TY - JOUR AB - Ulcerative colitis is an idiopathic gastrointestinal disease described by chronic inflammation of the digestive system. Cytokines may be responsible for immunopathogenesis, mucosal and tissue damage, and even treatment response. In addition to its role in calcium and phosphorus homeostasis and bone health, vitamin D is an immunomodulatory and anti-inflammatory agent. Understanding the role of cytokines may lead to improving the pathogenesis and treatment of this disease, therefore we aimed to investigate the relative gene expression of pro- and anti-inflammatory cytokines in biopsy samples taken from the affected area in the colon of ulcerative colitis patients and its association with serum vitamin D levels. A total of 47 ulcerative colitis patients were enrolled in this case-control study. The case group consisted of 23 patients with treatment-resistant ulcerative colitis, and the control group consisted of 24 ulcerative colitis patients responding to routine treatment. Serum vitamin D levels were measured by ELISA method. Real-time PCR was employed to quantify the relative expression of pro- and anti-inflammatory cytokines in colon biopsy samples from case and control groups. The pro-inflammatory cytokines included tumor necrosis factor-α (TNF-α), interferon-gamma (IFN-γ), interleukin-1β (IL-1β), IL-6, IL-8, IL-17 A, and IL-33, while the anti-inflammatory cytokines were IL-10, IL-35, and TGF-β. Data are showed as mean ± standard deviation (SD), and p values < 0.05 were considered statistically significant. The mean age of the control group was 45.88 ± 18.51 years, while that of the case group was 41.30 ± 13.01 years. The relative gene expression of TNF-α, IFN-γ, IL-1β, IL-6, IL-8, IL-17 A, IL-33, TGF-β, IL-10, and IL-35, in the case and control groups did not exhibit statistically significant differences (p > 0.05). However, the gene expression levels of the principal pro-inflammatory cytokines, including IL-6, IL-1β, and TNF-α, were elevated in treatment-resistant patients compared to patients who responded to treatments. No correlation was observed between serum vitamin D levels and the gene expression of pro- and anti-inflammatory cytokines (p > 0.05). The present study did not identify a statistically significant correlation between the expression of pro- or anti-inflammatory cytokines and treatment response. Therefore, routine treatments had no effect on the expression of these cytokines in treatment-resistant patients. Additionally, serum vitamin D levels were not related to the relative expression of pro- and anti-inflammatory cytokines in the affected area of the colon of these patients. Despite the need for further research on the protective and pathological roles of cytokines and vitamin D, regular screening and early and complementary treatment may be beneficial in reducing inflammatory symptoms in these patients. AU - Ahmadi, A.* AU - Yousefimashouf, R.* AU - Mohammadi, A.* AU - Nikkhoo, B.* AU - Shokoohizadeh, L.* AU - Khan Mirzaei, M. AU - Alikhani, M.Y.* AU - Sheikhesmaili, F.* AU - Khodaei, H.* C1 - 73590 C2 - 57126 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Investigating the expression of anti/pro-inflammatory cytokines in the pathogenesis and treatment of ulcerative colitis and its association with serum level of vitamin D. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Many scientific datasets are compositional in nature. Important biological examples include species abundances in ecology, cell-type compositions derived from single-cell sequencing data, and amplicon abundance data in microbiome research. Here, we provide a causal view on compositional data in an instrumental variable setting where the composition acts as the cause. First, we crisply articulate potential pitfalls for practitioners regarding the interpretation of compositional causes from the viewpoint of interventions and warn against attributing causal meaning to common summary statistics such as diversity indices in microbiome data analysis. We then advocate for and develop multivariate methods using statistical data transformations and regression techniques that take the special structure of the compositional sample space into account while still yielding scientifically interpretable results. In a comparative analysis on synthetic and real microbiome data we show the advantages and limitations of our proposal. We posit that our analysis provides a useful framework and guidance for valid and informative cause-effect estimation in the context of compositional data. AU - Ailer, E. AU - Müller, C.L. AU - Kilbertus, N. C1 - 73371 C2 - 57020 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Instrumental variable estimation for compositional treatments. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Glioblastoma multiforme continues to be one of the most aggressive brain cancers, posing a serious health challenge, as it offers a median survival of only 15-23 months and a 5-year survival rate of less than 6%. Current treatments often prove inadequate, underscoring the urgency for new therapeutic strategies. This study investigated the potential of silencing the PFKFB4 and HMOX1 genes in U87-MG glioblastoma cells using small interfering RNAs (siRNAs), both alone and alongside the chemotherapeutic agents temozolomide (TMZ) and doxorubicin (DOX). Through MTT assays, qPCR, and wound healing techniques, we assessed cell viability, gene expression, and cell migration. Notably, siPFKFB4 enhanced DOX's cytotoxic effect, reducing its IC50 by six-fold, while having a milder impact with TMZ. When both siRNAs were combined with DOX, the IC50 decreased by two-fold without harming normal cells. Although siHMOX1 reduced cell migration, it only modestly affected cell proliferation with either DOX or TMZ. The gene expression analysis demonstrated that the siPFKFB4/DOX treatment led to an upregulation of pro-apoptotic genes such as DPYSL4, while simultaneously downregulating anti-apoptotic genes, including BCL-2 and PARP2. In contrast, the siHMOX1 combination influenced the expression of 14 genes, significantly enhancing the levels of CYLD, FAS, and CASP3, which are key promoters of apoptosis. In migration assays, siPFKFB4/DOX and siHMOX1/DOX reduced cell migration by 65 and 75%, respectively. These findings suggest that siPFKFB4 combined with DOX offers a promising pathway for GBM therapy, advocating further exploration into effective central nervous system drug delivery methods. AU - Al-Ameer, H.J.* AU - Zihlif, M.* AU - Maslat, A.* AU - Al-Awaida, W.J.* AU - Ayyash, A.M.* AU - Imraish, A.* AU - Al-Qinna, N.* AU - Al-Omari, T.* AU - Al-Qaisi, T.* AU - Al-Zyoud, W.* AU - Alzubi, B.T.* AU - Atoom, A.M.* AU - Fattash, I.A.* AU - Ambike, S. AU - Goh, K.W.* AU - Gushchina, Y.S.* C1 - 75274 C2 - 57886 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Targeting the proliferation of glioblastoma cells and enhancement of doxorubicin and temozolomide cytotoxicity through inhibition of PFKFB4 and HMOX1 genes with siRNAs. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - The preservation of organic compounds under extreme environmental conditions remains a critical challenge for both terrestrial ecology applications on Earth and astrobiology. In a novel long-term field experiment over 8 months, we exposed biomolecules and a model organism to natural hyperarid conditions of the Atacama Desert, one of the best Mars analog environments. We used custom-designed sample plates for long-term exposure to simulate environmental stresses that biomolecules are exposed naturally in a hyperarid environment. The multiple stressors included extreme temperature fluctuations, associated humidity changes, and intense solar irradiation. Our field experiment complements and extends the insights obtained from previously conducted short-term laboratory experiments. To investigate biomolecule stability, we embedded adenosine triphosphate (ATP), chlorophyll-a, and the cyanobacterium Chrooccoccidiopsis in various Mars-relevant sediments with addition of chloride and perchlorate. Our findings, which include the rapid degradation of these biomolecules, the detection of more stable degradation products, and the identification of non-enzymatic degradation pathways, reveal the critical influence of substrate and salt types on biomolecule stability. Valuable insights into biosignature preservation under extreme terrestrial conditions and a better understanding of organic signal interpretations were gained, which will provide critical insights for future Mars missions, especially when searching for past or present life. AU - Arens, F.L.* AU - Uhl, J. AU - Schmitt-Kopplin, P. AU - Karger, C.* AU - Mangelsdorf, K.* AU - Sager, C.* AU - Airo, A.* AU - Valenzuela, B.* AU - Zamorano, P.* AU - Schulze-Makuch, D.* C1 - 75356 C2 - 58137 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Exploring organic compound preservation through long-term in situ experiments in the Atacama desert and the relevance for Mars. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - While the effect of time-of-day (morning versus evening) on hormones, lipids and lipolysis has been studied in relation to meals and exercise, there are no studies that have investigated the effects of time-of-day on ice bath induced hormone and lipidome responses. In this crossover-designed study, a group of six women and six men, 26 ± 5 years old, 176 ± 7 cm tall, weighing 75 ± 10 kg, and a BMI of 23 ± 2 kg/m2 had an ice bath (8-12 °C for 5 min) both in the morning and evening on separate days. Absence from intense physical exercise, nutrient intake and meal order was standardized in the 24 h prior the ice baths to account for confounders such as diet or exercise. We collected venous blood samples before and after (5 min and 30 min) the ice baths to measure hormones (noradrenaline, adrenaline, and cortisol) and lipid levels in plasma via liquid chromatography mass spectrometry shotgun lipidomics. We found that ice baths in the morning increase plasma fatty acids more than in the evening. Overall plasma lipid composition significantly differed in-between the morning and evening, and only in the morning ice bathing is accompanied by significantly increased plasma fatty acids from 5.1 ± 2.2% to 6.0 ± 2.4% (P = 0.029) 5 min after and to 6.3 ± 3.1% (P = 0.008) 30 min after. Noradrenaline was not affected by time-of-day and increased significantly immediately after the ice baths in the morning by 127 ± 2% (pre: 395 ± 158 pg/ml, post 5 min: 896 ± 562 pg/ml, P = 0.025) and in the evening by 144 ± 2% (pre: 385 ± 146 pg/ml, post 5 min: 937 ± 547 pg/ml, P = 0.015). Cortisol was generally higher in the morning than in the evening (pre: 179 ± 108 pg/ml versus 91 ± 59 pg/ml, P = 0.013; post 5 min: 222 ± 96 pg/ml versus 101 ± 52 pg/ml, P = 0.001; post 30 min: 190 ± 96 pg/ml versus 98 ± 54 pg/ml, P = 0.009). There was no difference in the hormonal and lipidome response to an ice bath between women and men. The main finding of the study was that noradrenaline, adrenaline, cortisol and plasma lipidome responses are similar after an ice bath in the morning and evening. However, ice baths in the morning increase plasma fatty acids more than in the evening. AU - Braunsperger, A.* AU - Bauer, M.* AU - Brahim, C.B.* AU - Seep, L.* AU - Tischer, D.* AU - Peitzsch, M.* AU - Hasenauer, J. AU - Figueroa, S.H.* AU - Worthmann, A.* AU - Heeren, J.* AU - Dyar, K.A. AU - Koehler, K.* AU - Soriano-Arroquia, A.* AU - Schönfelder, M.* AU - Wackerhage, H.* C1 - 72991 C2 - 56888 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Effects of time-of-day on the noradrenaline, adrenaline, cortisol and blood lipidome response to an ice bath. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Post COVID-19 condition (PCC) is a substantial burden for patients, society, and the healthcare system. Participants of the German National Cohort (NAKO) were asked in an online survey about their self-perceived health, symptoms related to PCC, and infection status. PCC was defined as reporting symptoms for the time window 4-12 months after infection. Of 110,375 respondents (73% response), 86,833 were included in this analysis. Of these, 44,451 (51%) did not report a SARS-CoV-2 infection (no infection), 26,726 (31%) reported an infection but no symptoms 4-12 months after infection (infection/no PCC), and 15,656 (18%) reported an infection and symptoms (PCC). The median number of current symptoms at the time of the survey was two for the "no infection" and the "infection/no PCC" group, and five for the "PCC" group. Participants with PCC had a substantially higher probability of having worse self-perceived health (OR 1.84, 95% CI [1.75; 1.93] compared to the "no infection" group, adjusting for sex, age, education and chronic diseases with elevated risk for developing PCC. After adjusting for the number of current symptoms related to PCC, this difference disappeared, suggesting that the symptoms collected explain the impairment of self-perceived health in the PCC group. AU - Diexer, S.* AU - Frost, J.* AU - Ahnert, P.* AU - Baernighausen, T.W.* AU - Brenner, H.* AU - Fricke, J.* AU - Gabrysch, S.* AU - Greiser, K.H.* AU - Harth, V.* AU - Heise, J.K.* AU - Kaaks, R.* AU - Karch, A.* AU - Keil, T.* AU - Klee, B.* AU - Klett-Tammen, C.J.* AU - Krist, L.* AU - Lampl, B.M.J.* AU - Leitzmann, M.F.* AU - Lieb, W.* AU - Meinke-Franze, C.* AU - Michels, K.B.* AU - Velásquez, I.M.* AU - Obi, N.* AU - Peters, A. AU - Pfrommer, L.R.* AU - Pischon, T.* AU - Purschke, O.* AU - Rübsamen, N.* AU - Schikowski, T.* AU - Schmidt, B.* AU - Thierry, S. AU - Völzke, H.* AU - Wright, M.N.* AU - Zeeb, H.* AU - Mikolajczyk, R.* C1 - 75163 C2 - 57810 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Cross-sectional study of health impairment related to post COVID-19 condition among participants of a large population-based cohort in Germany. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - The harvesting time of pomegranates is crucial for maximizing their health benefits and market value. However, traditional methods often fail to consider the intricate interactions between environmental conditions and fruit maturity. This study is the first of its kind in Lebanon to address this limitation by applying advanced machine learning techniques to predict key food quality indicators, which can aid in forecasting or determining the optimal harvesting date. The focus is on technological and phenolic maturity. Over three months, 548 pomegranates were meticulously harvested from three distinct geographic regions in Lebanon: Hasbaya, El Jahliye, and Rachiine. By integrating environmental, physical, and geographical data, we developed predictive models, including Linear Regression (LR) and Multi-Layer Perceptron (MLP) Regressor, to estimate key food quality indicators such as Total Soluble Solids (TSS), Titratable Acidity (TA), Maturity Index (MI), phenolic content, and Color Intensity (CI). Our results demonstrated that the MLP regressor achieved high predictive accuracy, with an R-squared value of 0.84 for TA, making it a reliable tool for predicting acidity levels. The model also showed strong performance in predicting phenolic content and color intensity, with R-squared values of 0.70 and 0.65 respectively, and an average classification accuracy of 71% for categorizing polyphenol levels. Principal Component Analysis (PCA) revealed significant geographic variation in phenolic content. In El Jahliye, phenolic levels ranged from low (<185 mg Gallic Acid Equivalent (GAE) per yield of juice) to moderate (185-400 mg GAE/yield of juice). In Rachiine, levels ranged from moderate to high (>400 mg GAE/yield of juice), while Hasbaya displayed all three phenolic content levels. These findings underscore the importance of region-specific harvesting strategies. As the first study in Lebanon to utilize machine learning for predicting food quality indicators in pomegranates, it provides a novel, data-driven approach to linking these indicators with optimal harvest timing. By accurately forecasting maturity-related metrics using simple physical, geographical, and environmental features, this study offers significant implications for refining agricultural practices in Lebanon and other similar agro-ecological regions, enhancing product quality and market value. AU - Ghannoum, R.* AU - Taha, N.* AU - Gaviria, D.D.* AU - Rajha, H.N.* AU - Darra, N.E.* AU - Albarqouni, S. C1 - 74847 C2 - 57628 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Unleashing the power of AI in predicting the technological and phenolic maturity of pomegranates cultivated in Lebanon. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - COVID-19 had a devastating impact on humanity. We investigated how residential air pollution (ozone (O3), nitrogen dioxide (NO2), fine particulate matter (PM2.5)) and meteorological factors (temperature (Temp), precipitation (Prec)) are associated with COVID-19 incidence in Baden-Württemberg (BW), Germany. We utilized data from the Copernicus Atmosphere Monitoring Service and the Copernicus Climate Change Service to model environmental exposure from 2020 to 2022 in postal code areas in BW. Health insurance data on SARS-CoV-2 infections were provided from the health insurance AOK BW on a quarterly level covering approximately 12 million person-years. We examined the spatiotemporal variability with a generalized additive model including various stressors, demographic factors, and area-wide data, offering a comprehensive analysis of the environmental stressor- COVI-10 incidence associations. In 2022, during the prevalence of the Omicron variant, the number of COVID-19 cases tripled compared to 2020. During the pre-Omicron period, COVID-19 incidence showed a positive association with PM2.5 (relative risk [RR] 2.41; 95% confidence interval [CI] (2.31, 2.52)), a negative association with Temp (RR 0.39 (0.32, 0.48)), and no clear or slight associations with O3, Prec, and NO2. During the Omicron period, there were either no clear or slight negative associations with Temp (RR 0.92 (0.74, 1.30)), PM2·5 (RR 0.70 (0.64, 0.79)), NO2, and Prec and a negative association with O3 (RR 0.46 (0.40, 0.53)). The analysis found clear links between environmental stressors and COVID-19 incidence, which strongly differed between pre-Omicron and Omicron periods. Consideration of environmental stressor concentration could be relevant in the management of the pandemic. AU - Hoffmann, L.* AU - Gilardi, L.* AU - Antoni, T.* AU - Baltruweit, M.* AU - Bittner, M.* AU - Breitner-Busch, S. AU - Dally, S.* AU - Erbertseder, T.* AU - Hawighorst-Knapstein, S.* AU - Schmitz, M.T.* AU - Schneider, R.* AU - Wüst, S.* AU - Rittweger, J.* C1 - 75266 C2 - 57881 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Modulation of COVID-19 incidence by environmental stressors is variant between pre-Omicron and Omicron periods. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Magnetic iron-oxide nanoparticles in the form of magnetite (Fe3O4) are present in the human brain. They have been hypothesized to biomineralize in situ, as a result of dysfunctional iron homeostasis related to Alzheimer's disease, or to enter the brain as airborne pollution particles. Regardless of their origin, magnetic iron-oxides pose a potential hazard to human health due to their high redox activity and surface charge. Here we report measurements on four post-mortem human brainstems, with one brainstem showing approximately 100 times higher magnetite concentrations than the other cases. This brainstem came from a subject with alcohol-associated liver disease (ALD) that manifested in liver cirrhosis and massive hepatic iron overload. Laser ablation - inductively coupled plasma - mass spectrometry showed the highest levels of trace metals (iron, copper and manganese) in the ALD brainstem. It is well established that a dysfunctional liver can result in the accumulation of trace metals in the brain. Our data indicate a similar pathway for magnetite particles, yet liver pathology has not been linked to magnetite occurrence in the brain so far. It may prove to be a crucial factor in understanding the high variation of magnetite concentrations found in human brains. AU - Kaub, L.* AU - Milz, S.* AU - Barapatre, N.* AU - Büttner, A.* AU - Michalke, B. AU - Schmitz, C.* AU - Gilder, S.A.* C1 - 75110 C2 - 57817 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Magnetic iron-oxide nanoparticles in the brain connected to alcohol-associated liver disease. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Abdominal adipose tissue (AT) amounts are increasingly considered as potential biomarkers for a variety of diseases and clinical questions, for instance, in diabetology, oncology or cardiovascular medicine. Despite the emergence of automated deep-learning methods for tissue quantification, interactive (supervised) segmentation tools will typically be used for model training. In comparison with CT-based approaches, MRI segmentation tools are more complex and less common. This work aims to validate a novel MRI-based tissue volumetry against a reference method in patients with (pre-) obesity. The new tool (segfatMR) was developed under a Matlab-based, open-source software framework and combines fast automatic pre-segmentation followed by manual (expert) corrections where needed. Analyses were performed retrospectively on a subset of clinical research MRI datasets (1.5 T Achieva XR, Philips Healthcare) and involved the segmentation of datasets from 20 patients (10 women/men) aged 25.1-63.1 (mean 48.5) years with BMIs between 28.3 and 58.8 (mean 36.8) kg/m2. Two independent expert readers analyzed the abdominopelvic data (30-40 slices, mean 35.8) with segfatMR and a widely used commercial tool (sliceOmatic). Coefficients of determination (R2), bias and limits of agreement (Bland Altman) were determined. Segmentation performance (R2 between methods) was excellent for both readers for SAT (> 0.99) and very high for VAT (around 0.90). The novel method was almost twice as fast as the reference standard - 25 and 19 s/slice (R1 and R2) vs. 40 and 34 s/slice. The presented semiautomatic segmentation tool enables a fast and accurate quantification of whole abdominopelvic adipose tissue volume in obesity studies. Use, adjustments and extensions of the MRI volumetry tool are facilitated by the open-source design on a standard PC. AU - Linder, A.* AU - Eggebrecht, T.* AU - Linder, N.* AU - Stange, R.* AU - Schaudinn, A.* AU - Blüher, M. AU - Denecke, T.* AU - Busse, H.* C1 - 73721 C2 - 57190 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Stand-alone MRI tool for semiautomatic volumetry of abdominal adipose compartments in patients with obesity. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Modelling of pollutants provides valuable insights into air quality dynamics, aiding exposure assessment where direct measurements are not viable. Machine learning (ML) models can be employed to explore such dynamics, including the prediction of air pollution concentrations, yet demanding extensive training data. To address this, techniques like transfer learning (TL) leverage knowledge from a model trained on a rich dataset to enhance one trained on a sparse dataset, provided there are similarities in data distribution. In our experimental setup, we utilize meteorological and pollutant data from multiple governmental air quality measurement stations in Graz, Austria, supplemented by data from one station in Zagreb, Croatia to simulate data scarcity. Common ML models such as Random Forests, Multilayer Perceptrons, Long-Short-Term Memory, and Convolutional Neural Networks are explored to predict particulate matter in both cities. Our detailed analysis of PM10 suggests that similarities between the cities and the meteorological features exist and can be further exploited. Hence, TL appears to offer a viable approach to enhance PM10 predictions for the Zagreb station, despite the challenges posed by data scarcity. Our results demonstrate the feasibility of different TL techniques to improve particulate matter prediction on transferring a ML model trained from all stations of Graz and transferred to Zagreb. Through our investigation, we discovered that selectively choosing time spans based on seasonal patterns not only aids in reducing the amount of data needed for successful TL but also significantly improves prediction performance. Specifically, training a Random Forest model using data from all measurement stations in Graz and transferring it with only 20% of the labelled data from Zagreb resulted in a 22% enhancement compared to directly testing the trained model on Zagreb. AU - Poelzl, M.* AU - Kern, R.* AU - Kecorius, S. AU - Lovrić, M.* C1 - 73167 C2 - 56943 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Exploration of transfer learning techniques for the prediction of PM10. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Hypertrophic cardiomyopathy (HCM) caused by autosomal-dominant mutations in genes coding for structural sarcomeric proteins, is the most common inherited heart disease. HCM is associated with myocardial hypertrophy, fibrosis and ventricular dysfunction. Hypoxia-inducible transcription factor-1α (Hif-1α) is the central master regulators of cellular hypoxia response and associated with HCM. Yet its exact role remains to be elucidated. Therefore, the effect of a cardiomyocyte-specific Hif-1a knockout (cHif1aKO) was studied in an established α-MHC719/+ HCM mouse model that exhibits the classical features of human HCM. The results show that Hif-1α protein and HIF targets were upregulated in left ventricular tissue of α-MHC719/+ mice. Cardiomyocyte-specific abolishment of Hif-1a blunted the disease phenotype, as evidenced by decreased left ventricular wall thickness, reduced myocardial fibrosis, disordered SRX/DRX state and ROS production. cHif1aKO induced normalization of pro-hypertrophic and pro-fibrotic left ventricular remodeling signaling evidenced on whole transcriptome and proteomics analysis in α-MHC719/+ mice. Proteomics of serum samples from patients with early onset HCM revealed significant modulation of HIF. These results demonstrate that HIF signaling is involved in mouse and human HCM pathogenesis. Cardiomyocyte-specific knockout of Hif-1a attenuates disease phenotype in the mouse model. Targeting Hif-1α might serve as a therapeutic option to mitigate HCM disease progression. AU - Raj Murthi, S.* AU - Petry, A.* AU - Shashikadze, B.* AU - Stöckl, J.B.* AU - Schmid, M.* AU - Santamaria, G.* AU - Klingel, K.* AU - Kračun, D.* AU - Chen, X.* AU - Bauer, S.* AU - Schmitt, J.P.* AU - Flenkenthaler, F.* AU - Gorham, J.M.* AU - Toepfer, C.N.* AU - Potěšil, D.* AU - Hruška, P.* AU - Zdráhal, Z.* AU - Mayer, Z.* AU - Klop, M.* AU - Lehmann, L.* AU - Qin, Y.* AU - Papanakli, L.* AU - Spielmann, N. AU - Moretti, A.* AU - Fröhlich, T.* AU - Ewert, P.* AU - Holdenrieder, S.* AU - Seidman, J.G.* AU - Seidman, C.E.* AU - Görlach, A.* AU - Wolf, C.M.* C1 - 73096 C2 - 56854 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Contribution of hypoxia-inducible factor 1alpha to pathogenesis of sarcomeric hypertrophic cardiomyopathy. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - If health impairments due to coronavirus disease 2019 (COVID-19) persist for 12 weeks or longer, patients are diagnosed with Post-COVID Syndrome (PCS), or Long-COVID. Although the COVID-19 pandemic has largely subsided in 2024, PCS is still a major health burden worldwide, and identifying potential genetic modifiers of PCS remains of great clinical and scientific interest. We therefore performed a case-control type genome-wide association study (GWAS) of three recently developed PCS (severity) scores in 2,247 participants of COVIDOM, a prospective, multi-centre, population-based cohort study of SARS-CoV-2-infected individuals in Germany. Each PCS score originally represented the weighted sum of the binary indicators of all, or a subset, of 12 PCS symptom complexes, assessed six months or later after the PCR test-confirmed SARS-CoV-2 infection of a participant. For various methodical reasons, however, the PCS scores were dichotomized along their respective median values in the present study, prior to the GWAS. Of the 6,383,167 single nucleotide polymorphisms included, various variants were found to be associated with at least one of the PCS scores, although not at the stringent genome-wide statistical significance level of 5 × 10- 8. With p = 6.6 × 10- 8, however, the genotype-phenotype association of SNP rs9792535 at position chr9:127,166,653 narrowly missed this threshold. The SNP is located in a region including the NEK6, PSMB7 and ADGRD2 genes which, however, does not immediately suggest an etiological connection to PCS. As regards functional plausibility, variants of a possible effect mapped to the olfactory receptor gene region (lead SNP rs10893121 at position chr11:123,854,744; p = 2.5 × 10- 6). Impairment of smell and taste is a pathognomonic feature of both, acute COVID-19 and PCS, and our results suggest that this connection may have a genetic basis. Three other genotype-phenotype associations pointed towards a possible etiological role in PCS of cellular virus repression (CHD6 gene region), activation of macrophages (SLC7A2) and the release of virus particles from infected cells (ARHGAP44). All other gene regions highlighted by our GWAS did not relate to pathophysiological processes currently discussed for PCS. Therefore, and because the genotype-phenotype associations observed in our GWAS were generally not very strong, the complexity of the genetic background of PCS appears to be as high as that of most other multifactorial traits in humans. AU - Ruß, A.K.* AU - Schreiber, S.* AU - Lieb, W.* AU - Vehreschild, J.J.* AU - Heuschmann, P.U.* AU - Illig, T.* AU - Appel, K.S.* AU - Vehreschild, M.J.G.T.* AU - Krefting, D.* AU - Reinke, L.* AU - Viebke, A.* AU - Poick, S.* AU - Störk, S.* AU - Reese, J.P.* AU - Zöller, T.* AU - Krist, L.* AU - Ellinghaus, D.* AU - Fösel, B. AU - Gieger, C. AU - Lorenz-Depiereux, B. AU - Witzenrath, M.* AU - Anton, G.* AU - Krawczak, M.* AU - Heyckendorf, J.* AU - Bahmer, T.* C1 - 74316 C2 - 57459 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Genome-wide association study of post COVID-19 syndrome in a population-based cohort in Germany. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - The pulsed nature of laser-driven ion sources and their relative large emission angles result in the production of secondary, undesired, pulsed neutron (and photon) radiation. Conventional neutron monitors struggle to accurately measure in such environments, yet characterizing these fields is crucial for applications like hadron therapy. Parasitic neutron dose measurements were performed at the Petawatt beam of the Dresden Laser Acceleration Source (DRACO) employing laser energies from 4.5 to 18 J. An active extended-range neutron REM counter specifically developed for pulsed neutron fields, the LUPIN-II, was employed, as well as a passive extended-range neutron REM counter, the Passive LINUS. Neutron doses were recorded on a single-bunch level with values up to about 260 nSv per proton bunch characterized by a proton cutoff energy of about 60 MeV at about 2 m from the DRACO vacuum chamber, confirming the expected pulsed nature of the neutron field. Results of passive measurements were compared to the LUPIN-II results, integrated over the same period, and showed a reasonable agreement, confirming the presence of pulsed neutron radiation in the proximity of the DRACO ion source. These results demonstrate for the first time that this kind of radiation can be monitored, in terms of H*(10) on a single-shot basis by using the LUPIN-II neutron REM counter. AU - Tisi, M.* AU - Bolzonella, M.* AU - Caresana, M.* AU - Hohmann, E.* AU - Kroll, F.* AU - Mares, V. AU - Metzkes-Ng, J.* AU - Urlass, S.* AU - Zeil, K.* AU - Rühm, W.* C1 - 74993 C2 - 57767 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Secondary neutron dose measurements at the DRACO laser-driven ion source. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - 17β-estradiol (E2), the main circulating estrogen hormone, is a critical signaling factor for the growth, differentiation, and function of breast epithelial cells. The effects of E2 on the breast tissue are primarily mediated by the estrogen receptor α (ERα). Deregulation of the E2-ERα signaling contributes to the initiation/progression of breast cancer and resistance to treatments. Cell lines from breast adenocarcinomas as in vitro model systems provide invaluable insight into cellular events, drug discovery, and drug resistance. Among ERα-synthesizing cell lines, MCF7 and T47D cells are widely used to elucidate cell cycle phase-specific molecular events that coordinate cellular proliferation mediated by E2-ERα. Due to variable results in generating phase-enriched populations with various approaches, we wanted to reassess cell cycle synchronization-coupled phase enrichment with charcoal dextran-treated fetal bovine serum, CD-FBS, as an effective hormone withdrawal approach, alone or in combination with excess thymidine, as a DNA replication inhibitor, and/or nocodazole, a microtubule poison, in MCF7 and T47D cells. We find that hormone withdrawal synchronizes both MCF7 and T47D cells at the G0/G1 phase. Supplementation of CD-FBS with E2 enriches the S phase population. E2 with nocodazole and nocodazole-coupled mitotic shake-off augments the G2/M phase population of MCF7 cells. However, the double thymidine block approach with nocodazole or nocodazole-coupled mitotic shake-off is more effective in enriching S and G2/M phase populations of T47D cells. Our results highlight the differential efficacy of synchronization approaches in MCF7 and T47D cells that could provide a framework for cell cycle-specific applications in breast cancer research. AU - Toker, P.* AU - Ayten, H.* AU - Demiralay, Ö.D. AU - Bınarcı, B.* AU - Turan, G.* AU - Olgun, E.* AU - Yaşar, P.* AU - Akman, H.B.* AU - Muyan, M.* C1 - 73425 C2 - 57074 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A reappraisal of cell cycle phase enrichment in synchronized estrogen receptor-positive cell models derived from breast adenocarcinomas. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Impaired awareness of hypoglycaemia (IAH) is a complication of diabetes treatment, whereby individuals are no longer able to feel an oncoming hypoglycaemic event. IAH may be a result of central nervous system adaptation to low recurrent hypoglycaemias, however the precise pathways involved remain unknown. This study employed proteomics analysis to explore potential pathophysiological pathways in IAH, using a nested case-control design within the Dutch Type 1 Diabetes Biomarker study. The Olink® Cardiovascular II panel was used for targeted proteomics, comparing 67 individuals with IAH to 108 age- and sex-matched individuals with normal awareness of hypoglycaemia (NAH). Univariate analysis revealed that agouti-related protein (AGRP) levels were significantly lower in individuals with IAH compared to NAH (6.12 NPX vs. 6.44 NPX, FDR-adjusted P = 0.012). In multivariate models adjusted for sex and diabetes duration, AGRP remained significant before p-value adjustment (P < 0.001) but not after adjusting for false discovery rate (FDR) (P = 0.057). AGRP, known for its orexigenic effects and expression in the arcuate nucleus of the hypothalamus, is involved in glucose sensing and hypothalamic-pituitary-adrenal (HPA) axis stimulation, suggesting its potential role in the pathophysiology of IAH. This study highlights the need for further research to clarify AGRP's role and its possible implications for managing IAH in diabetes. AU - Varkevisser, R.D.M.* AU - Petrera, A. AU - Hauck, S.M. AU - Mul, D.* AU - Aanstoot, H.J.* AU - Paterson, A.* AU - Wolffenbuttel, B.H.R.* AU - van der Klauw, M.M.* C1 - 75810 C2 - 58104 TI - Targeted proteomics analysis in type 1 diabetes identifies lower agouti-related protein levels in individuals with impaired hypoglycaemia awareness. JO - Sci. Rep. VL - 15 IS - 1 PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Prostate-specific membrane antigen (PSMA)-targeted positron emission tomography (PET) has improved localization of prostate cancer (PC) lesions in biochemical recurrence (BCR) for salvage radiotherapy (SRT). We conducted a retrospective review of patients undergoing 18F-rhPSMA-7 or 18F-flotufolastat (18F-rhPSMA-7.3)-PET-guided SRT compared with conventional-SRT (C-SRT) without PET. We evaluated biochemical failure-free survival (bFS) and overall rates of bFS in 110 evaluable patients with recurrent PC after radical prostatectomy who received SRT. 82 patients received 18F-rhPSMA-7/18F-flotufolastat-PET-guided SRT and 28 received C-SRT. Median bFS for patients with 18F-rhPSMA-7/18F-flotufolastat-PET-guided SRT was not reached while median bFS was 45.6 months for patients with C-SRT (p = 0.101). %bFS were 95% (52/55) vs 87% (20/23), 90% (27/30) vs 75% (15/20), 89% (16/18) vs 68% (13/19) and 100% (3/3) vs 57% (8/14) for PET-guided vs C-SRT at 12, 24, 36, and 48 months, respectively. Among patients treated in the prostate bed only, median bFS was not reached for PSMA-PET-guided SRT (n = 52) vs 55.1 months in the C-SRT group (n = 25; p = 0.063). %bFS was greater for PSMA-PET-guided SRT than C-SRT at all evaluated timepoints. 18F-rhPSMA-7/18F-flotufolastat-guided SRT yielded favorable disease outcomes. Although statistical significance was not reached, likely due to the limited sample size in this preliminary analysis, our data illustrate potential for 18F-flotufolastat-PET-guided SRT. AU - Vogel, M.M. AU - Rauscher, I.* AU - Gschwend, J.E.* AU - Hekimsoy, T.* AU - Gabler, N.* AU - Olufs, C.* AU - D'Alessandria, C.* AU - Peeken, J.C. AU - Combs, S.E. AU - Eiber, M.* C1 - 73107 C2 - 56914 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Biochemical failure-free survival of 18F-rhPSMA-7 and 18F-flotufolastat PET-guided salvage radiotherapy for patients with recurrent prostate cancer. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Fermentable carbohydrates and resulting short-chain fatty acids (SCFAs) received attention via modifying potential on obesity-associated systemic low-grade inflammation. However, their effects on inflammation remain poorly understood. In this study, the anti-inflammatory properties of pectin or inulin supplementation were investigated in an atherogenic-fed pig obesity model. Pigs were divided into three atherogenic-fed groups with or without 5% pectin/inulin supplementation (AD, ADp, ADi, n = 10) and a conventional-fed group (CD, n = 10) for a 15-week feeding period. We demonstrated that faecal SCFA concentrations decreased and faecal pH increased in all groups over the feeding period (P < 0.05). SCFA concentrations were comparable between colon and faeces in all groups. Liver inflammatory-marker expressions were on average < 1 in all groups, except TNF-α (AD < CD and ADi; P < 0.01). Inflammatory-marker expressions in abdominal adipose tissue exceeded subcutaneous marker expressions in all groups. AD showed significantly lower IL-1β and CD68 mRNA levels than CD (P < 0.03). Comparing the atherogenic diet groups, the IL-1β mRNA levels were higher in ADi versus AD and ADp (P = 0.02). Our data indicated that fermentable carbohydrates added to an atherogenic diet cannot resolve low-grade adipose tissue inflammatory associated with obesity. AU - Wahl, L.* AU - Rau, S.* AU - Dawczynski, C.A.* AU - Lorkowski, S.* AU - Ulrich, R.* AU - Blüher, M. AU - Vervuert, I.* C1 - 73664 C2 - 57160 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Type of diet has no major influence on inflammatory response in a Saddleback pig model. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - An increasing number of studies have used multi-armed bandit tasks to investigate individual differences in exploration behavior. However, the psychometric properties of exploration measures remain unexplored. We examine the test-retest reliability, convergent, divergent, and external validity of model-based estimates of exploration strategies using three canonical paradigms. Our results revealed poor to moderate reliability, with minimal correlations for the same strategy across tasks. We then provide actionable recommendations for how to improve reliability and convergence across tasks: Simplifying common computational models enabled us to identify two convergently valid latent factors representing value-guided and directed exploration. Still, these factors showed neither a significant correlation with self-reported exploration tendencies nor with mood fluctuations, symptoms of anxiety, and depression. The exploration factors were, however, highly correlated with working memory capacity, questioning whether they provide additional information beyond performance-related constructs. To improve future research, we suggest simplifying common computational models and using multiple tasks to more accurately measure exploration strategies and mitigate spurious correlations arising from task-specific factors. AU - Witte, K. AU - Thalmann, M. AU - Schulz, E. C1 - 75258 C2 - 57894 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Model-based exploration is measurable across tasks but not linked to personality and psychiatric assessments. JO - Sci. Rep. VL - 15 IS - 1 PB - Nature Portfolio PY - 2025 SN - 2045-2322 ER - TY - JOUR AB - Aim of this study was to analyse the associations of cardiovascular health and adrenal gland volume as a rather new imaging biomarker of chronic hypothalamic-pituitary-adrenal (HPA) axis activation. The study population originates from the KORA population-based cross-sectional prospective cohort. 400 participants without known cardiovascular disease underwent a whole-body MRI. Manual segmentation of adrenal glands was performed on VIBE-Dixon gradient-echo sequence. MRI based evaluation of cardiac parameters was achieved semi-automatically. Cardiometabolic risk factors were obtained through standardized interviews and medical examination. Univariate and multivariate associations were derived. Bi-directional causal mediation analysis was performed. 351 participants were eligible for analysis (56 ± 9.1 years, male 58.7%). In multivariate analysis, significant associations were observed between adrenal gland volume and hypertension (outcome hypertension: Odds Ratio = 1.11, 95% CI [1.01, 1.21], p = 0.028), left ventricular remodelling index (LVRI) (outcome LVRI: β = 0.01, 95% CI [0.00, 0.02], p = 0.011), and left ventricular (LV) wall thickness (outcome LV wall thickness: β = 0.06, 95% CI [0.02, 0.09], p = 0.005). In bi-directional causal mediation analysis adrenal gland volume had a borderline significant mediating effect on the association between hypertension and LVRI (p = 0.052) as well as wall thickness (p = 0.054). MRI-based assessment of adrenal gland enlargement is associated with hypertension and LV remodelling. Adrenal gland volume may serve as an indirect cardiovascular imaging biomarker. AU - Askani, E.* AU - Rospleszcz, S. AU - Lorbeer, R.* AU - Wintergerst, C.* AU - Müller-Peltzer, K.* AU - Nattenmüller, J.* AU - Hasic, D.* AU - von Krüchten, R.* AU - Kellner, E.* AU - Reisert, M.* AU - Rathmann, W.* AU - Peters, A. AU - Schlett, C.L.* AU - Bamberg, F.* AU - Storz, C.* C1 - 70923 C2 - 55819 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - MRI-based adrenal gland volume is associated with cardiovascular alterations in individuals without prior cardiovascular disease. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Sleep facilitates declarative memory consolidation, which is assumed to rely on the reactivation of newly encoded memories orchestrated by the temporal interplay of slow oscillations (SO), fast spindles and ripples. SO as well as the number of spindles coupled to SO are more frequent during slow wave sleep (SWS) compared to lighter sleep stage 2 (S2). But, it is unclear whether memory reactivation is more effective during SWS than during S2. To test this question, we applied Targeted Memory Reactivation (TMR) in a declarative memory design by presenting learning-associated sound cues during SWS vs. S2 in a counterbalanced within-subject design. Contrary to our hypothesis, memory performance was not significantly better when cues were presented during SWS. Event-related potential (ERP) amplitudes were significantly higher for cues presented during SWS than S2, and the density of SO and SO-spindle complexes was generally higher during SWS than during S2. Whereas SO density increased during and after the TMR period, SO-spindle complexes decreased. None of the parameters were associated with memory performance. These findings suggest that the efficacy of TMR does not depend on whether it is administered during SWS or S2, despite differential processing of memory cues in these sleep stages. AU - Carbone, J.* AU - Bibián, C.* AU - Born, J. AU - Forcato, C.* AU - Diekelmann, S.* C1 - 70528 C2 - 55644 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Comparing targeted memory reactivation during slow wave sleep and sleep stage 2. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Intelectin-1 (ITLN1; also Omentin-1, OMNT1) is secreted by adipose tissue (AT) and plays an important role in glucose metabolism regulation, with links to obesity-associated diseases. ITLN1 activity so far has rarely been investigated using RNA-sequencing and in larger cohorts. We evaluated ITLN1 expression among three clinical cohorts of the Leipzig Obesity BioBank-a cross-sectional cohort comprising of 1480 people, a cohort of people with metabolically healthy or unhealthy obesity (31 insulin-sensitive, 42 insulin-resistant individuals with obesity), and a longitudinal two-step bariatric surgery cohort (n = 65). We hypothesized that AT ITLN1 expression is associated with serum omentin-1, clinical parameters associated with obesity, and with weight loss after bariatric surgery. We also investigated the correlation of AT ITLN1 expression with genes related to inflammatory response, lipid metabolism, obesity, and regulation of energy balance. Likewise, we inspected gene group expression and metabolic pathways associated with ITLN1 expression using gene set enrichment and gene correlation analysis. We show that ITLN1 expression differs in VAT and SAT, and should therefore be analyzed separately. Furthermore, ITLN1 expression increases with VAT tissue mass, but is negatively affected by AT tissue dysfunction among individuals with unhealthy obesity, corroborated by interplay with genes related to tissue inflammation. Gene set enrichment and gene correlation analysis of ITLN1 expression suggest that AT ITLN1 expression is related to local inflammatory processes in AT, but also in processes such as regulation of appetite, energy balance, and maintenance of body weight. AU - Czechowski, P. AU - Hagemann, T. AU - Ghosh, A.* AU - Sun, W.* AU - Dong, H.* AU - Noé, F.* AU - Niersmann, C.* AU - Reinisch, I.* AU - Wolfrum, C.* AU - Herder, C.* AU - Dietrich, A.* AU - Blüher, M. AU - Hoffmann, A. C1 - 71859 C2 - 56438 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Expression of Intelectin-1, also known as Omentin-1, is related to clinical phenotypes such as overweight, obesity, insulin resistance, and changes after bariatric surgery. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected between February 2020 and January 2021 at a university hospital in Munich, Germany, and analysed along with the place of work, duration of hospital stay, and ward transfers. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. An additional dataset collected at the same time at another university hospital in the same city was used to account for multiple independent introductions. Clustering analysis of 619 viral genomes generated 19 clusters ranging from 3 to 31 individuals. Sequencing-based transmission clusters showed little overlap with those based on contact tracing data. The viral genomes were significantly more closely related to each other than comparable genomes collected simultaneously at other hospitals in the same city (n = 829), suggesting nosocomial transmission. Longitudinal sampling from individual patients suggested possible cross-infection events during the hospital stay in 19.2% of individuals (14 of 73 individuals). Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals. AU - Esser, E. AU - Schulte, E.C. AU - Graf, A.* AU - Karollus, A.* AU - Smith, N.H.* AU - Michler, T. AU - Dvoretskii, S.* AU - Angelov, A.* AU - Sonnabend, M.* AU - Peter, S.A.* AU - Engesser, C.* AU - Radonić, A.* AU - Thürmer, A.* AU - von Kleist, M.* AU - Gebhardt, F.* AU - da Costa, C.P.* AU - Busch, D.H.* AU - Muenchhoff, M.* AU - Blum, H.* AU - Keppler, O.T.* AU - Gagneur, J. AU - Protzer, U. C1 - 70167 C2 - 55436 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - The hypothalamus is the key regulator for energy homeostasis and is functionally connected to striatal and cortical regions vital for the inhibitory control of appetite. Hence, the ability to non-invasively modulate the hypothalamus network could open new ways for the treatment of metabolic diseases. Here, we tested a novel method for network-targeted transcranial direct current stimulation (net-tDCS) to influence the excitability of brain regions involved in the control of appetite. Based on the resting-state functional connectivity map of the hypothalamus, a 12-channel net-tDCS protocol was generated (Neuroelectrics Starstim system), which included anodal, cathodal and sham stimulation. Ten participants with overweight or obesity were enrolled in a sham-controlled, crossover study. During stimulation or sham control, participants completed a stop-signal task to measure inhibitory control. Overall, stimulation was well tolerated. Anodal net-tDCS resulted in faster stop signal reaction time (SSRT) compared to sham (p = 0.039) and cathodal net-tDCS (p = 0.042). Baseline functional connectivity of the target network correlated with SSRT after anodal compared to sham stimulation (p = 0.016). These preliminary data indicate that modulating hypothalamus functional network connectivity via net-tDCS may result in improved inhibitory control. Further studies need to evaluate the effects on eating behavior and metabolism. AU - Ester-Nacke, T. AU - Berti, K. AU - Veit, R. AU - Dannecker, C. AU - Salvador, R.* AU - Ruffini, G.* AU - Heni, M. AU - Birkenfeld, A.L. AU - Plewnia, C.* AU - Preissl, H. AU - Kullmann, S. C1 - 70701 C2 - 55704 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Network-targeted transcranial direct current stimulation of the hypothalamus appetite-control network: A feasibility study. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Season of birth, viral infections, HLA haplogenotypes and non-HLA variants are implicated in the development of celiac disease and celiac disease autoimmunity, suggesting a combined role of genes and environmental exposures. The aim of the study was to further decipher the biological pathways conveying the season of birth effect in celiac disease autoimmunity to gain novel insights into the early pathogenesis of celiac disease. Interactions between season of birth, genetics, and early-life environmental factors on the risk of celiac autoimmunity were investigated in the multicenter TEDDY birth cohort study. Altogether 6523 genetically predisposed children were enrolled to long-term follow-up with prospective sampling and data collection at six research centers in the USA, Germany, Sweden and Finland. Celiac disease autoimmunity was defined as positive tissue transglutaminase antibodies in two consecutive serum samples. There was a significant season of birth effect on the risk of celiac autoimmunity. The effect was dependent on polymorphisms in CD247 gene encoding for CD3ζ chain of TCR-CD3 complex. In particular, children with major alleles for SNP rs864537A > G, in CD247 (AA genotype) had an excess risk of celiac autoimmunity when born March-August as compared to other months. The interaction of CD247 with season of birth on autoimmunity risk was accompanied by interactions with febrile infections between the ages of 3-6 months. Considering the important role of TCR-CD3 complex in the adaptive immune response and our findings here, CD247 variants and their possible effect of subgroups in autoimmunity development could be of interest in the design of future gene-environment studies of celiac disease. ClinicalTrials.gov Identifier: NCT00279318. AU - Eurén, A.* AU - Lynch, K.* AU - Lindfors, K.* AU - Parikh, H.* AU - Koletzko, S.* AU - Liu, E.* AU - Akolkar, B.* AU - Hagopian, W.* AU - Krischer, J.* AU - Rewers, M.* AU - Toppari, J.* AU - Ziegler, A.-G. AU - Agardh, D.* AU - Kurppa, K.* C1 - 72169 C2 - 56414 TI - Risk of celiac disease autoimmunity is modified by interactions between CD247 and environmental exposures. JO - Sci. Rep. VL - 14 IS - 1 PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Following the Coronavirus disease 2019 (COVID-19) pandemic, a large number of people continue to report Post-COVID symptoms (PCS). A wide variety of symptoms are described, including fatigue, post-exertional malaise and cognitive impairment. However, adequate objective diagnostic tests for PCS are not yet available. Since the neurotropism of SARS-CoV-2 could be a possible factor for cognitive impairment, the aim of this study was to clarify whether visual reaction time (RT) in a stereoscopic setting can be a marker in PCS diagnostics. The Virtual-Reality-Oculomotor-Test-System (VR-OTS) was used testing binocular vision in 9 gaze directions via stereoscopic stimuli displayed in a virtual reality (VR)-environment (disparity: 275″, 550″, 1100″) in 179 individuals: 130 patients with PCS and 49 healthy controls. The results from the generalized linear models indicated that both group membership (PCS vs. control) and covariates (age and sex) yielded statistically significant different RT across the models. Accounting for the effect of covariates a statistically significant difference of RT was observed between patients with PCS and controls (disparity 275″ p-value = 0.001; 550″ p-value = 0.001; 1100″ p-value = 0.003). Patients with PCS performed worse in RT in all gaze directions, respectively. Adjusting for the influence of covariates, correct responses (CR) differed significantly between patients with PCS and controls (disparity 275″ p-value < 0.001; 550″ p-value = 0.003; 1100″ p-value = 0.019). Statistically significant effects of covariates on RT were observed for sex (disparity 275″ p-value = 0.047; 550″ p-value = 0.012; 1100″ p-value = 0.005) and age (disparity 275″ p-value < 0.001; 550″ p-value < 0.001; 1100″ p-value < 0.001). However, regarding covariates, no significant effects were found for CR, except for age at disparity 275″ (p-value = 0.035). The present data suggested that the mentioned variables uniquely contributed to explain the variation of the response variable (RT, CR). RT and CR detecting 3D-stimuli in a virtual 3D- environment might offer novel functional diagnostic approaches in PCS. AU - Güttes, M.* AU - Lucio, M. AU - Skornia, A.* AU - Rühl, E.* AU - Steußloff, F.* AU - Zott, J.* AU - Mardin, C.* AU - Mehringer, W.* AU - Ganslmayer, M.* AU - Michelson, G.* AU - Hohberger, B.* C1 - 72314 C2 - 56591 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A case-control study of reaction time deficits in a 3D virtual reality in patients with Post-COVID syndrome. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies, presenting a persisting global health burden. Neutrophils have a double-edged role in tumor progression exhibiting both pro-tumor and anti-tumor functions. CD71, also known as transferrin receptor 1, performs a critical role in cellular iron uptake and is highly expressed on proliferating cells, and especially on activated immune cells. CD71 is known to be elevated in various types of solid cancers and is associated with poor prognosis, however, the expression of CD71 on neutrophils in PDAC and its potential clinical impact is still unknown. Therefore, we analyzed CD71 on circulating neutrophils in PDAC and clinical control patients and found a significant increased expression in PDAC patients. High expression of CD71 on neutrophils in PDAC patients was associated with reduced outcome compared to low expression. CD71 on neutrophils correlated positively with the levels of proinflammatory cytokines IL-6, IFN-γ, and growth factor ligands CD40-L, and BAFF in plasma of PDAC patients. Finally, we have demonstrated that high expression of CD71 on neutrophils was also associated with an increased expression of CD39 and CD25 on circulating T-cells. Based on our findings, we hypothesize that CD71 on neutrophils is associated with tumor progression in PDAC. Further studies are required to investigate the distinct functionality of CD71 expressing neutrophils and their potential clinical application. AU - Hansen, F.J.* AU - Mittelstädt, A.* AU - Clausen, F.N.* AU - Knoedler, S. AU - Knoedler, L.* AU - Klöckner, S.* AU - Kuchenreuther, I.* AU - Mazurie, J.* AU - Arnold, L.S.* AU - Anthuber, A.* AU - Jacobsen, A.V.* AU - Merkel, S.* AU - Weisel, N.* AU - Klösch, B.* AU - Karabiber, A.* AU - Tacyildiz, I.* AU - Czubayko, F.* AU - Reitberger, H.* AU - Gendy, A.E.* AU - Brunner, M.* AU - Krautz, C.* AU - Wolff, K.* AU - Mihai, S.* AU - Neufert, C.* AU - Siebler, J.* AU - Grützmann, R.* AU - Weber, G.F.* AU - David, P.* C1 - 71666 C2 - 56375 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - CD71 expressing circulating neutrophils serve as a novel prognostic biomarker for metastatic spread and reduced outcome in pancreatic ductal adenocarcinoma patients. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - The decrease in sperm count and infertility is a global issue that remains unresolved. By screening environmental bacterial isolates, we have found that a novel lactic acid bacterium, Lactiplantibacillus plantarum SNI3, increased testis size, testosterone levels, sperm count, sexual activity and fertility in mice that have consumed the bacteria for four weeks. The abundance of L. plantarum in the colon microbiome was positively associated with sperm count. Fecal microbiota transplantation (FMT) from L. plantarum SNI3-dosed mice improved testicular functions in microbiome-attenuated recipient animals. To identify mediators that confer pro-reproductive effects on the host, untargeted in situ mass spectrometry metabolomics was performed on testis samples of L. plantarum SNI3-treated and control mice. Enrichment pathway analysis revealed several perturbed metabolic pathways in the testis of treated mice. Within the testis, a dipeptide, glutamyl-glutamate (GluGlu) was the most upregulated metabolite following L. plantarum SNI3 administration. To validate the pro-reproductive feature of GluGlu, systemic and local injections of the dipeptide have been performed. γ-GluGlu increased sperm count but had no effect on testosterone. These findings highlight the role of γ-GluGlu in mediating spermatogenetic effects of L. plantarum on the male mouse host and -following relevant human clinical trials- may provide future tools for treating certain forms of male infertility. AU - Juhász, B.* AU - Horváth, K.* AU - Kuti, D.* AU - Shen, J. AU - Feuchtinger, A. AU - Zhang, C.-Y. AU - Bata-Vidács, I.* AU - Nagy, I.* AU - Kukolya, J.* AU - Witting, M. AU - Baranyi, M.* AU - Ferenczi, S.* AU - Walch, A.K. AU - Sun, N. AU - Kovács, K.J.* C1 - 71780 C2 - 56288 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Dipeptide metabolite, glutamyl-glutamate mediates microbe-host interaction to boost spermatogenesis. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - MEIS1 and MEIS2 encode highly conserved homeodomain transcription factors crucial for developmental processes in a wide range of tissues, including the brain. They can execute redundant functions when co-expressed in the same cell types, but their roles during early stages of neural differentiation have not been systematically compared. By separate knockout and overexpression of MEIS1 and MEIS2 in human neural stem cells, we find they control specific sets of target genes, associated with distinct biological processes. Integration of DNA binding sites with differential transcriptomics implicates MEIS1 to co-regulate gene expression by interaction with transcription factors of the SOX and FOX families. MEIS1 harbors the strongest risk factor for restless legs syndrome (RLS). Our data suggest that MEIS1 can directly regulate the RLS-associated genes NTNG1, MDGA1 and DACH1, constituting new approaches to study the elusive pathomechanism or RLS. AU - Kittke, V. AU - Zhao, C. AU - Lam, D.D. AU - Harrer, P. AU - Krezel, W.* AU - Schormair, B. AU - Oexle, K. AU - Winkelmann, J. C1 - 72491 C2 - 56631 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - RLS-associated MEIS transcription factors control distinct processes in human neural stem cells. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Inflammation is an important factor in Alzheimer's disease (AD). An NMR measurement in plasma, glycoprotein acetyls (GlycA), captures the overall level of protein production and glycosylation implicated in systemic inflammation. With its additional advantage of reducing biological variability, GlycA might be useful in monitoring the relationship between peripheral inflammation and brain changes relevant to AD. However, the associations between GlycA and these brain changes have not been fully evaluated. Here, we performed Spearman's correlation analyses to evaluate these associations cross-sectionally and determined whether GlycA can inform AD-relevant longitudinal measurements among participants in the Alzheimer's Disease Neuroimaging Initiative (n = 1506), with additional linear models and stratification analyses to evaluate the influences of sex or diagnosis status and confirm findings from Spearman's correlation analyses. We found that GlycA was elevated in AD patients compared to cognitively normal participants. GlycA correlated negatively with multiple concurrent regional brain volumes in females diagnosed with late mild cognitive impairment (LMCI) or AD. Baseline GlycA level was associated with executive function decline at 3-9 year follow-up in participants diagnosed with LMCI at baseline, with similar but not identical trends observed in the future decline of memory and entorhinal cortex volume. Results here indicated that GlycA is an inflammatory biomarker relevant to AD pathogenesis and that the stage of LMCI might be relevant to inflammation-related intervention. AU - Liang, N.* AU - Nho, K.* AU - Newman, J.W.* AU - Arnold, M. AU - Huynh, K.* AU - Meikle, P.J.* AU - Borkowski, K.* AU - Kaddurah-Daouk, R.* C1 - 71347 C2 - 56078 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Peripheral inflammation is associated with brain atrophy and cognitive decline linked to mild cognitive impairment and Alzheimer's disease. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Skin inflammation with the potential sequel of moist epitheliolysis and edema constitute the most frequent breast radiotherapy (RT) acute side effects. The aim of this study was to compare the predictive value of tissue-derived radiomics features to the total breast volume (TBV) for the moist cells epitheliolysis as a surrogate for skin inflammation, and edema. Radiomics features were extracted from computed tomography (CT) scans of 252 breast cancer patients from two volumes of interest: TBV and glandular tissue (GT). Machine learning classifiers were trained on radiomics and clinical features, which were evaluated for both side effects. The best radiomics model was a least absolute shrinkage and selection operator (LASSO) classifier, using TBV features, predicting moist cells epitheliolysis, achieving an area under the receiver operating characteristic (AUROC) of 0.74. This was comparable to TBV breast volume (AUROC of 0.75). Combined models of radiomics and clinical features did not improve performance. Exclusion of volume-correlated features slightly reduced the predictive performance (AUROC 0.71). We could demonstrate the general propensity of planning CT-based radiomics models to predict breast RT-dependent side effects. Mammary tissue was more predictive than glandular tissue. The radiomics features performance was influenced by their high correlation to TBV volume. AU - Llorián-Salvador, O.* AU - Windeler, N.* AU - Martin, N.* AU - Etzel, L.* AU - Andrade-Navarro, M.A.* AU - Bernhardt, D. AU - Rost, B.* AU - Borm, K.J.* AU - Combs, S.E. AU - Duma, M.N.* AU - Peeken, J.C. C1 - 71547 C2 - 56272 TI - CT-based radiomics for predicting breast cancer radiotherapy side effects. JO - Sci. Rep. VL - 14 IS - 1 PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-023-39841-9, published online 07 August 2023 The original version of this Article contained errors in Figure 4c. The values for ‘Storage temperature’, displayed on the X-axis, were inadvertently changed into the mean values of the depicted bars. The original Figure 4 and accompanying legend appear below. (Figure presented.) Stability of labile Cu2+ in serum. Repeatability and reproducibility of the assay are shown, including relative standard deviation (RSD) (a). Labile Cu2+ concentration in the reference serum depending on the number of freeze–thaw cycles (b) and storage temperature (c) are depicted. The labile Cu2+ concentration in 1% human reference serum upon spiking with 0 or 20 nM CuSO4 (N = 4) is presented (d). Statistically significant differences between labile Cu2+ values were determined with non-parametric Kruskal–Wallis with Dunn’s multiple comparison test (b), ordinary one way ANOVA followed by Tukey multiple comparison test (c), and unpaired t-test (*p < 0.05, **p < 0.01; ***p < 0.001). Results are presented as data points including mean ± SD of at least three independent experiments. The original Article has been corrected. AU - Maares, M.* AU - Haupt, A.* AU - Schüßler, C.* AU - Kulike-Koczula, M.* AU - Hackler, J.* AU - Keil, C.* AU - Mohr, I.* AU - Schomburg, L.* AU - Süssmuth, R.D.* AU - Zischka, H. AU - Merle, U.* AU - Haase, H.* C1 - 70523 C2 - 55363 TI - Correction to: A fluorometric assay to determine labile copper(II) ions in serum (Scientific Reports, (2023), 13, 1, (12807), 10.1038/s41598-023-39841-9). JO - Sci. Rep. VL - 14 IS - 1 PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - In this study, we aimed to understand the potential role of the gut microbiome in the development of Alzheimer's disease (AD). We took a multi-faceted approach to investigate this relationship. Urine metabolomics were examined in individuals with AD and controls, revealing decreased formate and fumarate concentrations in AD. Additionally, we utilised whole-genome sequencing (WGS) data obtained from a separate group of individuals with AD and controls. This information allowed us to create and investigate host-microbiome personalised whole-body metabolic models. Notably, AD individuals displayed diminished formate microbial secretion in these models. Additionally, we identified specific reactions responsible for the production of formate in the host, and interestingly, these reactions were linked to genes that have correlations with AD. This study suggests formate as a possible early AD marker and highlights genetic and microbiome contributions to its production. The reduced formate secretion and its genetic associations point to a complex connection between gut microbiota and AD. This holistic understanding might pave the way for novel diagnostic and therapeutic avenues in AD management. AU - Martinelli, F.* AU - Heinken, A.* AU - Henning, A.K.* AU - Ulmer, M.A. AU - Hensen, T.* AU - González, A.* AU - Arnold, M. AU - Asthana, S.* AU - Budde, K.* AU - Engelman, C.D.* AU - Estaki, M.* AU - Grabe, H.J.* AU - Heston, M.B.* AU - Johnson, S.* AU - Kastenmüller, G. AU - Martino, C.* AU - McDonald, D.* AU - Rey, F.E.* AU - Kilimann, I.* AU - Peters, O.* AU - Wang, X.* AU - Spruth, E.J.* AU - Schneider, A.* AU - Fliessbach, K.* AU - Wiltfang, J.* AU - Hansen, N.* AU - Glanz, W.* AU - Buerger, K.* AU - Janowitz, D.* AU - Laske, C.* AU - Munk, M.H.* AU - Spottke, A.* AU - Roy, N.* AU - Nauck, M.* AU - Teipel, S.* AU - Knight, R.* AU - Kaddurah-Daouk, R.F.* AU - Bendlin, B.B.* AU - Hertel, J.* AU - Thiele, I.* C1 - 70253 C2 - 55469 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AU - Martinelli, F.* AU - Heinken, A.* AU - Henning, A.K.* AU - Ulmer, M.A. AU - Hensen, T.* AU - González, A.* AU - Arnold, M. AU - Asthana, S.* AU - Budde, K.* AU - Engelman, C.D.* AU - Estaki, M.* AU - Grabe, H.J.* AU - Heston, M.B.* AU - Johnson, S.* AU - Kastenmüller, G. AU - Martino, C.* AU - McDonald, D.* AU - Rey, F.E.* AU - Kilimann, I.* AU - Peters, O.* AU - Wang, X.* AU - Spruth, E.J.* AU - Schneider, A.* AU - Fliessbach, K.* AU - Wiltfang, J.* AU - Hansen, N.* AU - WenzelGlanz* AU - Buerger, K.* AU - Janowitz, D.* AU - Laske, C.* AU - Munk, M.H.* AU - Spottke, A.* AU - Roy, N.* AU - Nauck, M.* AU - Teipel, S.* AU - Knight, R.* AU - Kaddurah-Daouk, R.F.* AU - Bendlin, B.B.* AU - Hertel, J.* AU - Thiele, I.* C1 - 72296 C2 - 56556 TI - Author Correction: Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. JO - Sci. Rep. VL - 14 IS - 1 PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - When planning for epilepsy surgery, multiple potential sites for resection may be identified through anatomical imaging. Magnetoencephalography (MEG) using optically pumped sensors (OP-MEG) is a non-invasive functional neuroimaging technique which could be used to help identify the epileptogenic zone from these candidate regions. Here we test the utility of a-priori information from anatomical imaging for differentiating potential lesion sites with OP-MEG. We investigate a number of scenarios: whether to use rigid or flexible sensor arrays, with or without a-priori source information and with or without source modelling errors. We simulated OP-MEG recordings for 1309 potential lesion sites identified from anatomical images in the Multi-centre Epilepsy Lesion Detection (MELD) project. To localise the simulated data, we used three source inversion schemes: unconstrained, prior source locations at centre of the candidate sites, and prior source locations within a volume around the lesion location. We found that prior knowledge of the candidate lesion zones made the inversion robust to errors in sensor gain, orientation and even location. When the reconstruction was too highly restricted and the source assumptions were inaccurate, the utility of this a-priori information was undermined. Overall, we found that constraining the reconstruction to the region including and around the participant’s potential lesion sites provided the best compromise of robustness against modelling or measurement error. AU - Mellor, S.* AU - Timms, R.C.* AU - O’Neill, G.C.* AU - Tierney, T.M.* AU - Spedden, M.E.* AU - Brookes, M.J.* AU - Wagstyl, K.* AU - Barnes, G.R.* AU - MELD Project Consortium (Spitzer, H.) C1 - 70010 C2 - 55359 TI - Combining OPM and lesion mapping data for epilepsy surgery planning: A simulation study. JO - Sci. Rep. VL - 14 IS - 1 PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery. AU - Atomwise AIMS Program (Popowicz, G.M.) C1 - 70598 C2 - 55591 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - AI is a viable alternative to high throughput screening: A 318-target study. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-024-54655-z, published online 02 April 2024 The original version of this Article contained errors. In the original version of this article, Ellie Giles was omitted from the Author list. Additionally, the following Affiliation information has been updated: 1. Affiliation 25 was incorrect. Affiliation 25 ‘Queensland University of Technology, Brisbane, USA.’ now reads, ‘Queensland University of Technology, Brisbane, Australia.’ 2. Marta Giorgis was incorrectly affiliated with the ‘University of Aberdeen, Aberdeen, UK.’ The correct Affiliation is listed below: ‘University of Turin, Turin, Italy.’ 3. Affiliations 52, 125 and 261 were duplicated. As a result, the correct Affiliation for Andrew B. Herr, Benjamin Liou, David A. Hildeman, Joseph J. Maciag, Ying Sun, Durga Krishnamurthy, and Stephen N. Waggoner is: ‘Cincinnati Children’s Hospital Medical Center, Cincinnati, USA.’ Furthermore, an outdated version of Figure 1 was typeset. The original Figure 1 and accompanying legend appear below. (Figure presented.) Pairs of representative compounds extracted from AI patents (right) and corresponding prior patents (left) for clinical-stage programs (CDK792,93, A2Ar-antagonist94,95, MALT196,97, QPCTL98,99, USP1100,101, and 3CLpro102,103). The identical atoms between the chemical structures are highlighted in red. Lastly, The Acknowledgements section contained an error. “See Supplementary section S1.” now reads, “See Supplementary section S2.” The original Article has been corrected. AU - Atomwise AIMS Program (Popowicz, G.M.) C1 - 71863 C2 - 56295 TI - Correction to: AI is a viable alternative to high throughput screening: A 318-target study (Scientific Reports, (2024), 14, 1, (7526), 10.1038/s41598-024-54655-z). JO - Sci. Rep. VL - 14 IS - 1 PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Investigating acute stress responses is crucial to understanding the underlying mechanisms of stress. Current stress assessment methods include self-reports that can be biased and biomarkers that are often based on complex laboratory procedures. A promising additional modality for stress assessment might be the observation of body movements, which are affected by negative emotions and threatening situations. In this paper, we investigated the relationship between acute psychosocial stress induction and body posture and movements. We collected motion data from N = 59 individuals over two studies (Pilot Study: N = 20, Main Study: N = 39) using inertial measurement unit (IMU)-based motion capture suits. In both studies, individuals underwent the Trier Social Stress Test (TSST) and a stress-free control condition (friendly-TSST; f-TSST) in randomized order. Our results show that acute stress induction leads to a reproducible freezing behavior, characterized by less overall motion as well as more and longer periods of no movement. Based on these data, we trained machine learning pipelines to detect acute stress solely from movement information, achieving an accuracy of 75.0 ± 17.7 % (Pilot Study) and 73.4 ± 7.7 % (Main Study). This, for the first time, suggests that body posture and movements can be used to detect whether individuals are exposed to acute psychosocial stress. While more studies are needed to further validate our approach, we are convinced that motion information can be a valuable extension to the existing biomarkers and can help to obtain a more holistic picture of the human stress response. Our work is the first to systematically explore the use of full-body body posture and movement to gain novel insights into the human stress response and its effects on the body and mind. AU - Richer, R.* AU - Koch, V.* AU - Abel, L.* AU - Hauck, F.* AU - Kurz, M.* AU - Ringgold, V.* AU - Müller, V.* AU - Küderle, A.* AU - Schindler-Gmelch, L.* AU - Eskofier, B.M. AU - Rohleder, N.* C1 - 70418 C2 - 55610 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Machine learning-based detection of acute psychosocial stress from body posture and movements. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - FLASH-radiotherapy may provide significant sparing of healthy tissue through ultra-high dose rates in protons, electrons, and x-rays while maintaining the tumor control. Key factors for the FLASH effect might be oxygen depletion, the immune system, and the irradiated blood volume, but none could be fully confirmed yet. Therefore, further investigations are necessary. We investigated the protective (tissue sparing) effect of FLASH in proton treatment using an in-vivo mouse ear model. The right ears of Balb/c mice were irradiated with 20 MeV protons at the ion microprobe SNAKE in Garching near Munich by using three dose rates (Conv = 0.06 Gy/s, Flash9 = 9.3 Gy/s and Flash930 = 930 Gy/s) at a total dose of 23 Gy or 33 Gy. The ear thickness, desquamation, and erythema combined in an inflammation score were measured for 180 days. The cytokines TGF-β1, TNF-α, IL1α, and IL1β were analyzed in the blood sampled in the first 4 weeks and at termination day. No differences in inflammation reactions were visible in the 23 Gy group for the different dose rates. In the 33 Gy group, the ear swelling and the inflammation score for Flash9 was reduced by (57 ± 12) % and (67 ± 17) % and for Flash930 by (40 ± 13) % and (50 ± 17) % compared to the Conv dose rate. No changes in the cytokines in the blood could be measured. However, an estimation of the irradiated blood volume demonstrates, that 100-times more blood is irradiated when using Conv compared to using Flash9 or Flash930. This indicates that blood might play a role in the underlying mechanisms in the protective effect of FLASH. AU - Rudigkeit, S.* AU - Schmid, T.E. AU - Dombrowsky, A. AU - Stolz, J. AU - Bartzsch, S. AU - Chen, C.B.* AU - Matejka, N.* AU - Sammer, M.* AU - Bergmaier, A.* AU - Dollinger, G.* AU - Reindl, J.* C1 - 69829 C2 - 55271 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Proton-FLASH: Effects of ultra-high dose rate irradiation on an in-vivo mouse ear model. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-022-06014-z, published online 10 February 2022 The original version of this Article contained errors in Figure 3 where the panels (q) and (r) with the two hormones, estrone and estradiol, were omitted. The original Figure 3 and accompanying legend appear below. (Figure presented.) The caption to be typeset alongside it: Steroid hormones in serum. Changes of the steroid concentrations (ng/mL) in serum of cows with normal versus high body condition score (NBCS, HBCS) at week 7 ante partum, as well as week 1, 3 and 12 postpartum. Data are given as means ± SEM. Asterisks (*) indicate differences (P ≤ 0.05) between HBCS and NBCS cows within the time points. Trends (P ≤ 0.10) for differences between the groups are indicated by daggers (†). The original Article has been corrected. AU - Schuh, K.* AU - Häussler, S.* AU - Sadri, H.* AU - Prehn, C. AU - Lintelmann, J. AU - Adamski, J. AU - Koch, C.* AU - Frieten, D.* AU - Ghaffari, M.H.* AU - Dusel, G.* AU - Sauerwein, H.* C1 - 69980 C2 - 55348 TI - Author Correction: Blood and adipose tissue steroid metabolomics and mRNA expression of steroidogenic enzymes in periparturient dairy cows differing in body condition. JO - Sci. Rep. VL - 14 IS - 1 PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - In contemporary healthcare, effective risk stratification in the general population is vital amidst rising chronic disease rates and an ageing demographic. Deceleration Capacity of the heart rate (DC), derived from 24-hour Holter electrocardiograms, holds promise in risk stratification for cardiac patients. However, the potential of short-term electrocardiograms of five minutes duration for population screening has not been fully explored. Our study aims to investigate the utility of Deceleration Capacity derived from short-term electrocardiograms as a scalable, fully-automated screening tool for predicting long-term mortality risk in the general population. Within a cohort of a representative population-based survey in Germany (KORA-KMC-study), 823 participants with sinus rhythm aged 27 to 76 years at enrollment (females 47.4%) were followed for a median of 13.4 years (IQR 13.1-13.6). All-cause mortality was defined as the primary endpoint and observed in 159 participants. Deceleration Capacity was calculated from 5-minute 12-lead electrocardiograms by a fully automated approach. Participants were divided into three predefined risk categories: DCcategory0 - low-risk (> 4.5ms); DCcategory1 - intermediate-risk (2.5-4.5ms); and DCcategory2 - high-risk (≤ 2.5ms). More than two-thirds of the participants (n = 564, 68.5%) fell into DCcategory0, about one-fifth (n = 168, 20.4%) into DCcategory1, and about one-tenth (n = 91, 11.1%) into DCcategory2. Estimated 13-years mortality in the risk groups was 16.7%, 23.5%, and 49.1%, respectively (p < 0.001). Adjusting for age, life-style-related risk factors, and comorbidities, increased mortality risk was observed for DCcategory2 (HR 2.34, 95%-CI 1.56-3.50). Deceleration Capacity, derived automatically from brief 5-minute electrocardiogram recordings, emerges as a robust, feasible, and independent predictor of long-term mortality risk in the general population. AU - Steger, A.* AU - Barthel, P.* AU - Müller, A.* AU - Rückert-Eheberg, I.-M. AU - Linkohr, B. AU - Allescher, J.* AU - Maier, M.* AU - Hapfelmeier, A.* AU - Martens, E.* AU - Heidegger, H.H.* AU - Müller, A.M.* AU - Rizas, K.D.* AU - Kääb, S.* AU - Sinner, M.F.* AU - Sinnecker, D.* AU - Laugwitz, K.L.* AU - Peters, A. AU - Schmidt, G.* C1 - 72868 C2 - 56761 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Deceleration capacity derived from a five-minute electrocardiogram predicts mortality in the general population. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - This study investigates impaired awareness of hypoglycaemia (IAH), a complication of insulin therapy affecting 20-40% of individuals with type 1 diabetes. The exact pathophysiology is unclear, therefore we sought to identify metabolic signatures in IAH to elucidate potential pathophysiological pathways. Plasma samples from 578 individuals of the Dutch type 1 diabetes biomarker cohort, 67 with IAH and 108 without IAH (NAH) were analysed using the targeted metabolomics Biocrates AbsoluteIDQ p180 assay. Eleven metabolites were significantly associated with IAH. Genome-wide association studies of these 11 metabolites identified significant single nucleotide polymorphisms (SNPs) in C22:1-OH and phosphatidylcholine diacyl C36:6. After adjusting for the SNPs, 11 sphingomyelins and phosphatidylcholines were significantly higher in the IAH group in comparison to NAH. These metabolites are important components of the cell membrane and have been implicated to play a role in cell signalling in diabetes. These findings demonstrate the potential role of phosphatidylcholine and sphingomyelins in IAH. AU - Varkevisser, R.D.M.* AU - Cecil, A. AU - Prehn, C. AU - Mul, D.* AU - Aanstoot, H.J.* AU - Paterson, A.D.* AU - Wolffenbuttel, B.H.R.* AU - van der Klauw, M.M.* C1 - 70037 C2 - 55370 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Metabolomic associations of impaired awareness of hypoglycaemia in type 1 diabetes. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Large population-based cohort studies utilizing device-based measures of physical activity are crucial to close important research gaps regarding the potential protective effects of physical activity on chronic diseases. The present study details the quality control processes and the derivation of physical activity metrics from 100 Hz accelerometer data collected in the German National Cohort (NAKO). During the 2014 to 2019 baseline assessment, a subsample of NAKO participants wore a triaxial ActiGraph accelerometer on their right hip for seven consecutive days. Auto-calibration, signal feature calculations including Euclidean Norm Minus One (ENMO) and Mean Amplitude Deviation (MAD), identification of non-wear time, and imputation, were conducted using the R package GGIR version 2.10-3. A total of 73,334 participants contributed data for accelerometry analysis, of whom 63,236 provided valid data. The average ENMO was 11.7 ± 3.7 mg (milli gravitational acceleration) and the average MAD was 19.9 ± 6.1 mg. Notably, acceleration summary metrics were higher in men than women and diminished with increasing age. Work generated in the present study will facilitate harmonized analysis, reproducibility, and utilization of NAKO accelerometry data. The NAKO accelerometry dataset represents a valuable asset for physical activity research and will be accessible through a specified application process. AU - Weber, A.* AU - van Hees, V.T.* AU - Stein, M.J.* AU - Gastell, S.* AU - Steindorf, K.* AU - Herbolsheimer, F.* AU - Ostrzinski, S.* AU - Pischon, T.* AU - Brandes, M.* AU - Krist, L.* AU - Marschollek, M.* AU - Greiser, K.H.* AU - Nimptsch, K.* AU - Brandes, B.* AU - Jochem, C.* AU - Sedlmeier, A.M.* AU - Berger, K.* AU - Brenner, H.* AU - Buck, C.* AU - Castell, S.* AU - Dörr, M.* AU - Emmel, C.* AU - Fischer, B.* AU - Flexeder, C. AU - Harth, V.* AU - Hebestreit, A.* AU - Heise, J.K.* AU - Holleczek, B.* AU - Keil, T.* AU - Koch-Gallenkamp, L.* AU - Lieb, W.* AU - Meinke-Franze, C.* AU - Michels, K.B.* AU - Mikolajczyk, R.* AU - Kluttig, A.* AU - Obi, N.* AU - Peters, A. AU - Schmidt, B.* AU - Schipf, S.* AU - Schulze, M.B.* AU - Teismann, H.* AU - Waniek, S.* AU - Willich, S.N.* AU - Leitzmann, M.F.* AU - Baurecht, H.* C1 - 70432 C2 - 55242 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Large-scale assessment of physical activity in a population using high-resolution hip-worn accelerometry: The German National Cohort (NAKO). JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Left atrial (LA) physiology and hemodynamics are intimately connected to cardiac and lung function in health and disease. This study examined the relationship between MRI-based left atrial (LA) size and function with MRI-based lung volume and pulmonary function testing (PFT) parameters in the population-based KORA study cohort of 400 participants without overt cardiovascular disease. MRI quantification assessed LA size/function in sequences with and without ECG synchronization, alongside lung volume. Regression analysis explored the relationship of LA with MRI lung volume and PFT parameters. Among 378 participants (average age 56.3 ± 9.2 years; 42.3% women), non-gated LA size averaged 16.8 cm2, while maximal and minimal LA size from gated measurements were 19.6 cm2 and 11.9 cm2 respectively. The average MRI-derived lung volume was 4.0 L, with PFT showing a total lung capacity of 6.2 L, residual lung volume of 2.1 L, and forced vital capacity of 4.1 L. Multivariate regression analysis, adjusted for age, gender, and cardiovascular risk factors, revealed an inverse association between maximum LA size, non-gated LA, and LA area fraction with lung volume (ß = - 0.03, p = 0.006; ß = - 0.03, p = 0.021; ß = - 0.01, p = 0.012), with no significant association with PFT parameters. This suggests that MRI-based assessment may offer greater sensitivity in detecting subclinical LA impairment than PFT. AU - Wintergerst, C.* AU - Lorbeer, R.* AU - Mujaj, B.* AU - Bulwer, B.E.* AU - Rospleszcz, S.* AU - Askani, E.* AU - Schulz, H. AU - Karrasch, S. AU - Peters, A. AU - Schlett, C.L.* AU - Bamberg, F.* AU - von Krüchten, R.* C1 - 71661 C2 - 56374 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Subclinical impairment of the left atrium is associated with MRI-based lung volume but not with parameters from pulmonary function testing. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - The significant advances in the differentiation of human pluripotent stem (hPS) cells into pancreatic endocrine cells, including functional β-cells, have been based on a detailed understanding of the underlying developmental mechanisms. However, the final differentiation steps, leading from endocrine progenitors to mono-hormonal and mature pancreatic endocrine cells, remain to be fully understood and this is reflected in the remaining shortcomings of the hPS cell-derived islet cells (SC-islet cells), which include a lack of β-cell maturation and variability among different cell lines. Additional signals and modifications of the final differentiation steps will have to be assessed in a combinatorial manner to address the remaining issues and appropriate reporter lines would be useful in this undertaking. Here we report the generation and functional validation of hPS cell reporter lines that can monitor the generation of INS+ and GCG+ cells and their resolution into mono-hormonal cells (INSeGFP, INSeGFP/GCGmCHERRY) as well as β-cell maturation (INSeGFP/MAFAmCHERRY) and function (INSGCaMP6). The reporter hPS cell lines maintained strong and widespread expression of pluripotency markers and differentiated efficiently into definitive endoderm and pancreatic progenitor (PP) cells. PP cells from all lines differentiated efficiently into islet cell clusters that robustly expressed the corresponding reporters and contained glucose-responsive, insulin-producing cells. To demonstrate the applicability of these hPS cell reporter lines in a high-content live imaging approach for the identification of optimal differentiation conditions, we adapted our differentiation procedure to generate SC-islet clusters in microwells. This allowed the live confocal imaging of multiple SC-islets for a single condition and, using this approach, we found that the use of the N21 supplement in the last stage of the differentiation increased the number of monohormonal β-cells without affecting the number of α-cells in the SC-islets. The hPS cell reporter lines and the high-content live imaging approach described here will enable the efficient assessment of multiple conditions for the optimal differentiation and maturation of SC-islets. AU - Zanfrini, E. AU - Bandral, M. AU - Jarc, L. AU - Ramirez-Torres, M.A. AU - Pezzolla, D. AU - Kufrin, V. AU - Rodriguez-Aznar, E. AU - Mojica Avila, A.K. AU - Cohrs, C.M. AU - Speier, S. AU - Neumann, K.* AU - Gavalas, A. C1 - 71531 C2 - 56261 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Generation and application of novel hES cell reporter lines for the differentiation and maturation of hPS cell-derived islet-like clusters. JO - Sci. Rep. VL - 14 IS - 1 PB - Nature Portfolio PY - 2024 SN - 2045-2322 ER - TY - JOUR AB - Integration of the omics data, including metabolomics and proteomics, provides a unique opportunity to search for new associations within metabolic disorders, including Alzheimer's disease. Using metabolomics, we have previously profiled oxylipins, endocannabinoids, bile acids, and steroids in 293 CSF and 202 matched plasma samples from AD cases and healthy controls and identified both central and peripheral markers of AD pathology within inflammation-regulating cytochrome p450/soluble epoxide hydrolase pathway. Additionally, using proteomics, we have identified five cerebrospinal fluid protein panels, involved in the regulation of energy metabolism, vasculature, myelin/oligodendrocyte, glia/inflammation, and synapses/neurons, affected in AD, and reflective of AD-related changes in the brain. In the current manuscript, using metabolomics-proteomics data integration, we describe new associations between peripheral and central lipid mediators, with the above-described CSF protein panels. Particularly strong associations were observed between cytochrome p450/soluble epoxide hydrolase metabolites, bile acids, and proteins involved in glycolysis, blood coagulation, and vascular inflammation and the regulators of extracellular matrix. Those metabolic associations were not observed at the gene-co-expression level in the central nervous system. In summary, this manuscript provides new information regarding Alzheimer's disease, linking both central and peripheral metabolism, and illustrates the necessity for the "omics" data integration to uncover associations beyond gene co-expression. AU - Borkowski, K.* AU - Seyfried, N.T.* AU - Arnold, M. AU - Lah, J.J.* AU - Levey, A.I.* AU - Hales, C.M.* AU - Dammer, E.B.* AU - Blach, C.* AU - Louie, G.* AU - Kaddurah-Daouk, R.* AU - Newman, J.W.* C1 - 67964 C2 - 54442 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Integration of plasma and CSF metabolomics with CSF proteomic reveals novel associations between lipid mediators and central nervous system vascular and energy metabolism. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Adeno-associated viral (AAV) vector suspensions produced in either human derived HEK cells or in Spodoptera frugiperda (Sf9) insect cells differ in terms of residual host cell components as well as species-specific post-translational modifications displayed on the AAV capsid proteins. Here we analysed the impact of these differences on the immunogenic properties of the vector. We stimulated human plasmacytoid dendritic cells with various lots of HEK cell-produced and Sf9 cell-produced AAV-CMV-eGFP vectors derived from different manufacturers. We found that AAV8-CMV-eGFP as well as AAV2-CMV-eGFP vectors induced lot-specific but not production platform-specific or manufacturer-specific inflammatory cytokine responses. These could be reduced or abolished by blocking toll-like receptor 9 signalling or by enzymatically reducing DNA in the vector lots using DNase. Successful HEK cell transduction by DNase-treated AAV lots and DNA analyses demonstrated that DNase did not affect the integrity of the vector but degraded extra-viral DNA. We conclude that both HEK- and Sf9-cell derived AAV preparations can contain immunogenic extra-viral DNA components which can trigger lot-specific inflammatory immune responses. This suggests that improved strategies to remove extra-viral DNA impurities may be instrumental in reducing the immunogenic properties of AAV vector preparations. AU - Bücher, K.* AU - Rodríguez-Bocanegra, E.* AU - Wissinger, B.* AU - Strasser, T.* AU - Clark, S.J.* AU - Birkenfeld, A.L. AU - Siegel-Axel, D. AU - Fischer, M.D.* C1 - 67398 C2 - 54163 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Extra-viral DNA in adeno-associated viral vector preparations induces TLR9-dependent innate immune responses in human plasmacytoid dendritic cells. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Clival tumors present challenging entities regarding their treatment options. Due to their proximity to critical neurovascular structures, the operative goal of gross total tumor resection is rendered more difficult by a high risk of neurological deficits. Retrospective cohort study of patients treated for clival neoplasms through a transnasal endoscopic approach between 2009 and 2020. Assessment of preoperative clinical status, length of operation, number of approaches, pre- and postoperative radiotherapy, and the clinical outcome. Presentation and clinical correlation with our new classification. In total, 59 transnasal endoscopic operations were performed on 42 patients over 12 years. Most lesions were clival chordomas; 63% of the lesions did not reach the brainstem. Cranial nerve impairment was present in 67% of the patients, and 75% of the patients with cranial nerve palsy improved after surgical treatment. Interrater reliability for our proposed tumor extension classification showed a substantial agreement (Cohen's κ = 0.766). The transnasal approach was sufficient to achieve a complete tumor resection in 74% of the patients. Clival tumors exhibit heterogeneous characteristics. Depending on clival tumor extension, the transnasal endoscopic approach can present a safe surgical technique for upper and middle clival tumor resection, with a low risk of perioperative complications and a high rate of postoperative improvement. AU - Butenschoen, V.M.* AU - Krauss, P.* AU - Bernhardt, D. AU - Negwer, C.* AU - Combs, S.E. AU - Meyer, B.* AU - Gempt, J.* C1 - 67450 C2 - 54110 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - The transnasal endoscopic approach for resection of clival tumors: a single-center experience. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - The availability of polygenic scores for type 2 diabetes (T2D) raises the question, whether assessing family history might become redundant. However, family history not only involves shared genetics, but also shared environment. It was the aim of this study to assess the independent and combined effects of one family risk score (FamRS) and a polygenic score (PGS) on prevalent and incident T2D risk in a population-based study from Germany (n = 3071). The study was conducted in 2004/2005 with up to 12 years of follow-up. The FamRS takes into account not only the number of diseased first grade relatives, but also age at onset of the relatives and age of participants. 256 prevalent and additional 163 incident T2D cases were recorded. Prevalence of T2D increased sharply for those within the top quantile of the PGS distribution resulting in an OR of 19.16 (p < 2 × 10-16) for the top 20% compared to the remainder of the population, independent of age, sex, BMI, physical activity and FamRS. On the other hand, having a very strong family risk compared to average was still associated with an OR of 2.78 (p = 0.001), independent of the aforementioned factors and the PGS. The PGS and FamRS were only slightly correlated (r2Spearman = 0.018). The combined contribution of both factors varied with varying age-groups, though, with decreasing influence of the PGS with increasing age. To conclude, both, genetic information and family history are relevant for the prediction of T2D risk and might be used for identification of high risk groups to personalize prevention measures. AU - Duschek, E.* AU - Forer, L.* AU - Schönherr, S.* AU - Gieger, C. AU - Peters, A. AU - Kronenberg, F.* AU - Grallert, H. AU - Lamina, C.* C1 - 67693 C2 - 54000 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A polygenic and family risk score are both independently associated with risk of type 2 diabetes in a population-based study. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Microscopic compartmentalization is beneficial in synthetic chemistry and indispensable for the evolution of life to separate a reactive “inside” from a hydrolyzing “outside”. Here, we show compartmentalization in aqueous solution containing mixtures of fatty acids up to 19 carbon atoms which were synthesized by one-pot reactions of acetylene and carbon monoxide in contact with nickel sulfide at 105 °C, reaction requirements which are compatible to Hadean Early Earth conditions. Based on confocal, dynamic light scattering (DLS) and transmission electron microscopy (TEM) measurements, vesicle-like structures with diameters of 10–150 nm are formed after solvent extraction and resolubilisation. Moreover fluorescent dye was encapsulated into the structures proving their vesicular properties. This self-assembly could also have occurred on Early Earth as a crucial step in establishing simple membranes of proto-cells as a prerequisite in the evolution of metabolism and life. AU - Geisberger, T.* AU - Diederich, P. AU - Kaiser, C.J.O.* AU - Vogele, K.* AU - Ruf, A.* AU - Seitz, C.* AU - Simmel, F.* AU - Eisenreich, W.* AU - Schmitt-Kopplin, P. AU - Huber, C.* C1 - 68274 C2 - 54799 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 8 TI - Formation of vesicular structures from fatty acids formed under simulated volcanic hydrothermal conditions. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Lyme borreliosis (LB) is caused by the transmission of Borrelia burgdorferi s.l. from ticks to humans. Climate affects tick abundance, and climate change is projected to promote shifts in abundance in Europe, potentially increasing human exposure. We analyzed serum samples collected between the years 2014-2019 from German National Cohort (NAKO) participants at four study sites (Augsburg, Berlin, Hanover, Münster) for immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies using an enzyme-linked immunosorbent assay (ELISA) and line blot immunoassay as confirmatory test for positive and equivocal ELISA samples. We reported crude and weighted seropositivity proportions for local estimates. We used mixed model analysis to investigate associated factors, such as age, sex, migration background, or animal contacts. We determined the serostatus of 14,207 participants. The weighted seropositivity proportions were 3.4% (IgG) and 0.4% (IgM) in Augsburg, 4.1% (IgG) and 0.6% (IgM) in northern Berlin, 3.0% (IgG) and 0.9% (IgM) in Hanover, and 2.7% (IgG) and 0.6% (IgM) in Münster. We found higher odds for IgG seropositivity with advancing age (p < 0.001), among males compared to females (p < 0.001) and reduced odds among participants with migration background compared to those without (p = 0.001). We did not find evidence for an association between serostatus and depression, children within the household, or animal contact, respectively. We found low seropositivity proportions and indications of differences across the study locations, although between-group comparisons did not yield significant results. Comparisons to earlier research are subject to important limitations; however, our results indicate no major increases in seropositivity over time. Nevertheless, monitoring of seropositivity remains critical in light of potential climate-related Borrelia exposure. AU - Hassenstein, M.J.* AU - Pischon, T.* AU - Karch, A.* AU - Peters, A. AU - Kerrinnes, T.* AU - Teismann, H.* AU - Schneider, A.E. AU - Thierry, S. AU - Moreno Velásquez, I.* AU - Janke, J.* AU - Kemmling, Y.* AU - Castell, S.* C1 - 68885 C2 - 53743 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Seropositivity of Borrelia burgdorferi s.l. in Germany-an analysis across four German National Cohort (NAKO) study sites. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Nausea often occurs in stressful situations, such as chemotherapy or surgery. Clinically relevant placebo effects in nausea have been demonstrated, but it remains unclear whether stress has an impact on these effects. The aim of this experimental study was to investigate the interplay between acute stress and placebo effects in nausea. 80 healthy female volunteers susceptible to motion sickness were randomly assigned to either the Maastricht Acute Stress Test or a non-stress control condition, and to either placebo treatment or no treatment. Nausea was induced by a virtual vection drum and behavioral, psychophysiological as well as humoral parameters were repeatedly assessed. Manipulation checks confirmed increased cortisol levels and negative emotions in the stressed groups. In the non-stressed groups, the placebo intervention improved nausea, symptoms of motion sickness, and gastric myoelectrical activity (normo-to-tachy (NTT) ratio). In the stressed groups, the beneficial effects of the placebo intervention on nausea and motion sickness remained unchanged, whereas no improvement of the gastric NTT ratio was observed. Results suggest that placebo effects on symptoms of nausea and motion sickness are resistant to experimentally-induced stress. Stress most likely interfered with the validity of the gastric NTT ratio to measure nausea and thus the gastric placebo effect. AU - Jacob, C.* AU - Olliges, E.* AU - Haile, A.* AU - Hoffmann, V.* AU - Jacobi, B.* AU - Steinkopf, L.* AU - Lanz, M.* AU - Wittmann, M.* AU - Tschöp, M.H. AU - Meissner, K.* C1 - 68501 C2 - 54675 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Placebo effects on nausea and motion sickness are resistant to experimentally-induced stress. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Differentiating benign renal oncocytic tumors and malignant renal cell carcinoma (RCC) on imaging and histopathology is a critical problem that presents an everyday clinical challenge. This manuscript aims to demonstrate a novel methodology integrating metabolomics with radiomics features (RF) to differentiate between benign oncocytic neoplasia and malignant renal tumors. For this purpose, thirty-three renal tumors (14 renal oncocytic tumors and 19 RCC) were prospectively collected and histopathologically characterised. Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) was used to extract metabolomics data, while RF were extracted from CT scans of the same tumors. Statistical integration was used to generate multilevel network communities of -omics features. Metabolites and RF critical for the differentiation between the two groups (delta centrality > 0.1) were used for pathway enrichment analysis and machine learning classifier (XGboost) development. Receiver operating characteristics (ROC) curves and areas under the curve (AUC) were used to assess classifier performance. Radiometabolomics analysis demonstrated differential network node configuration between benign and malignant renal tumors. Fourteen nodes (6 RF and 8 metabolites) were crucial in distinguishing between the two groups. The combined radiometabolomics model achieved an AUC of 86.4%, whereas metabolomics-only and radiomics-only classifiers achieved AUC of 72.7% and 68.2%, respectively. Analysis of significant metabolite nodes identified three distinct tumour clusters (malignant, benign, and mixed) and differentially enriched metabolic pathways. In conclusion, radiometabolomics integration has been presented as an approach to evaluate disease entities. In our case study, the method identified RF and metabolites important in differentiating between benign oncocytic neoplasia and malignant renal tumors, highlighting pathways differentially expressed between the two groups. Key metabolites and RF identified by radiometabolomics can be used to improve the identification and differentiation between renal neoplasms. AU - Klontzas, M.E.* AU - Koltsakis, E.* AU - Kalarakis, G.* AU - Trpkov, K.* AU - Papathomas, T.* AU - Sun, N. AU - Walch, A.K. AU - Karantanas, A.H.* AU - Tzortzakakis, A.* C1 - 68035 C2 - 54513 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A pilot radiometabolomics integration study for the characterization of renal oncocytic neoplasia. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Patients suffering from painful spinal bone metastases (PSBMs) often undergo palliative radiation therapy (RT), with an efficacy of approximately two thirds of patients. In this exploratory investigation, we assessed the effectiveness of machine learning (ML) models trained on radiomics, semantic and clinical features to estimate complete pain response. Gross tumour volumes (GTV) and clinical target volumes (CTV) of 261 PSBMs were segmented on planning computed tomography (CT) scans. Radiomics, semantic and clinical features were collected for all patients. Random forest (RFC) and support vector machine (SVM) classifiers were compared using repeated nested cross-validation. The best radiomics classifier was trained on CTV with an area under the receiver-operator curve (AUROC) of 0.62 ± 0.01 (RFC; 95% confidence interval). The semantic model achieved a comparable AUROC of 0.63 ± 0.01 (RFC), significantly below the clinical model (SVM, AUROC: 0.80 ± 0.01); and slightly lower than the spinal instability neoplastic score (SINS; LR, AUROC: 0.65 ± 0.01). A combined model did not improve performance (AUROC: 0,74 ± 0,01). We could demonstrate that radiomics and semantic analyses of planning CTs allowed for limited prediction of therapy response to palliative RT. ML predictions based on established clinical parameters achieved the best results. AU - Llorián-Salvador, O.* AU - Akhgar, J.* AU - Pigorsch, S.* AU - Borm, K.* AU - Münch, S.* AU - Bernhardt, D. AU - Rost, B.* AU - Andrade-Navarro, M.A.* AU - Combs, S.E. AU - Peeken, J.C. C1 - 68656 C2 - 54860 TI - The importance of planning CT-based imaging features for machine learning-based prediction of pain response. JO - Sci. Rep. VL - 13 IS - 1 PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - The "Patient Assessment of Chronic Illness Care" (PACIC) is a tool for evaluating outpatient health service for patients with chronic diseases. Our aim was to analyze the association between PACIC scores of primary care patients with depression and patients' or patients' general practitioners' (GPs) characteristics. In a data set including depressive primary care patients (N = 280) the association of patient characteristics (sex, age, depressive symptom severity, suicidal ideation) with PACIC scores were assessed by linear regression models. The association between GPs' characteristics (type, location of practice; age, qualification of practitioner) and PACIC scores was assessed by linear mixed models with individual practices as random effects. Patient Health Questionnaire (PHQ-9) scores at 12 months follow up and changes in PHQ-9 scores from baseline to follow up were significantly positive associated with higher PACIC scores (beta = 0.67, 95%-CI [0.02, 1.34]). PACIC scores were not associated with patients' sex (p = 0.473) or age (p = 0.531). GP's age was negatively associated with PACIC scores (p = 0.03). In conclusion, in patients with depression, the PACIC is independent from patients' and GPs' characteristics. The PACIC may be appropriate to assess patient-perspective on depression services in primary care. AU - Lukaschek, K.* AU - Beltz, C.* AU - Rospleszcz, S. AU - Schillok, H.* AU - Falkai, P.* AU - Margraf, J.* AU - Gensichen, J.* C1 - 67433 C2 - 54144 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Depressive primary care patients' assessment of received collaborative care. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Labile copper(II) ions (Cu2+) in serum are considered to be readily available for cellular uptake and to constitute the biologically active Cu2+ species in the blood. It might also be suitable to reflect copper dyshomeostasis during diseases such as Wilson's disease (WD) or neurological disorders. So far, no direct quantification method has been described to determine this small Cu2+ subset. This study introduces a fluorometric high throughput assay using the novel Cu2+ binding fluoresceine-peptide sensor FP4 (Kd of the Cu2+-FP4-complex 0.38 pM) to determine labile Cu2+ in human and rat serum. Using 96 human serum samples, labile Cu2+was measured to be 0.14 ± 0.05 pM, showing no correlation with age or other serum trace elements. No sex-specific differences in labile Cu2+ concentrations were noted, in contrast to the total copper levels in serum. Analysis of the effect of drug therapy on labile Cu2+ in the sera of 19 patients with WD showed a significant decrease in labile Cu2+ following copper chelation therapy, suggesting that labile Cu2+ may be a specific marker of disease status and that the assay could be suitable for monitoring treatment progress. AU - Maares, M.* AU - Haupt, A.* AU - Schüßler, C.* AU - Kulike-Koczula, M.* AU - Hackler, J.* AU - Keil, C.* AU - Mohr, I.* AU - Schomburg, L.* AU - Süssmuth, R.D.* AU - Zischka, H. AU - Merle, U.* AU - Haase, H.* C1 - 68022 C2 - 54500 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A fluorometric assay to determine labile copper(II) ions in serum. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - We present an artificial neural network architecture, termed STENCIL-NET, for equation-free forecasting of spatiotemporal dynamics from data. STENCIL-NET works by learning a discrete propagator that is able to reproduce the spatiotemporal dynamics of the training data. This data-driven propagator can then be used to forecast or extrapolate dynamics without needing to know a governing equation. STENCIL-NET does not learn a governing equation, nor an approximation to the data themselves. It instead learns a discrete propagator that reproduces the data. It therefore generalizes well to different dynamics and different grid resolutions. By analogy with classic numerical methods, we show that the discrete forecasting operators learned by STENCIL-NET are numerically stable and accurate for data represented on regular Cartesian grids. A once-trained STENCIL-NET model can be used for equation-free forecasting on larger spatial domains and for longer times than it was trained for, as an autonomous predictor of chaotic dynamics, as a coarse-graining method, and as a data-adaptive de-noising method, as we illustrate in numerical experiments. In all tests, STENCIL-NET generalizes better and is computationally more efficient, both in training and inference, than neural network architectures based on local (CNN) or global (FNO) nonlinear convolutions. AU - Maddu, S.* AU - Sturm, D.* AU - Cheeseman, B.L.* AU - Müller, C.L. AU - Sbalzarini, I.F.* C1 - 68024 C2 - 54502 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - STENCIL-NET for equation-free forecasting from data. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Obesity is characterized by the accumulation of adipose tissue in different body compartments. Whether adipose tissue directly affects kidney function is still unknown. We aimed to investigate the role of the adipose tissue and circulating creatinine, cystatin C and kidney function in subjects free of cardio-renal diseases. In the KORA-MRI population-based study, 377 subjects (mean age 56.2 ± 9.2 years; 41.6% female) underwent whole-body 3T-MRI examination. Adipose tissue defined as visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) were quantified from T1-DIXON sequence using a semi-automatic algorithm. Serum creatinine and cystatin C were measured using standard laboratory and estimated glomerular filtration rate (e-GFR) was performed based on creatinine (e-GFRcrea), cystatin C (e-GFRcys) and creatinine-cystatin C (e-GFRcc). Linear regression analysis, adjusted for risk factors, was used to investigate the relationship between adipose tissue and circulating creatinine, cystatin C, and kidney function. In multivariate analyses VAT was inversely associated with eGFRcys (ß = - 4.88, p =  < 0.001), and positively associated with serum cystatin C (ß = 0.05, p =  < 0.001), respectively. No association was found between other adipose parameters such as total adipose tissue (TAT) and subcutaneous adipose tissue (SAT) and serum creatinine, urine microalbumin and eGFRcrea. Stratified analyses according to BMI revealed confirmatory results for category of BMI > 30. VAT is positively associated with serum cystatin C and inversely with eGFR based on cystatin C, suggesting a direct involvement of visceral adipose tissue in increased metabolism of cystatin C and consequently decreased kidney function. AU - Mueller-Peltzer, K.* AU - von Krüchten, R.* AU - Lorbeer, R.* AU - Rospleszcz, S. AU - Schulz, H. AU - Peters, A. AU - Bamberg, F.* AU - Schlett, C.L.* AU - Mujaj, B.* C1 - 67846 C2 - 54324 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Adipose tissue is associated with kidney function parameters. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - The selective inhibition of kinases from the diabetic kinome is known to promote the regeneration of beta cells and provide an opportunity for the curative treatment of diabetes. The effect can be achieved by carefully tailoring the selectivity of inhibitor toward a particular kinase, especially DYRK1A, previously associated with Down syndrome and Alzheimer's disease. Recently DYRK1A inhibition has been shown to promote both insulin secretion and beta cells proliferation. Here, we show that commonly available flavones are effective inhibitors of DYRK1A. The observed biochemical activity of flavone compounds is confirmed by crystal structures solved at 2.06 Å and 2.32 Å resolution, deciphering the way inhibitors bind in the ATP-binding pocket of the kinase, which is driven by the arrangement of hydroxyl moieties. We also demonstrate antidiabetic properties of these biomolecules and prove that they could be further improved by therapy combined with TGF-β inhibitors. Our data will allow future structure-based optimization of the presented scaffolds toward potent, bioavailable and selective anti-diabetic drugs. AU - Pustelny, K.* AU - Grygier, P.* AU - Barzowska, A.* AU - Pucelik, B.* AU - Matsuda, A.* AU - Mrowiec, K.* AU - Slugocka, E.* AU - Popowicz, G.M. AU - Dubin, G.* AU - Czarna, A.* C1 - 68707 C2 - 54916 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Binding mechanism and biological effects of flavone DYRK1A inhibitors for the design of new antidiabetics. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Neuronal ceroid lipofuscinosis 6 (CLN6) is a rare and fatal autosomal recessive disease primarily affecting the nervous system in children. It is caused by a pathogenic mutation in the CLN6 gene for which no therapy is available. Employing an untargeted metabolomics approach, we analyzed the metabolic changes in CLN6 subjects to see if this system could potentially yield biomarkers for diagnosis and monitoring disease progression. Neuronal-like cells were derived from human fibroblast lines from CLN6-affected subjects (n = 3) and controls (wild type, n = 3). These were used to assess the potential of a neuronal-like cell-based metabolomics approach to identify CLN6 distinctive and specific biomarkers. The most impacted metabolic profile is associated with sphingolipids, glycerophospholipids metabolism, and calcium signaling. Over 2700 spectral features were screened, and fifteen metabolites were identified that differed significantly between both groups, including the sphingolipids C16 GlcCer, C24 GlcCer, C24:1 GlcCer and glycerophospholipids PG 40:6 and PG 40:7. Of note, these fifteen metabolites were downregulated in the CLN6 disease group. This study is the first to analyze the metabolome of neuronal-like cells with a pathogenic mutation in the CLN6 gene and to provide insights into their metabolomic alterations. This could allow for the development of novel biomarkers for monitoring CLN6 disease. AU - Rus, C.M.* AU - Polla, D.L.* AU - Di Bucchianico, S. AU - Fischer, S.* AU - Hartkamp, J.* AU - Hartmann, G.* AU - Alpagu, Y.* AU - Cozma, C.* AU - Zimmermann, R. AU - Bauer, P.* C1 - 68744 C2 - 54954 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Neuronal progenitor cells-based metabolomics study reveals dysregulated lipid metabolism and identifies putative biomarkers for CLN6 disease. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - The risk of enteric hyperoxaluria is significantly increased after malabsorptive bariatric surgery (MBS). However, its underlying determinants are only poorly characterized. In this case-control study, we aimed at identifying clinical and genetic factors to dissect their individual contributions to the development of post-surgical hyperoxaluria. We determined the prevalence of hyperoxaluria and nephrolithiasis after MBS by 24-h urine samples and clinical questionnaires at our obesity center. Both hyperoxaluric and non-hyperoxaluric patients were screened for sequence variations in known and candidate genes implicated in hyperoxaluria (AGXT, GRHPR, HOGA1, SLC26A1, SLC26A6, SLC26A7) by targeted next generation sequencing (tNGS). The cohort comprised 67 patients, 49 females (73%) and 18 males (27%). While hyperoxaluria was found in 29 patients (43%), only one patient reported postprocedural nephrolithiasis within 41 months of follow-up. Upon tNGS, we did not find a difference regarding the burden of (rare) variants between hyperoxaluric and non-hyperoxaluric patients. However, patients with hyperoxaluria showed significantly greater weight loss accompanied by markers of intestinal malabsorption compared to non-hyperoxaluric controls. While enteric hyperoxaluria is very common after MBS, genetic variation of known hyperoxaluria genes contributes little to its pathogenesis. In contrast, the degree of postsurgical weight loss and levels of malabsorption parameters may allow for predicting the risk of enteric hyperoxaluria and consecutive kidney stone formation. AU - Scherer, L.* AU - Schönauer, R.* AU - Nemitz-Kliemchen, M.* AU - Hagemann, T. AU - Hantmann, E.* AU - de Fallois, J.* AU - Petzold, F.* AU - Blüher, M. AU - Halbritter, J.* C1 - 67854 C2 - 54332 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Delta weight loss unlike genetic variation associates with hyperoxaluria after malabsorptive bariatric surgery. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - In magnetic resonance imaging (MRI), the perception of substandard image quality may prompt repetition of the respective image acquisition protocol. Subsequently selecting the preferred high-quality image data from a series of acquisitions can be challenging. An automated workflow may facilitate and improve this selection. We therefore aimed to investigate the applicability of an automated image quality assessment for the prediction of the subjectively preferred image acquisition. Our analysis included data from 11,347 participants with whole-body MRI examinations performed as part of the ongoing prospective multi-center German National Cohort (NAKO) study. Trained radiologic technologists repeated any of the twelve examination protocols due to induced setup errors and/or subjectively unsatisfactory image quality and chose a preferred acquisition from the resultant series. Up to 11 quantitative image quality parameters were automatically derived from all acquisitions. Regularized regression and standard estimates of diagnostic accuracy were calculated. Controlling for setup variations in 2342 series of two or more acquisitions, technologists preferred the repetition over the initial acquisition in 1116 of 1396 series in which the initial setup was retained (79.9%, range across protocols: 73-100%). Image quality parameters then commonly showed statistically significant differences between chosen and discarded acquisitions. In regularized regression across all protocols, 'structured noise maximum' was the strongest predictor for the technologists' choice, followed by 'N/2 ghosting average'. Combinations of the automatically derived parameters provided an area under the ROC curve between 0.51 and 0.74 for the prediction of the technologists' choice. It is concluded that automated image quality assessment can, despite considerable performance differences between protocols and anatomical regions, contribute substantially to identifying the subjective preference in a series of MRI acquisitions and thus provide effective decision support to readers. AU - Schuppert, C.* AU - Rospleszcz, S. AU - Hirsch, J.G.* AU - Hoinkiss, D.C.* AU - Köhn, A.* AU - von Krüchten, R.* AU - Russe, M.F.* AU - Keil, T.* AU - Krist, L.* AU - Schmidt, B.* AU - Michels, K.B.* AU - Schipf, S.* AU - Brenner, H.* AU - Kröncke, T.J.* AU - Pischon, T.* AU - Niendorf, T.* AU - Schulz-Menger, J.* AU - Forsting, M.* AU - Völzke, H.* AU - Hosten, N.* AU - Bülow, R.* AU - Zaitsev, M.A.* AU - Kauczor, H.U.* AU - Bamberg, F.* AU - Günther, M.* AU - Schlett, C.L.* C1 - 69054 C2 - 53832 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Automated image quality assessment for selecting among multiple magnetic resonance image acquisitions in the German National Cohort study. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Laser diodes are small and inexpensive but don't afford the pulse energy and beam profile required for optoacoustic (photoacoustic) microscopy. Using two novel modulation concepts, i.e. overdriving continuous-wave laser diodes (CWLD) and frequency-wavelength multiplexing (FWM) based on illumination pulse-trains, we demonstrate concurrent multi-wavelength optoacoustic microscopy with signal-to-noise ratios of > 17 dB, < 2 µm resolution at repetition rates of 1 MHz. This unprecedented performance based on an adaptable trigger engine allowed us to contrast FWM to wavelength alternating acquisition using identical optical components. We showcase this concept's superiority over conventional optoacoustic microscopes by visualizing vascular oxygenation dynamics and circulating tumor cells in mice. This work positions laser diodes as a technology allowing affordable, tunable, and miniaturizable optoacoustic microscopy. AU - Seeger, M. AU - Stylogiannis, A. AU - Prade, L. AU - Glasl, S. AU - Ntziachristos, V. C1 - 68759 C2 - 54969 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Overdriven laser diode optoacoustic microscopy. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Epigenetic sex differences and their resulting implications for human health have been studied for about a decade. The objective of this paper is to use permutation-based inference and a new ranked-based test statistic to identify sex-based epigenetic differences in the human DNA methylome. In particular, we examine whether we could identify separations between the female and male distributions of DNA methylation across hundred of thousands CpG sites in two independent cohorts, the Swedish Adoption Twin study and the Lamarck study. Based on Fisherian p-values, we set a threshold for methylation differences “worth further scrutiny”. At this threshold, we were able to confirm previously-found CpG sites that stratify with respect to sex. These CpG sites with sex differences in DNA methylation should be further investigated for their possible contribution to various physiological and pathological functions in the human body. We followed-up our statistical analyses with a literature review in order to inform the proposed disease implications for the loci we uncovered. AU - Sommer, A. AU - Okonkwo, J.* AU - Monteiro, J.* AU - Bind, M.A.C.* C1 - 68300 C2 - 54721 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - There is a growing literature investigating the effects of selenium on the central nervous system and cognitive function. However, little is known about the role of selenoprotein P, the main selenium transporter, which can also have adverse biological effects. We conducted a prospective cohort study of individuals aged 42-81 years who received a clinical diagnosis of mild cognitive impairment. Using sandwich ELISA methods, we measured full-length selenoprotein P concentrations in serum and cerebrospinal fluid to assess the relation with dementia incidence during a median follow-up of 47.3 months. We used Cox proportional hazards regression and restricted cubic splines to model such relation. Of the 54 participants, 35 developed dementia during follow-up (including 26 cases of Alzheimer's dementia). Selenoprotein P concentrations in serum and cerebrospinal fluid were highly correlated, and in spline regression analyses they each showed a positive non-linear association with dementia risk, particularly after excluding dementia cases diagnosed within 24 months of follow-up. We also observed differences in association according to the dementia subtypes considered. Risk ratios of dementia peaked at 2-6 at the highest levels of selenoprotein P, when compared to its median level, also depending on matrix, analytical methodology and dementia subtype. Findings of this study, the first to assess selenoprotein P levels in the central nervous system in vivo and the first to use a prospective study design to evaluate associations with dementia, suggest that higher circulating concentrations of selenoprotein P, both in serum and cerebrospinal fluid, predict progression of MCI to dementia. However, further confirmation of these findings is required, given the limited statistical precision of the associations and the potential for residual confounding. AU - Vinceti, M.* AU - Urbano, T.* AU - Chiari, A.* AU - Filippini, T.* AU - Wise, L.A.* AU - Tondelli, M.* AU - Michalke, B. AU - Shimizu, M.* AU - Saito, Y.* C1 - 67864 C2 - 54342 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Selenoprotein P concentrations and risk of progression from mild cognitive impairment to dementia. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has changed the clinical day-to-day practice. The aim of this study was to evaluate the impact of the pandemic on patients with high-grade glioma (HGG) as well as to derive best practice recommendations. We compared a multi-institutional cohort with HGG (n = 251) from 03/2020 to 05/2020 (n = 119) to a historical cohort from 03/2019 to 05/2019 (n = 132). The endpoints were outcome (progression-free survival (PFS) and overall survival (OS)) as well as patterns of care and time intervals between treatment steps. The median OS for WHO grade 4 gliomas was 12 months in 2019 (95% Confidence Interval 9.7-14.3 months), and not reached in 2020 (p = .026). There were no other significant differences in the Kaplan-Meier estimates for OS and PFS between cohorts of 2019 and 2020, neither did stratification by WHO grade reveal any significant differences for OS, PFS or for patterns of care. The time interval between cranial magnetic resonance imaging (cMRI) and biopsy was significantly longer in 2020 cohort (11 versus 21 days, p = .031). Median follow-up was 10 months (range 0-30 months). Despite necessary disease containment policies, it is crucial to ensure that patients with HGG are treated in line with the recent guidelines and standard of care (SOC) algorithms. Therefore, we strongly suggest pursuing no changes to SOC treatment, a timely diagnosis and treatment with short time intervals between first symptoms, initial diagnosis, and treatment, as well as a guideline-based cMRI follow-up. AU - Vogel, M.M. AU - Wagner, A.* AU - Gempt, J.* AU - Krenzlin, H.* AU - Zeyen, T.* AU - Drexler, R.* AU - Voss, M.* AU - Nettekoven, C.* AU - Abboud, T.* AU - Mielke, D.* AU - Rohde, V.* AU - Timmer, M.* AU - Goldbrunner, R.* AU - Steinbach, J.P.* AU - Dührsen, L.* AU - Westphal, M.* AU - Herrlinger, U.* AU - Ringel, F.* AU - Meyer, B.* AU - Combs, S.E. C1 - 67462 C2 - 54119 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Impact of the SARS-CoV-2 pandemic on the survival of patients with high-grade glioma and best practice recommendations. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - This study aimed to determine the retest variability of quantitative fundus autofluorescence (QAF) in patients with and without age-related macular degeneration (AMD) and evaluate the predictive value of patient reliability indices on retest reliability. A total of 132 eyes from 68 patients were examined, including healthy individuals and those with various stages of AMD. Duplicate QAF imaging was conducted at baseline and 2 weeks later across six study sites. Intraclass correlation (ICC) analysis was used to evaluate the consistency of imaging, and mean opinion scores (MOS) of image quality were generated by two researchers. The contribution of MOS and other factors to retest variation was assessed using mixed-effect linear models. Additionally, a Random Forest Regressor was trained to evaluate the extent to which manual image grading of image quality could be replaced by automated assessment (inferred MOS). The results showed that ICC values were high for all QAF images, with slightly lower values in AMD-affected eyes. The average inter-day ICC was found to be 0.77 for QAF segments within the QAF8 ring and 0.74 for peripheral segments. Image quality was predicted with a mean absolute error of 0.27 on a 5-point scale, and of all evaluated reliability indices, MOS/inferred MOS proved most important. The findings suggest that QAF allows for reliable testing of autofluorescence levels at the posterior pole in patients with AMD in a multicenter, multioperator setting. Patient reliability indices could serve as eligibility criteria for clinical trials, helping identify patients with adequate retest reliability. AU - von der Emde, L.* AU - Mallwitz, M.* AU - Vaisband, M.* AU - Hasenauer, J. AU - Saßmannshausen, M.* AU - Terheyden, J.H.* AU - Sloan, K.R.* AU - Schmitz-Valckenberg, S.* AU - Finger, R.P.* AU - Holz, F.G.* AU - Ach, T.* C1 - 68655 C2 - 54859 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Retest variability and patient reliability indices of quantitative fundus autofluorescence in age-related macular degeneration: Aa MACUSTAR study report. JO - Sci. Rep. VL - 13 IS - 1 PB - Nature Portfolio PY - 2023 SN - 2045-2322 ER - TY - JOUR AB - Adipose tissue expansion involves both differentiation of new precursors and size increase of mature adipocytes. While the two processes are well balanced in healthy tissues, obesity and diabetes type II are associated with abnormally enlarged adipocytes and excess lipid accumulation. Previous studies suggested a link between cell stiffness, volume and stem cell differentiation, although in the context of preadipocytes, there have been contradictory results regarding stiffness changes with differentiation. Thus, we set out to quantitatively monitor adipocyte shape and size changes with differentiation and lipid accumulation. We quantified by optical diffraction tomography that differentiating preadipocytes increased their volumes drastically. Atomic force microscopy (AFM)-indentation and -microrheology revealed that during the early phase of differentiation, human preadipocytes became more compliant and more fluid-like, concomitant with ROCK-mediated F-actin remodelling. Adipocytes that had accumulated large lipid droplets were more compliant, and further promoting lipid accumulation led to an even more compliant phenotype. In line with that, high fat diet-induced obesity was associated with more compliant adipose tissue compared to lean animals, both for drosophila fat bodies and murine gonadal adipose tissue. In contrast, adipose tissue of diabetic mice became significantly stiffer as shown not only by AFM but also magnetic resonance elastography. Altogether, we dissect relative contributions of the cytoskeleton and lipid droplets to cell and tissue mechanical changes across different functional states, such as differentiation, nutritional state and disease. Our work therefore sets the basis for future explorations on how tissue mechanical changes influence the behaviour of mechanosensitive tissue-resident cells in metabolic disorders. AU - Abuhattum, S.* AU - Kotzbeck, P. AU - Schlüßler, R.* AU - Harger, A. AU - Ariza de Schellenberger, A.* AU - Kim, K.* AU - Escolano, J.C.* AU - Müller, T.* AU - Braun, J.* AU - Wabitsch, M.* AU - Tschöp, M.H. AU - Sack, I.* AU - Brankatschk, M.* AU - Guck, J.* AU - Stemmer, K. AU - Taubenberger, A.V.* C1 - 65549 C2 - 52734 TI - Adipose cells and tissues soften with lipid accumulation while in diabetes adipose tissue stiffens. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Gender specific all-cause mortality risk associated with a high somatic symptom burden (SSB) in a population-based cohort was investigated. The study population included 5679 women and 5861 men aged 25-74 years from the population-based MONICA/KORA Cohort. SSB was assessed following the Somatic Symptom Scale-8 and categorized as very high (≥ 95th percentile), high (60-95th percentile), moderate (30-60th percentile), and low (≤ 30th percentile). The impact of SSB on all-cause mortality risk within a mean follow-up period of 22.6 years (SD 7.1; 267,278 person years) was estimated by gender-specific Cox regression models adjusted for sociodemographic, lifestyle, somatic and psychosocial risk factors, as well as pre-existing medical conditions. Approximately 5.7% of men and 7.3% of women had very high SSB. During follow-up, 3638 (30.6%) mortality cases were observed. Men with a very-high SSB had 48% increased relative risk of mortality in comparison to men with a low SSB after adjustment for concurrent risk factors (1.48, 95% CI 1.20-1.81, p < .0001), corresponding to 2% increased risk of mortality for each 1-point increment in SSB (1.02; 95% CI 1.01-1.03; p = 0.03). In contrast, women with a very high SSB had a 22% lower risk of mortality (0.78, 95% CI 0.61-1.00, p = 0.05) and women with high SSB had an 18% lower risk of mortality (0.82; 95% CI 0.68-0.98, p = 0.03) following adjustment for concurrent risk factors. The current findings indicate that an increasing SSB is an independent risk factor for mortality in men but not in women, pointing in the direction of critical gender differences in the management of SSB, including women's earlier health care utilization than men. AU - Atasoy, S. AU - Hausteiner-Wiehle, C.* AU - Sattel, H.* AU - Johar, H. AU - Roenneberg, C.* AU - Peters, A. AU - Ladwig, K.H.* AU - Henningsen, P.* C1 - 66108 C2 - 52631 TI - Gender specific somatic symptom burden and mortality risk in the general population. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The original version of this Article contained an error in the spelling of the author Hamimatunnisa Johar, which was incorrectly given as Hamimatunissa Johar. The original Article has been corrected. AU - Atasoy, S. AU - Hausteiner-Wiehle, C.* AU - Sattel, H.* AU - Johar, H. AU - Roenneberg, C.* AU - Peters, A. AU - Ladwig, K.H.* AU - Henningsen, P.* C1 - 66772 C2 - 53225 TI - Author Correction: Gender specific somatic symptom burden and mortality risk in the general population. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Early school times fundamentally clash with the late sleep of teenagers. This mismatch results in chronic sleep deprivation posing acute and long-term health risks and impairing students' learning. Despite immediate short-term benefits for sleep, the long-term effects of later starts remain unresolved. In a pre-post design over 1 year, we studied a unique flexible school start system, in which 10-12th grade students chose daily between an 8:00 or 8:50AM-start. Missed study time (8:00-8:50) was compensated for during gap periods or after classes. Based on 2 waves (6-9 weeks of sleep diary each), we found that students maintained their ~ 1-h-sleep gain on later days, longitudinally (n = 28) and cross-sectionally (n = 79). This gain was independent of chronotype and frequency of later starts but attenuated for boys after 1 year. Students showed persistently better sleep quality and reduced alarm-driven waking and reported psychological benefits (n = 93) like improved motivation, concentration, and study quality on later days. Nonetheless, students chose later starts only infrequently (median 2 days/week), precluding detectable sleep extensions in the flexible system overall. Reasons for not choosing late starts were the need to make up lost study time, preference for extra study time and transport issues. Whether flexible systems constitute an appealing alternative to fixed delays given possible circadian and psychological advantages warrants further investigation. AU - Biller, A.M.* AU - Molenda, C.* AU - Zerbini, G.* AU - Roenneberg, T.* AU - Winnebeck, E.C. C1 - 64348 C2 - 52187 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Sleep improvements on days with later school starts persist after 1 year in a flexible start system. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The mismatch between teenagers' late sleep phase and early school start times results in acute and chronic sleep reductions. This is not only harmful for learning but may reduce career prospects and widen social inequalities. Delaying school start times has been shown to improve sleep at least short-term but whether this translates to better achievement is unresolved. Here, we studied whether 0.5-1.5 years of exposure to a flexible school start system, with the daily choice of an 8 AM or 8:50 AM-start, allowed secondary school students (n = 63-157, 14-21 years) to improve their quarterly school grades in a 4-year longitudinal pre-post design. We investigated whether sleep, changes in sleep or frequency of later starts predicted grade improvements. Mixed model regressions with 5111-16,724 official grades as outcomes did not indicate grade improvements in the flexible system per se or with observed sleep variables nor their changes-the covariates academic quarter, discipline and grade level had a greater effect in our sample. Importantly, our finding that intermittent sleep benefits did not translate into detectable grade changes does not preclude improvements in learning and cognition in our sample. However, it highlights that grades are likely suboptimal to evaluate timetabling interventions despite their importance for future success. AU - Biller, A.M.* AU - Molenda, C.* AU - Obster, F.* AU - Zerbini, G.* AU - Förtsch, C.* AU - Roenneberg, T.* AU - Winnebeck, E.C. C1 - 64470 C2 - 52226 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A 4-year longitudinal study investigating the relationship between flexible school starts and grades. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - To examine the effect of night shift on salivary cortisol at awakening (C1), 30 min later (C2), and on the cortisol awakening response (CAR, the difference between C2 and C1). We compared shift and non-shift workers with a focus on the impact of worker chronotype. Our study included 66 shift-working females (mean age = 37.3 years, SD = 10.2) and 21 non-shift working females (mean age = 47.0 years, SD = 8.9). The shift workers collected their saliva samples at C1 and C2 on each two consecutive day shifts and night shifts. Non-shift workers collected their samples on two consecutive day shifts. We applied linear mixed-effects models (LMM) to determine the effect of night shift on CAR and log-transformed C1 and C2 levels. LMMs were stratified by chronotype group. Compared to non-shift workers, shift workers before day shifts (i.e. after night sleep) showed lower cortisol at C1 (exp [Formula: see text]=0.58, 95% CI 0.42, 0.81) but not at C2. In shift workers, the CARs after night shifts (i.e. after day sleep) were lower compared to CARs before day shifts ([Formula: see text]= - 11.07, 95% CI - 15.64, - 6.50). This effect was most pronounced in early chronotypes (early: [Formula: see text]= - 16.61, 95% CI - 27.87, - 5.35; intermediate: [Formula: see text]= - 11.82, 95% CI - 18.35, - 5.29; late: [Formula: see text]= - 6.27, 95% CI - 14.28, 1.74). Chronotype did not modify the association between night shift and CAR. In our population of shift workers, there was a mismatch between time of waking up and their natural cortisol peak at waking up (CAR) both during day and night shift duties. AU - Burek, K.* AU - Rabstein, S.* AU - Kantermann, T.* AU - Vetter, C.* AU - Rotter, M. AU - Wang-Sattler, R. AU - Lehnert, M.* AU - Pallapies, D.* AU - Jöckel, K.H.* AU - Brüning, T.* AU - Behrens, T.* C1 - 64891 C2 - 52545 TI - Night work, chronotype and cortisol at awakening in female hospital employees. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Breakdown of synthesis, excretion and detoxification defines liver failure. Post-hepatectomy liver failure (PHLF) is specific for liver resection and a rightfully feared complication due to high lethality and limited therapeutic success. Individual cytokine and growth factor profiles may represent potent predictive markers for recovery of liver function. We aimed to investigate these profiles in post-hepatectomy regeneration. This study combined a time-dependent cytokine and growth factor profiling dataset of a training (30 patients) and a validation (14 patients) cohorts undergoing major liver resection with statistical and predictive models identifying individual pathway signatures. 2319 associations were tested. Primary hepatocytes isolated from patient tissue samples were stimulated and their proliferation was analysed through DNA content assay. Common expression trajectories of cytokines and growth factors with strong correlation to PHLF, morbidity and mortality were identified despite highly individual perioperative dynamics. Especially, dynamics of EGF, HGF, and PLGF were associated with mortality. PLGF was additionally associated with PHLF and complications. A global association-network was calculated and validated to investigate interdependence of cytokines and growth factors with clinical attributes. Preoperative cytokine and growth factor signatures were identified allowing prediction of mortality following major liver resection by regression modelling. Proliferation analysis of corresponding primary human hepatocytes showed associations of individual regenerative potential with clinical outcome. Prediction of PHLF was possible on as early as first postoperative day (POD1) with AUC above 0.75. Prediction of PHLF and mortality is possible on POD1 with liquid-biopsy based risk profiling. Further utilization of these models would allow tailoring of interventional strategies according to individual profiles. AU - Dehlke, K.* AU - Krause, L.* AU - Tyufekchieva, S.* AU - Murtha-Lemekhova, A.* AU - Mayer, P.* AU - Vlasov, A.* AU - Klingmüller, U.* AU - Müller, N.S. AU - Hoffmann, K.* C1 - 65849 C2 - 52940 TI - Predicting liver regeneration following major resection. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Parkinson´s disease (PD) pathology progresses throughout the nervous system. Whereas motor symptoms are always present, there is a high variability in the prevalence of non-motor symptoms. It has been postulated that the progression of the pathology is based on a prion-like disease mechanism partly due to the seeding effect of endocytosed-alpha-synuclein (ASYN) on the endogenous ASYN. Here, we analyzed the role of endogenous ASYN in the progression of PD-like pathology in vivo and in vitro and compared the effect of endocytosed-ASYN as well as paraquat and rotenone on primary enteric, dopaminergic and cortical neurons from wild-type and ASYN-KO mice. Our results show that, in vivo, pathology progression did not occur in the absence of endogenous ASYN. Remarkably, the damage caused by endocytosed-ASYN, rotenone or paraquat was independent from endogenous ASYN and related to the alteration of the host´s mitochondrial membrane potential. Dopaminergic neurons were very sensitive to these noxae compared to other neuronal subtypes. These results suggest that ASYN-mitochondrial interactions play a major role in initiating the pathological process in the host neuron and endogenous ASYN is essential for the transsynaptical transmission of the pathology. Our results also suggest that protecting mitochondrial function is a valid primary therapeutic target. AU - Dening, Y.* AU - Straßl, T.* AU - Ruf, V.* AU - Dirscherl, P. AU - Chovsepian, A.* AU - Stievenard, A.* AU - Khairnar, A.* AU - Schmidt, F.* AU - Giesert, F. AU - Herms, J.* AU - Levin, J.* AU - Dieterich, M.* AU - Falkai, P.* AU - Weisenhorn, D.M. AU - Wurst, W. AU - Giese, A.* AU - Pan-Montojo, F.* C1 - 67079 C2 - 53451 TI - Toxicity of extracellular alpha-synuclein is independent of intracellular alpha-synuclein. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - During 2020, the infection rate of COVID-19 has been investigated by many scholars from different research fields. In this context, reliable and interpretable forecasts of disease incidents are a vital tool for policymakers to manage healthcare resources. In this context, several experts have called for the necessity to account for human mobility to explain the spread of COVID-19. Existing approaches often apply standard models of the respective research field, frequently restricting modeling possibilities. For instance, most statistical or epidemiological models cannot directly incorporate unstructured data sources, including relational data that may encode human mobility. In contrast, machine learning approaches may yield better predictions by exploiting these data structures yet lack intuitive interpretability as they are often categorized as black-box models. We propose a combination of both research directions and present a multimodal learning framework that amalgamates statistical regression and machine learning models for predicting local COVID-19 cases in Germany. Results and implications: the novel approach introduced enables the use of a richer collection of data types, including mobility flows and colocation probabilities, and yields the lowest mean squared error scores throughout the observational period in the reported benchmark study. The results corroborate that during most of the observational period more dispersed meeting patterns and a lower percentage of people staying put are associated with higher infection rates. Moreover, the analysis underpins the necessity of including mobility data and showcases the flexibility and interpretability of the proposed approach. AU - Fritz, C.* AU - Dorigatti, E. AU - Rügamer, D.* C1 - 64608 C2 - 52342 TI - Combining graph neural networks and spatio-temporal disease models to improve the prediction of weekly COVID-19 cases in Germany. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - We searched a database of single-gene knockout (KO) mice produced by the International Mouse Phenotyping Consortium (IMPC) to identify candidate ciliopathy genes. We first screened for phenotypes in mouse lines with both ocular and renal or reproductive trait abnormalities. The STRING protein interaction tool was used to identify interactions between known cilia gene products and those encoded by the genes in individual knockout mouse strains in order to generate a list of "candidate ciliopathy genes." From this list, 32 genes encoded proteins predicted to interact with known ciliopathy proteins. Of these, 25 had no previously described roles in ciliary pathobiology. Histological and morphological evidence of phenotypes found in ciliopathies in knockout mouse lines are presented as examples (genes Abi2, Wdr62, Ap4e1, Dync1li1, and Prkab1). Phenotyping data and descriptions generated on IMPC mouse line are useful for mechanistic studies, target discovery, rare disease diagnosis, and preclinical therapeutic development trials. Here we demonstrate the effective use of the IMPC phenotype data to uncover genes with no previous role in ciliary biology, which may be clinically relevant for identification of novel disease genes implicated in ciliopathies. AU - Higgins, K.* AU - Moore, B.A.* AU - Berberovic, Z.* AU - Adissu, H.A.* AU - Eskandarian, M.* AU - Flenniken, A.M.* AU - Shao, A.* AU - Imai, D.M.* AU - Clary, D.* AU - Lanoue, L.* AU - Newbigging, S.* AU - Nutter, L.M.J.* AU - Adams, D.J.* AU - Bosch, F.* AU - Braun, R.E.* AU - Brown, S.D.M.* AU - Dickinson, M.E.* AU - Dobbie, M.S.* AU - Flicek, P.* AU - Gao, X.* AU - Galande, S.* AU - Grobler, A.* AU - Heaney, J.D.* AU - Herault, Y.* AU - Hrabě de Angelis, M. AU - Chin, H.G.* AU - Mammano, F.* AU - Qin, C.* AU - Shiroishi, T.* AU - Sedlacek, R.* AU - Seong, J.K.* AU - Xu, Y.* AU - Lloyd, K.C.K.* AU - McKerlie, C.* AU - Moshiri, A.* C1 - 66841 C2 - 53313 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The replication complex (RC) of SARS-CoV-2 was recently shown to be one of the fastest RNA-dependent RNA polymerases of any known coronavirus. With this rapid elongation, the RC is more prone to incorporate mismatches during elongation, resulting in a highly variable genomic sequence. Such mutations render the design of viral protein targets difficult, as drugs optimized for a given viral protein sequence can quickly become inefficient as the genomic sequence evolves. Here, we use biochemical experiments to characterize features of RNA template recognition and elongation fidelity of the SARS-CoV-2 RdRp, and the role of the exonuclease, nsp14. Our study highlights the 2'OH group of the RNA ribose as a critical component for RdRp template recognition and elongation. We show that RdRp fidelity is reduced in the presence of the 3' deoxy-terminator nucleotide 3'dATP, which promotes the incorporation of mismatched nucleotides (leading to U:C, U:G, U:U, C:U, and A:C base pairs). We find that the nsp10-nsp14 heterodimer is unable to degrade RNA products lacking free 2'OH or 3'OH ribose groups. Our results suggest the potential use of 3' deoxy-terminator nucleotides in RNA-derived oligonucleotide inhibitors as antivirals against SARS-CoV-2. AU - Jones, A. AU - Mourao, A. AU - Czarna, A.* AU - Matsuda, A.* AU - Fino, R. AU - Pyrc, K.* AU - Sattler, M. AU - Popowicz, G.M. C1 - 65440 C2 - 52683 TI - Characterization of SARS-CoV-2 replication complex elongation and proofreading activity. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - We studied whether in patients with COPD the use of metformin for diabetes treatment was linked to a pattern of lung function decline consistent with the hypothesis of anti-aging effects of metformin. Patients of GOLD grades 1–4 of the COSYCONET cohort with follow-up data of up to 4.5 y were included. The annual decline in lung function (FEV1, FVC) and CO diffusing capacity (KCO, TLCO) in %predicted at baseline was evaluated for associations with age, sex, BMI, pack-years, smoking status, baseline lung function, exacerbation risk, respiratory symptoms, cardiac disease, as well as metformin-containing therapy compared to patients without diabetes and metformin. Among 2741 patients, 1541 (mean age 64.4 y, 601 female) fulfilled the inclusion criteria. In the group with metformin treatment vs. non-diabetes the mean annual decline in KCO and TLCO was significantly lower (0.2 vs 2.3, 0.8 vs. 2.8%predicted, respectively; p < 0.05 each), but not the decline of FEV1 and FVC. These results were confirmed using multiple regression and propensity score analyses. Our findings demonstrate an association between the annual decline of lung diffusing capacity and the intake of metformin in patients with COPD consistent with the hypothesis of anti-aging effects of metformin as reflected in a surrogate marker of emphysema. AU - Kahnert, K.* AU - Andreas, S.* AU - Kellerer, C.* AU - Lutter, J. AU - Lucke, T.* AU - Yildirim, A.O.E.* AU - Lehmann, M.* AU - Seissler, J.* AU - Behr, J.* AU - Frankenberger, M.* AU - Bals, R.* AU - Watz, H.* AU - Welte, T.* AU - Trudzinski, F.C.* AU - Vogelmeier, C.F.* AU - Alter, P.* AU - Jörres, R.A.* C1 - 64220 C2 - 52111 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Reduced decline of lung diffusing capacity in COPD patients with diabetes and metformin treatment. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Large epidemiological studies such as the UK Biobank (UKBB) or German National Cohort (NAKO) provide unprecedented health-related data of the general population aiming to better understand determinants of health and disease. As part of these studies, Magnetic Resonance Imaging (MRI) is performed in a subset of participants allowing for phenotypical and functional characterization of different organ systems. Due to the large amount of imaging data, automated image analysis is required, which can be performed using deep learning methods, e. g. for automated organ segmentation. In this paper we describe a computational pipeline for automated segmentation of abdominal organs on MRI data from 20,000 participants of UKBB and NAKO and provide results of the quality control process. We found that approx. 90% of data sets showed no relevant segmentation errors while relevant errors occurred in a varying proportion of data sets depending on the organ of interest. Image-derived features based on automated organ segmentations showed relevant deviations of varying degree in the presence of segmentation errors. These results show that large-scale, deep learning-based abdominal organ segmentation on MRI data is feasible with overall high accuracy, but visual quality control remains an important step ensuring the validity of down-stream analyses in large epidemiological imaging studies. AU - Kart, T.* AU - Fischer, M.* AU - Winzeck, S.* AU - Glocker, B.* AU - Bai, W.* AU - Bülow, R.* AU - Emmel, C.* AU - Friedrich, L.* AU - Kauczor, H.U.* AU - Keil, T.* AU - Kröncke, T.* AU - Mayer, P.* AU - Niendorf, T.* AU - Peters, A. AU - Pischon, T.* AU - Schaarschmidt, B.M.* AU - Schmidt, B.* AU - Schulze, M.B.* AU - Umutle, L.* AU - Völzke, H.* AU - Küstner, T.* AU - Bamberg, F.* AU - Schölkopf, B.* AU - Rueckert, D.* AU - Gatidis, S.* C1 - 66608 C2 - 53050 TI - Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Gastro-intestinal stromal tumors and acute myeloid leukemia induced by activating stem cell factor receptor tyrosine kinase (KIT) mutations are highly malignant. Less clear is the role of KIT mutations in the context of breast cancer. Treatment success of KIT-induced cancers is still unsatisfactory because of primary or secondary resistance to therapy. Mouse models offer essential platforms for studies on molecular disease mechanisms in basic cancer research. In the course of the Munich N-ethyl-N-nitrosourea (ENU) mutagenesis program a mouse line with inherited polycythemia was established. It carries a base-pair exchange in the Kit gene leading to an amino acid exchange at position 824 in the activation loop of KIT. This KIT variant corresponds to the N822K mutation found in human cancers, which is associated with imatinib-resistance. C3H KitN824K/WT mice develop hyperplasia of interstitial cells of Cajal and retention of ingesta in the cecum. In contrast to previous Kit-mutant models, we observe a benign course of gastrointestinal pathology associated with prolonged survival. Female mutants develop mammary carcinomas at late onset and subsequent lung metastasis. The disease model complements existing oncology research platforms. It allows for addressing the role of KIT mutations in breast cancer and identifying genetic and environmental modifiers of disease progression. AU - Klein-Rodewald, T. AU - Micklich, K. AU - Sanz-Moreno, A. AU - Tost, M. AU - Calzada-Wack, J. AU - Adler, T. AU - Klaften, M. AU - Sabrautzki, S. AU - Aigner, B.* AU - Kraiger, M. AU - Gailus-Durner, V. AU - Fuchs, H. AU - German Mouse Clinic Consortium (Aguilar-Pimentel, J.A. AU - Becker, L. AU - Garrett, L. AU - Hölter, S.M. AU - Prehn, C. AU - Rácz, I. AU - Rozman, J. AU - Puk, O. AU - Schrewe, A. AU - Adamski, J. AU - Esposito, I. AU - Wurst, W. AU - Stoeger, C.) AU - Gründer, A.* AU - Pahl, H.* AU - Wolf, E.* AU - Hrabě de Angelis, M. AU - Rathkolb, B. C1 - 66766 C2 - 53200 TI - New C3H KitN824K/WT cancer mouse model develops late-onset malignant mammary tumors with high penetrance. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Animal models are an indispensable platform used in various research disciplines, enabling, for example, studies of basic biological mechanisms, pathological processes and new therapeutic interventions. In this study, we applied magnetic resonance imaging (MRI) to characterize the clinical picture of a novel N-ethyl-N-nitrosourea-induced Kit-mutant mouse in vivo. Seven C3H KitN824K/WT mutant animals each of both sexes and their littermates were monitored every other month for a period of twelve months. MRI relaxometry data of hematopoietic bone marrow and splenic tissue as well as high-resolution images of the gastrointestinal organs were acquired. Compared with controls, the mutants showed a dynamic change in the shape and volume of the cecum and enlarged Peyer´s patches were identified throughout the entire study. Mammary tumors were observed in the majority of mutant females and were first detected at eight months of age. Using relaxation measurements, a substantial decrease in longitudinal relaxation times in hematopoietic tissue was detected in mutants at one year of age. In contrast, transverse relaxation time of splenic tissue showed no differences between genotypes, except in two mutant mice, one of which had leukemia and the other hemangioma. In this study, in vivo MRI was used for the first time to thoroughly characterize the evolution of systemic manifestations of a novel Kit-induced tumor model and to document the observable organ-specific disease cascade. AU - Kraiger, M. AU - Klein-Rodewald, T. AU - Rathkolb, B. AU - Calzada-Wack, J. AU - Sanz-Moreno, A. AU - Fuchs, H. AU - Wolf, E.* AU - Gailus-Durner, V. AU - Hrabě de Angelis, M. C1 - 65972 C2 - 52578 TI - Monitoring longitudinal disease progression in a novel murine Kit tumor model using high-field MRI. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Haematological traits are linked to cardiovascular, metabolic, infectious and immune disorders, as well as cancer. Here, we examine the role of genetic variation in shaping haematological traits in two isolated Mediterranean populations. Using whole-genome sequencing data at 22× depth for 1457 individuals from Crete (MANOLIS) and 1617 from the Pomak villages in Greece, we carry out a genome-wide association scan for haematological traits using linear mixed models. We discover novel associations (p < 5 × 10–9) of five rare non-coding variants with alleles conferring effects of 1.44–2.63 units of standard deviation on red and white blood cell count, platelet and red cell distribution width. Moreover, 10.0% of individuals in the Pomak population and 6.8% in MANOLIS carry a pathogenic mutation in the Haemoglobin Subunit Beta (HBB) gene. The mutational spectrum is highly diverse (10 different mutations). The most frequent mutation in MANOLIS is the common Mediterranean variant IVS-I-110 (G>A) (rs35004220). In the Pomak population, c.364C>A (“HbO-Arab”, rs33946267) is most frequent (4.4% allele frequency). We demonstrate effects on haematological and other traits, including bilirubin, cholesterol, and, in MANOLIS, height and gestation age. We find less severe effects on red blood cell traits for HbS, HbO, and IVS-I-6 (T>C) compared to other b+ mutations. Overall, we uncover allelic diversity of HBB in Greek isolated populations and find an important role for additional rare variants outside of HBB. AU - Kuchenbaecker, K.* AU - Gilly, A. AU - Suveges, D.* AU - Southam, L. AU - Giannakopoulou, O.* AU - Kilian, B.* AU - Tsafantakis, E.* AU - Karaleftheri, M.* AU - Farmaki, A.E.* AU - Gurdasani, D.* AU - Kundu, K.* AU - Sandhu, M.S.* AU - Danesh, J.* AU - Butterworth, A.* AU - Barroso, I.* AU - Dedoussis, G.* AU - Zeggini, E. C1 - 64191 C2 - 52098 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Insights into the genetic architecture of haematological traits from deep phenotyping and whole-genome sequencing for two Mediterranean isolated populations. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - This study aims to identify key anatomic features that govern the individual variability of lung doses from breast-cancer radiotherapy. 3D conformal, intensity-modulated and hybrid techniques with 50.4 Gy whole-breast dose were planned for 128 patients. From their CT images, 17 anatomic measures were assessed and tested as predictors for lung dose-volume characteristics. Tangential techniques yielded mean ipsilateral lung doses in the range of 3–11 Gy. This inter-patient variability was explained to almost 40% by central lung distance, and to almost 60% if this measure was complemented by midplane lung width and maximum heart distance. Also the variability in further dose-volume metrics such as volume fractions receiving 5, 20 or 40 Gy could be largely explained by the anatomy. Multi-field intensity-modulated radiotherapy reduced high-exposed lung volumes, but resulted in higher mean ipsilateral lung doses and larger low-dose burden. Contralateral lung doses ranged from 0.3 to 1 Gy. The results highlight that there are large differences in lung doses among breast-cancer patients. Most of this inter-individual variability can be explained by a few anatomic features. The results will be implemented in a dedicated software tool to provide personalized estimates of long-term health risks related to breast-cancer radiotherapy. The results may also be used to identify favourable as well as problematic anatomies, and serve as a quick quantitative benchmark for individual treatment plans. AU - Kundrát, P. AU - Rennau, H.* AU - Remmele, J.* AU - Sebb, S.* AU - Simonetto, C. AU - Kaiser, J.C. AU - Hildebrandt, G.* AU - Wolf, U.* AU - Eidemüller, M. C1 - 65619 C2 - 52744 TI - Anatomy-dependent lung doses from 3D-conformal breast-cancer radiotherapy. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Aim of this study was to validate the prognostic impact of clinical parameters and baseline 18F-FDG-PET/CT derived textural features to predict histopathologic response and survival in patients with esophageal squamous cell carcinoma undergoing neoadjuvant chemoradiation (nCRT) and surgery. Between 2005 and 2014, 38 ESCC were treated with nCRT and surgery. For all patients, the 18F-FDG-PET-derived parameters metabolic tumor volume (MTV), SUVmax, contrast and busyness were calculated for the primary tumor using a SUV-threshold of 3. The parameter uniformity was calculated using contrast-enhanced computed tomography. Based on histopathological response to nCRT, patients were classified as good responders (< 10% residual tumor) (R) or non-responders (≥ 10% residual tumor) (NR). Regression analyses were used to analyse the association of clinical parameters and imaging parameters with treatment response and overall survival (OS). Good response to nCRT was seen in 27 patients (71.1%) and non-response was seen in 11 patients (28.9%). Grading was the only parameter predicting response to nCRT (Odds Ratio (OR) = 0.188, 95% CI: 0.040–0.883; p = 0.034). No association with histopathologic treatment response was seen for any of the evaluated imaging parameters including SUVmax, MTV, busyness, contrast and uniformity. Using multivariate Cox-regression analysis, the heterogeneity parameters busyness (Hazard Ratio (HR) = 1.424, 95% CI: 1.044–1.943; p = 0.026) and contrast (HR = 6.678, 95% CI: 1.969–22.643;p = 0.002) were independently associated with OS, while no independent association with OS was seen for SUVmax and MTV. In patients with ESCC undergoing nCRT and surgery, baseline 18F-FDG-PET/CT derived parameters could not predict histopathologic response to nCRT. However, the PET/CT derived features busyness and contrast were independently associated with OS and should be further investigated. AU - Marr, L.* AU - Haller, B.* AU - Pyka, T.* AU - Peeken, J.C. AU - Jesinghaus, M.* AU - Scheidhauer, K.* AU - Friess, H.* AU - Combs, S.E. AU - Münch, S.* C1 - 64952 C2 - 52587 TI - Predictive value of clinical and 18F-FDG-PET/CT derived imaging parameters in patients undergoing neoadjuvant chemoradiation for esophageal squamous cell carcinoma. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - We provide a descriptive characterization of the unfolded protein response (UPR) in skeletal muscle of human patients with peritoneal sepsis and a sepsis model of C57BL/6J mice. Patients undergoing open surgery were included in a cross-sectional study and blood and skeletal muscle samples were taken. Key markers of the UPR and cluster of differentiation 68 (CD68) as surrogate of inflammatory injury were evaluated by real-time PCR and histochemical staining. CD68 mRNA increased with sepsis in skeletal muscle of patients and animals (p < 0.05). Mainly the inositol-requiring enzyme 1α branch of the UPR was upregulated as shown by elevated X-box binding-protein 1 (XBP1u) and its spliced isoform (XBP1s) mRNA (p < 0.05, respectively). Increased expression of Gadd34 indicated activation of PRKR-Like Endoplasmic Reticulum Kinase (PERK) branch of the UPR, and was only observed in mice (p < 0.001) but not human study subjects. Selected cell death signals were upregulated in human and murine muscle, demonstrated by increased bcl-2 associated X protein mRNA and TUNEL staining (p < 0.05). In conclusion we provide a first characterization of the UPR in skeletal muscle in human sepsis. AU - Metzing, U.B.* AU - von Loeffelholz, C.* AU - Steidl, R.* AU - Romeike, B.* AU - Winkler, R.* AU - Rauchfuß, F.* AU - Settmacher, U.* AU - Stoppe, C.* AU - Coldewey, S.M.* AU - Weinmann, C.* AU - Weickert, M.O.* AU - Claus, R.A.* AU - Birkenfeld, A.L. AU - Kosan, C.* AU - Horn, P.* C1 - 64076 C2 - 52077 TI - Endoplasmic reticulum stress and the unfolded protein response in skeletal muscle of subjects suffering from peritoneal sepsis. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Epidemiological analyses of health risks associated with non-optimal temperature are traditionally based on ground observations from weather stations that offer limited spatial and temporal coverage. Climate reanalysis represents an alternative option that provide complete spatio-temporal exposure coverage, and yet are to be systematically explored for their suitability in assessing temperature-related health risks at a global scale. Here we provide the first comprehensive analysis over multiple regions to assess the suitability of the most recent generation of reanalysis datasets for health impact assessments and evaluate their comparative performance against traditional station-based data. Our findings show that reanalysis temperature from the last ERA5 products generally compare well to station observations, with similar non-optimal temperature-related risk estimates. However, the analysis offers some indication of lower performance in tropical regions, with a likely underestimation of heat-related excess mortality. Reanalysis data represent a valid alternative source of exposure variables in epidemiological analyses of temperature-related risk. AU - Mistry, M.N.* AU - Schneider, R.* AU - Masselot, P.* AU - Royé, D.* AU - Armstrong, B.* AU - Kyselý, J.* AU - Orru, H.* AU - Sera, F.* AU - Tong, S.* AU - Lavigne, E.* AU - Urban, A.* AU - Madureira, J.* AU - García-León, D.* AU - Ibarreta, D.* AU - Ciscar, J.C.* AU - Feyen, L.* AU - de Schrijver, E.* AU - de Sousa Zanotti Stagliorio Coélho, M.* AU - Pascal, M.* AU - Tobias, A.* AU - Guo, Y.* AU - Vicedo-Cabrera, A.M.* AU - Gasparrini, A.* AU - Multi-Country Multi-City (MCC) Collaborative Research Network (Schneider, A.E.) AU - Multi-Country Multi-City (MCC) Collaborative Research Network (Huber, V.) C1 - 66503 C2 - 52859 TI - Comparison of weather station and climate reanalysis data for modelling temperature-related mortality. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AU - Mistry, M.N.* AU - Schneider, R.* AU - Masselot, P.* AU - Royé, D.* AU - Armstrong, B.* AU - Kyselý, J.* AU - Orru, H.* AU - Sera, F.* AU - Tong, S.* AU - Lavigne, E.* AU - Urban, A.* AU - Madureira, J.* AU - García-León, D.* AU - Ibarreta, D.* AU - Ciscar, J.C.* AU - Feyen, L.* AU - de Schrijver, E.* AU - de Sousa Zanotti Stagliorio Coélho, M.* AU - Pascal, M.* AU - Tobias, A.* AU - Guo, Y.* AU - Vicedo-Cabrera, A.M.* AU - Gasparrini, A.* AU - Multi-Country Multi-City (MCC) Collaborative Research Network (Schneider, A.E. AU - Huber, V.) C1 - 67023 C2 - 53422 TI - Author Correction: Comparison of weather station and climate reanalysis data for modelling temperature-related mortality. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Trypanosomiases are life-threatening infections of humans and livestock, and novel effective therapeutic approaches are needed. Trypanosoma compartmentalize glycolysis into specialized organelles termed glycosomes. Most of the trypanosomal glycolytic enzymes harbor a peroxisomal targeting signal-1 (PTS1) which is recognized by the soluble receptor PEX5 to facilitate docking and translocation of the cargo into the glycosomal lumen. Given its pivotal role in the glycosomal protein import, the PEX5-PTS1 interaction represents a potential target to inhibit import of glycolytic enzymes and thus kill the parasite. We developed a fluorescence polarization (FP)-based assay for monitoring the PEX5-PTS1 interaction and performed a High Throughput Screening (HTS) campaign to identify small molecule inhibitors of the interaction. Six of the identified hits passed orthogonal selection criteria and were found to inhibit parasite growth in cell culture. Our results validate PEX5 as a target for small molecule inhibitors and provide scaffolds suitable for further pre-clinical development of novel trypanocidal compounds. AU - Napolitano, V.* AU - Softley, C. AU - Blat, A.* AU - Kalel, V.C.* AU - Schorpp, K.K. AU - Siebenmorgen, T. AU - Hadian, K. AU - Erdmann, R.* AU - Sattler, M. AU - Popowicz, G.M. AU - Dubin, G.* C1 - 65961 C2 - 53005 TI - Small molecule mediated inhibition of protein cargo recognition by peroxisomal transport receptor PEX5 is toxic to Trypanosoma. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Inflammatory cytokines and non-esterified fatty acids (NEFAs) are obesity-linked factors that disturb insulin secretion. The aim of this study was to investigate whether pancreatic adipose tissue (pWAT) is able to generate a NEFA/cytokine overload within the pancreatic environment and as consequence to impact on insulin secretion. Pancreatic fat is a minor fat depot, therefore we used high-fat diet (HFD) feeding to induce pancreatic steatosis in mice. Relative Adipoq and Lep mRNA levels were higher in pWAT of HFD compared to chow diet mice. Regardless of HFD, Adipoq and Lep mRNA levels of pWAT were at least 10-times lower than those of epididymal fat (eWAT). Lipolysis stimulating receptors Adrb3 and Npr1 were expressed in pWAT and eWAT, and HFD reduced their expression in eWAT only. In accordance, HFD impaired lipolysis in eWAT but not in pWAT. Despite expression of Npr mRNA, lipolysis was stimulated solely by the adrenergic agonists, isoproterenol and adrenaline. Short term co-incubation of islets with CD/HFD pWAT did not alter insulin secretion. In the presence of CD/HFD eWAT, glucose stimulated insulin secretion only upon isoproterenol-induced lipolysis, i.e. in the presence of elevated NEFA. Isoproterenol augmented Il1b and Il6 mRNA levels both in pWAT and eWAT. These results suggest that an increased sympathetic activity enhances NEFA and cytokine load of the adipose microenvironment, including that of pancreatic fat, and by doing so it may alter beta-cell function. AU - Oquendo, M.B.* AU - Lorza-Gil, E. AU - Juarez Lopez, D.A. AU - Wagner, R. AU - Birkenfeld, A.L. AU - Ullrich, S. AU - Gerst, F. C1 - 66262 C2 - 53123 TI - Effects of adrenergic-stimulated lipolysis and cytokine production on in vitro mouse adipose tissue-islet interactions. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The extent of elective nodal irradiation (ENI) in patients undergoing definitive chemoradiotherapy (dCRT) for esophageal squamous cell carcinoma (ESCC) remains unclear. The aim of this dosimetric study was to evaluate the extent of incidental nodal irradiation using modern radiation techniques. A planning target volume (PTV) was generated for 30 patients with node-negative esophageal carcinoma (13 cervical/upper third, 7 middle third, 10 lower third/abdomen). Thereby, no elective nodal irradiation (ENI) was intended. Both three-dimensional conformal radiotherapy (3D-CRT) and volumetric-modulated arc therapy (VMAT) treatment plans (50 Gy in 25 fractions) were calculated for all patients. Fifteen nodal stations were contoured according to the definitions of the AJCC and investigated in regard to dosimetric parameters. Compared to 3D-CRT, VMAT was associated with lower dose distribution to the organs at risk (lower Dmean, V20 and V30 for the lungs and lower Dmean and V30 for the heart). For both techniques, the median Dmean surpassed 40 Gy in 12 of 15 (80%) nodal stations. However, VMAT resulted in significantly lower Dmeans and equivalent uniform doses (EUD) compared to 3D-CRT for eight nodal stations (1L, 2L, 2R, 4L, 7, 8L, 10L, 15), while differences did not reach significance for seven nodal station (1R, 4R, 8U, 8M, 10R, 16). For dCRT of ESCC, the use of VMAT was associated with significantly lower median (incidental) doses to eight of 15 regional lymph node areas compared to 3D-CRT. However, given the small absolute differences, these differences probably do not impair (regional) tumor control rates. AU - Peschel, D.P.* AU - Düsberg, M.* AU - Peeken, J.C. AU - Kaiser, J.C. AU - Borm, K.J.* AU - Sommer, K.* AU - Combs, S.E. AU - Münch, S.* C1 - 67106 C2 - 53427 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Incidental nodal irradiation in patients with esophageal cancer undergoing (chemo)radiation with 3D-CRT or VMAT. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - A historical beer, dated to the German Empire era, was recently found in northern Germany. Its chemical composition represents a unique source of insights into brewing culture of the late nineteenth century when pioneer innovations laid the foundations for industrial brewing. Complementary analytics including metabolomics, microbiological, sensory, and beer attribute analysis revealed its molecular profile and certify the unprecedented good storage condition even after 130 years in the bottle. Comparing its chemical signature to that of four hundred modern brews allowed to describe molecular fingerprints teaching us about technological aspects of historical beer brewing. Several critical production steps such as malting and germ treatment, wort preparation and fermentation, filtration and storage, and compliance with the Bavarian Purity Law left detectable molecular imprints. In addition, the aging process of the drinkable brew could be analyzed on a chemical level and resulted in an unseen diversity of hops- and Maillard-derived compounds. Using this archeochemical forensic approach, the historical production process of a culturally significant beverage could be traced and the ravages of time made visible. AU - Pieczonka, S. AU - Zarnkow, M.* AU - Diederich, P. AU - Hutzler, M.* AU - Weber, N.* AU - Jacob, F.* AU - Rychlik, M.* AU - Schmitt-Kopplin, P. C1 - 65395 C2 - 52290 TI - Archeochemistry reveals the first steps into modern industrial brewing. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AU - Pieczonka, S. AU - Zarnkow, M.* AU - Diederich, P. AU - Hutzler, M.* AU - Weber, N.* AU - Jacob, F.* AU - Rychlik, M.* AU - Schmitt-Kopplin, P. C1 - 66181 C2 - 53118 TI - Author Correction: Archeochemistry reveals the first steps into modern industrial brewing. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Patients with locally advanced head and neck squamous cell carcinoma (HNSCC) may benefit from personalised treatment, requiring biomarkers that characterize the tumour and predict treatment response. We integrate pre-treatment CT radiomics and whole-transcriptome data from a multicentre retrospective cohort of 206 patients with locally advanced HNSCC treated with primary radiochemotherapy to classify tumour molecular subtypes based on radiomics, develop surrogate radiomics signatures for gene-based signatures related to different biological tumour characteristics and evaluate the potential of combining radiomics features with full-transcriptome data for the prediction of loco-regional control (LRC). Using end-to-end machine-learning, we developed and validated a model to classify tumours of the atypical subtype (AUC [95% confidence interval] 0.69 [0.53-0.83]) based on CT imaging, observed that CT-based radiomics models have limited value as surrogates for six selected gene signatures (AUC < 0.60), and showed that combining a radiomics signature with a transcriptomics signature consisting of two metagenes representing the hedgehog pathway and E2F transcriptional targets improves the prognostic value for LRC compared to both individual sources (validation C-index [95% confidence interval], combined: 0.63 [0.55-0.73] vs radiomics: 0.60 [0.50-0.71] and transcriptomics: 0.59 [0.49-0.69]). These results underline the potential of multi-omics analyses to generate reliable biomarkers for future application in personalized oncology. AU - Rabasco Meneghetti, A.* AU - Zwanenburg, A.* AU - Linge, A.* AU - Lohaus, F.* AU - Grosser, M.* AU - Kalinauskaite, G.* AU - Tinhofer, I.* AU - Guberina, M.* AU - Stuschke, M.* AU - Balermpas, P.* AU - Von der Grün, J.* AU - Ganswindt, U. AU - Belka, C. AU - Peeken, J.C. AU - Combs, S.E. AU - Böke, S.* AU - Zips, D.* AU - Baumann, M.* AU - Löck, S.* C1 - 66344 C2 - 53142 TI - Integrated radiogenomics analyses allow for subtype classification and improved outcome prognosis of patients with locally advanced HNSCC. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Heated tobacco products (HTP) are novel nicotine delivery products with limited toxicological data. HTP uses heating instead of combustion to generate aerosol (HTP-smoke). Physiologically relevant human bronchial and alveolar lung mucosa models developed at air-liquid interface were exposed to HTP-smoke to assess broad toxicological response (n = 6-7; ISO puffing regimen; compared to sham; non-parametric statistical analysis; significance: p < 0.05). Elevated levels of total cellular reactive oxygen species, stress responsive nuclear factor kappa-B, and DNA damage markers [8-hydroxy-2'-deoxyguanosine, phosphorylated histone H2AX, cleaved poly-(ADP-Ribose) polymerase] were detected in HTP-smoke exposed bronchial and/or alveolar models. RNA sequencing detected differential regulation of 724 genes in the bronchial- and 121 genes in the alveolar model following HTP-smoke exposure (cut off: p ≤ 0.01; fold change: ≥ 2). Common enriched pathways included estrogen biosynthesis, ferroptosis, superoxide radical degradation, xenobiotics, and α-tocopherol degradation. Secreted levels of interleukin (IL)1ꞵ and IL8 increased in the bronchial model whereas in the alveolar model, interferon-γ and IL4 increased and IL13 decreased following HTP-smoke exposure. Increased lipid peroxidation was detected in HTP-smoke exposed bronchial and alveolar models which was inhibited by ferrostatin-1. The findings form a basis to perform independent risk assessment studies on different flavours of HTP using different puffing topography and corresponding chemical characterization. AU - Rahman, M.* AU - Irmler, M. AU - Introna, M.* AU - Beckers, J. AU - Palmberg, L.* AU - Johanson, G.* AU - Upadhyay, S.* AU - Ganguly, K.* C1 - 66371 C2 - 52920 TI - Insight into the pulmonary molecular toxicity of heated tobacco products using human bronchial and alveolar mucosa models at air-liquid interface. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Anal cancer and the related treatment are generally known to affect patients’ quality of life. The aim of this study was to assess self-reported quality of life (QoL) of anal cancer patients after combined radiation and chemotherapy, and to identify patient-, disease-, and therapy-related factors associated with QoL. A total of 94 patients treated with definitive chemoradiation for anal cancer at our institution in the period from 2004 to 2018 were identified from our database. QoL was assessed in the remaining 52 patients using the EORTC QLQ-C30 questionnaire (cancer-specific QoL) and the newly developed anal cancer module QLQ-ANL27 (site-specific QoL). Differences in QoL between anal cancer patients and a German age and sex adjusted reference population were examined. The median follow-up was 71 months (range, 7–176). In the cancer-specific QoL module, the anal cancer cohort presented with significantly lower scores in role (− 12.2 points), emotional (− 6.6 points), and social functioning (− 6.8 points), but higher scores in diarrhea (+ 36.3 points) and constipation (+ 13.3 points) than the German reference population. There were no significant differences in disease- or therapy-related factors, but age greater than 70 years and a follow-up time greater than 71 months had a negative impact on global QoL. As for the site-specific QoL, patients with a tumor relapse showed significantly higher symptom scores than patients with a complete clinical remission in all scales except of micturition frequency. Compared to 3D conformal radiotherapy, IMRT treatment seemed to improve non-stoma bowel function (+ 23.3 points), female sexual functioning (+ 24.2 points), and came along with less scores in the symptom scales pain (− 35.9 points), toilet proximity (− 28.6 points), and cleanliness (− 26.2 points). Most of the functional scores of anal cancer patients were lower compared to the general German population, but did not seem to affect the general QoL. Fatigue, physical, and role functioning had the strongest impact on global QoL causing psychological symptoms as important as physical. AU - Sauter, C.* AU - Peeken, J.C. AU - Borm, K.* AU - Diehl, C.* AU - Münch, S.* AU - Combs, S.E. AU - Dapper, H.* C1 - 64610 C2 - 52344 TI - Quality of life in patients treated with radiochemotherapy for primary diagnosis of anal cancer. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - We compared our institutional experience with intensity-modulated radiotherapy (IMRT) and 3D-conformal radiotherapy (3D-RT) for definitive treatment of primary anal cancer. We performed a single-institution retrospective review of all patients with anal squamous cell carcinoma treated with definitive (chemo) radiotherapy with curative intent from 2004 through 2018. We assessed several prognostic factors in respect to relevant survival endpoints. In addition, acute toxicities were determined and compared between IMRT and 3D-RT patients. This study included 94 patients (58 IMRT, 36 3D-RT). Mean follow up for all patients, for IMRT and 3D-RT patients was 61 months (range 6–176), 46 months (range 6–118), and 85 months (range 6–176), respectively. 5-year overall survival (OS) was 86%, disease-free survival (DFS) was 72%, and colostomy-free survival (CFS) was 75% in the IMRT cohort. In the 3D-RT cohort, OS was 87%, DFS was 71%, and CFS was 81% (all p > 0.05). Male gender and Karnofsky Index (KI) were revealed as independent prognostic factors for 5-year OS (p = 0.017; p = 0.023). UICC stage was an independent prognostic factor for DFS and CFS (p = 0.023; p = 0.042). In addition, the pre-treatment leukocyte count was an independent prognostic factor for CFS (p = 0.042). Acute grade ≥ 3 toxicity was not significantly different between IMRT and 3D-RT patients, but the IMRT cohort had favorable outcomes. This study confirmed IMRT as the primary definitive treatment of anal cancer. With similar survival rates, IMRT had the potential to reduce acute toxicity by sparing organs at risk. Promising prognostic factors such as BMI, KI, and leucocyte and hemoglobin levels should be further investigated. AU - Sauter, C.* AU - Peeken, J.C. AU - Borm, K.* AU - Diehl, C.D.* AU - Münch, S.* AU - Combs, S.E. AU - Dapper, H.* C1 - 66754 C2 - 53290 TI - Influence of radiation treatment technique (IMRT vs. 3D-RT) on acute toxicity and prognostic factors for survival for anal cancer. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - In high-yielding dairy cows, the rapidly increasing milk production after parturition can result in a negative nutrient balance, since feed intake is insufficient to cover the needs for lactation. Mobilizing body reserves, mainly adipose tissue (AT), might affect steroid metabolism. We hypothesized, that cows differing in the extent of periparturient lipomobilization, will have divergent steroid profiles measured in serum and subcutaneous (sc)AT by a targeted metabolomics approach and steroidogenic enzyme profiles in scAT and liver. Fifteen weeks antepartum, 38 multiparous Holstein cows were allocated to a high (HBCS) or normal body condition (NBCS) group fed differently until week 7 antepartum to either increase (HBCS BCS: 3.8 ± 0.1 and BFT: 2.0 ± 0.1 cm; mean ± SEM) or maintain BCS (NBCS BCS: 3.0 ± 0.1 and BFT: 0.9 ± 0.1 cm). Blood samples, liver, and scAT biopsies were collected at week -7, 1, 3, and 12 relative to parturition. Greater serum concentrations of progesterone, androsterone, and aldosterone in HBCS compared to NBCS cows after parturition, might be attributed to the increased mobilization of AT. Greater glucocorticoid concentrations in scAT after parturition in NBCS cows might either influence local lipogenesis by differentiation of preadipocytes into mature adipocytes and/or inflammatory response. AU - Schuh, K.* AU - Häussler, S.* AU - Sadri, H.* AU - Prehn, C. AU - Lintelmann, J. AU - Adamski, J. AU - Koch, C.* AU - Frieten, D.* AU - Ghaffari, M.H.* AU - Dusel, G.* AU - Sauerwein, H.* C1 - 64311 C2 - 52022 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Blood and adipose tissue steroid metabolomics and mRNA expression of steroidogenic enzymes in periparturient dairy cows differing in body condition. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Fetal behavioural states (fBS) describe periods of fetal wakefulness and sleep and are commonly defined by features such as body and eye movements and heart rate. Automatic state detection through algorithms relies on different parameters and thresholds derived from both the heart rate variability (HRV) and the actogram, which are highly dependent on the specific datasets and are prone to artefacts. Furthermore, the development of the fetal states is dynamic over the gestational period and the evaluation usually only separated into early and late gestation (before and after 32 weeks). In the current work, fBS detection was consistent between the classification algorithm and visual inspection in 87 fetal magnetocardiographic data segments between 27 and 39 weeks of gestational age. To identify how automated fBS detection could be improved, we first identified commonly used parameters for fBS classification in both the HRV and the actogram, and investigated their distribution across the different fBS. Then, we calculated a receiver operating characteristics (ROC) curve to determine the performance of each parameter in the fBS classification. Finally, we investigated the development of parameters over gestation through linear regression. As a result, the parameters derived from the HRV have a higher classification accuracy compared to those derived from the body movement as defined by the actogram. However, the overlapping distributions of several parameters across states limit a clear separation of states based on these parameters. The changes over gestation of the HRV parameters reflect the maturation of the fetal autonomic nervous system. Given the higher classification accuracy of the HRV in comparison to the actogram, we suggest to focus further research on the HRV. Furthermore, we propose to develop probabilistic fBS classification approaches to improve classification in less prototypical datasets. AU - Semeia, L. AU - Sippel, K. AU - Moser, J. AU - Preissl, H. C1 - 64528 C2 - 52254 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Evaluation of parameters for fetal behavioural state classification. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Radiomics analyses commonly apply imaging features of different complexity for the prediction of the endpoint of interest. However, the prognostic value of each feature class is generally unclear. Furthermore, many radiomics models lack independent external validation that is decisive for their clinical application. Therefore, in this manuscript we present two complementary studies. In our modelling study, we developed and validated different radiomics signatures for outcome prediction after neoadjuvant chemoradiotherapy (nCRT) in patients with locally advanced rectal cancer (LARC) based on computed tomography (CT) and T2-weighted (T2w) magnetic resonance (MR) imaging datasets of 4 independent institutions (training: 122, validation 68 patients). We compared different feature classes extracted from the gross tumour volume for the prognosis of tumour response and freedom from distant metastases (FFDM): morphological and first order (MFO) features, second order texture (SOT) features, and Laplacian of Gaussian (LoG) transformed intensity features. Analyses were performed for CT and MRI separately and combined. Model performance was assessed by the area under the curve (AUC) and the concordance index (CI) for tumour response and FFDM, respectively. Overall, intensity features of LoG transformed CT and MR imaging combined with clinical T stage (cT) showed the best performance for tumour response prediction, while SOT features showed good performance for FFDM in independent validation (AUC = 0.70, CI = 0.69). In our external validation study, we aimed to validate previously published radiomics signatures on our multicentre cohort. We identified relevant publications on comparable patient datasets through a literature search and applied the reported radiomics models to our dataset. Only one of the identified studies could be validated, indicating an overall lack of reproducibility and the need of further standardization of radiomics before clinical application. AU - Shahzadi, I.* AU - Zwanenburg, A.* AU - Lattermann, A.* AU - Linge, A.* AU - Baldus, C.* AU - Peeken, J.C. AU - Combs, S.E. AU - Diefenhardt, M.* AU - Rödel, C.* AU - Kirste, S.* AU - Grosu, A.L.* AU - Baumann, M.* AU - Löck, S.* C1 - 65556 C2 - 52739 TI - Analysis of MRI and CT-based radiomics features for personalized treatment in locally advanced rectal cancer and external validation of published radiomics models. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - For gene expression analysis, the raw data obtained from RT-qPCR are preferably normalized to reference genes, which should be constantly expressed regardless of experimental conditions. Selection of reference genes is particularly challenging for the developing lung because of the complex transcriptional and epigenetic regulation of genes during organ maturation and injury repair. To date, there are only limited experimental data addressing reliable reference genes for this biological circumstance. In this study, we evaluated reference genes for the lung in neonatal C57BL/6 mice under consideration of biological, technical and experimental conditions. For that, we thoroughly selected candidates from commonly used reference genes side-by-side with novel ones by analyzing publicly available microarray datasets. We performed RT-qPCR of the selected candidate genes and analyzed their expression variability using GeNorm and Normfinder. Cell-specific expression of the candidate genes was analyzed using our own single-cell RNA-sequencing data from the developing mouse lung. Depending on the investigated conditions, i.e., developmental stages, sex, RNA quality, experimental condition (hyperoxia) and cell types, distinct candidate genes demonstrated stable expression confirming their eligibility as reliable reference genes. Our results provide valuable information for the selection of proper reference genes in studies investigating the neonatal mouse lung. AU - Shin, H. AU - Morty, R.E.* AU - Sucre, J.M.S.* AU - Negretti, N.M.* AU - Markmann, M.* AU - Hossain, H.* AU - Krauss-Etschmann, S. AU - Dehmel, S. AU - Hilgendorff, A. C1 - 66467 C2 - 53184 TI - Reference genes for the developing mouse lung under consideration of biological, technical and experimental confounders. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - There is large inter-individual heterogeneity in risk of coronary heart disease (CHD). Risk factors traditionally used in primary risk assessment only partially explain this heterogeneity. Residual, unobserved heterogeneity leads to age-related attenuation of hazard rates and underestimation of hazard ratios. Its magnitude is unknown. Therefore, we aimed to estimate a lower and an approximate upper bound. Heterogeneity was parametrized by a log-normal distribution with shape parameter σ. Analysis was based on published data. From concordance indices of studies including traditional risk factors and additional diagnostic imaging data, we calculated the part of heterogeneity explained by imaging data. For traditional risk assessment, this part typically remains unexplained, thus constituting a lower bound on unobserved heterogeneity. Next, the potential impact of heterogeneity on CHD hazard rates in several large countries was investigated. CHD rates increase with age but the increase attenuates with age. Presuming this attenuation to be largely caused by heterogeneity, an approximate upper bound on σ was derived. Taking together both bounds, unobserved heterogeneity in studies without imaging information can be described by a shape parameter in the range σ = 1-2. It substantially contributes to observed age-dependences of hazard ratios and may lead to underestimation of hazard ratios by a factor of about two. Therefore, analysis of studies for primary CHD risk assessment should account for unobserved heterogeneity. AU - Simonetto, C. AU - Rospleszcz, S. AU - Kaiser, J.C. AU - Furukawa, K.* C1 - 65560 C2 - 52362 TI - Heterogeneity in coronary heart disease risk. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - This Article contains an error in Table 1 where the mean value and standard deviation of pregnancy week for the "screening group:NGT women" was incorrectly given as 23.0 +/- 9.5. The correct numbers are 26.5 +/- 2.1. Incorrect: (Table presented.) Correct: (Table presented.). AU - Stirm, L. AU - Huypens, P. AU - Sass, S. AU - Batra, R. AU - Fritsche, L. AU - Brucker, S.* AU - Abele, H.* AU - Hennige, A.M. AU - Theis, F.J. AU - Beckers, J. AU - Hrabě de Angelis, M. AU - Fritsche, A. AU - Häring, H.-U. AU - Staiger, H. C1 - 64938 C2 - 52012 TI - Author Correction: Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin (Scientific Reports, (2018), 8, 1, (1366), 10.1038/s41598-018-19200-9). JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The Environmental Determinants of Diabetes in the Young (TEDDY) study enrolled 8676 children, 3-4 months of age, born with HLA-susceptibility genotypes for islet autoimmunity (IA) and type 1 diabetes (T1D). Whole-genome sequencing (WGS) was performed in 1119 children in a nested case-control study design. Telomere length was estimated from WGS data using five tools: Computel, Telseq, Telomerecat, qMotif and Motif_counter. The estimated median telomere length was 5.10 kb (IQR 4.52-5.68 kb) using Computel. The age when the blood sample was drawn had a significant negative correlation with telomere length (P = 0.003). European children, particularly those from Finland (P = 0.041) and from Sweden (P = 0.001), had shorter telomeres than children from the U.S.A. Paternal age (P = 0.019) was positively associated with telomere length. First-degree relative status, presence of gestational diabetes in the mother, and maternal age did not have a significant impact on estimated telomere length. HLA-DR4/4 or HLA-DR4/X children had significantly longer telomeres compared to children with HLA-DR3/3 or HLA-DR3/9 haplogenotypes (P = 0.008). Estimated telomere length was not significantly different with respect to any IA (P = 0.377), IAA-first (P = 0.248), GADA-first (P = 0.248) or T1D (P = 0.861). These results suggest that telomere length has no major impact on the risk for IA, the first step to develop T1D. Nevertheless, telomere length was shorter in the T1D high prevalence populations, Finland and Sweden. AU - Törn, C.* AU - Liu, X.* AU - Onengut-Gumuscu, S.* AU - Counts, K.M.* AU - Moreno, J.L.* AU - Remedios, C.L.* AU - Chen, W.M.* AU - LeFaive, J.* AU - Butterworth, M.D.* AU - Akolkar, B.* AU - Krischer, J.P.* AU - Lernmark, Å.* AU - Rewers, M.* AU - She, J.X.* AU - Toppari, J.* AU - Ziegler, A.-G. AU - Ratan, A.* AU - Smith, A.V.* AU - Hagopian, W.A.* AU - Rich, S.S.* AU - Parikh, H.M.* C1 - 64634 C2 - 52361 TI - Telomere length is not a main factor for the development of islet autoimmunity and type 1 diabetes in the TEDDY study. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Endothelial cells (ECs) lining blood vessels are exposed to mechanical forces, such as shear stress. These forces control many aspects of EC biology, including vascular tone, cell migration and proliferation. Despite a good understanding of the genes responding to shear stress, our insight into the transcriptional regulation of these genes is much more limited. Here, we set out to study alterations in the chromatin landscape of human umbilical vein endothelial cells (HUVEC) exposed to laminar shear stress. To do so, we performed ChIP-Seq for H3K27 acetylation, indicative of active enhancer elements and ATAC-Seq to mark regions of open chromatin in addition to RNA-Seq on HUVEC exposed to 6 h of laminar shear stress. Our results show a correlation of gained and lost enhancers with up and downregulated genes, respectively. DNA motif analysis revealed an over-representation of KLF transcription factor (TF) binding sites in gained enhancers, while lost enhancers contained more ETV/ETS motifs. We validated a subset of flow responsive enhancers using luciferase-based reporter constructs and CRISPR-Cas9 mediated genome editing. Lastly, we characterized the shear stress response in ECs of zebrafish embryos using RNA-Seq. Our results lay the groundwork for the exploration of shear stress responsive elements in controlling EC biology. AU - Tsaryk, R.* AU - Yucel, N.* AU - Leonard, E.V.* AU - Diaz, N.* AU - Bondareva, O. AU - Odenthal-Schnittler, M.* AU - Arany, Z.* AU - Vaquerizas, J.M.* AU - Schnittler, H.J.* AU - Siekmann, A.F.* C1 - 64620 C2 - 52348 TI - Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The mutational spectrum of asthma and allergy associated genes is not known although recent biobank based exome sequencing studies included these traits. We therefore conducted a secondary analysis of exome data from 281,104 UK Biobank samples for association of mostly rare variants with asthma, allergic rhinitis and atopic dermatitis. Variants of interest (VOI) were tabulated, shared genes annotated and compared to earlier genome-wide SNP association studies (GWAS), whole genome sequencing, exome and bisulfit sequencing studies. 354 VOI were significantly associated with asthma, allergic rhinitis and atopic dermatitis. They cluster mainly in two large regions on chromosome 6 and 17. After exclusion of the variants associated with atopic dermatitis and redundant variants, 321 unique VOI remain in 122 unique genes. 30 genes are shared among the 87 genes with increased and the 65 genes with decreased risk for allergic disease. 85% of genes identified earlier by common GWAS SNPs are not replicated here. Most identified genes are located in interferon ɣ and IL33 signaling pathway. These genes include already known but also new pharmacological targets, including the IL33 receptor ST2/IL1RL1, as well as TLR1, ALOX15, GSDMA, BTNL2, IL13 and IKZF3. Future pharmacological studies will need to included these VOI for stratification of the study population paving the way to individualized treatment. AU - Wjst, M. C1 - 66926 C2 - 53353 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Exome variants associated with asthma and allergy. JO - Sci. Rep. VL - 12 IS - 1 PB - Nature Portfolio PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The adverse effects of maternal prenatal stress (PS) on child's neurodevelopment warrant the establishment of biomarkers that enable early interventional therapeutic strategies. We performed a prospective matched double cohort study screening 2000 pregnant women in third trimester with Cohen Perceived Stress Scale-10 (PSS-10) questionnaire; 164 participants were recruited and classified as stressed and control group (SG, CG). Fetal cord blood iron parameters of 107 patients were measured at birth. Transabdominal electrocardiograms-based Fetal Stress Index (FSI) was derived. We investigated sex contribution to group differences and conducted causal inference analyses to assess the total effect of PS exposure on iron homeostasis using a directed acyclic graph (DAG) approach. Differences are reported for p < 0.05 unless noted otherwise. Transferrin saturation was lower in male stressed neonates. The minimum adjustment set of the DAG to estimate the total effect of PS exposure on fetal ferritin iron biomarkers consisted of maternal age and socioeconomic status: SG revealed a 15% decrease in fetal ferritin compared with CG. Mean FSI was higher among SG than among CG. FSI-based timely detection of fetuses affected by PS can support early individualized iron supplementation and neurodevelopmental follow-up to prevent long-term sequelae due to PS-exacerbated impairment of the iron homeostasis. AU - Zimmermann, P.* AU - Antonelli, M.C.* AU - Sharma, R. AU - Müller, A.* AU - Zelgert, C.* AU - Fabre, B.* AU - Wenzel, N.* AU - Wu, H.T.* AU - Frasch, M.G.* AU - Lobmaier, S.M.* C1 - 65464 C2 - 52695 TI - Prenatal stress perturbs fetal iron homeostasis in a sex specific manner. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - The northern white rhinoceros (NWR) is probably the earth's most endangered mammal. To rescue the functionally extinct species, we aim to employ induced pluripotent stem cells (iPSCs) to generate gametes and subsequently embryos in vitro. To elucidate the regulation of pluripotency and differentiation of NWR PSCs, we generated iPSCs from a deceased NWR female using episomal reprogramming, and observed surprising similarities to human PSCs. NWR iPSCs exhibit a broad differentiation potency into the three germ layers and trophoblast, and acquire a naïve-like state of pluripotency, which is pivotal to differentiate PSCs into primordial germ cells (PGCs). Naïve culturing conditions induced a similar expression profile of pluripotency related genes in NWR iPSCs and human ESCs. Furthermore, naïve-like NWR iPSCs displayed increased expression of naïve and PGC marker genes, and a higher integration propensity into developing mouse embryos. As the conversion process was aided by ectopic BCL2 expression, and we observed integration of reprogramming factors, the NWR iPSCs presented here are unsuitable for gamete production. However, the gained insights into the developmental potential of both primed and naïve-like NWR iPSCs are fundamental for in future PGC-specification in order to rescue the species from extinction using cryopreserved somatic cells. AU - Zywitza, V.* AU - Rusha, E. AU - Shaposhnikov, D. AU - Ruiz-Orera, J.* AU - Telugu, N.* AU - Rishko, V. AU - Hayashi, M.* AU - Michel, G.* AU - Wittler, L.* AU - Stejskal, J.* AU - Holtze, S.* AU - Göritz, F.* AU - Hermes, R.* AU - Wang, J.* AU - Izsvák, Z.* AU - Colleoni, S.* AU - Lazzari, G.* AU - Galli, C.* AU - Hildebrandt, T.B.* AU - Hayashi, K.* AU - Diecke, S.* AU - Drukker, M. C1 - 64578 C2 - 52333 TI - Naïve-like pluripotency to pave the way for saving the northern white rhinoceros from extinction. JO - Sci. Rep. VL - 12 IS - 1 PY - 2022 SN - 2045-2322 ER - TY - JOUR AB - Radiological hazards to the residents of the Gaza Strip, Palestine and the north of the Sinai Peninsula, Egypt, were determined using the naturally occurring radionuclides (226Ra, 232Th and 40K) in 69 samples of building materials (demolition debris, plasters, concretes, from recycling plants and raw cements from suppliers), soils and sands collected in the field. The radiological hazard indices and dose rates calculated with the activity concentrations of radionuclides in those materials determined by gamma-ray spectrometry indicate that the values are all within the global limits recommended by the United Nations Scientific Committee on the Effects of Atomic Radiation 2000 and European Commission 1999. The results of Spearman's correlation and hierarchical cluster analysis for 210Pb in the building materials, soils and sands suggest that the samples include 210Pb from the atmospheric fallout. The medium correlation between 232Th and 40K in demolition debris implies that their activity concentrations are characteristic of the building materials and constituents of the demolition debris. Non-natural ratio of 238U/235U was found in the soil and sand samples collected in the Gaza Strip. Furthermore, 137Cs and 241Am were detected in some soil, sand and demolition debris samples analyzed in this study. The origins of those anthropogenic radionuclides were considered. AU - Abd Elkader, M.M AU - Shinonaga, T. AU - Sherif, M.M.* C1 - 63732 C2 - 51681 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Radiological hazard assessments of radionuclides in building materials, soils and sands from the Gaza Strip and the north of Sinai Peninsula. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Endoscopic ultrasonography (EUS) is a safe, real-time diagnostic and therapeutic tool. Speckle noise, inherent to ultrasonography, degrades the diagnostic precision of EUS. Elevational angular compounding (EAC) can provide real-time speckle noise reduction; however, EAC has never been applied to EUS because current implementations require costly and bulky arrays and are incompatible with the tight spatial constraints of hollow organs. Here we develop a radial implementation of a refraction-based elevational angular compounding technique (REACT) for EUS and demonstrate for the first time spatial compounding in a radial endoscopy. The proposed implementation was investigated in cylindrical phantoms and demonstrated superior suppression of ultrasound speckle noise and up to a two-fold improvement in signal- and contrast- ratios, compared to standard image processing techniques and averaging. The effect of elevational angular deflection on image fidelity was further investigated in a phantom with lymph node-like structures to determine the optimum elevational angular width for high speckle reduction efficiency while maintaining image fidelity. This study introduces REACT as a potential compact and low-cost solution to impart current radial echo-endoscopes with spatial compounding, which could enable accurate identification and precise sizing of lymph nodes in staging of gastrointestinal tract cancers. AU - Afshari, P. AU - Zakian Dominguez, C.M. AU - Bachmann, J.* AU - Ntziachristos, V. C1 - 63051 C2 - 51245 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Speckle reduction in ultrasound endoscopy using refraction based elevational angular compounding. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Image performance in optoacoustic endoscopy depends markedly on the design of the transducer employed. Ideally, high-resolution performance is required over an expanded depth of focus. Current optoacoustic focused transducers achieve lateral resolutions in the range of tens of microns in the mesoscopic regime, but their depth of focus is limited to hundreds of microns by the nature of their spherical geometry. We designed an ultra-broadband axicon detector with a 2 mm central aperture and investigated whether the imaging characteristics exceeded those of a spherical detector of similar size. We show a previously undocumented ability to achieve a broadband elongated pencil-beam optoacoustic sensitivity with an axicon detection geometry, providing approximately 40 μm-lateral resolution maintained over a depth of focus of 950 μm-3.8 times that of the reference spherical detector. This performance could potentially lead to optoacoustic endoscopes that can visualize optical absorption deeper and with higher resolution than any other optical endoscope today. AU - Ali, Z. AU - Zakian Dominguez, C.M. AU - Ntziachristos, V. C1 - 61092 C2 - 50042 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Ultra-broadband axicon transducer for optoacoustic endoscopy. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Limited data on prehospital and early in-hospital coronary heart disease (CHD) deaths is available. Aims of this study were to provide a comprehensive description on CHD cases and to analyse determinants of prehospital death. From a population-based myocardial infarction (MI) registry in Augsburg, Germany we included 12,572 CHD cases aged 25-74 years between 2003-2017 and 4754 CHD cases aged 75-84 years between 2009-2017. Multivariable logistic regression models were conducted to identify patient characteristics associated with prehospital death compared to 28-day survival. In patients aged 25-74 years, 1713 (13.6%) died prehospital, 941 (7.5%) died within the first 24 h in-hospital and 560 (4.5%) died within the 2nd and 28th day after the acute event; in patients aged 75-84 years the numbers were 1263 (26.6%), 749 (15.8%) and 329 (6.9%), respectively. In both age groups increasing age, actual smoking or nicotine abuse, previous MI, angina pectoris and previous stroke were more likely and hypertension was less likely in cases, who died prehospital compared to 28-day survivors. For example, in the 25-74 years old we revealed an adjusted odds ratio (OR) of 4.53 (95% CI 3.84-5.34) for angina pectoris and an OR of 0.69 (95% CI 0.57-0.85) for hypertension. In cases aged 25-74 years, an association of living alone (OR 1.26, 95% CI 1.06-1.49) and diabetes (OR 1.20, 95% CI 1.03-1.41) with prehospital death was found. Whereas in cases aged 75-84 years, chronic obstructive pulmonary disease (OR 2.20, 95%CI 1.69-0.2.85) was associated with prehospital death. In summary, we observed high prehospital and early in-hospital case fatality. Besides classical cardiac risk factors, the impact of living alone on prehospital death was more important in patients aged 25-74 years than in older patients. AU - Amann, U. AU - Heier, M. AU - Thilo, C.* AU - Linseisen, J. AU - Meisinger, C. C1 - 62882 C2 - 51077 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Determinants of prehospital coronary heart disease death. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Cilia are protrusions of the cell surface and composed of hundreds of proteins many of which are evolutionary and functionally well conserved. In cells assembling motile cilia the expression of numerous ciliary components is under the control of the transcription factor FOXJ1. Here, we analyse the evolutionary conserved FOXJ1 target CFAP161 in Xenopus and mouse. In both species Cfap161 expression correlates with the presence of motile cilia and depends on FOXJ1. Tagged CFAP161 localises to the basal bodies of multiciliated cells of the Xenopus larval epidermis, and in mice CFAP161 protein localises to the axoneme. Surprisingly, disruption of the Cfap161 gene in both species did not lead to motile cilia-related phenotypes, which contrasts with the conserved expression in cells carrying motile cilia and high sequence conservation. In mice mutation of Cfap161 stabilised the mutant mRNA making genetic compensation triggered by mRNA decay unlikely. However, genes related to microtubules and cilia, microtubule motor activity and inner dyneins were dysregulated, which might buffer the Cfap161 mutation. AU - Beckers, A.* AU - Fuhl, F.* AU - Ott, T.* AU - Boldt, K.* AU - Brislinger, M.M.* AU - Walentek, P.* AU - Schuster-Gossler, K.* AU - Hegermann, J.* AU - Alten, L.* AU - Kremmer, E. AU - Przykopanski, A.* AU - Serth, K.* AU - Ueffing, M.* AU - Blum, M.* AU - Gossler, A.* C1 - 62459 C2 - 50884 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - The highly conserved FOXJ1 target CFAP161 is dispensable for motile ciliary function in mouse and Xenopus. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Nowadays droplet microfluidics is widely used to perform high throughput assays and for the synthesis of micro- and nanoparticles. These applications usually require packaging several reagents into droplets and their mixing to start a biochemical reaction. For rapid mixing microfluidic devices usually require additional functional elements that make their designs more complex. Here we perform a series of 2D numerical simulations, followed by experimental studies, and introduce a novel asymmetric flow-focusing droplet generator, which enhances mixing during droplet formation due to a 2D or 3D asymmetric vortex, located in the droplet formation area of the microfluidic device. Our results suggest that 2D numerical simulations can be used for qualitative analysis of two-phase flows and droplet generation process in quasi-two-dimensional devices, while the relative simplicity of such simulations allows them to be easily applied to fairly complicated microfluidic geometries. Mixing inside droplets formed in the asymmetric generator occurs up to six times faster than in a conventional symmetric one. The best mixing efficiency is achieved in a specific range of droplet volumes, which can be changed by scaling the geometry of the device. Thus, the droplet generator suggested here can significantly simplify designs of microfluidic devices because it enables both the droplet formation and fast mixing of the reagents within droplets. Moreover, it can be used to precisely estimate reaction kinetics. AU - Belousov, K.I.* AU - Filatov, N.A.* AU - Kukhtevich, I. AU - Kantsler, V.* AU - Evstrapov, A.A.* AU - Bukatin, A.S.* C1 - 61886 C2 - 50502 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - An asymmetric flow-focusing droplet generator promotes rapid mixing of reagents. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Peptide glycation is an important, yet poorly understood reaction not only found in food but also in biological systems. The enormous heterogeneity of peptides and the complexity of glycation reactions impeded large-scale analysis of peptide derived glycation products and to understand both the contributing factors and how this affects the biological activity of peptides. Analyzing time-resolved Amadori product formation, we here explored site-specific glycation for 264 peptides. Intensity profiling together with in-depth computational sequence deconvolution resolved differences in peptide glycation based on microheterogeneity and revealed particularly reactive peptide collectives. These peptides feature potentially important sequence patterns that appear in several established bio- and sensory-active peptides from independent sources, which suggests that our approach serves system-wide applicability. We generated a pattern peptide map and propose that in peptide glycation the herein identified molecular checkpoints can be used as indication of sequence reactivity. AU - Berger, M. AU - Hemmler, D. AU - Walker, A. AU - Rychlik, M.* AU - Marshall, J.W.* AU - Schmitt-Kopplin, P. C1 - 62462 C2 - 50886 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Molecular characterization of sequence-driven peptide glycation. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Modern high-throughput sequencing technologies provide low-cost microbiome survey data across all habitats of life at unprecedented scale. At the most granular level, the primary data consist of sparse counts of amplicon sequence variants or operational taxonomic units that are associated with taxonomic and phylogenetic group information. In this contribution, we leverage the hierarchical structure of amplicon data and propose a data-driven and scalable tree-guided aggregation framework to associate microbial subcompositions with response variables of interest. The excess number of zero or low count measurements at the read level forces traditional microbiome data analysis workflows to remove rare sequencing variants or group them by a fixed taxonomic rank, such as genus or phylum, or by phylogenetic similarity. By contrast, our framework, which we call trac (tree-aggregation of compositional data), learns data-adaptive taxon aggregation levels for predictive modeling, greatly reducing the need for user-defined aggregation in preprocessing while simultaneously integrating seamlessly into the compositional data analysis framework. We illustrate the versatility of our framework in the context of large-scale regression problems in human gut, soil, and marine microbial ecosystems. We posit that the inferred aggregation levels provide highly interpretable taxon groupings that can help microbiome researchers gain insights into the structure and functioning of the underlying ecosystem of interest. AU - Bien, J.* AU - Yan, X.* AU - Simpson, L. AU - Müller, C.L. C1 - 62570 C2 - 50951 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Tree-aggregated predictive modeling of microbiome data. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Cognitive decline is associated with both normal aging and early pathologies leading to dementia. Here we used quantitative profiling of metabolites involved in the regulation of inflammation, vascular function, neuronal function and energy metabolism, including oxylipins, endocannabinoids, bile acids, and steroid hormones to identify metabolic biomarkers of mild cognitive impairment (MCI). Serum samples (n = 212) were obtained from subjects with or without MCI opportunistically collected with incomplete fasting state information. To maximize power and stratify the analysis of metabolite associations with MCI by the fasting state, we developed an algorithm to predict subject fasting state when unknown (n = 73). In non-fasted subjects, linoleic acid and palmitoleoyl ethanolamide levels were positively associated with perceptual speed. In fasted subjects, soluble epoxide hydrolase activity and tauro-alpha-muricholic acid levels were negatively associated with perceptual speed. Other cognitive domains showed associations with bile acid metabolism, but only in the non-fasted state. Importantly, this study shows unique associations between serum metabolites and cognitive function in the fasted and non-fasted states and provides a fasting state prediction algorithm based on measurable metabolites. AU - Borkowski, K.* AU - Taha, A.Y.* AU - Pedersen, T.L.* AU - de Jager, P.L.* AU - Bennett, D.A.* AU - Arnold, M. AU - Kaddurah-Daouk, R. AU - Newman, J.W.* C1 - 63118 C2 - 51329 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Serum metabolomic biomarkers of perceptual speed in cognitively normal and mildly impaired subjects with fasting state stratification. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The current study aims to assess the effect of cone beam computed tomography (CBCT) frequency during adjuvant breast cancer radiotherapy with simultaneous integrated boost (SIB) on target volume coverage and dose to the organs at risk (OAR). 50 breast cancer patients receiving either non-hypofractionated or hypofractionated radiotherapy after lumpectomy including a SIB to the tumor bed were selected for this study. All patients were treated in volumetric modulated arc therapy (VMAT) technique and underwent daily CBCT imaging. In order to estimate the delivered dose during the treatment, the applied fraction doses were recalculated on daily CBCT scans and accumulated using deformable image registration. Based on a total of 2440 dose recalculations, dose coverage in the clinical target volumes (CTV) and OAR was compared depending on the CBCT frequency. The estimated delivered dose (V95%) for breast-CTV and SIB-CTV was significantly lower than the planned dose distribution, irrespective of the CBCT-frequency. Between daily CBCT and CBCT on alternate days, no significant dose differences were found regarding V95% for both, breast-CTV and SIB-CTV. Dose distribution in the OAR was similar for both imaging protocols. Weekly CBCT though led to a significant decrease in dose coverage compared to daily CBCT and a small but significant dose increase in most OAR. Daily CBCT imaging might not be necessary to ensure adequate dose coverage in the target volumes while efficiently sparing the OAR during adjuvant breast cancer radiotherapy with SIB. AU - Borm, K.J.* AU - Junker, Y.* AU - Düsberg, M.* AU - Devečka, M.* AU - Münch, S.* AU - Dapper, H.* AU - Oechsner, M.* AU - Combs, S.E. C1 - 62925 C2 - 51169 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Impact of CBCT frequency on target coverage and dose to the organs at risk in adjuvant breast cancer radiotherapy. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - It is unknown whether indoles, metabolites of tryptophan that are derived entirely from bacterial metabolism in the gut, are associated with symptoms of depression and anxiety. Serum samples (baseline, 12 weeks) were drawn from participants (n = 196) randomized to treatment with cognitive behavioral therapy (CBT), escitalopram, or duloxetine for major depressive disorder. Baseline indoxyl sulfate abundance was positively correlated with severity of psychic anxiety and total anxiety and with resting state functional connectivity to a network that processes aversive stimuli (which includes the subcallosal cingulate cortex (SCC-FC), bilateral anterior insula, right anterior midcingulate cortex, and the right premotor areas). The relation between indoxyl sulfate and psychic anxiety was mediated only through the metabolite’s effect on the SCC-FC with the premotor area. Baseline indole abundances were unrelated to post-treatment outcome measures, and changes in symptoms were not correlated with changes in indole concentrations. These results suggest that CBT and antidepressant medications relieve anxiety via mechanisms unrelated to modulation of indoles derived from gut microbiota; it remains possible that treatment-related improvement stems from their impact on other aspects of the gut microbiome. A peripheral gut microbiome-derived metabolite was associated with altered neural processing and with psychiatric symptom (anxiety) in humans, which provides further evidence that gut microbiome disruption can contribute to neuropsychiatric disorders that may require different therapeutic approaches. Given the exploratory nature of this study, findings should be replicated in confirmatory studies. Clinical trial NCT00360399 “Predictors of Antidepressant Treatment Response: The Emory CIDAR” https://clinicaltrials.gov/ct2/show/NCT00360399. AU - Brydges, C.R.* AU - Fiehn, O.* AU - Mayberg, H.S.* AU - Schreiber, H.* AU - Dehkordi, S.M.* AU - Bhattacharyya, S.* AU - Cha, J.* AU - Choi, K.S.* AU - Craighead, W.E.* AU - Krishnan, R.R.* AU - Rush, A.J.* AU - Dunlop, B.W.* AU - Kaddurah-Daouk, R.* AU - Mood Disorders Precision Medicine Consortium (Kastenmüller, G.) AU - Mood Disorders Precision Medicine Consortium (Arnold, M.) C1 - 63388 C2 - 51520 TI - Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature. JO - Sci. Rep. VL - 11 IS - 1 PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Bamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Sequence comparisons identified one important amino acid, which was located in the DNA-binding basic region and was altered between BtFD1 and BtFD2 (Ala146 of BtFD1 vs. Leu100 of BtFD2). Electrophoretic mobility shift assay revealed that this alteration had resulted into ten times higher binding efficiency of BtFD1 than BtFD2 to its target ACGT motif present at the promoter of the APETALA1 gene. Expression analyses in different tissues and seasons indicated the involvement of BtFD1 in flower and vegetative development, while BtFD2 was very lowly expressed throughout all the tissues and conditions studied. Finally, a tenfold increase of the AtAP1 transcript level by p35S::BtFD1 Arabidopsis plants compared to wild type confirms a positively regulatory role of BtFD1 towards flowering. However, constitutive expression of BtFD1 had led to dwarfisms and apparent reduction in the length of flowering stalk and numbers of flowers/plant, whereas no visible phenotype was observed for BtFD2 overexpression. This signifies that timely expression of BtFD1 may be critical to perform its programmed developmental role in planta. AU - Dutta, S.* AU - Deb, A.* AU - Biswas, P.* AU - Chakraborty, S.* AU - Guha, S.* AU - Mitra, D.* AU - Geist, B. AU - Schäffner, A. AU - Das, M.* C1 - 61778 C2 - 50455 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Breast cancer metastasis accounts for most of the deaths from breast cancer. Identification of germline variants associated with survival in aggressive types of breast cancer may inform understanding of breast cancer progression and assist treatment. In this analysis, we studied the associations between germline variants and breast cancer survival for patients with distant metastases at primary breast cancer diagnosis. We used data from the Breast Cancer Association Consortium (BCAC) including 1062 women of European ancestry with metastatic breast cancer, 606 of whom died of breast cancer. We identified two germline variants on chromosome 1, rs138569520 and rs146023652, significantly associated with breast cancer-specific survival (P = 3.19 × 10-8 and 4.42 × 10-8). In silico analysis suggested a potential regulatory effect of the variants on the nearby target genes SDE2 and H3F3A. However, the variants showed no evidence of association in a smaller replication dataset. The validation dataset was obtained from the SNPs to Risk of Metastasis (StoRM) study and included 293 patients with metastatic primary breast cancer at diagnosis. Ultimately, larger replication studies are needed to confirm the identified associations. AU - Escala-Garcia, M.* AU - Canisius, S.* AU - Keeman, R.* AU - Beesley, J.* AU - Anton-Culver, H.* AU - Arndt, V.* AU - Augustinsson, A.* AU - Becher, H.* AU - Beckmann, M.W.* AU - Behrens, S.* AU - Bermisheva, M.* AU - Bojesen, S.E.* AU - Bolla, M.K.* AU - Brenner, H.* AU - Canzian, F.* AU - Castelao, J.E.* AU - Chang-Claude, J.* AU - Chanock, S.J.* AU - Couch, F.J.* AU - Czene, K.* AU - Daly, M.B.* AU - Dennis, J.* AU - Devilee, P.* AU - Dörk, T.* AU - Dunning, A.M.* AU - Easton, D.F.* AU - Ekici, A.B.* AU - Eliassen, A.H.* AU - Fasching, P.A.* AU - Flyger, H.* AU - Gago-Dominguez, M.* AU - Garcia-Closas, M.* AU - García-Sáenz, J.A.* AU - Geisler, J.* AU - Giles, G.G.* AU - Grip, M.* AU - Gündert, M. AU - Hahnen, E.* AU - Haiman, C.A.* AU - Håkansson, N.* AU - Hall, P.* AU - Hamann, U.* AU - Hartikainen, J.M.* AU - Heemskerk-Gerritsen, B.A.M.* AU - Hollestelle, A.* AU - Hoppe, R.* AU - Hopper, J.L.* AU - Hunter, D.J.* AU - Jacot, W.* AU - Jakubowska, A.* AU - John, E.M.* AU - Jung, A.Y.* AU - Kaaks, R.* AU - Khusnutdinova, E.* AU - Koppert, L.B.* AU - Kraft, P.* AU - Kristensen, V.N.* AU - Kurian, A.W.* AU - Lambrechts, D.* AU - Le Marchand, L.* AU - Lindblom, A.* AU - Luben, R.N.* AU - Lubiński, J.* AU - Mannermaa, A.* AU - Manoochehri, M.* AU - Margolin, S.* AU - Mavroudis, D.* AU - Muranen, T.A.* AU - Nevanlinna, H.* AU - Olshan, A.F.* AU - Olsson, H.* AU - Park-Simon, T.W.* AU - Patel, A.V.* AU - Peterlongo, P.* AU - Pharoah, P.D.P.* AU - Punie, K.* AU - Radice, P.* AU - Rennert, G.* AU - Rennert, H.S.* AU - Romero, A.* AU - Roylance, R.* AU - Rudiger, T.* AU - Ruebner, M.* AU - Saloustros, E.* AU - Sawyer, E.J.* AU - Schmutzler, R.K.* AU - Schoemaker, M.J.* AU - Scott, C.* AU - Southey, M.C.* AU - Surowy, H.M.* AU - Swerdlow, A.J.* AU - Tamimi, R.M.* AU - Teras, L.R.* AU - Thomas, E.L.* AU - Tomlinson, I.* AU - Troester, M.A.* AU - Vachon, C.M.* AU - Wang, Q.* AU - Winqvist, R.* AU - Wolk, A.* AU - Ziogas, A.* AU - Michailidou, K.* AU - Chenevix-Trench, G.* AU - Bachelot, T.* AU - Schmidt, M.K.* C1 - 64441 C2 - 51841 TI - Germline variants and breast cancer survival in patients with distant metastases at primary breast cancer diagnosis. JO - Sci. Rep. VL - 11 IS - 1 PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Chronic obstructive pulmonary disease (COPD) is a destructive inflammatory disease and the genes expressed within the lung are crucial to its pathophysiology. We have determined the RNAseq transcriptome of bronchial brush cells from 312 stringently defined ex-smoker patients. Compared to healthy controls there were for males 40 differentially expressed genes (DEGs) and 73 DEGs for females with only 26 genes shared. The gene ontology (GO) term "response to bacterium" was shared, with several different DEGs contributing in males and females. Strongly upregulated genes TCN1 and CYP1B1 were unique to males and females, respectively. For male emphysema (E)-dominant and airway disease (A)-dominant COPD (defined by computed tomography) the term "response to stress" was found for both sub-phenotypes, but this included distinct up-regulated genes for the E-sub-phenotype (neutrophil-related CSF3R, CXCL1, MNDA) and for the A-sub-phenotype (macrophage-related KLF4, F3, CD36). In E-dominant disease, a cluster of mitochondria-encoded (MT) genes forms a signature, able to identify patients with emphysema features in a confirmation cohort. The MT-CO2 gene is upregulated transcriptionally in bronchial epithelial cells with the copy number essentially unchanged. Both MT-CO2 and the neutrophil chemoattractant CXCL1 are induced by reactive oxygen in bronchial epithelial cells. Of the female DEGs unique for E- and A-dominant COPD, 88% were detected in females only. In E-dominant disease we found a pronounced expression of mast cell-associated DEGs TPSB2, TPSAB1 and CPA3. The differential genes discovered in this study point towards involvement of different types of leukocytes in the E- and A-dominant COPD sub-phenotypes in males and females. AU - Esteve-Codina, A.* AU - Hofer, T.P. AU - Burggraf, D. AU - Heiss-Neumann, M.S. AU - Gesierich, W. AU - Boland, A.* AU - Olaso, R.* AU - Bihoreau, M.T.* AU - Deleuze, J.F.* AU - Möller, W. AU - Schmid, O. AU - Soler Artigas, M.* AU - Renner, K.* AU - Hohlfeld, J.M.* AU - Welte, T.* AU - Fuehner, T.* AU - Jerrentrup, L.* AU - Koczulla, A.R.* AU - Greulich, T.* AU - Prasse, A.* AU - Müller-Quernheim, J.* AU - Gupta, S.* AU - Brightling, C.* AU - Subramanian, D.R.* AU - Parr, D.G.* AU - Kolsum, U.* AU - Gupta, V.* AU - Barta, I.* AU - Döme, B.* AU - Strausz, J.* AU - Stendardo, M.* AU - Piattella, M.* AU - Boschetto, P.* AU - Korzybski, D.* AU - Gorecka, D.* AU - Nowinski, A.* AU - Dabad, M.* AU - Fernández-Callejo, M.* AU - Endesfelder, D. AU - zu Castell, W. AU - Hiemstra, P.S.* AU - Venge, P.* AU - Nößner, E. AU - Griebel, T.* AU - Heath, S.* AU - Singh, D.* AU - Gut, I.* AU - Ziegler-Heitbrock, L. C1 - 62321 C2 - 50631 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Gender specific airway gene expression in COPD sub-phenotypes supports a role of mitochondria and of different types of leukocytes. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The preservation of biosignatures on Mars is largely associated with extensive deposits of clays formed under mild early Noachian conditions (> 3.9 Ga). They were followed by widespread precipitation of acidic sulfates considered adverse for biomolecule preservation. In this paper, an exhaustive mass spectrometry investigation of ferric subsurface materials in the Rio Tinto gossan deposit (~ 25 Ma) provides evidence of well-preserved molecular biosignatures under oxidative and acidic conditions. Time of flight secondary ion mass spectrometry (ToF-SIMS) analysis shows a direct association between physical-templating biological structures and molecular biosignatures. This relation implies that the quality of molecular preservation is exceptional and provides information on microbial life formerly operating in the shallow regions of the Rio Tinto subsurface. Consequently, low-pH oxidative environments on Mars could also record molecular information about ancient life in the same way as the Noachian clay-rich deposits. AU - Fernández-Remolar, D.C.* AU - Carrizo, D.* AU - Harir, M. AU - Huang, T.* AU - Amils, R.* AU - Schmitt-Kopplin, P. AU - Sánchez-García, L.* AU - Gomez-Ortiz, D.* AU - Malmberg, P.* C1 - 63421 C2 - 51527 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Unveiling microbial preservation under hyperacidic and oxidizing conditions in the Oligocene Rio Tinto deposit. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The original version of this Article contained errors. Firstly, citation numbers after reference 11 (with the exception of citations to References 7 and 10) were inaccurate by two. Additionally, in the Introduction, “Although different authors report neutral to alkaline conditions for underground Mars7,8, the upper part of the planet interior has certainly been affected by the circulation and downwelling of low-pH and oxidizing solutions8- 10.” now reads: “Although different authors report neutral to alkaline conditions for underground Mars7,8, the upper part of the planet interior has certainly been affected by the circulation and downwelling of low-pH and oxidizing solutions9- 11.” Furthermore, in the Materials and methods section, the subheading ‘Sample 010,109-1’ now reads ‘Sample 010109-1’, and “Thin sections of sample 010,109-1 were prepared for mineral and textural analysis under an optical microscope and a Scanning Electron Microscope (SEM) coupled with an Electron Dispersive Spectroscopy (EDS) probe, and molecular surface analysis by ToF-SIMS105.” now reads: “Thin sections of sample 010109-1 were prepared for mineral and textural analysis under an optical microscope and a Scanning Electron Microscope (SEM) coupled with an Electron Dispersive Spectroscopy (EDS) probe, and molecular surface analysis by ToF-SIMS107.” Finally, in the Materials and methods section, under the subheading ‘ToF-SIMS analysis’, exponents were incorrectly captured as citations, and “To prevent this problem, the thin sections of samples 010,109-1 and BH8-24c were cleaned by surface sputtering with a 100 nA 500 eV oxygen ion beam for 3 s.” now reads: “To prevent this problem, the thin sections of sample 010109-1 were cleaned by surface sputtering with a 100 nA 500 eV oxygen ion beam for 3 s.” The original Article has been corrected. AU - Fernández-Remolar, D.C.* AU - Carrizo, D.* AU - Harir, M. AU - Huang, T.* AU - Amils, R.* AU - Schmitt-Kopplin, P. AU - Sánchez-García, L.* AU - Gomez-Ortiz, D.* AU - Malmberg, P.* C1 - 63887 C2 - 52014 TI - Publisher Correction: Unveiling microbial preservation under hyperacidic and oxidizing conditions in the Oligocene Rio Tinto deposit. JO - Sci. Rep. VL - 11 IS - 1 PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Rapid, high-throughput diagnostic tests are essential to decelerate the spread of the novel coronavirus disease 2019 (COVID-19) pandemic. While RT-PCR tests performed in centralized laboratories remain the gold standard, rapid point-of-care antigen tests might provide faster results. However, they are associated with markedly reduced sensitivity. Bedside breath gas analysis of volatile organic compounds detected by ion mobility spectrometry (IMS) may enable a quick and sensitive point-of-care testing alternative. In this proof-of-concept study, we investigated whether gas analysis by IMS can discriminate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from other respiratory viruses in an experimental set-up. Repeated gas analyses of air samples collected from the headspace of virus-infected in vitro cultures were performed for 5 days. A three-step decision tree using the intensities of four spectrometry peaks correlating to unidentified volatile organic compounds allowed the correct classification of SARS-CoV-2, human coronavirus-NL63, and influenza A virus H1N1 without misassignment when the calculation was performed with data 3 days post infection. The forward selection assignment model allowed the identification of SARS-CoV-2 with high sensitivity and specificity, with only one of 231 measurements (0.43%) being misclassified. Thus, volatile organic compound analysis by IMS allows highly accurate differentiation of SARS-CoV-2 from other respiratory viruses in an experimental set-up, supporting further research and evaluation in clinical studies. AU - Feuerherd, M. AU - Sippel, A.K.* AU - Erber, J.* AU - Baumbach, J.I.* AU - Schmid, R.M.* AU - Protzer, U. AU - Voit, F.* AU - Spinner, C.D.* C1 - 63282 C2 - 51419 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A proof of concept study for the differentiation of SARS-CoV-2, hCoV-NL63, and IAV-H1N1 in vitro cultures using ion mobility spectrometry. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Childhood maltreatment has been shown to relate to adult obesity. In this epidemiological study, we investigate the association between childhood maltreatment and waist-to-height-ratio (WHtR) in a sample of the German adult population, comprising of N = 2936 participants. WHtR, an indicator for risk of obesity, was the primary outcome. Childhood maltreatment was assessed by the Childhood Trauma Screener (CTS), which assesses emotional and physical neglect, abuse as well as sexual abuse. Cohort-data were harmonized and analyzed within DataSHIELD. We used multivariable regression models to estimate the association of childhood maltreatment and WHtR at different levels of adjustments for potential confounders. Overall childhood maltreatment was associated with a higher WHtR in both sexes (women: p = 0.004, men: p < 0.001); associations were no longer significant in women after adding socioeconomic variables, but remained significant in men (p = 0.013). Additionally, we were able to identify sex specific patterns for childhood maltreatment predicting the WHtR. Emotional neglect and abuse had stronger impacts on the WHtR in women than in men, whereas physical neglect and abuse had stronger impacts in men. To our knowledge, this is the first comprehensive population-based study testing various types of childhood maltreatment with WHtR in sex-, region- and weight-stratified analyses. Future studies in clinical populations are warranted to examine U-shaped correlations between increased WHtR and childhood maltreatment. AU - Fleischer, T.* AU - Ulke, C.* AU - Beutel, M.* AU - Binder, H.* AU - Brähler, E.* AU - Johar, H. AU - Atasoy, S. AU - Kruse, J.* AU - Otten, D.* AU - Tibubos, A.N.* AU - Zoller, D.* AU - Speerforck, S.* AU - Grabe, H.J.* AU - Ladwig, K.-H. AU - Schomerus, G.* C1 - 62527 C2 - 50862 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - The relation between childhood adversity and adult obesity in a population-based study in women and men. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Podoconiosis, a debilitating lymphoedema of the leg, results from barefoot exposure to volcanic clay soil in genetically susceptible individuals. A previous genome-wide association study (GWAS) conducted in the Wolaita ethnic group from Ethiopia showed association between single nucleotide polymorphisms (SNPs) in the HLA class II region and podoconiosis. We aimed to conduct a second GWAS in a new sample (N = 1892) collected from the Wolaita and two other Ethiopian populations, the Amhara and the Oromo, also affected by podoconiosis. Fourteen SNPs in the HLA class II region showed significant genome-wide association (P < 5.0 × 10-8) with podoconiosis. The lead SNP was rs9270911 (P = 5.51 × 10-10; OR 1.53; 95% CI 1.34-1.74), located near HLA-DRB1. Inclusion of data from the first GWAS (combined N = 2289) identified 47 SNPs in the class II HLA region that were significantly associated with podoconiosis (lead SNP also rs9270911 (P = 2.25 × 10-12). No new loci outside of the HLA class II region were identified in this more highly-powered second GWAS. Our findings confirm the HLA class II association with podoconiosis suggesting HLA-mediated abnormal induction and regulation of immune responses may have a direct role in its pathogenesis. AU - Gebresilase, T.* AU - Finan, C.* AU - Suveges, D.* AU - Tessema, T.S.* AU - Aseffa, A.* AU - Davey, G.* AU - Hatzikotoulas, K. AU - Zeggini, E. AU - Newport, M.J.* AU - Tekola-Ayele, F.* C1 - 61325 C2 - 50124 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Replication of HLA class II locus association with susceptibility to podoconiosis in three Ethiopian ethnic groups. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - To identify the most important parameters associated with cerebral white matter hyperintensities (WMH), in consideration of potential collinearity, we used a data-driven machine-learning approach. We analysed two independent cohorts (KORA and SHIP). WMH volumes were derived from cMRI-images (FLAIR). 90 (KORA) and 34 (SHIP) potential determinants of WMH including measures of diabetes, blood-pressure, medication-intake, sociodemographics, life-style factors, somatic/depressive-symptoms and sleep were collected. Elastic net regression was used to identify relevant predictor covariates associated with WMH volume. The ten most frequently selected variables in KORA were subsequently examined for robustness in SHIP. The final KORA sample consisted of 370 participants (58% male; age 55.7 ± 9.1 years), the SHIP sample comprised 854 participants (38% male; age 53.9 ± 9.3 years). The most often selected and highly replicable parameters associated with WMH volume were in descending order age, hypertension, components of the social environment (i.e. widowed, living alone) and prediabetes. A systematic machine-learning based analysis of two independent, population-based cohorts showed, that besides age and hypertension, prediabetes and components of the social environment might play important roles in the development of WMH. Our results enable personal risk assessment for the development of WMH and inform prevention strategies tailored to the individual patient. AU - Grosu, S.* AU - Rospleszcz, S. AU - Hartmann, F.* AU - Habes, M.* AU - Bamberg, F.* AU - Schlett, C.L.* AU - Galiè, F.* AU - Lorbeer, R.* AU - Auweter, S.* AU - Selder, S.* AU - Buelow, R.* AU - Heier, M. AU - Rathmann, W.* AU - Mueller-Peltzer, K.* AU - Ladwig, K.-H. AU - Grabe, H.J.* AU - Peters, A. AU - Ertl-Wagner, B.B.* AU - Stoecklein, S.* C1 - 61138 C2 - 49816 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Associated factors of white matter hyperintensity volume: A machine-learning approach. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The selection of carbohydrates or fat to generate intracellular energy is thought to be crucial for long-term metabolic health. While most studies assess fuel selection after a metabolic challenge, the determinants of substrate oxidation in the fasted state remain largely unexplored. We therefore assessed the respiratory quotient by indirect calorimetry as a read-out for substrate oxidation following an overnight fast. This cross-sectional analysis consisted of 192 (92 women, 100 men) either lean or obese participants. Following an overnight fast, the respiratory quotient (RQ) was assessed, after which a 5-point 75-g oral glucose tolerance test was performed. Unlike glucose and insulin, fasting free fatty acids (FFA) correlated negatively with fasting RQ (p < 0.0001). Participants with high levels of the ketone body β-hydroxybutyric acid had significantly lower RQ values. Fasting levels of glucose-dependent insulinotropic polypeptide (GIP) and glicentin were positively associated with fasting RQ (all p ≤ 0.03), whereas GLP-1 showed no significant association. Neither BMI, nor total body fat, nor body fat distribution correlated with fasting RQ. No relationship between the RQ and diabetes or the metabolic syndrome could be observed. In the fasting state, FFA concentrations were strongly linked to the preferentially oxidized substrate. Our data did not indicate any relationship between fasting substrate oxidation and metabolic diseases, including obesity, diabetes, and the metabolic syndrome. Since glicentin and GIP are linked to fuel selection in the fasting state, novel therapeutic approaches that target these hormones may have the potential to modulate substrate oxidation. AU - Hummel, J. AU - Fritsche, L. AU - Vosseler, A. AU - Dannecker, C. AU - Hoene, M.* AU - Kantartzis, K. AU - Häring, H.-U. AU - Stefan, N. AU - Machann, J. AU - Birkenfeld, A.L. AU - Weigert, C. AU - Wagner, R. AU - Peter, A. AU - Fritsche, A. AU - Heni, M. C1 - 62836 C2 - 51089 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Free fatty acids, glicentin and glucose-dependent insulinotropic polypeptide as potential major determinants of fasting substrate oxidation. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Non-alcoholic fatty liver disease (NAFLD) is common in Metabolic Syndrome and type 2 diabetes (T2DM), driven by energy imbalance, saturated fats and simple carbohydrates. NAFLD requires screening and monitoring for late complications. Liver fat indices may predict NAFLD avoiding expensive or invasive gold-standard methods, but they are poorly validated for use in interventional settings. Recent data indicate a particular insensitivity to weight-independent liver fat reduction. We evaluated 31 T2DM patients, completing a randomized intervention study on isocaloric high-protein diets. We assessed anthropometric measures, intrahepatic lipid (IHL) content and serum liver enzymes, allowing AUROC calculations as well as cross-sectional and longitudinal Spearman correlations between the fatty liver index, the NAFLD-liver fat score, the Hepatosteatosis Index, and IHL. At baseline, all indices predicted NAFLD with moderate accuracy (AUROC 0.731-0.770), supported by correlation analyses. Diet-induced IHL changes weakly correlated with changes of waist circumference, but no other index component or the indices themselves. Liver fat indices may help to easily detect NAFLD, allowing cost-effective allocation of further diagnostics to patients at high risk. IHL reduction by weight-independent diets is not reflected by a proportional change in liver fat scores. Further research on the development of treatment-sensitive indices is required.Trial registration: The trial was registered at clinicaltrials.gov: NCT02402985. AU - Kabisch, S.* AU - Markova, M.* AU - Hornemann, S.* AU - Sucher, S.* AU - Pivovarova-Ramich, O.* AU - Machann, J. AU - Hierholzer, J.* AU - Rohn, S.* AU - Pfeiffer, A.F.H. C1 - 61883 C2 - 50500 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Liver fat scores do not reflect interventional changes in liver fat content induced by high-protein diets. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Gene therapy revolves around modifying genetic makeup by inserting foreign nucleic acids into targeted cells via gene delivery methods to treat a particular disease. While the genes targeted play a key role in gene therapy, the gene delivery system used is also of utmost importance as it determines the success of gene therapy. As primary cells and stem cells are often the target cells for gene therapy in clinical trials, the delivery system would need to be robust, and viral-based entries such as lentiviral vectors work best at transporting the transgene into the cells. However, even within lentiviral vectors, several parameters can affect the functionality of the delivery system. Using cardiac-derived c-kit expressing cells (CCs) as a model system, this study aims to optimize lentiviral production by investigating various experimental factors such as the generation of the lentiviral system, concentration method, and type of selection marker. Our findings showed that the 2nd generation system with pCMV-dR8.2 dvpr as the packaging plasmid produced a 7.3-fold higher yield of lentiviral production compared to psPAX2. Concentrating the virus with ultracentrifuge produced a higher viral titer at greater than 5 × 105 infectious unit values/ml (IFU/ml). And lastly, the minimum inhibitory concentration (MIC) of puromycin selection marker was 10 μg/mL and 7 μg/mL for HEK293T and CCs, demonstrating the suitability of antibiotic selection for all cell types. This encouraging data can be extrapolated and applied to other difficult-to-transfect cells, such as different types of stem cells or primary cells. AU - Kalidasan, V.* AU - Ng, W.H.* AU - Ishola, O.A. AU - Ravichantar, N.* AU - Tan, J.J.* AU - Das, K.T.* C1 - 63197 C2 - 51239 TI - A guide in lentiviral vector production for hard-to-transfect cells, using cardiac-derived c-kit expressing cells as a model system. JO - Sci. Rep. VL - 11 IS - 1 PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - In Figure 2, the colours and the positions of the labels are incorrect. The correct Figure 2 appears below as Figure 1. As a result, the legend of Figure 2, “Sky blue: edgetic gains as a result of more genes being expressed in the cancer state, dark brown (left of zero intercept): edgetic gains as a result of isoform/domain changes (left of zero intercept). Light brown: edgetic losses as a result of the depletion of genes in the cancer state (right of zero intercept), light green: edgetic losses as a result of isoform/domain changes (right of zero intercept).” should read: “Sky blue: edgetic gains as a result of more genes being expressed in the cancer state, red: edgetic gains as a result of isoform/domain changes (right of zero intercept): Light brown: edgetic losses as a result of the depletion of genes in the cancer state (left of zero intercept), light green: edgetic losses as a result of isoform/domain changes (left of zero intercept).” In Figure 3, the labels of the gene CALM1 are incorrectly given as CALM2. The correct Figure 3 appears below as Figure 2. AU - Kataka, E.* AU - Zaucha, J.* AU - Frishman, G. AU - Ruepp, A. AU - Frishman, D.* C1 - 61299 C2 - 49843 TI - Author Correction: Edgetic perturbation signatures represent known and novel cancer biomarkers (Scientific Reports, (2020), 10, 1, (4350), 10.1038/s41598-020-61422-3). JO - Sci. Rep. VL - 11 IS - 1 PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Chemotherapy resistance is the main impediment in the treatment of acute myeloid leukaemia (AML). Despite rapid advances, the various mechanisms inducing resistance development remain to be defined in detail. Here we report that loss-of-function mutations (LOF) in the histone methyltransferase EZH2 have the potential to confer resistance against the chemotherapeutic agent cytarabine. We identify seven distinct EZH2 mutations leading to loss of H3K27 trimethylation via multiple mechanisms. Analysis of matched diagnosis and relapse samples reveal a heterogenous regulation of EZH2 and a loss of EZH2 in 50% of patients. We confirm that loss of EZH2 induces resistance against cytarabine in the cell lines HEK293T and K562 as well as in a patient-derived xenograft model. Proteomics and transcriptomics analysis reveal that resistance is conferred by upregulation of multiple direct and indirect EZH2 target genes that are involved in apoptosis evasion, augmentation of proliferation and alteration of transmembrane transporter function. Our data indicate that loss of EZH2 results in upregulation of its target genes, providing the cell with a selective growth advantage, which mediates chemotherapy resistance. AU - Kempf, J.M.* AU - Weser, S.* AU - Bartoschek, M.D.* AU - Metzeler, K.H.* AU - Vick, B. AU - Herold, T.* AU - Völse, K. AU - Mattes, R.* AU - Scholz, M.* AU - Wange, L.E.* AU - Festini, M.* AU - Ugur, E.* AU - Roas, M.* AU - Weigert, O.* AU - Bultmann, S.* AU - Leonhardt, H.* AU - Schotta, G.* AU - Hiddemann, W.* AU - Jeremias, I. AU - Spiekermann, K.* C1 - 61544 C2 - 50334 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Loss-of-function mutations in the histone methyltransferase EZH2 promote chemotherapy resistance in AML. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Stereotactic body radiotherapy (SBRT) applies high doses and requires advanced techniques to spare surrounding tissue in the presence of organ motion. In this work patient individual phase gating is investigated. We studied peripheral and central primary lung tumors. The internal target volume (ITV) was defined including different numbers of phases picked from a 4D Computed tomography (CT) defining the gating window (gw). Planning target volume (PTV) reductions depending on the gw were analyzed. A treatment plan was calculated on a reference phase CT (rCT) and the dose for each breathing phase was calculated and accumulated on the rCT. We compared the dosimetric results with the dose calculated when all breathing phases were included for ITV definition. GWs including 1 to 10 breathing phases were analyzed. We found PTV reductions up to 38.4%. The mean reduction of the lung volume receiving 20 Gy due to gating was found to be 25.7% for peripheral tumors and 16.7% for central tumors. Gating considerably reduced esophageal doses. However, we found that simple reduction of the gw does not necessarily influence the dose in a clinically relevant range. Thus, we suggest a patient individual definition of the breathing phases included within the gw. AU - Kraus, K.M.* AU - Oechsner, M.* AU - Wilkens, J.J.* AU - Kessel, K.A. AU - Münch, S.* AU - Combs, S.E. C1 - 61543 C2 - 50333 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Patient individual phase gating for stereotactic radiation therapy of early stage non-small cell lung cancer (NSCLC). JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The results of this survey reveal current clinical practice in the handling of combined radioimmunotherapy with Immune Checkpoint Inhibitors (RT + ICI). We aim to provide a basis to open a discussion for clinical application of RT + ICI by analyzation of experts’ assessment. We conducted a survey with 24 items with a focus on side effects of RT + ICI, common practice of scheduling and handling of adverse events. After pilot testing by radiation oncology experts the link to the online survey was sent to all members of the German Society of Radiation Oncology (DEGRO). In total, 51 radiation oncologists completed the questionnaire. Pulmonary toxicity under RT + ICI with ICIs was reported most frequently. Consensus was observed for bone and soft tissue RT of the limbs in favor for no interruption of ICIs. For cranial RT half of the participants do not suspend ICIs during normofractionated radiotherapy (nfRT) or stereotactic hypofractionated RT (SRT). More participants pause ICIs for central than for peripheral thoracic region. Maintenance therapy with ICIs is mostly not interrupted prior to RT. For management of RT associated pneumonitis under durvalumab the majority of 86.3% suggest corticosteroid therapy and 76.5% would postpone the next cycle of ICI therapy. The here obtained assessment and experiences by radiation oncologists reveal a large variability in practical handling of combined RT + ICI. Until scientific evidence is available a discussion for current clinical application of RT + ICI should be triggered. Interdisciplinary consensus guidelines with practical recommendations are required. AU - Kraus, K.M.* AU - Fischer, J.C.* AU - Borm, K.J.* AU - Vogel, M.M.E.* AU - Pigorsch, S.U.* AU - Devečka, M.* AU - Combs, S.E. C1 - 61770 C2 - 50136 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Evaluation of practical experiences of German speaking radiation oncologists in combining radiation therapy with checkpoint blockade. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Current screening algorithms for type 2 diabetes (T2D) rely on fasting plasma glucose (FPG) and/or HbA1c. This fails to identify a sizeable subgroup of individuals in early stages of metabolic dysregulation who are at high risk for developing diabetes or cardiovascular disease. The Matsuda index, a combination of parameters derived from a fasting and postprandial insulin assay, is an early biomarker for metabolic dysregulation (i.e. insulin resistance/compensatory hyperinsulinemia). The aim of this analysis was to compare four widely available anthropometric and biochemical markers indicative of this condition [waist-to-height ratio (WHtR), hypertriglyceridemic-waist phenotype (HTW), triglycerides-to-HDL-C ratio (TG/HDL-C) and FPG] to the Matsuda index. This cross-sectional analysis included 2231 individuals with normal fasting glucose (NFG, n = 1333), impaired fasting glucose (IFG, n = 599) and T2D (n = 299) from an outpatient diabetes clinic in Germany and thus extended a prior analysis from our group done on the first two subgroups. We analyzed correlations of the Matsuda index with WHtR, HTW, TG/HDL-C and FPG and their predictive accuracies by correlation and logistic regression analyses and receiver operating characteristics. In the entire group and in NFG, IFG and T2D, the best associations were observed between the Matsuda index and the WHtR (r = - 0.458), followed by HTW phenotype (r = - 0.438). As for prediction accuracy, WHtR was superior to HTW, TG/HDL-C and FPG in the entire group (AUC 0.801) and NFG, IFG and T2D. A multivariable risk score for the prediction of insulin resistance was tested and demonstrated an area under the ROC curve of 0.765 for WHtR and its interaction with sex as predictor controlled by age and sex. The predictive power increased to 0.845 when FPG and TG/HDL-C were included. Using as a comparator the Matsuda index, WHtR, compared to HTW, TG/HDL-C and FPG, showed the best predictive value for detecting metabolic dysregulation. We conclude that WHtR, a widely available anthropometric index, could refine phenotypic screening for insulin resistance/hyperinsulinemia. This may ameliorate early identification of individuals who are candidates for appropriate therapeutic interventions aimed at addressing the twin epidemic of metabolic and cardiovascular disease in settings where more extended testing such as insulin assays are not feasible. AU - Lechner, K.* AU - Lechner, B.* AU - Crispin, A.* AU - Schwarz, P.E. AU - von Bibra, H.* C1 - 61846 C2 - 50196 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Waist-to-height ratio and metabolic phenotype compared to the Matsuda index for the prediction of insulin resistance. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - CRISPR/Cas9 represents a valuable tool to determine protein function, but technical hurdles limit its use in challenging settings such as cells unable to grow in vitro like primary leukemia cells and xenografts derived thereof (PDX). To enrich CRISPR/Cas9-edited cells, we improved a dual-reporter system and cloned the genomic target sequences of the gene of interest (GOI) upstream of an out-of-frame fluorochrome which was expressed only upon successful gene editing. To reduce rounds of in vivo passaging required for PDX leukemia growth, targets of 17 GOI were cloned in a row, flanked by an improved linker, and PDX cells were lentivirally transduced for stable expression. The reporter enriched scarce, successfully gene-edited PDX cells as high as 80%. Using the reporter, we show that KO of the SRC-family kinase LYN increased the response of PDX cells of B precursor cell ALL towards Vincristine, even upon heterozygous KO, indicating haploinsufficiency. In summary, our reporter system enables enriching KO cells in technically challenging settings and extends the use of gene editing to highly patient-related model systems. AU - Liu, W.-H. AU - Völse, K. AU - Senft, D. AU - Jeremias, I. C1 - 62335 C2 - 50777 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A reporter system for enriching CRISPR/Cas9 knockout cells in technically challenging settings like patient models. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Living with dogs appears to protect against allergic diseases and airway infections, an effect possibly linked with immunomodulation by microbial exposures associated with dogs. The aim of this study was to characterize the influence of dog ownership on house dust microbiota composition. The bacterial and fungal microbiota was characterized with Illumina MiSeq sequencing from floor dust samples collected from homes in a Finnish rural-suburban (LUKAS2, N = 182) birth cohort, and the results were replicated in a German urban (LISA, N = 284) birth cohort. Human associated bacteria variable was created by summing up the relative abundances of five bacterial taxa. Bacterial richness, Shannon index and the relative abundances of seven bacterial genera, mostly within the phyla Proteobacteria and Firmicutes, were significantly higher in the dog than in the non-dog homes, whereas the relative abundance of human associated bacteria was lower. The results were largely replicated in LISA. Fungal microbiota richness and abundance of Leucosporidiella genus were higher in dog homes in LUKAS2 and the latter association replicated in LISA. Our study confirms that dog ownership is reproducibly associated with increased bacterial richness and diversity in house dust and identifies specific dog ownership-associated genera. Dogs appeared to have more limited influence on the fungal than bacterial indoor microbiota. AU - Mäki, J.M.* AU - Kirjavainen, P.V.* AU - Täubel, M.* AU - Piippo-Savolainen, E.* AU - Backman, K.* AU - Hyvärinen, A.* AU - Tuoresmäki, P.* AU - Jayaprakash, B.* AU - Heinrich, J. AU - Herberth, G.* AU - Standl, M. AU - Pekkanen, J.* AU - Karvonen, A.M.* C1 - 61445 C2 - 50161 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Associations between dog keeping and indoor dust microbiota. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Preterm birth (PTB) is associated with increased risk of type 2 diabetes and neurocognitive impairment later in life. We analyzed for the first time the associations of PTB with blood miRNA levels in adulthood. We also investigated the relationship of PTB associated miRNAs and adulthood phenotypes previously linked with premature birth. Blood MicroRNA profiling, genome-wide gene expression analysis, computer-based cognitive testing battery (CANTAB) and serum NMR metabolomics were performed for Young Finns Study subjects (aged 34-49 years, full-term n = 682, preterm n = 84). Preterm birth (vs. full-term) was associated with adulthood levels of hsa-miR-29b-3p in a fully adjusted regression model (p = 1.90 × 10-4, FDR = 0.046). The levels of hsa-miR-29b-3p were down-regulated in subjects with PTB with appropriate birthweight for gestational age (p = 0.002, fold change [FC] = - 1.20) and specifically in PTB subjects with small birthweight for gestational age (p = 0.095, FC = - 1.39) in comparison to individuals born full term. Hsa-miR-29b-3p levels correlated with the expressions of its target-mRNAs BCL11A and CS and the gene set analysis results indicated a target-mRNA driven association between hsa-miR-29b-3p levels and Alzheimer's disease, Parkinson's disease, Insulin signaling and Regulation of Actin Cytoskeleton pathway expression. The level of hsa-miR-29b-3p was directly associated with visual processing and sustained attention in CANTAB test and inversely associated with serum levels of VLDL subclass component and triglyceride levels. In conlcusion, adult blood levels of hsa-miR-29b-3p were lower in subjects born preterm. Hsa-miR-29b-3p associated with cognitive function and may be linked with adulthood morbidities in subjects born preterm, possibly through regulation of gene sets related to neurodegenerative diseases and insulin signaling as well as VLDL and triglyceride metabolism. AU - Marttila, S.* AU - Rovio, S.* AU - Mishra, P.P.* AU - Seppälä, I.* AU - Lyytikäinen, L.P.* AU - Juonala, M.* AU - Waldenberger, M. AU - Oksala, N.* AU - Ala-Korpela, M.* AU - Harville, E.* AU - Hutri-Kähönen, N.* AU - Kähönen, M.* AU - Raitakari, O.* AU - Lehtimäki, T.* AU - Raitoharju, E.* C1 - 61970 C2 - 50314 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Adulthood blood levels of hsa-miR-29b-3p associate with preterm birth and adult metabolic and cognitive health. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - We found the hepatic transcription factor Cyclic-AMP Responsive Element Binding Protein 3-like-3 (CREB3L3) to be expressed in adipose tissue, and selectively downregulated in the more metabolically protective subcutaneous adipose tissue in obese mice and humans. We sought to elucidate the specific role of this factor in adipose biology. CREB3L3 fat-specific knockout mice were fed a high-fat diet to induce obesity and metabolic dysfunction. Additionally, we injected a flip-excision adeno-associated virus directly into the subcutaneous inguinal adipose tissue of Adiponectin-Cre mice to create a depot-specific overexpression model for further assessment. Fat-specific ablation of CREB3L3 enhanced weight gain and insulin resistance following high-fat feeding, as fat-specific knockout mice expended less energy and possessed more inflammatory adipose tissue. Conversely, inguinal fat CREB3L3 overexpression deterred diet-induced obesity and ameliorated metabolic dysfunction. Together, this study highlights the relevance of CREB3L3 in obese adipose tissue and demonstrates its role as a powerful body weight modulator. AU - McCann, M.A.* AU - Li, Y.* AU - Munoz, M.L.* AU - Gil, V.* AU - Qiang, G.* AU - Cordoba-Chacon, J.* AU - Blüher, M. AU - Duncan, S.R.* AU - Liew, C.W.* C1 - 63191 C2 - 51287 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Adipose expression of CREB3L3 modulates body weight during obesity. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The Acknowledgements section in the original version of this Article was incomplete. “The authors thank Kezhong Zhang of Wayne State University for providing the anti-CREB3L3 antibody. The work was supported by R00 DK090210, R01 DK109015, University of Chicago DRTC (DK020595) Pilot & Feasibility award, Central for Society for Clinical and Translational Research Early Career Development Award and UIC Startup fund (C.W.L.); M.A.M. was supported by an American Heart Association Predoctoral Fellowship (Grant No. 16PRE30190011). M.B. was funded by the Deutsche Forschungsgemeinschaft: Collaborative Research Center SFB1052, project B1.” now reads: “The authors thank Kezhong Zhang of Wayne State University for providing the anti-CREB3L3 antibody. The authors also acknowledge the Research Open Access Publishing (ROAAP) Fund of the University of Illinois at Chicago for financial support towards the open access publishing fee for this article. The work was supported by R00 DK090210, R01 DK109015, University of Chicago DRTC (DK020595) Pilot & Feasibility award, Central for Society for Clinical and Translational Research Early Career Development Award and UIC Startup fund (C.W.L.); M.A.M. was supported by an American Heart Association Predoctoral Fellowship. M.B. was funded by the Deutsche Forschungsgemeinschaft: Collaborative Research Center SFB1052, project B1.” The original Article has been corrected. AU - McCann, M.A.* AU - Li, Y.* AU - Munoz, M.L.* AU - Gil, V.* AU - Qiang, G.* AU - Cordoba-Chacon, J.* AU - Blüher, M. AU - Duncan, S.R.* AU - Liew, C.W.* C1 - 63222 C2 - 51286 TI - Author Correction: Adipose expression of CREB3L3 modulates body weight during obesity (Scientific Reports, (2021), 11, 1, (19400), 10.1038/s41598-021-98627-z). JO - Sci. Rep. VL - 11 IS - 1 PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The human mitochondrial ClpXP protease complex (HsClpXP) has recently attracted major attention as a target for novel anti-cancer therapies. Despite its important role in disease progression, the cellular role of HsClpXP is poorly characterized and only few small molecule inhibitors have been reported. Herein, we screened previously established S. aureus ClpXP inhibitors against the related human protease complex and identified potent small molecules against human ClpXP. The hit compounds showed anti-cancer activity in a panoply of leukemia, liver and breast cancer cell lines. We found that the bacterial ClpXP inhibitor 334 impairs the electron transport chain (ETC), enhances the production of mitochondrial reactive oxygen species (mtROS) and thereby promotes protein carbonylation, aberrant proteostasis and apoptosis. In addition, 334 induces cell death in re-isolated patient-derived xenograft (PDX) leukemia cells, potentiates the effect of DNA-damaging cytostatics and re-sensitizes resistant cancers to chemotherapy in non-apoptotic doses. AU - Meßner, M.* AU - Mandl, M.M.* AU - Hackl, M.W.* AU - Reinhardt, T.* AU - Ardelt, M.A.* AU - Szczepanowska, K.* AU - Frädrich, J.E.* AU - Waschke, J.* AU - Jeremias, I. AU - Fux, A.* AU - Stahl, M.* AU - Vollmar, A.M.* AU - Sieber, S.A.* AU - Pachmayr, J.* C1 - 62176 C2 - 50679 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Small molecule inhibitors of the mitochondrial ClpXP protease possess cytostatic potential and re-sensitize chemo-resistant cancers. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - The heterozygous human Klotho KL-VS haplotype has been associated with improved cognitive performance but results are inconsistent. Here we assessed Klotho KL-VS haplotype and cognition using data from the third examination of the population-based Heinz Nixdorf Recall Study. We analyzed cognition tests (immediate and delayed word list, Trail-Making Test [TMT] part A and B, Maze test, interference condition of the Stroop color-word test, verbal fluency) and their associations with Klotho KL-VS haplotype. The Klotho KL-VS haplotype is classified by the V-allele at SNP rs9536314 (F352V) and the S-allele at SNP rs9527025 (C370S). Heterozygotes for the KL-VS haplotype were compared with non-carriers. Analyses were performed in 1812 subjects (55-87 years). We found consistent but only slightly lower performance in heterozygous carriers of the KL-VS haplotype in all tasks with Z-scores ranging between Z = - 0.042 (verbal fluency) and - 0.17 (TMT part A). Differences between carriers and non-carriers were similar for men and women for all tests but TMT part B (interaction contrast = 8.4 s (95% CI - 2.3; 19.1)). While cognition declined with age, we found an effect modification by age (55-65 years, 66-75 years, > 75 years). In the 66-75 years KL-VS heterozygous age group, lower performance was seen in memory, visual attention and motor speed. Contrary to our hypothesis, heterozygous carriers of the KL-VS haplotype did not show enhanced performance in cognitive tests in our study. AU - Müller, B.W.* AU - Hinney, A.* AU - Scherbaum, N.* AU - Weimar, C.* AU - Kleinschnitz, C.* AU - Peters, T.* AU - Hochfeld, L.* AU - Pechlivanis, S. AU - Stang, A.* AU - Jokisch, M.* AU - Kowall, B.* C1 - 62411 C2 - 50857 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 13852 TI - Klotho KL-VS haplotype does not improve cognition in a population-based sample of adults age 55-87 years. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Our aim was to investigate the associations between erythrocyte fatty acids and the risk of islet autoimmunity in children. The Environmental Determinants of Diabetes in the Young Study (TEDDY) is a longitudinal cohort study of children at high genetic risk for type 1 diabetes (n = 8676) born between 2004 and 2010 in the U.S., Finland, Sweden, and Germany. A nested case-control design comprised 398 cases with islet autoimmunity and 1178 sero-negative controls matched for clinical site, family history, and gender. Fatty acids composition was measured in erythrocytes collected at the age of 3, 6, and 12 months and then annually up to 6 years of age. Conditional logistic regression models were adjusted for HLA risk genotype, ancestry, and weight z-score. Higher eicosapentaenoic and docosapentaenoic acid (n - 3 polyunsaturated fatty acids) levels during infancy and conjugated linoleic acid after infancy were associated with a lower risk of islet autoimmunity. Furthermore, higher levels of some even-chain saturated (SFA) and monounsaturated fatty acids (MUFA) were associated with increased risk. Fatty acid status in early life may signal the risk for islet autoimmunity, especially n - 3 fatty acids may be protective, while increased levels of some SFAs and MUFAs may precede islet autoimmunity. AU - Niinistö, S.* AU - Erlund, I.* AU - Lee, H.S.* AU - Uusitalo, U.* AU - Salminen, I.* AU - Aronsson, C.A.* AU - Parikh, H.M.* AU - Liu, X.* AU - Hummel, S. AU - Toppari, J.* AU - She, J.X.* AU - Lernmark, A.* AU - Ziegler, A.-G. AU - Rewers, M.* AU - Akolkar, B.* AU - Krischer, J.P.* AU - Galas, D.* AU - Das, S.* AU - Sakhanenko, N.* AU - Rich, S.S.* AU - Hagopian, W.* AU - Norris, J.M.* AU - Virtanen, S.M.* C1 - 61310 C2 - 50146 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Children's erythrocyte fatty acids are associated with the risk of islet autoimmunity. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Constantly decreasing costs of high-throughput profiling on many molecular levels generate vast amounts of multi-omics data. Studying one biomedical question on two or more omic levels provides deeper insights into underlying molecular processes or disease pathophysiology. For the majority of multi-omics data projects, the data analysis is performed level-wise, followed by a combined interpretation of results. Hence the full potential of integrated data analysis is not leveraged yet, presumably due to the complexity of the data and the lacking toolsets. We propose a versatile approach, to perform a multi-level fully integrated analysis: The Knowledge guIded Multi-Omics Network inference approach, KiMONo ( https://github.com/cellmapslab/kimono ). KiMONo performs network inference by using statistical models for combining omics measurements coupled to a powerful knowledge-guided strategy exploiting prior information from existing biological sources. Within the resulting multimodal network, nodes represent features of all input types e.g. variants and genes while edges refer to knowledge-supported and statistically derived associations. In a comprehensive evaluation, we show that our method is robust to noise and exemplify the general applicability to the full spectrum of multi-omics data, demonstrating that KiMONo is a powerful approach towards leveraging the full potential of data sets for detecting biomarker candidates. AU - Ogris, C. AU - Hu, Y. AU - Knauer-Arloth, J. AU - Müller, N.S. C1 - 61690 C2 - 50395 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Infection of hepatocytes by hepatitis B virus (HBV) depends on surface expression of its receptor Na+-taurocholate-cotransporting polypeptide (NTCP), but sufficient NTCP expression is lacking in most cell lines. NTCP can be introduced by plasmid transfection or transduction by viral vectors to render cells permissive for HBV. However, transient transfection of hepatocyte-derived cell lines is inefficient, resulting in inhomogeneous protein expression and does not allow to adapt the level of NTCP expression. We therefore utilized in vitro transcribed mRNA to introduce NTCP into cells. Optimization using alternative cap structures and nucleotide modifications rendered mRNA transfection into different non-hepatic and hepatic cell lines very efficient. After transfection of mRNA, surface expression and functionality of NTCP was demonstrated by staining with an N-terminal HBV-preS peptide and bile acid uptake. Introduction of NTCP by mRNA transfection increased susceptibility of hepatoma cells to HBV in a dose-dependent manner. Transfection of NTCP mRNA into non-liver cells, in contrast, supported bile acid uptake but did still not render the cells permissive for HBV, demonstrating the requirement for additional host factors. Introduction of candidate host factors by mRNA transfection will allow for fast and convenient analysis of the viral life cycle using a transient, but reliable expression system. AU - Oswald, A. AU - Chakraborty, A. AU - Ni, Y.* AU - Wettengel, J.M. AU - Urban, S.* AU - Protzer, U. C1 - 63221 C2 - 51389 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Concentration of Na+-taurocholate-cotransporting polypeptide expressed after in vitro-transcribed mRNA transfection determines susceptibility of hepatoma cells for hepatitis B virus. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - We investigated the genetic causes of major mental disorders (MMDs) including schizophrenia, bipolar disorder I, major depressive disorder and attention deficit hyperactive disorder, in a large family pedigree from Alpujarras, South of Spain, a region with high prevalence of psychotic disorders. We applied a systematic genomic approach based on karyotyping (n = 4), genotyping by genome-wide SNP array (n = 34) and whole-genome sequencing (n = 12). We performed genome-wide linkage analysis, family-based association analysis and polygenic risk score estimates. Significant linkage was obtained at chromosome 9 (9q33.1-33.2, LOD score = 4.11), a suggestive region that contains five candidate genes ASTN2, BRINP1, C5, TLR4 and TRIM32, previously associated with MMDs. Comprehensive analysis associated the MMD phenotype with genes of the immune system with dual brain functions. Moreover, the psychotic phenotype was enriched for genes involved in synapsis. These results should be considered once studying the genetics of psychiatric disorders in other families, especially the ones from the same region, since founder effects may be related to the high prevalence. AU - Pol-Fuster, J.* AU - Canellas, F.* AU - Ruiz-Guerra, L.* AU - Medina-Dols, A.* AU - Bisbal-Carrio, B.* AU - Ortega-Vila, B.* AU - Llinàs, J.* AU - Hernandez-Rodriguez, J.* AU - Llado, J.* AU - Olmos, G.* AU - Strauch, K. AU - Heine-Suner, D.* AU - Vives-Bauza, C.* AU - Flaquer, A. C1 - 62569 C2 - 50950 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - The conserved ASTN2/BRINP1 locus at 9q33.1-33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - In 2007 the German government passed smoke-free legislation, leaving the details of implementation to the individual federal states. In January 2008 Bavaria implemented one of the strictest laws in Germany. We investigated its impact on pregnancy outcomes and applied an interrupted time series (ITS) study design to assess any changes in preterm birth, small for gestational age (primary outcomes), and low birth weight, stillbirth and very preterm birth. We included 1,236,992 singleton births, comprising 83,691 preterm births and 112,143 small for gestational age newborns. For most outcomes we observed unclear effects. For very preterm births, we found an immediate drop of 10.4% (95%CI − 15.8, − 4.6%; p = 0.0006) and a gradual decrease of 0.5% (95%CI − 0.7, − 0.2%, p = 0.0010) after implementation of the legislation. The majority of subgroup and sensitivity analyses confirm these results. Although we found no statistically significant effect of the Bavarian smoke-free legislation on most pregnancy outcomes, a substantial decrease in very preterm births was observed. We cannot rule out that despite our rigorous methods and robustness checks, design-inherent limitations of the ITS study as well as country-specific factors, such as the ambivalent German policy context have influenced our estimation of the effects of the legislation. AU - Polus, S.* AU - Burns, J.* AU - Hoffmann, S.* AU - Mathes, T.* AU - Mansmann, U.* AU - Been, J.V.* AU - Lack, N.* AU - Koller, D.* AU - Maier, W. AU - Rehfuess, E.A.* C1 - 61405 C2 - 50215 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Interrupted time series study found mixed effects of the impact of the Bavarian smoke-free legislation on pregnancy outcomes. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Inclusion of clinical parameters limits the application of most cardiovascular disease (CVD) prediction models to clinical settings. We developed and externally validated a non-clinical CVD risk score with a clinical extension and compared the performance to established CVD risk scores. We derived the scores predicting CVD (non-fatal and fatal myocardial infarction and stroke) in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam cohort (n = 25,992, cases = 683) using competing risk models and externally validated in EPIC-Heidelberg (n = 23,529, cases = 692). Performance was assessed by C-indices, calibration plots, and expected-to-observed ratios and compared to a non-clinical model, the Pooled Cohort Equation, Framingham CVD Risk Scores (FRS), PROCAM scores, and the Systematic Coronary Risk Evaluation (SCORE). Our non-clinical score included age, gender, waist circumference, smoking, hypertension, type 2 diabetes, CVD family history, and dietary parameters. C-indices consistently indicated good discrimination (EPIC-Potsdam 0.786, EPIC-Heidelberg 0.762) comparable to established clinical scores (thereof highest, FRS: EPIC-Potsdam 0.781, EPIC-Heidelberg 0.764). Additional clinical parameters slightly improved discrimination (EPIC-Potsdam 0.796, EPIC-Heidelberg 0.769). Calibration plots indicated very good calibration with minor overestimation in the highest decile of predicted risk. The developed non-clinical 10-year CVD risk score shows comparable discrimination to established clinical scores, allowing assessment of individual CVD risk in physician-independent settings. AU - Schiborn, C.* AU - Kuhn, T.* AU - Mühlenbruch, K.* AU - Kuxhaus, O.* AU - Weikert, C.* AU - Fritsche, A. AU - Kaaks, R.* AU - Schulze, M.B.* C1 - 63172 C2 - 51365 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A newly developed and externally validated non-clinical score accurately predicts 10-year cardiovascular disease risk in the general adult population. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Calcium plays an essential role in physiology of the cardiovascular system. Aberrations from normal serum calcium levels are known to be associated with several cardiovascular diseases. Its possible role as a predictor for long-term mortality after acute myocardial infarction (AMI) is still uncertain. In this study, a total of 3732 patients (aged 25–74 years) with incident AMI surviving at least 28 days after AMI was included. The median follow-up time was 6.0 years. Admission total serum calcium levels were divided into quartiles. The Kaplan–Meier-Curve suggested a division of the follow up time in two different time periods. So, Cox regression models were calculated to assess association between admission serum calcium levels and all-cause long-term mortality with two observation periods: 28–2500 days and > 2500 days. The final model was adjusted for various comorbidities, clinical characteristics, in-hospital treatment and medication. The third quartile (normal-high Calcium levels) served as the reference group. The fully adjusted Cox-regression model shows significantly higher mortality risk for low serum calcium (quartile 1) within the timeframe 28–2500 days after the event (OR 1.53 [1.19–1.98]). The other groups did not differ significantly from each other. In the later observation period (from 2500 days until death or censoring) no more significant differences were seen between the four calcium quartiles. In summary, low serum calcium is an independent predictor of adverse outcome in the first 2500 days (about 7 years) after AMI. On later points in time this effect attenuates, so that no more significant differences can be observed. AU - Schmitz, T.* AU - Thilo, C.* AU - Linseisen, J. AU - Heier, M. AU - Peters, A. AU - Kuch, B.* AU - Meisinger, C. C1 - 61170 C2 - 49834 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Low serum calcium is associated with higher long-term mortality in myocardial infarction patients from a population-based registry. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Prior studies examined association between short-term mortality and certain changes in the admission ECG in acute myocardial infarction (AMI). Nevertheless, little is known about possible differences between patients with diabetes and without diabetes in this regard. So the aim of the study was to investigate the association between 28-day case fatality according to certain ECG changes comparing AMI cases with and without diabetes from the general population. From 2000 until 2017 a total of 9756 AMI cases was prospectively recorded in the study Area of Augsburg, Germany. Each case was assigned to one of the following groups according to admission ECG: ‘ST-elevation’, ‘ST-depression’, ‘only T-negativity’, ‘predominantly bundle branch block’, ‘unspecific changes’ and ‘normal ECG’ (the last two were put together for regression analyses). Multivariable adjusted logistic regression models were calculated to compare 28-day case-fatality between the ECG groups for the total sample and separately for diabetes and non-diabetes cases. For the non-diabetes group, the parsimonious logistic regression model revealed significantly better 28-day-outcome for the ‘normal ECG / unspecific changes’ group (OR: 0.47 [0.29–0.76]) compared to the reference group (STEMI). Contrary, in AMI cases with diabetes the category ‘normal ECG / unspecific changes’ was not significantly associated with lower short-term mortality (OR: 0.87 [0.49–1.54]). Neither of the other ECG groups was significantly associated with 28-day-mortality in the parsimonious logistic regression models. Consequently, the absence of AMI-typical changes in the admission ECG predicts favorable short-term mortality only in non-diabetic cases, but not so in patients with diabetes. AU - Schmitz, T.* AU - Thilo, C.* AU - Linseisen, J. AU - Heier, M. AU - Peters, A. AU - Kuch, B.* AU - Meisinger, C. C1 - 61649 C2 - 50166 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Admission ECG changes predict short term-mortality after acute myocardial infarction less reliable in patients with diabetes. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Convolutional neural networks (CNNs) excel as powerful tools for biomedical image classification. It is commonly assumed that training CNNs requires large amounts of annotated data. This is a bottleneck in many medical applications where annotation relies on expert knowledge. Here, we analyze the binary classification performance of a CNN on two independent cytomorphology datasets as a function of training set size. Specifically, we train a sequential model to discriminate non-malignant leukocytes from blast cells, whose appearance in the peripheral blood is a hallmark of leukemia. We systematically vary training set size, finding that tens of training images suffice for a binary classification with an ROC-AUC over 90%. Saliency maps and layer-wise relevance propagation visualizations suggest that the network learns to increasingly focus on nuclear structures of leukocytes as the number of training images is increased. A low dimensional tSNE representation reveals that while the two classes are separated already for a few training images, the distinction between the classes becomes clearer when more training images are used. To evaluate the performance in a multi-class problem, we annotated single-cell images from a acute lymphoblastic leukemia dataset into six different hematopoietic classes. Multi-class prediction suggests that also here few single-cell images suffice if differences between morphological classes are large enough. The incorporation of deep learning algorithms into clinical practice has the potential to reduce variability and cost, democratize usage of expertise, and allow for early detection of disease onset and relapse. Our approach evaluates the performance of a deep learning based cytology classifier with respect to size and complexity of the training data and the classification task. AU - Schouten, J.P.E. AU - Matek, C. AU - Jacobs, L.F.P.* AU - Buck, M.C.* AU - Bošnački, D.* AU - Marr, C. C1 - 61779 C2 - 50472 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Tens of images can suffice to train neural networks for malignant leukocyte detection. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Morphological and functional optoacoustic imaging is enhanced by dedicated transgene reporters, in analogy to fluorescence methods. The development of optoacoustic reporters using protein engineering and directed evolution would be accelerated by high-throughput in-flow screening for intracellular, genetically encoded, optoacoustic contrast. However, accurate characterization of such contrast is impeded because the optoacoustic signals depend on the cell’s size and position in the flow chamber. We report herein an optoacoustic flow cytometer (OA-FCM) capable of precise measurement of intracellular optoacoustic signals of genetically-encoded chromoproteins in flow. The novel system records light-scattering as a reference for the detected optoacoustic signals in order to account for cell size and position, as well as excitation light flux in the focal volume, which we use to reference the detected optoacoustic signals to enhance the system’s precision. The OA-FCM was calibrated using micrometer-sized particles to showcase the ability to assess in-flow objects in the size range of single-cells. We demonstrate the capabilities of our OA-FCM to identify sub-populations in a mixture of two E. coli stocks expressing different reporter-proteins with a precision of over 90%. High-throughput screening of optoacoustic labels could pave the way for identifying genetically encoded optoacoustic reporters by transferring working concepts of the fluorescence field such as directed evolution and activated cell sorting. AU - Seeger, M. AU - Stiel, A.-C. AU - Ntziachristos, V. C1 - 61135 C2 - 50058 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - In vitro optoacoustic flow cytometry with light scattering referencing. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Ordinary differential equation (ODE) models are a key tool to understand complex mechanisms in systems biology. These models are studied using various approaches, including stability and bifurcation analysis, but most frequently by numerical simulations. The number of required simulations is often large, e.g., when unknown parameters need to be inferred. This renders efficient and reliable numerical integration methods essential. However, these methods depend on various hyperparameters, which strongly impact the ODE solution. Despite this, and although hundreds of published ODE models are freely available in public databases, a thorough study that quantifies the impact of hyperparameters on the ODE solver in terms of accuracy and computation time is still missing. In this manuscript, we investigate which choices of algorithms and hyperparameters are generally favorable when dealing with ODE models arising from biological processes. To ensure a representative evaluation, we considered 142 published models. Our study provides evidence that most ODEs in computational biology are stiff, and we give guidelines for the choice of algorithms and hyperparameters. We anticipate that our results will help researchers in systems biology to choose appropriate numerical methods when dealing with ODE models. AU - Städter, P. AU - Schälte, Y. AU - Schmiester, L. AU - Hasenauer, J. AU - Stapor, P. C1 - 61195 C2 - 50082 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Benchmarking of numerical integration methods for ODE models of biological systems. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Countries around the world implement nonpharmaceutical interventions (NPIs) to mitigate the spread of COVID-19. Design of efficient NPIs requires identification of the structure of the disease transmission network. We here identify the key parameters of the COVID-19 transmission network for time periods before, during, and after the application of strict NPIs for the first wave of COVID-19 infections in Germany combining Bayesian parameter inference with an agent-based epidemiological model. We assume a Watts–Strogatz small-world network which allows to distinguish contacts within clustered cliques and unclustered, random contacts in the population, which have been shown to be crucial in sustaining the epidemic. In contrast to other works, which use coarse-grained network structures from anonymized data, like cell phone data, we consider the contacts of individual agents explicitly. We show that NPIs drastically reduced random contacts in the transmission network, increased network clustering, and resulted in a previously unappreciated transition from an exponential to a constant regime of new cases. In this regime, the disease spreads like a wave with a finite wave speed that depends on the number of contacts in a nonlinear fashion, which we can predict by mean field theory. AU - Syga, S.* AU - David-Rus, D.* AU - Schälte, Y. AU - Hatzikirou, H.* AU - Deutsch, A.* C1 - 63498 C2 - 51559 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Inferring the effect of interventions on COVID-19 transmission networks. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - At the Center for Advanced Laser Applications (CALA), Garching, Germany, the LION (Laser-driven ION Acceleration) experiment is being commissioned, aiming at the production of laser-driven bunches of protons and light ions with multi-MeV energies and repetition frequency up to 1 Hz. A Geant4 Monte Carlo-based study of the secondary neutron and photon fields expected during LION's different commissioning phases is presented. Goal of this study is the characterization of the secondary radiation environment present inside and outside the LION cave. Three different primary proton spectra, taken from experimental results reported in the literature and representative of three different future stages of the LION's commissioning path are used. Together with protons, also electrons are emitted through laser-target interaction and are also responsible for the production of secondary radiation. For the electron component of the three source terms, a simplified exponential model is used. Moreover, in order to reduce the simulation complexity, a two-components simplified geometrical model of proton and electron sources is proposed. It has been found that the radiation environment inside the experimental cave is either dominated by photons or neutrons depending on the position in the room and the source term used. The higher the intensity of the source, the higher the neutron contribution to the total dose for all scored positions. Maximum neutron and photon ambient dose equivalent values normalized to 109 simulated incident primaries were calculated at the exit of the vacuum chamber, where values of about 85 nSv (109 primaries)-1 and 1.0 μSv (109 primaries)-1 were found. AU - Tisi, M. AU - Mares, V. AU - Schreiber, J.* AU - Englbrecht, F.S.* AU - Rühm, W. C1 - 63872 C2 - 51680 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Geant4 Monte Carlo simulation study of the secondary radiation fields at the laser-driven ion source LION. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - To evaluate the relationship of cardiac function, including time-volume-curves, with lung volumes derived from pulmonary function tests (PFT) and MRI in subjects without cardiovascular diseases. 216 subjects underwent whole-body MRI and spirometry as part of the KORA-FF4 cohort study. Lung volumes derived semi-automatically using an in-house algorithm. Forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and residual volume were measured. Cardiac parameters derived from Cine-SSFP-sequence using cvi42, while left ventricle (LV) time-volume-curves were evaluated using pyHeart. Linear regression analyses assessed the relationships of cardiac parameters with PFT and MRI-based lung volumes. Mean age was 56.3 ± 9.2 years (57% males). LV and right ventricular (RV) end-diastolic-, end-systolic-, stroke volume, LV peak ejection- and early/late diastolic filling rate were associated with FEV1, FVC, and residual volume (excluding late diastolic filling rate with FEV1, LV end-systolic/stroke volume and RV end-diastolic/end-systolic volumes with residual volume). In contrast, LV end-diastolic volume (ß = − 0.14, p = 0.01), early diastolic filling rate (ß = − 0.11, p = 0.04), and LV/RV stroke volume (ß = − 0.14, p = 0.01; ß = − 0.11, p = 0.01) were inversely associated with MRI-based lung volume. Subclinical cardiac impairment was associated with reduced FEV1, FVC, and residual volume. Cardiac parameters decreased with increasing MRI-based lung volume contrasting the results of PFT. AU - von Krüchten, R.* AU - Lorbeer, R.* AU - Schuppert, C.* AU - Storz, C.* AU - Mujaj, B.* AU - Schulz, H. AU - Kauczor, H.U.* AU - Peters, A. AU - Bamberg, F.* AU - Karrasch, S. AU - Schlett, C.L.* C1 - 62795 C2 - 51066 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Subclinical cardiac impairment relates to traditional pulmonary function test parameters and lung volume as derived from whole-body MRI in a population-based cohort study. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Parasympathetic nervous system innervates peripheral organs including pancreas, hepatic portal system, and gastrointestinal tract. It thereby contributes to the regulation of whole-body glucose metabolism especially in the postprandial state when it promotes secretion of insulin and enhances its action in major target organs. We now aimed to evaluate the effect of parasympathetic modulation on human glucose metabolism. We used slow deep breathing maneuvers to activate the parasympathetic nervous system and tested for effects on metabolism during an oral glucose tolerance test in a randomized, controlled, cross-over trial in 15 healthy young men. We used projections towards the heart as a readout for parasympathetic activity. When analyzing heart rate variability, there was a significant increase of RMSSD (root mean square of successive differences) when participants performed slow deep breathing compared to the control condition, indicating a modulation of parasympathetic activity. However, no statistically significant effects on peripheral glucose metabolism or energy expenditure after the glucose tolerance test were detected. Of note, we detected a significant association between mean heart rate and serum insulin and C-peptide concentrations. While we did not find major effects of slow deep breathing on glucose metabolism, our correlational results suggest a link between the autonomic nervous system and insulin secretion after oral glucose intake. Future studies need to unravel involved mechanisms and develop potential novel treatment approaches for impaired insulin secretion in diabetes. AU - Vosseler, A. AU - Zhao, D. AU - Hummel, J. AU - Gholamrezaei, A.* AU - Hudak, S. AU - Kantartzis, K. AU - Peter, A. AU - Birkenfeld, A.L. AU - Häring, H.-U. AU - Wagner, R. AU - Preissl, H. AU - Kullmann, S. AU - Heni, M. C1 - 63275 C2 - 51449 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Slow deep breathing modulates cardiac vagal activity but does not affect peripheral glucose metabolism in healthy men. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Genome-wide association studies have identified numerous common genetic variants associated with spirometric measures of pulmonary function, including forced expiratory volume in one second (FEV1), forced vital capacity, and their ratio. However, variants with lower minor allele frequencies are less explored. We conducted a large-scale gene-smoking interaction meta-analysis on exonic rare and low-frequency variants involving 44,429 individuals of European ancestry in the discovery stage and sought replication in the UK BiLEVE study with 45,133 European ancestry samples and UK Biobank study with 59,478 samples. We leveraged data on cigarette smoking, the major environmental risk factor for reduced lung function, by testing gene-by-smoking interaction effects only and simultaneously testing the genetic main effects and interaction effects. The most statistically significant signal that replicated was a previously reported low-frequency signal in GPR126, distinct from common variant associations in this gene. Although only nominal replication was obtained for a top rare variant signal rs142935352 in one of the two studies, interaction and joint tests for current smoking and PDE3B were significantly associated with FEV1. This study investigates the utility of assessing gene-by-smoking interactions and underscores their effects on potential pulmonary function. AU - Yang, T.* AU - Jackson, V.E.* AU - Smith, A.V.* AU - Chen, H.* AU - Bartz, T.M.* AU - Sitlani, C.M.* AU - Psaty, B.M.* AU - Gharib, S.A.* AU - O'Connor, G.T.* AU - Dupuis, J.* AU - Xu, J.* AU - Lohman, K.* AU - Liu, Y.* AU - Kritchevsky, S.B.* AU - Cassano, P.A.* AU - Flexeder, C. AU - Gieger, C. AU - Karrasch, S. AU - Peters, A. AU - Schulz, H. AU - Harris, S.E.* AU - Starr, J.M.* AU - Deary, I.J.* AU - Manichaikul, A.* AU - Oelsner, E.C.* AU - Barr, R.G.* AU - Taylor, K.D.* AU - Rich, S.S.* AU - Bonten, T.N.* AU - Mook-Kanamori, D.O.* AU - Noordam, R.* AU - Li-Gao, R.* AU - Jarvelin, M.R.* AU - Wielscher, M.* AU - Terzikhan, N.* AU - Lahousse, L.* AU - Brusselle, G.* AU - Weiss, S.* AU - Ewert, R.* AU - Gläser, S.* AU - Homuth, G.* AU - Shrine, N.* AU - Hall, I.P.* AU - Tobin, M.* AU - London, S.J.* AU - Wei, P.* AU - Morrison, A.C.* C1 - 63192 C2 - 51288 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Rare and low-frequency exonic variants and gene-by-smoking interactions in pulmonary function. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Bacteria-mediated cancer-targeted therapy is a novel experimental strategy for the treatment of cancers. Bacteria can be engineered to overcome a major challenge of existing therapeutics by differentiating between malignant and healthy tissue. A prerequisite for further development and study of engineered bacteria is a suitable imaging concept which allows bacterial visualization in tissue and monitoring bacterial targeting and proliferation. Optoacoustics (OA) is an evolving technology allowing whole-tumor imaging and thereby direct observation of bacterial colonization in tumor regions. However, bacterial detection using OA is currently hampered by the lack of endogenous contrast or suitable transgene fluorescent labels. Here, we demonstrate improved visualization of cancer-targeting bacteria using OA imaging and E. coli engineered to express tyrosinase, which uses L-tyrosine as the substrate to produce the strong optoacoustic probe melanin in the tumor microenvironment. Tumors of animals injected with tyrosinase-expressing E. coli showed strong melanin signals, allowing to resolve bacterial growth in the tumor over time using multispectral OA tomography (MSOT). MSOT imaging of melanin accumulation in tumors was confirmed by melanin and E. coli staining. Our results demonstrate that using tyrosinase-expressing E. coli enables non-invasive, longitudinal monitoring of bacterial targeting and proliferation in cancer using MSOT. AU - Yun, M. AU - You, S.H.* AU - Nguyen, V.H.* AU - Prakash, J. AU - Glasl, S. AU - Gujrati, V. AU - Choy, H.E.* AU - Stiel, A.-C. AU - Min, J.J.* AU - Ntziachristos, V. C1 - 63871 C2 - 51667 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Reporter gene-based optoacoustic imaging of E. coli targeted colon cancer in vivo. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Portfolio PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Despite broad application of different analytical techniques for studies on organic matter of chondrite meteorites, information about composition and structure of individual compounds is still very limited due to extreme molecular diversity of extraterrestrial organic matter. Here we present the first application of isotopic exchange assisted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for analysis of alkali extractable fraction of insoluble organic matter (IOM) of the Murchison and Allende meteorites. This allowed us to determine the individual S-containing ions with different types of sulfur atoms in IOM. Thiols, thiophenes, sulfoxides, sulfonyls and sulfonates were identified in both samples but with different proportions, which contribution corroborated with the hydrothermal and thermal history of the meteorites. The results were supported by XPS and thermogravimetric analysis coupled to FTICR MS. The latter was applied for the first time for analysis of chondritic IOM. To emphasize the peculiar extraterrestrial origin of IOM we have compared it with coal kerogen, which is characterized by the comparable complexity of molecular composition but its aromatic nature and low oxygen content can be ascribed almost exclusively to degradation of biomacromolecules. AU - Zherebker, A.* AU - Kostyukevich, Y.* AU - Volkov, D.S.* AU - Chumakov, R.G.* AU - Friederici, L.* AU - Rüger, C.P.* AU - Kononikhin, A.S.* AU - Kharybin, O.* AU - Korochantsev, A.* AU - Zimmermann, R. AU - Perminova, I.V.* AU - Nikolaev, E.* C1 - 61747 C2 - 50433 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Speciation of organosulfur compounds in carbonaceous chondrites. JO - Sci. Rep. VL - 11 IS - 1 PB - Nature Research PY - 2021 SN - 2045-2322 ER - TY - JOUR AB - Recent studies have shown that high-risk patients with type 2 diabetes mellitus (T2DM) treated with sodium glucose cotransporter 2 (SGLT2) inhibitors have improved cardiovascular (CV) outcomes. In an exploratory analysis of data from the EMPA-REG study, elevations in haematocrit were shown to be strongly associated with beneficial CV effects. As insulin treatment has been shown to be antinatriuretic, with an associated increase in extracellular fluid volume, it is important to confirm whether haematocrit increase is maintained with concomitant insulin therapy. Here, we investigate the effect of the SGLT2 inhibitor dapagliflozin on haematocrit, red blood cell (RBC) counts and reticulocyte levels in high-risk patients with T2DM receiving insulin. A 24-week, double-blinded, randomised, placebo-controlled trial (ClinicalTrials.gov: NCT00673231) was reported previously with extension periods of 24 and 56 weeks (total of 104 weeks). Patients receiving insulin were randomised 1:1:1:1 to placebo or dapagliflozin at 2.5, 5 or 10 mg. Haematocrit, RBC and reticulocyte measurements were conducted during this study, and a longitudinal repeated-measures analysis was performed here to examine change from baseline during treatment. Dapagliflozin treatment in combination with insulin resulted in a dose-dependent increase in haematocrit levels and RBCs over a 104 week period. There was a short-term increase in reticulocyte levels at the start of treatment, which dropped to below baseline after 8 weeks. SGLT2 inhibition with dapagliflozin leads to a sustained increase in haematocrit in patients receiving chronic insulin treatment. AU - Aberle, J.* AU - Menzen, M.* AU - Schmid, S.M.* AU - Terkamp, C.* AU - Jaeckel, E.* AU - Rohwedder, K.* AU - Scheerer, M.F.* AU - Xu, J.* AU - Tang, W.* AU - Birkenfeld, A.L. C1 - 60962 C2 - 49771 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Dapagliflozin effects on haematocrit, red blood cell count and reticulocytes in insulin-treated patients with type 2 diabetes. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Ultrasound imaging is affected by coherent noise or speckle, which reduces contrast and overall image quality and degrades the diagnostic precision of the collected images. Elevational angular compounding (EAC) is an attractive means of addressing this limitation, since it reduces speckle noise while operating in real-time. However, current EAC implementations rely on mechanically rotating a one-dimensional (1D) transducer array or electronically beam steering of two-dimensional (2D) arrays to provide different elevational imaging angles, which increases the size and cost of the systems. Here we present a novel EAC implementation based on a 1D array, which does not necessitate mechanically rotating the transducer. The proposed refraction-based elevational angular compounding technique (REACT) instead utilizes a translating cylindrical acoustic lens that steers the ultrasound beam along the elevational direction. Applying REACT to investigate phantoms and excised tissue samples demonstrated superior suppression of ultrasound speckle noise compared to previous EAC methods, with up to a two-fold improvement in signal- and contrast-to-noise ratios. The effects of elevational angular width on speckle reduction was further investigated to determine the appropriate conditions for applying EAC. This study introduces acoustic refractive elements as potential low cost solutions to noise reduction, which could be integrated into current medical ultrasound devices. AU - Afshari, P. AU - Zakian Dominguez, C.M. AU - Ntziachristos, V. C1 - 60410 C2 - 49433 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Improving ultrasound images with elevational angular compounding based on acoustic refraction. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Sex steroids, such as estrogens and androgens, are important regulators of the humoral immune response. Studies in female mice have demonstrated that alteration of circulating estrogen concentration regulates antibody-mediated immunity. As males have normally little endogenous estrogen, we hypothesized that in males high estrogens and low androgens affect the immune system and enhance the allergic inflammatory response. Here, we studied transgenic male mice expressing human aromatase (AROM+). These animals have a high circulating estrogen to androgen ratio (E/A), causing female traits such as gynecomastia. We found that AROM+ male mice had significantly higher plasma immunoglobulin levels, particularly IgE. Flow cytometry analyses of splenocytes revealed changes in mature/immature B cell ratio together with a transcriptional upregulation of the Igh locus. Furthermore, higher proliferation rate and increased IgE synthesis after IgE class-switching was found. Subsequently, we utilized an ovalbumin airway challenge model to test the allergic response in AROM+ male mice. In line with above observations, an increase in IgE levels was measured, albeit no impact on immune cell infiltration into the lungs was detected. Together, our findings suggest that high circulating E/A in males significantly alters B cell function without any significant enhancement in allergic inflammation. AU - Aguilar-Pimentel, J.A. AU - Cho, Y.-L. AU - Gerlini, R. AU - Calzada-Wack, J. AU - Wimmer, M. AU - Mayer-Kuckuk, P. AU - Adler, T. AU - Schmidt-Weber, C.B. AU - Busch, D.H.* AU - Fuchs, H. AU - Gailus-Durner, V. AU - Ollert, M.* AU - Hrabě de Angelis, M. AU - Ohlsson, C.* AU - Poutanen, M.* AU - Teperino, R. AU - Strauss, L.* C1 - 60433 C2 - 49250 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Increased estrogen to androgen ratio enhances immunoglobulin levels and impairs B cell function in male mice. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - An amendment to this paper has been published and can be accessed via a link at the top of the paper. AU - Angelini, G.* AU - Gissey, L.C.* AU - Del Corpo, G.* AU - Giordano, C.* AU - Cerbelli, B.* AU - Severino, A.* AU - Manco, M.* AU - Basso, N.* AU - Birkenfeld, A.L. AU - Bornstein, S.R. AU - Genco, A.* AU - Mingrone, G.* AU - Casella, G.* C1 - 58199 C2 - 48140 TI - Publisher Correction: New insight into the mechanisms of ectopic fat deposition improvement after bariatric surgery (Scientific reports (2019) 9 1 (17315)). JO - Sci. Rep. VL - 10 IS - 1 PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Improving spatial accessibility to hospitals is a major task for health care systems which can be facilitated using recent methodological improvements of spatial accessibility measures. We used the integrated floating catchment area (iFCA) method to analyze spatial accessibility of general inpatient care (internal medicine, surgery and neurology) on national level in Germany determining an accessibility index (AI) by integrating distances, hospital beds and morbidity data. The analysis of 358 million distances between hospitals and population locations revealed clusters of lower accessibility indices in areas in north east Germany. There was a correlation of urbanity and accessibility up to r = 0.31 (p < 0.001). Furthermore, 10% of the population lived in areas with significant clusters of low spatial accessibility for internal medicine and surgery (neurology: 20%). The analysis revealed the highest accessibility for heart failure (AI = 7.33) and the lowest accessibility for stroke (AI = 0.69). The method applied proofed to reveal important aspects of spatial accessibility i.e. geographic variations that need to be addressed. However, for the majority of the German population, accessibility of general inpatient care was either high or at least not significantly low, which suggests rather adequate allocation of hospital resources for most parts of Germany. AU - Bauer, J.* AU - Klingelhöfer, D.* AU - Maier, W. AU - Schwettmann, L. AU - Groneberg, D.A.* C1 - 60500 C2 - 49355 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Spatial accessibility of general inpatient care in Germany: An analysis of surgery, internal medicine and neurology. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Little is known about trends in the age of onset of first myocardial infarction. Thus, we examined trends in the age of onset distribution of first myocardial infarction using two population-based datasets from Germany. First, we used German claims data based on an annual case number of approximately 2 million women and men covering the period from 2006 to 2016. Second, we used data from the KORA (Cooperative Health Research in the Region of Augsburg) Myocardial Infarction Registry covering the period from 2000-2016. Analyses were performed by means of quantile regression to estimate trends across the whole distribution of age of onset. Overall, N-Sample 1=69627 and N-Sample 2=9954 first myocardial infarctions were observed. In both samples, we found highly heterogeneous trends in age of onset. In men, we consistently found that age of onset increased before 50 and after 70 but decreased within this age bracket. For women, on the other hand, we consistently found that age of onset decreased for first myocardial infarctions before 70 but increased slightly or remained relatively stable thereafter. Therefore, late myocardial infarctions tended to occur later in life, while regular myocardial infarctions tended to occur earlier. These results suggest that in myocardial infarction, both morbidity compression and morbidity expansion might have occurred at the same time but for different parts of the age at onset distribution. AU - Beller, J.* AU - Bauersachs, J.* AU - Schäfer, A.* AU - Schwettmann, L. AU - Heier, M. AU - Peters, A. AU - Meisinger, C. AU - Geyer, S.* C1 - 59385 C2 - 48797 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Diverging trends in age at first myocardial infarction: Evidence from two German population-based studies. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Light sheet fluorescence microscopy (LSFM) of optically cleared biological samples represents a powerful tool to analyze the 3-dimensional morphology of tissues and organs. Multimodal combinations of LSFM with additional analyses of the identical sample help to limit the consumption of restricted specimen and reduce inter-sample variation. Here, we demonstrate the proof-of-concept that LSFM of cleared brain tissue samples can be combined with Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI) for detection and quantification of proteins. Samples of freshly dissected murine brain and of archived formalin-fixed paraffin-embedded (FFPE) human brain tissue were cleared (3DISCO). Tissue regions of interest were defined by LSFM and excised, (re)-embedded in paraffin, and sectioned. Mouse sections were coated with sinapinic acid matrix. Human brain sections were pre-digested with trypsin and coated with α-cyano-4-hydroxycinnamic acid matrix. Subsequently, sections were subjected to MALDI-time-of-flight (TOF)-MSI in mass ranges between 0.8 to 4 kDa (human tissue sections), or 2.5–25 kDa (mouse tissue sections) with a lateral resolution of 50 µm. Protein- and peptide-identities corresponding to acquired MALDI-MSI spectra were confirmed by parallel liquid chromatography tandem mass spectrometry (LC–MS/MS) analysis. The spatial abundance- and intensity-patterns of established marker proteins detected by MALDI-MSI were also confirmed by immunohistochemistry. AU - Blutke, A. AU - Sun, N. AU - Xu, Z. AU - Buck, A. AU - Harrison, L. AU - Schriever, S.C. AU - Pfluger, P.T. AU - Wiles, D.* AU - Kunzke, T. AU - Huber, K. AU - Schlegel, J.* AU - Aichler, M. AU - Feuchtinger, A. AU - Matiasek, K.* AU - Hauck, S.M. AU - Walch, A.K. C1 - 60007 C2 - 48967 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Light sheet fluorescence microscopy guided MALDI-imaging mass spectrometry of cleared tissue samples. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Among obese subjects, metabolically healthy (MHO) and unhealthy obese (MUHO) subjects exist, the latter being characterized by whole-body insulin resistance, hepatic steatosis, and subclinical inflammation. Insulin resistance and obesity are known to associate with alterations in mitochondrial density, morphology, and function. Therefore, we assessed mitochondrial function in human subcutaneous preadipocytes as well as in differentiated adipocytes derived from well-matched donors. Primary subcutaneous preadipocytes from 4 insulin-resistant (MUHO) versus 4 insulin-sensitive (MHO), non-diabetic, morbidly obese Caucasians (BMI > 40 kg/m(2)), matched for sex, age, BMI, and percentage of body fat, were differentiated in vitro to adipocytes. Real-time cellular respiration was measured using an XF24 Extracellular Flux Analyzer (Seahorse). Lipolysis was stimulated by forskolin (FSK) treatment. Mitochondrial respiration was fourfold higher in adipocytes versus preadipocytes (p = 1.6*10(-9)). In adipocytes, a negative correlation of mitochondrial respiration with donors' insulin sensitivity was shown (p = 0.0008). Correspondingly, in adipocytes of MUHO subjects, an increased basal respiration (p = 0.002), higher proton leak (p = 0.04), elevated ATP production (p = 0.01), increased maximal respiration (p = 0.02), and higher spare respiratory capacity (p = 0.03) were found, compared to MHO. After stimulation with FSK, the differences in ATP production, maximal respiration and spare respiratory capacity were blunted. The differences in mitochondrial respiration between MUHO/MHO were not due to altered mitochondrial content, fuel switch, or lipid metabolism. Thus, despite the insulin resistance of MUHO, we could clearly show an elevated mitochondrial respiration of MUHO adipocytes. We suggest that the higher mitochondrial respiration reflects a compensatory mechanism to cope with insulin resistance and its consequences. Preserving this state of compensation might be an attractive goal for preventing or delaying the transition from insulin resistance to overt diabetes. AU - Böhm, A. AU - Keuper, M. AU - Meile, T.* AU - Zdichavsky, M.* AU - Fritsche, A. AU - Häring, H.-U. AU - Hrabě de Angelis, M. AU - Staiger, H. AU - Frankó, A. C1 - 59776 C2 - 48942 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Increased mitochondrial respiration of adipocytes from metabolically unhealthy obese compared to healthy obese individuals. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - This Article contains an error in the legend of Table 2, where the axes width is incorrect. “The beam spots had elliptical shape with semi-axes ?x and ?y, and different methods were performed for spot size characterization.” should read: “The beam spots had elliptical shape with axes ?x and ?y, and different methods were performed for spot size characterization.” Additionally, there is an error in Figure 2, where the conversion between standard deviation and FWHM of a Gaussian distribution was performed by an incorrect factor. The correct Figure 2 appears below as Figure 1. (Figure presented.). AU - Friedrich, T.* AU - Ilicic, K. AU - Greubel, C.* AU - Girst, S.* AU - Reindl, J.* AU - Sammer, M.* AU - Schwarz, B.* AU - Siebenwirth, C.* AU - Walsh, D.W.M.* AU - Schmid, T.E. AU - Scholz, M.* AU - Dollinger, G.* C1 - 60488 C2 - 49839 TI - Author Correction: DNA damage interactions on both nanometer and micrometer scale determine overall cellular damage (Scientific Reports, (2018), 8, 1, (16063), 10.1038/s41598-018-34323-9). JO - Sci. Rep. VL - 10 IS - 1 PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - To identify the most important factors that impact brain volume, while accounting for potential collinearity, we used a data-driven machine-learning approach. Gray Matter Volume (GMV) was derived from magnetic resonance imaging (3T, FLAIR) and adjusted for intracranial volume (ICV). 93 potential determinants of GMV from the categories sociodemographics, anthropometric measurements, cardio-metabolic variables, lifestyle factors, medication, sleep, and nutrition were obtained from 293 participants from a population-based cohort from Southern Germany. Elastic net regression was used to identify the most important determinants of ICV-adjusted GMV. The four variables age (selected in each of the 1000 splits), glomerular filtration rate (794 splits), diabetes (323 splits) and diabetes duration (122 splits) were identified to be most relevant predictors of GMV adjusted for intracranial volume. The elastic net model showed better performance compared to a constant linear regression (mean squared error = 1.10 vs. 1.59, p<0.001). These findings are relevant for preventive and therapeutic considerations and for neuroimaging studies, as they suggest to take information on metabolic status and renal function into account as potential confounders. AU - Galiè, F.* AU - Rospleszcz, S. AU - Keeser, D.* AU - Beller, E.* AU - Illigens, B.* AU - Lorbeer, R.* AU - Grosu, S.* AU - Selder, S.* AU - Auweter, S.* AU - Schlett, C.L.* AU - Rathmann, W.* AU - Schwettmann, L. AU - Ladwig, K.-H. AU - Linseisen, J. AU - Peters, A. AU - Bamberg, F.* AU - Ertl-Wagner, B.* AU - Stoecklein, S.* C1 - 59169 C2 - 48651 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Machine-learning based exploration of determinants of gray matter volume in the KORA-MRI study. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Overcoming the global health threat of HIV infection requires continuous pipelines of novel drug candidates. We identified the gamma-pyrone polyketides Aureothin/Neoaureothin as potent hits by anti-HIV screening of an extensive natural compound collection. Total synthesis of a structurally diverse group of Aureothin-derivatives successfully identified a lead compound (#7) superior to Aureothin that combines strong anti-HIV activity (IC90<45 nM), photostability and improved cell safety. Compound #7 inhibited de novo virus production from integrated proviruses by blocking the accumulation of HIV RNAs that encode the structural components of virions and include viral genomic RNAs. Thus, the mode-of-action displayed by compound #7 is different from those of all current clinical drugs. Proteomic analysis indicated that compound #7 does not affect global protein expression in primary blood cells and may modulate cellular pathways linked to HIV infection. Compound #7 inhibited multiple HIV genotypes, including HIV-type 1 and 2 and synergistically inhibited HIV in combination with clinical reverse transcriptase and integrase inhibitors. We conclude that compound #7 represents a promising new class of HIV inhibitors that will facilitate the identification of new virus-host interactions exploitable for antiviral attack and holds promise for further drug development. AU - Herrmann, A. AU - Roesner, M.* AU - Werner, T.* AU - Hauck, S.M. AU - Koch, A. AU - Bauer A. AU - Schneider, M. AU - Brack-Werner, R. C1 - 57994 C2 - 48320 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Potent inhibition of HIV replication in primary human cells by novel synthetic polyketides inspired by Aureothin. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - To investigate factors associated with time in physical activity intensities, we assessed physical activity of 249 men and women (mean age 51.3 years) by 7-day 24h-accelerometry (ActiGraph GT3X+). Triaxial vector magnitude counts/minute were extracted to determine time in inactivity, in low-intensity, moderate, and vigorous-to-very-vigorous activity. Cross-sectional associations with sex, age, body mass index, waist circumference, smoking, alcohol consumption, education, employment, income, marital status, diabetes, and dyslipidaemia were investigated in multivariable regression analyses. Higher age was associated with more time in low-intensity (mean difference, 7.3min/d per 5 years; 95% confidence interval 2.0,12.7) and less time in vigorous-to-very-vigorous activity (-0.8min/d; -1.4, -0.2), while higher BMI was related to less time in low-intensity activity (-3.7min/d; -6.3, -1.2). Current versus never smoking was associated with more time in low-intensity (29.2min/d; 7.5, 50.9) and less time in vigorous-to-very-vigorous activity (-3.9min/d; -6.3, -1.5). Finally, having versus not having a university entrance qualification and being not versus full time employed were associated with more inactivity time (35.9min/d; 13.0, 58.8, and 66.2min/d; 34.7, 97.7, respectively) and less time in low-intensity activity (-31.7min/d; -49.9, -13.4, and -50.7; -76.6, -24.8, respectively). The assessed factors show distinct associations with activity intensities, providing targets for public health measures aiming to increase activity. AU - Jaeschke, L.* AU - Steinbrecher, A.* AU - Boeing, H.* AU - Gastell, S.* AU - Ahrens, W.* AU - Berger, K.* AU - Brenner, H.* AU - Ebert, N.* AU - Fischer, B.* AU - Greiser, K.H.* AU - Hoffmann, W.* AU - Jöckel, K.-H.* AU - Kaaks, R.* AU - Keil, T.* AU - Kemmling, Y.* AU - Kluttig, A.* AU - Krist, L.* AU - Leitzmann, M.* AU - Leib, W.* AU - Linseisen, J. AU - Löffler, M.* AU - Michels, K.B.* AU - Obi, N.* AU - Peters, A. AU - Schipf, S.* AU - Schmidt, B.* AU - Zinkhan, M.* AU - Pischon, T.* C1 - 57896 C2 - 48168 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Factors associated with habitual time spent in different physical activity intensities using multiday accelerometry. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Determining exact viral titers in a given sample is essential for many environmental and clinical applications, e.g., for studying viral ecology or application of bacteriophages for food safety. However, virus quantification is not a simple task, especially for complex environmental samples. While clonal viral isolates can be quantified with relative high accuracy using virus-specific methods, i.e., plaque assay or quantitative real-time PCR, these methods are not valid for complex and diverse environmental samples. Moreover, it is not yet known how precisely laser-based methods, i.e., epifluorescence microscopy, flow cytometry, and nanoparticle tracking analysis, quantify environmental viruses. In the present study, we compared five state-of-the-art viral quantification methods by enumerating four model viral isolates of different genome and size characteristics as well as four different environmental water samples. Although Nanoparticle tracking analysis combined with gentle staining at 30 degrees C could be confirmed by this study to be a reliable quantification technique for tested environmental samples, environmental samples still lack an universally applicable and accurate quantification method. Special attention has to be put on optimal sample concentrations as well as optimized sample preparations, which are specific for each method. As our results show the inefficiency when enumerating small, or single-stranded DNA or RNA viruses, the global population of viruses is presumably higher than expected. AU - Kaletta, J. AU - Pickl, C.* AU - Griebler, C. AU - Klingl, A.* AU - Kurmayer, R.* AU - Deng, L. C1 - 60450 C2 - 49462 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A rigorous assessment and comparison of enumeration methods for environmental viruses. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Isoform switching is a recently characterized hallmark of cancer, and often translates to the loss or gain of domains mediating protein interactions and thus, the re-wiring of the interactome. Recent computational tools leverage domain-domain interaction data to resolve the condition-specific interaction networks from RNA-Seq data accounting for the domain content of the primary transcripts expressed. Here, we used The Cancer Genome Atlas RNA-Seq datasets to generate 642 patient-specific pairs of interactomes corresponding to both the tumor and the healthy tissues across 13 cancer types. The comparison of these interactomes provided a list of patient-specific edgetic perturbations of the interactomes associated with the cancerous state. We found that among the identified perturbations, select sets are robustly shared between patients at the multi-cancer, cancer-specific and cancer subtype specific levels. Interestingly, the majority of the alterations do not directly involve significantly mutated genes, nevertheless, they strongly correlate with patient survival. The findings (available at EdgeExplorer: "http://webclu.bio.wzw.tum.de/EdgeExplorer") are a new source of potential biomarkers for classifying cancer types and the proteins we identified are potential anti-cancer therapy targets. AU - Kataka, E.* AU - Zaucha, J.* AU - Frishman, G. AU - Ruepp, A. AU - Frishman, D.* C1 - 58543 C2 - 48170 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Edgetic perturbation signatures represent known and novel cancer biomarkers. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Most imaging studies of immunotherapy have focused on tracking labeled T cell biodistribution in vivo for understanding trafficking and homing parameters and predicting therapeutic efficacy by the presence of transferred T cells at or in the tumour mass. Conversely, we investigate here a novel concept for longitudinally elucidating anatomical and pathophysiological changes of solid tumours after adoptive T cell transfer in a preclinical set up, using previously unexplored in-tandem macroscopic and mesoscopic optoacoustic (photoacoustic) imaging. We show non-invasive in vivo observations of vessel collapse during tumour rejection across entire tumours and observe for the first time longitudinal tumour rejection in a label-free manner based on optical absorption changes in the tumour mass due to cellular decline. We complement these observations with high resolution episcopic fluorescence imaging of T cell biodistribution using optimized T cell labeling based on two near-infrared dyes targeting the cell membrane and the cytoplasm. We discuss how optoacoustic macroscopy and mesoscopy offer unique contrast and immunotherapy insights, allowing label-free and longitudinal observations of tumour therapy. The results demonstrate optoacoustic imaging as an invaluable tool in understanding and optimizing T cell therapy. AU - Kimm, M.A.* AU - Tzoumas, S. AU - Glasl, S. AU - Omar, M. AU - Symvoulidis, P. AU - Olefir, I. AU - Rummeny, E.J.* AU - Meier, R.* AU - Ntziachristos, V. C1 - 58623 C2 - 48512 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Longitudinal imaging of T cell-based immunotherapy with multi-spectral, multi-scale optoacoustic tomography. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The distribution of neurons in the cortex (cytoarchitecture) differs between cortical areas and constitutes the basis for structural maps of the human brain. Deep learning approaches provide a promising alternative to overcome throughput limitations of currently used cytoarchitectonic mapping methods, but typically lack insight as to what extent they follow cytoarchitectonic principles. We therefore investigated in how far the internal structure of deep convolutional neural networks trained for cytoarchitectonic brain mapping reflect traditional cytoarchitectonic features, and compared them to features of the current grey level index (GLI) profile approach. The networks consisted of a 10-block deep convolutional architecture trained to segment the primary and secondary visual cortex. Filter activations of the networks served to analyse resemblances to traditional cytoarchitectonic features and comparisons to the GLI profile approach. Our analysis revealed resemblances to cellular, laminar- as well as cortical area related cytoarchitectonic features. The networks learned filter activations that reflect the distinct cytoarchitecture of the segmented cortical areas with special regard to their laminar organization and compared well to statistical criteria of the GLI profile approach. These results confirm an incorporation of relevant cytoarchitectonic features in the deep convolutional neural networks and mark them as a valid support for high-throughput cytoarchitectonic mapping workflows. AU - Kiwitz, K.* AU - Schiffer, C.* AU - Spitzer, H. AU - Dickscheid, T.* AU - Amunts, K.* C1 - 60818 C2 - 49640 TI - Deep learning networks reflect cytoarchitectonic features used in brain mapping. JO - Sci. Rep. VL - 10 IS - 1 PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The helical tomotherapy (HT) Hi-ART system was installed at our department in April 2007. In July 2018 the first Radixact system in Germany has been launched for clinical use. We present differences, advantages and disadvantages and show future perspectives in patient treatment using two HT devices. We investigate patient characteristics, image quality, radiotherapy treatment specifications and analyze the time effort for treatments with the Hi-ART system from April 2010 until May 2017 and compare it to the data acquired in the first nine months of usage of the Radixact system. Comparing the Hi-ART and Radixact system, the unique option of integrated MVCT image acquisition has experienced distinct improvement in image quality. Time effort for irradiation treatment could be improved resulting in a mean beam on time for craniospinal axis treatment of 636.2 s for the Radixact system compared to 915.9 s for the Hi-ART system. The beneficial use of tomotherapy for complex target volumes is demonstrated by a head and neck tumor case and craniospinal axis treatment. With the Radixact system MVCT image quality has been improved allowing for fast and precise interfraction dose adaptation. The improved time effort for patient treatment could increase the accessibility for clinical usage. AU - Kraus, K.M.* AU - Kampfer, S.* AU - Wilkens, J.J.* AU - Schüttrumpf, L.* AU - Combs, S.E. C1 - 58640 C2 - 48514 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Helical tomotherapy: Comparison of Hi-ART and Radixact clinical patient treatments at the Technical University of Munich. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Track structure based simulations valuably complement experimental research on biological effects of ionizing radiation. They provide information at the highest level of detail on initial DNA damage induced by diverse types of radiation. Simulations with the biophysical Monte Carlo code PARTRAC have been used for testing working hypotheses on radiation action mechanisms, for benchmarking other damage codes and as input for modelling subsequent biological processes. To facilitate such applications and in particular to enable extending the simulations to mixed radiation field conditions, we present analytical formulas that capture PARTRAC simulation results on DNA single- and double-strand breaks and their clusters induced in cells irradiated by ions ranging from hydrogen to neon at energies from 0.5 GeV/u down to their stopping. These functions offer a means by which radiation transport codes at the macroscopic scale could easily be extended to predict biological effects, exploiting a large database of results from micro-/nanoscale simulations, without having to deal with the coupling of spatial scales and running full track-structure calculations. AU - Kundrát, P. AU - Friedland, W. AU - Becker, J. AU - Eidemüller, M. AU - Ottolenghi, A.* AU - Baiocco, G.* C1 - 60160 C2 - 49229 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Analytical formulas representing track-structure simulations on DNA damage induced by protons and light ions at radiotherapy-relevant energies. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Harmful algal blooms formed by colony-forming cyanobacteria deteriorate water resources by producing cyanotoxins, which frequently occur at high intracellular concentrations. We aimed to localize toxic microcystins (MCs) and bioactive anabaenopeptins (APs) at the subcellular level under noninvasive conditions. Since both metabolites are synthesized nonribosomally, the relaxed specificity of key enzymes catalyzing substrate activation allowed chemical labeling through a standard copper-catalyzed click chemistry reaction. The genera Planktothrix and Microcystis specifically incorporated unnatural amino acids such as N-propargyloxy-carbonyl-L-lysine or O-propargyl-L-tyrosine, resulting in modified AP or MC peptides carrying the incorporated alkyne moiety. The labeled cells were quantitatively differentiated from the unlabeled control cells. MCs and APs occurred intracellularly as distinct entities showing a cell-wide distribution but a lowered spatial overlap with natural autofluorescence. Using the immunofluorescence technique, colocalization with markers of individual organelles was utilized to relate the distribution of labeled MCs to cellular compartments, e.g., using RbcL and FtsZ (cytosol) and PsbA (thylakoids). The colocalization correlation coefficients calculated pairwise between organelles and autofluorescence were highly positive as opposed to the relatively low positive indices derived from labeled MCs. The lower correlation coefficients imply that only a portion of the labeled MC molecules were related spatially to the organelles in the cell. AU - Kurmayer, R.* AU - Entfellner, E.* AU - Weisse, T.* AU - Offterdinger, M.* AU - Rentmeister, A.* AU - Deng, L. C1 - 58468 C2 - 48231 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Chemically labeled toxins or bioactive peptides show a heterogeneous intracellular distribution and low spatial overlap with autofluorescence in bloom-forming cyanobacteria. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The study aimed to examine the sex specific association of obesity with cortisol metabolism in a sample of older community dwelling people. The cross-sectional analysis included 394 men and 375 women (aged 65-90 years) of the population-based KORA-Age study. Multivariable regression analyses were employed to examine the association between cortisol samples (serum and salivary samples of morning after awakening (M1), 30 min later (M2) and at late night (LNSC)). Obesity was calculated as waist-to-hip ratio (WHR) and body mass index (BMI). Cortisol levels were not significantly different between obesity measures except for elevated serum cortisol (P=0.02) levels in individuals with a low WHR. Higher M1 levels were especially apparent in women with normal BMI. Serum cortisol levels were inversely related to WHR (P=0.004) and CAR(AUC) was inversely associated with BMI (P=0.007). Sex-stratified analytic models revealed that both obesity measures showed a non-linear association with cortisol diurnal pattern (M1/LNSC) in men. Impaired cortisol patterns emerged at both very ends of the body weight distribution. These findings do not support a cortisol driven obesity etiology in an older population and even point to an inverse association of body weight with cortisol levels. Differences of cortisol secretion patterns in generalized and abdominal fat distribution were marginal. AU - Ladwig, K.-H. AU - Schriever, S.C. AU - Atasoy, S. AU - Bidlingmaier, M.* AU - Kruse, J.* AU - Johar, H. C1 - 60000 C2 - 48970 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Association of generalized and central obesity with serum and salivary cortisol secretion patterns in the elderly: Findings from the cross sectional KORA-Age study. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The original version of this Article contained a typographical error in the spelling of the author Ana Maria Ortega-Prieto, which was incorrectly given as Anna Maria Ortega-Prieto. This has now been corrected in the PDF and HTML versions of the Article. AU - Liu, P.J.* AU - Harris, J.M.* AU - Marchi, E.* AU - D’Arienzo, V.* AU - Michler, T. AU - Wing, P.A.C.* AU - Magri, A.* AU - Ortega-Prieto, A.M.* AU - van de Klundert, M. AU - Wettengel, J.M. AU - Durantel, D.* AU - Dorner, M.* AU - Klenerman, P.* AU - Protzer, U. AU - Giotis, E.S.* AU - McKeating, J.A.* C1 - 60472 C2 - 49878 TI - Author Correction: Hypoxic gene expression in chronic hepatitis B virus infected patients is not observed in state-of-the-art in vitro and mouse infection models (Scientific Reports, (2020), 10, 1, (14101), 10.1038/s41598-020-70865-7). JO - Sci. Rep. VL - 10 IS - 1 PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Hepatitis B virus (HBV) is the leading cause of hepatocellular carcinoma (HCC) worldwide. The prolyl hydroxylase domain (PHD)-hypoxia inducible factor (HIF) pathway is a key mammalian oxygen sensing pathway and is frequently perturbed by pathological states including infection and inflammation. We discovered a significant upregulation of hypoxia regulated gene transcripts in patients with chronic hepatitis B (CHB) in the absence of liver cirrhosis. We used state-of-the-art in vitro and in vivo HBV infection models to evaluate a role for HBV infection and the viral regulatory protein HBx to drive HIF-signalling. HBx had no significant impact on HIF expression or associated transcriptional activity under normoxic or hypoxic conditions. Furthermore, we found no evidence of hypoxia gene expression in HBV de novo infection, HBV infected human liver chimeric mice or transgenic mice with integrated HBV genome. Collectively, our data show clear evidence of hypoxia gene induction in CHB that is not recapitulated in existing models for acute HBV infection, suggesting a role for inflammatory mediators in promoting hypoxia gene expression. AU - Liu, P.J.* AU - Harris, J.M.* AU - Marchi, E.* AU - D’Arienzo, V.* AU - Michler, T. AU - Wing, P.A.C.* AU - Magri, A.* AU - Ortega-Prieto, A.M.* AU - van de Klundert, M. AU - Wettengel, J.M. AU - Durantel, D.* AU - Dorner, M.* AU - Klenerman, P.* AU - Protzer, U. AU - Giotis, E.S.* AU - McKeating, J.A.* C1 - 59974 C2 - 49151 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Hypoxic gene expression in chronic hepatitis B virus infected patients is not observed in state-of-the-art in vitro and mouse infection models. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Molecular imaging of atherosclerosis by Magnetic Resonance Imaging (MRI) has been impaired by a lack of validation of the specific substrate responsible for the molecular imaging signal. We therefore aimed to investigate the additive value of mass spectrometry imaging (MSI) of atherosclerosis-affine Gadofluorine P for molecular MRI of atherosclerotic plaques. Atherosclerotic Ldlr(-/-) mice were investigated by high-field MRI (7T) at different time points following injection of atherosclerosis-affine Gadofluorine P as well as at different stages of atherosclerosis formation (4, 8, 16 and 20 weeks of HFD). At each imaging time point mice were immediately sacrificed after imaging and aortas were excised for mass spectrometry imaging: Matrix Assisted Laser Desorption Ionization (MALDI) Imaging and Laser Ablation - Inductively Coupled Plasma - Mass Spectrometry (LA-ICP-MS) imaging. Mass spectrometry imaging allowed to visualize the localization and measure the concentration of the MR imaging probe Gadofluorine P in plaque tissue ex vivo with high spatial resolution and thus adds novel and more target specific information to molecular MR imaging of atherosclerosis. AU - Lohöfer, F.* AU - Buchholz, R.* AU - Glinzer, A.* AU - Huber, K. AU - Haas, H.* AU - Kaissis, G.* AU - Feuchtinger, A. AU - Aichler, M. AU - Sporns, P.B.* AU - Höltke, C.* AU - Stölting, M.* AU - Schilling, F.* AU - Botnar, R.M.* AU - Kimm, M.A.* AU - Faber, C.* AU - Walch, A.K. AU - Zernecke, A.* AU - Karst, U.* AU - Wildgruber, M.* C1 - 57860 C2 - 48163 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Mass Spectrometry imaging of atherosclerosis-affine Gadofluorine following Magnetic Resonance imaging. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The expression of short chain fatty acid receptors FFA2 and FFA3 in pancreatic islets raised interest in using them as drug targets for treating hyperglycemia in humans. This study aims to examine the efficacy of synthetic FFA2- and FFA3-ligands to modulate glucose-stimulated insulin secretion (GSIS) in human pseudoislets which display intact glucose responsiveness. The FFA2-agonists 4-CMTB and TUG-1375 inhibited GSIS, an effect reversed by the FFA2-antagonist CATPB. GSIS itself was not augmented by CATPB. The FFA3-agonists FHQC and 1-MCPC did not affect GSIS in human pseudoislets. For further drug evaluation we used mouse islets. The CATPB-sensitive inhibitory effect of 100 mu M 4-CMTB on GSIS was recapitulated. The inhibition was partially sensitive to the G(i/o)-protein inhibitor pertussis toxin. A previously described FFA2-dependent increase of GSIS was observed with lower concentrations of 4-CMTB (10 and 30 mu M). The stimulatory effect of 4-CMTB on secretion was prevented by the Gq-protein inhibitor FR900359. As in human pseudoislets, in mouse islets relative mRNA levels were FFAR2 > FFAR3 and FFA3-agonists did not affect GSIS. The FFA3-agonists, however, inhibited GSIS in a pertussis toxin-sensitive manner in INS-1E cells and this correlated with relative mRNA levels of Ffar3 > > Ffar2. Thus, in humans, when FFA2-activation impedes GSIS, FFA2-antagonism may reduce glycemia. AU - Lorza-Gil, E. AU - Kaiser, G. AU - Rexen Ulven, E.* AU - König, G.M.* AU - Gerst, F. AU - Oquendo, M.B.* AU - Birkenfeld, A.L. AU - Häring, H.-U. AU - Kostenis, E.* AU - Ulven, T.* AU - Ullrich, S. C1 - 60273 C2 - 49188 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - FFA2-, but not FFA3-agonists inhibit GSIS of human pseudoislets: A comparative study with mouse islets and rat INS-1E cells. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - We investigated the cognitive and behavioral profile of three distinct groups of epilepsies with a genetic background for intergroup differences: (1) idiopathic/genetic generalized epilepsies (IGE/GGE group); (2) idiopathic focal epilepsies (IFE group); and (3) epilepsies with proven or strongly suggested monogenic or structural/numeric chromosomal etiology (genetic epilepsies, GE group). Cognitive (total IQ and subcategories) and behavioral parameters (CBCL) were assessed at the tertiary epilepsy center of the University of Munich (Germany). We used ANOVA with post-hoc Bonferroni-correction to explore significant mean differences and Fisher's exact test for significant proportional differences of intelligence impairment and behavioral problems. 126 (56 IGE/GGE, 26 IFE, 44 GE) patients were available. Total IQ was 89.0 ± 15.9 (95% CI 84.5-93.4) for IGE/GGE, 94.8 ± 18.1 (95% CI 87.3-102.3) for IFE and 76.4 ± 22.4 (95% CI 67.6-85.3) for GE (p = 0.001). The same trend was significant for all but one IQ subcategory. The rate of patients with an intelligence impairment (total IQ < 70) was higher for GE (40%) than for IGE/GGE (14%) and for IFE (7%) patients (p = 0.033). There were no significant differences between groups for behavior scores and behavioral problems. This study shows that the current ILAE classification of epilepsies with genetic etiology creates a heterogeneous group of patients with respect to cognitive performance but not behavior. These findings may help in further delineating epilepsies as regards cognitive performance, notwithstanding their closely related etiological classification. AU - Moorhouse, F.J.* AU - Cornell, S.* AU - Gerstl, L.* AU - Tacke, M.* AU - Roser, T.* AU - Heinen, F.* AU - Bonfert, M.* AU - von Stülpnagel, C.* AU - Wagner, M. AU - Borggraefe, I.* C1 - 60768 C2 - 49520 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Cognitive performance and behavior across idiopathic/genetic epilepsies in children and adolescents. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Since family history of diabetes is a very strong risk factor for type 2 diabetes, which is one of the most important risk factors for cardiovascular disease (CVD), it might be also useful to assess the risk for CVD. Therefore, we aimed to investigate the relationship between a familial (parents and siblings) history of diabetes and the risk of incident CVD. Data from four prospective German cohort studies were used: EPIC-Potsdam study (n=26,054), CARLA study (n=1,079), SHIP study (n=3,974), and KORA study (n=15,777). A multivariable-adjusted Cox regression was performed to estimate associations between familial histories of diabetes, myocardial infarction or stroke and the risk of CVD in each cohort; combined hazard ratios (HRMeta) were derived by conducting a meta-analysis. The history of diabetes in first-degree relatives was not related to the development of CVD (HRMeta 0.99; 95% CI 0.88-1.10). Results were similar for the single outcomes myocardial infarction (MI) (HRMeta 1.07; 95% CI 0.92-1.23) and stroke (HRMeta 1.00; 95% CI 0.86-1.16). In contrast, parental history of MI and stroke were associated with an increased CVD risk. Our study indicates that diabetes in the family might not be a relevant risk factor for the incidence of CVD. However, the study confirmed the relationship between a parental history of MI or stroke and the onset of CVD. AU - Mühlenbruch, K.* AU - Menzel, J.* AU - Dörr, M.* AU - Ittermann, T.* AU - Meisinger, C. AU - Peters, A. AU - Kluttig, A.* AU - Medenwald, D.* AU - Bergmann, M.* AU - Boeing, H.* AU - Schulze, M.B.* AU - Weikert, C.* C1 - 60149 C2 - 49277 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Association of familial history of diabetes or myocardial infarction and stroke with risk of cardiovascular diseases in four German cohorts. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Natural products (NP) are a valuable drug resource. However, NP-inspired drug leads are declining, among other reasons due to high re-discovery rates. We developed a conceptual framework using the metabolic fingerprint of entire ecosystems (MeE) to facilitate the discovery of global bioactivity hotspots. We assessed the MeE of 305 sites of diverse aquatic ecosystems, worldwide. All samples were tested for antiviral effects against the human immunodeficiency virus (HIV), followed by a comprehensive screening for cell-modulatory activity by High-Content Screening (HCS). We discovered a very strong HIV-1 inhibition mainly in samples taken from fjords with a strong terrestrial input. Multivariate data integration demonstrated an association of a set of polyphenols with specific biological alterations (endoplasmic reticulum, lysosomes, and NFkB) caused by these samples. Moreover, we found strong HIV-1 inhibition in one unrelated oceanic sample closely matching to HIV-1-inhibitory drugs on a cytological and a chemical level. Taken together, we demonstrate that even without physical purification, a sophisticated strategy of differential filtering, correlation analysis, and multivariate statistics can be employed to guide chemical analysis, to improve de-replication, and to identify ecosystems with promising characteristics as sources for NP discovery. AU - Müller, C. AU - Kremb, S.* AU - Gonsior, M.* AU - Brack-Werner, R. AU - Voolstra, C.R.* AU - Schmitt-Kopplin, P. C1 - 57961 C2 - 48262 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Advanced identification of global bioactivity hotspots via screening of the metabolic fingerprint of entire ecosystems. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - ACO2 is a mitochondrial protein, which is critically involved in the function of the tricarboxylic acid cycle (TCA), the maintenance of iron homeostasis, oxidative stress defense and the integrity of mitochondrial DNA (mtDNA). Mutations in the ACO2 gene were identified in patients suffering from a broad range of symptoms, including optic nerve atrophy, cortical atrophy, cerebellar atrophy, hypotonia, seizures and intellectual disabilities. In the present study, we identified a heterozygous 51 bp deletion (c.1699_1749del51) in ACO2 in a family with autosomal dominant inherited isolated optic atrophy. A complementation assay using aco1-deficient yeast revealed a growth defect for the mutant ACO2 variant substantiating a pathogenic effect of the deletion. We used patient-derived fibroblasts to characterize cellular phenotypes and found a decrease of ACO2 protein levels, while ACO2 enzyme activity was not affected compared to two age- and gender-matched control lines. Several parameters of mitochondrial function, including mitochondrial morphology, mitochondrial membrane potential or mitochondrial superoxide production, were not changed under baseline conditions. However, basal respiration, maximal respiration, and spare respiratory capacity were reduced in mutant cells. Furthermore, we observed a reduction of mtDNA copy number and reduced mtDNA transcription levels in ACO2-mutant fibroblasts. Inducing oxidative stress led to an increased susceptibility for cell death in ACO2-mutant fibroblasts compared to controls. Our study reveals that a monoallelic mutation in ACO2 is sufficient to promote mitochondrial dysfunction and increased vulnerability to oxidative stress as main drivers of cell death related to optic nerve atrophy. AU - Neumann, M.A.C.* AU - Grossmann, D.* AU - Schimpf-Linzenbold, S.* AU - Dayan, D.* AU - Stingl, K.* AU - Ben-Menachem, R.* AU - Pines, O.* AU - Massart, F.* AU - Delcambre, S.* AU - Ghelfi, J.* AU - Bohler, J.* AU - Strom, T.M. AU - Kessel, A.* AU - Azem, A.* AU - Schöls, L.* AU - Grünewald, A.* AU - Wissinger, B.* AU - Krüger, R.* C1 - 60286 C2 - 49327 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Haploinsufficiency due to a novel ACO2 deletion causes mitochondrial dysfunction in fibroblasts from a patient with dominant optic nerve atrophy. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The autoimmune disease systemic sclerosis (SSc) causes microvascular changes that can be easily observed cutaneously at the finger nailfold. Optoacoustic imaging (OAI), a combination of optical and ultrasound imaging, specifically raster-scanning optoacoustic mesoscopy (RSOM), offers a noninvasive high-resolution 3D visualization of capillaries allowing for a better view of microvascular changes and an extraction of volumetric measures. In this study, nailfold capillaries of patients with SSc and healthy controls are imaged and compared with each other for the first time using OAI. The nailfolds of 23 patients with SSc and 19 controls were imaged using RSOM. The acquired images were qualitatively compared to images from state-of-the-art imaging tools for SSc, dermoscopy and high magnification capillaroscopy. The vascular volume in the nailfold capillaries were computed from the RSOM images. The vascular volumes differ significantly between both cohorts (0.216 +/- 0.085 mm(3) and 0.337 +/- 0.110 mm(3); p < 0.0005). In addition, an artificial neural network was trained to automatically differentiate nailfold images from both cohorts to further assess whether OAI is sensitive enough to visualize anatomical differences in the capillaries between the two cohorts. Using transfer learning, the model classifies images with an area under the ROC curve of 0.897, and a sensitivity of 0.783 and specificity of 0.895. In conclusion, this study demonstrates the capabilities of RSOM as an imaging tool for SSc and establishes it as a modality that facilitates more in-depth studies into the disease mechanisms and progression. AU - Nitkunanantharajah, S. AU - Haedicke, K.* AU - Moore, T.B.* AU - Manning, J.B.* AU - Dinsdale, G.* AU - Berks, M.* AU - Taylor, C.* AU - Dickinson, M.R.* AU - Jüstel, D. AU - Ntziachristos, V. AU - Herrick, A.L.* AU - Murray, A.K.* C1 - 60271 C2 - 49305 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Three-dimensional optoacoustic imaging of nailfold capillaries in systemic sclerosis and its potential for disease differentiation using deep learning. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The differential associations of adipose depots with metabolic risk during obesity have been proposed to be controlled by environmental and genetic factors. We evaluated the regional differences in transcriptome signatures between abdominal (aSAT) and gluteal subcutaneous adipose tissue (gSAT) in obese black South African women and tested the hypothesis that 12-week exercise training alters gene expression patterns in a depot-specific manner. Twelve young women performed 12-weeks of supervised aerobic and resistance training. Pre- and post-intervention measurements included peak oxygen consumption (VO2peak), whole-body composition and unbiased gene expression analysis of SAT depots. VO2peak increased, body weight decreased, and body fat distribution improved with exercise training (p<0.05). The expression of 15 genes, mainly associated with embryonic development, differed between SAT depots at baseline, whereas 318 genes were differentially expressed post-training (p<0.05). Four developmental genes were differentially expressed between these depots at both time points (HOXA5, DMRT2, DMRT3 and CSN1S1). Exercise training induced changes in the expression of genes associated with immune and inflammatory responses, and lipid metabolism in gSAT, and muscle-associated processes in aSAT. This study showed differences in developmental processes regulating SAT distribution and expandability of distinct depots, and depot-specific adaptation to exercise training in black South African women with obesity. AU - Nono Nankam, P.A.* AU - Blüher, M. AU - Kehr, S.* AU - Klöting, N. AU - Krohn, K.* AU - Adams, K.* AU - Stadler, P.F.* AU - Mendham, A.E.* AU - Goedecke, J.H.* C1 - 59498 C2 - 48883 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Distinct abdominal and gluteal adipose tissue transcriptome signatures are altered by exercise training in African women with obesity. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Obesity is one of the major risk factor for cardiovascular and metabolic diseases. A disproportional accumulation of fat at visceral (VAT) compared to subcutaneous sites (SAT) has been suspected as a key detrimental event. We used non-targeted metabolomics profiling to reveal metabolic pathways associated with higher VAT or SAT amount among subjects free of metabolic diseases to identify possible contributing metabolic pathways. The study population comprised 491 subjects [mean (standard deviation): age 44.6yrs (13.0), body mass index 25.4kg/m(2) (3.6), 60.1% females] without diabetes, hypertension, dyslipidemia, the metabolic syndrome or impaired renal function. We associated MRI-derived fat amounts with mass spectrometry-derived metabolites in plasma and urine using linear regression models adjusting for major confounders. We tested for sex-specific effects using interactions terms and performed sensitivity analyses for the influence of insulin resistance on the results. VAT and SAT were significantly associated with 155 (101 urine) and 49 (29 urine) metabolites, respectively, of which 45 (27 urine) were common to both. Major metabolic pathways were branched-chain amino acid metabolism (partially independent of insulin resistance), surrogate markers of oxidative stress and gut microbial diversity, and cortisol metabolism. We observed a novel positive association between VAT and plasma levels of the potential pharmacological agent piperine. Sex-specific effects were only a few, e.g. the female-specific association between VAT and O-methylascorbate. In brief, higher VAT was associated with an unfavorable metabolite profile in a sample of healthy, mostly non-obese individuals from the general population and only few sex-specific associations became apparent. AU - Otto, L.* AU - Budde, K.* AU - Kastenmüller, G. AU - Kaul, A.* AU - Völker, U.* AU - Völzke, H.* AU - Adamski, J. AU - Kühn, J.P.* AU - Krumsiek, J. AU - Artati, A. AU - Nauck, M.* AU - Friedrich, N.* AU - Pietzner, M.* C1 - 58789 C2 - 48325 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Associations between adipose tissue volume and small molecules in plasma and urine among asymptomatic subjects from the general population. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Hyperglycemia and insulin resistance contribute to vascular damage and are regulated by different pathophysiological processes. The aim of the study was to systematically investigate the relative contributions of multiple fasting state- and oral glucose tolerance test (oGTT)-derived glycemic traits to carotid intima-media thickness (cIMT), a surrogate parameter of subclinical atherosclerosis, in individuals with increased risk for type 2 diabetes mellitus (T2D). 667 volunteers (417 women and 250 men, mean age 44.1 years), who were free of cardiovascular disease (CVD), were included in this cross-sectional study. Glucose tolerance, insulin sensitivity, insulin secretion and insulin clearance were assessed by frequently sampled 75 g oGTT. CIMT was measured by high-resolution ultrasound. Insulin clearance was associated with cIMT in univariate analysis (ßst = − 0.17, p < 0.0001) and in a stepwise regression analysis on 15 variables possibly affecting cIMT, age (r2 = 0.3923, p < 0.0001), insulin clearance (r2 = 0.4564, p < 0.0001), systolic blood pressure (r2 = 0.4733, p < 0.0001), body mass index (BMI) (r2 = 0.4804, p = 0.002), gender (r2 = 0.4831, p = 0.013), and fasting insulin clearance (r2 = 0.4857, p = 0.030) turned out to be significant determinants of cIMT. In a cross-validated model resulting from this analysis, insulin clearance was found to be an independent determinant of cIMT (ßst = − 0.16, p < 0.0001) even after adjusting for traditional CVD risk factors. Reduced insulin clearance may be an early marker of damage on the vasculature, independent of classical CVD risk factors. Reduced insulin clearance should be considered with regard to vascular insulin resistance. AU - Randrianarisoa, E. AU - Lehn-Stefan, A. AU - Hieronimus, A. AU - Wagner, R. AU - Maucher, J.* AU - Rittig, K.* AU - Balletshofer, B.* AU - Birkenfeld, A.L. AU - Peter, A. AU - Stefan, N. AU - Häring, H.-U. AU - Fritsche, A. AU - Heni, M. C1 - 60895 C2 - 49734 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Reduced insulin clearance is linked to subclinical atherosclerosis in individuals at risk for type 2 diabetes mellitus. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - X-linked Adrenoleukodystrophy (X-ALD) is caused by mutations in the ABCD1 gene resulting in the accumulation of very long chain fatty acids (VLCFA). X-ALD is the most common peroxisomal disorder with adult patients (male and female) presenting with progressive spastic paraparesis with bladder disturbance, sensory ataxia with impaired vibration sense, and leg pain. 80% of male X-ALD patients have an adrenal failure, while adrenal dysfunction is rare in women with X-ALD. The objective of this study was to define optimal serum VLCFA cutoff values in patients with X-ALD-like phenotypes for the differentiation of genetically confirmed X-ALD and Non-X-ALD individuals. Three groups were included into this study: a) X-ALD cases with confirmed ABCD1 mutations (n=34) and two Non-X-ALD cohorts: b) Patients with abnormal serum VCLFA levels despite negative testing for ABCD1 mutations (n=15) resulting from a total of 1,953 VLCFA tests c) Phenotypically matching patients as Non-X-ALD controls (n=104). Receiver operating curve analysis was used to optimize VLCFA cutoff values, which differentiate patients with genetically confirmed X-ALD and Non-X-ALD individuals. The serum concentration of C26:0 was superior to C24:0 for the detection of X-ALD. The best differentiation of Non-X-ALD and X-ALD individuals was obtained with a cutoff value of<1.0 for the C24:0/C22:0 ratio resulting in a sensitivity of 97%, a specificity of 94.1% and a positive predictive value (PPV) of 83.8% for true X-ALD. Our findings further suggested a cutoff of<0.02 for the ratio C26:0/C22:0 leading to a sensitivity of 90.9%, a specificity of 95.0%, and a PPV of 80.6%. Pearson correlation indicated a significant positive association between total blood cholesterol and VLCFA values. Usage of serum VLCFA are economical and established biomarkers suitable for the guidance of genetic testing matching the X-ALD phenotype. We suggest using our new optimized cutoff values, especially the two ratios (C24:0/C22:0 and C26:0/C22:0), in combination with standard lipid profiles. AU - Rattay, T.W.* AU - Rautenberg, M.* AU - Söhn, A.S.* AU - Hengel, H.* AU - Traschütz, A.* AU - Röben, B.* AU - Hayer, S.N.* AU - Schüle, R.* AU - Wiethoff, S.* AU - Zeltner, L.* AU - Haack, T.B.* AU - Cegan, A.* AU - Schöls, L.* AU - Schleicher, E. AU - Peter, A. C1 - 60083 C2 - 49139 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Defining diagnostic cutoffs in neurological patients for serum very long chain fatty acids (VLCFA) in genetically confirmed X-Adrenoleukodystrophy. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Elevated serum uric acid (SUA) is associated with a variety of medical conditions, such as hypertension, diabetes and obesity. Analyses investigating uric acid and obesity were primarily conducted using anthropometric measures like BMI and waist circumference. However, different adipose tissue depots might be differentially affected in uric acid metabolism. We analyzed the relation of SUA with visceral, subcutaneous and hepatic fat as quantified by Magnetic Resonance Imaging in N = 371 individuals from a cross-sectional sample of a population-based cohort. Associations of SUA and fat depots were calculated by regressions adjusted for potential confounders. We found that SUA was correlated with all fat measures (e.g. Pearson's r between SUA and hepatic fat: 0.50, 95%-CI: 0.42, 0.57). Associations with visceral and hepatic fat, but not with subcutaneous fat, remained evident after adjustment for anthropometric measures (e.g. visceral fat: beta = 0.51 l, 95%-CI: 0.30 l, 0.72 l). In conclusion, these results show how different adipose tissue compartments are affected by SUA to varying degrees, thus emphasizing the different physiological roles of these adipose tissues in uric acid metabolism. AU - Rospleszcz, S. AU - Dermyshi, D.* AU - Müller-Peltzer, K.* AU - Strauch, K. AU - Bamberg, F.* AU - Peters, A. C1 - 57865 C2 - 48100 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Association of serum uric acid with visceral, subcutaneous and hepatic fat quantified by magnetic resonance imaging. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - As a complex microbial ecosystem, wine is a particularly interesting model for studying interactions between microorganisms as fermentation can be done by microbial consortia, a unique strain or mixed culture. The effect of a specific yeast strain on its environments is unique and characterized by its metabolites and their concentration. With its great resolution and excellent mass accuracy, ultrahigh resolution mass spectrometry (uHRMS) is the perfect tool to analyze the yeast metabolome at the end of alcoholic fermentation. This work reports the change in wine chemical composition from pure and mixed culture fermentation with Lachancea thermotolerans, Starmerella bacillaris, Metschnikowia pulcherrima and S. cerevisiae. We could clearly differentiate wines according to the yeast strain used in single cultures and markers, which reflect important differences between the yeast species, were extracted and annotated. Moreover, uHRMS revealed underlining intra species metabolomics differences, showing differences at the strain level between the two Starmerella bacillaris. Non volatile metabolomics analysis of single and sequential fermentations confirmed that mixed fermentations lead to a different composition. Distinct metabolites appeared in wines from sequential fermentation compared to single fermentation. This suggests that interactions between yeasts are not neutral. AU - Roullier-Gall, C.* AU - David, V.* AU - Hemmler, D. AU - Schmitt-Kopplin, P. AU - Alexandre, H.* C1 - 58834 C2 - 48338 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Exploring yeast interactions through metabolic profiling. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - In light of the limited treatment options of diabetic polyneuropathy (DPN) available, suitable animal models are essential to investigate pathophysiological mechanisms and to identify potential therapeutic targets. In vivo evaluation with current techniques, however, often provides only restricted information about disease evolution. In the study of patients with DPN, magnetic resonance neurography (MRN) has been introduced as an innovative diagnostic tool detecting characteristic lesions within peripheral nerves. We developed a novel multicontrast ultra high field MRN strategy to examine major peripheral nerve segments in diabetic mice non-invasively. It was first validated in a cross-platform approach on human nerve tissue and then applied to the popular streptozotocin(STZ)-induced mouse model of DPN. In the absence of gross morphologic alterations, a distinct MR-signature within the sciatic nerve was observed mirroring subtle changes of the nerves' fibre composition and ultrastructure, potentially indicating early re-arrangements of DPN. Interestingly, these signal alterations differed from previously reported typical nerve lesions of patients with DPN. The capacity of our approach to non-invasively assess sciatic nerve tissue structure and function within a given mouse model provides a powerful tool for direct translational comparison to human disease hallmarks not only in diabetes but also in other peripheral neuropathic conditions. AU - Schwarz, D.* AU - Hidmark, A.S.* AU - Sturm, V.* AU - Fischer, M.* AU - Milford, D.* AU - Hausser, I.* AU - Sahm, F.* AU - Breckwoldt, M.O.* AU - Agarwal, N.* AU - Kuner, R.* AU - Bendszus, M.* AU - Nawroth, P.P. AU - Heiland, S.* AU - Fleming, T.* C1 - 59039 C2 - 48657 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Characterization of experimental diabetic neuropathy using multicontrast magnetic resonance neurography at ultra high field strength. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Pancreatic cancer is one of the most aggressive malignancies and is characterized by a low 5-year survival rate, a broad genetic diversity and a high resistance to conventional therapies. As a result, novel therapeutic agents to improve the current situation are needed urgently. Curcumin, a polyphenolic colorant derived from Curcuma longa root, showed pleiotropic influences on cellular pathways in vitro and amongst others anti-cancer properties including sensitization of tumor cells to chemo- and radiation-therapy. In this study, we evaluated the impact of Curcumin on the radiosensitivity of the established human pancreatic cancer cell lines Panc-1 and MiaPaCa-2 in vitro. In contrast to MiaPaCa-2 cells, we found a significant radiosensitization by Curcumin in the more radioresistant Panc-1 cells, possibly caused by cell cycle arrest in the most radiation-sensitive G2/M-phase at the time of irradiation. Furthermore, a significant enhancement of radiation-induced apoptosis, DNA-double-strand breaks and G2/M-arrest after curcumin treatment was observed in both cell lines. These in vitro findings suggest that especially patients with more radioresistant tumors could benefit from a radiation-concomitant, phytotherapeutic therapy with Curcumin. AU - Schwarz, K.* AU - Dobiasch, S. AU - Nguyen, L. AU - Schilling, D. AU - Combs, S.E. C1 - 58505 C2 - 48511 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Modification of radiosensitivity by Curcumin in human pancreatic cancer cell lines. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - For treatment individualisation of patients with locally advanced head and neck squamous cell carcinoma (HNSCC) treated with primary radiochemotherapy, we explored the capabilities of different deep learning approaches for predicting loco-regional tumour control (LRC) from treatment-planning computed tomography images. Based on multicentre cohorts for exploration (206 patients) and independent validation (85 patients), multiple deep learning strategies including training of 3D- and 2D-convolutional neural networks (CNN) from scratch, transfer learning and extraction of deep autoencoder features were assessed and compared to a clinical model. Analyses were based on Cox proportional hazards regression and model performances were assessed by the concordance index (C-index) and the model’s ability to stratify patients based on predicted hazards of LRC. Among all models, an ensemble of 3D-CNNs achieved the best performance (C-index 0.31) with a significant association to LRC on the independent validation cohort. It performed better than the clinical model including the tumour volume (C-index 0.39). Significant differences in LRC were observed between patient groups at low or high risk of tumour recurrence as predicted by the model (p= 0.001). This 3D-CNN ensemble will be further evaluated in a currently ongoing prospective validation study once follow-up is complete. AU - Starke, S.* AU - Leger, S.* AU - Zwanenburg, A.* AU - Leger, K.* AU - Lohaus, F.* AU - Linge, A.* AU - Schreiber, A.* AU - Kalinauskaite, G.* AU - Tinhofer, I.* AU - Guberina, N.* AU - Guberina, M.* AU - Balermpas, P.* AU - Von der Grün, J.* AU - Ganswindt, U. AU - Belka, C. AU - Peeken, J.C. AU - Combs, S.E. AU - Boeke, S.* AU - Zips, D.* AU - Richter, C.* AU - Löck, S.* C1 - 60161 C2 - 49281 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - 2D and 3D convolutional neural networks for outcome modelling of locally advanced head and neck squamous cell carcinoma. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The extracellular matrix is known to modulate cell adhesion and migration during tissue regeneration. However, the molecular mechanisms that fine-tune cells to extra-cellular matrix dynamics during regeneration of the peripheral nervous system remain poorly understood. Using the RSC96 Schwann cell line, we show that Sox2 directly controls fibronectin fibrillogenesis in Schwann cells in culture, to provide a highly oriented fibronectin matrix, which supports their organization and directional migration. We demonstrate that Sox2 regulates Schwann cell behaviour through the upregulation of multiple extracellular matrix and migration genes as well as the formation of focal adhesions during cell movement. We find that mouse primary sensory neurons and human induced pluripotent stem cell-derived motoneurons require the Sox2-dependent fibronectin matrix in order to migrate along the oriented Schwann cells. Direct loss of fibronectin in Schwann cells impairs their directional migration affecting the alignment of the axons in vitro. Furthermore, we show that Sox2 and fibronectin are co-expressed in proregenerative Schwann cells in vivo in a time-dependent manner during sciatic nerve regeneration. Taken together, our results provide new insights into the mechanisms by which Schwann cells regulate their own extracellular microenvironment in a Sox2-dependent manner to ensure the proper migration of neurons. AU - Torres-Mejia, E. AU - Trümbach, D. AU - Kleeberger, C.* AU - Dornseifer, U.* AU - Orschmann, T. AU - Bäcker, T. AU - Brenke, J.K. AU - Hadian, K. AU - Wurst, W. AU - López-Schier, H. AU - Desbordes, S.C. C1 - 58106 C2 - 48076 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Sox2 controls Schwann cell self-organization through fibronectin fibrillogenesis. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - In this study we aim to evaluate the assessment of bronchial pathologies in a murine model of lung transplantation with grating-based X-ray interferometry in vivo. Imaging was performed using a dedicated grating-based small-animal X-ray dark-field and phase-contrast scanner. While the contrast modality of the dark-field signal already showed several promising applications for diagnosing various types of pulmonary diseases, the phase-shifting contrast mechanism of the phase contrast has not yet been evaluated in vivo. For this purpose, qualitative analysis of phase-contrast images was performed and revealed pathologies due to previous lung transplantation, such as unilateral bronchial stenosis or bronchial truncation. Dependent lung parenchyma showed a strong loss in dark-field and absorption signal intensity, possibly caused by several post transplantational pathologies such as atelectasis, pleural effusion, or pulmonary infiltrates. With this study, we are able to show that bronchial pathologies can be visualized in vivo using conventional X-ray imaging when phase-contrast information is analysed. Absorption and dark-field images can be used to quantify the severity of lack of ventilation in the affected lung. AU - Umkehrer, S.* AU - Morrone, C.* AU - Dinkel, J. AU - Aigner, L.* AU - Reiser, M.F. AU - Herzen, J.* AU - Yildirim, A.Ö. AU - Pfeiffer, F.* AU - Hellbach, K.* C1 - 60430 C2 - 49454 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A proof-of principal study using phase-contrast imaging for the detection of large airway pathologies after lung transplantation. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Experimental evidence suggests a crucial role of the autonomic nervous system in whole body metabolism with major regulatory effects of the parasympathetic branch in postprandial adaptation. However, the relative contribution of this mechanism is still not fully clear in humans. We therefore compared the effects of transcutaneous auricular vagus nerve stimulation (taVNS, Cerbomed Nemos) with sham stimulation during an oral glucose tolerance test in a randomized, single-blind, cross-over design in 15 healthy lean men. Stimulation was performed for 150 min, 30 min before and during the entire oral glucose tolerance test with stimulation cycles of 30 s of on-phase and 30 s of off-phase and a 25 Hz impulse. Heart rate variability and plasma catecholamine levels were assessed as proxies of autonomic tone in the periphery. Neither analyzed heart rate variability parameters nor plasma catecholamine levels were significantly different between the two conditions. Plasma glucose, insulin sensitivity and insulin secretion were also comparable between conditions. Thus, the applied taVNS device or protocol was unable to achieve significant effects on autonomic innervation in peripheral organs. Accordingly, glucose metabolism remained unaltered. Therefore, alternative approaches are necessary to investigate the importance of the autonomic nervous system in postprandial human metabolism. AU - Vosseler, A. AU - Zhao, D. AU - Fritsche, L. AU - Lehmann, R.* AU - Kantartzis, K. AU - Small, D.M.* AU - Peter, A. AU - Häring, H.-U. AU - Birkenfeld, A.L. AU - Fritsche, A. AU - Wagner, R. AU - Preissl, H. AU - Kullmann, S. AU - Heni, M. C1 - 60610 C2 - 49499 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - No modulation of postprandial metabolism by transcutaneous auricular vagus nerve stimulation: A cross-over study in 15 healthy men. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The incidence of Alzheimer's disease (AD) increases with age and is becoming a significant cause of worldwide morbidity and mortality. However, the metabolic perturbation behind the onset of AD remains unclear. In this study, we performed metabolite profiling in both brain (n = 109) and matching serum samples (n = 566) to identify differentially expressed metabolites and metabolic pathways associated with neuropathology and cognitive performance and to identify individuals at high risk of developing cognitive impairment. The abundances of 6 metabolites, glycolithocholate (GLCA), petroselinic acid, linoleic acid, myristic acid, palmitic acid, palmitoleic acid and the deoxycholate/cholate (DCA/CA) ratio, along with the dysregulation scores of 3 metabolic pathways, primary bile acid biosynthesis, fatty acid biosynthesis, and biosynthesis of unsaturated fatty acids showed significant differences across both brain and serum diagnostic groups (P-value < 0.05). Significant associations were observed between the levels of differential metabolites/pathways and cognitive performance, neurofibrillary tangles, and neuritic plaque burden. Metabolites abundances and personalized metabolic pathways scores were used to derive machine learning models, respectively, that could be used to differentiate cognitively impaired persons from those without cognitive impairment (median area under the receiver operating characteristic curve (AUC) = 0.772 for the metabolite level model; median AUC = 0.731 for the pathway level model). Utilizing these two models on the entire baseline control group, we identified those who experienced cognitive decline in the later years (AUC = 0.804, sensitivity = 0.722, specificity = 0.749 for the metabolite level model; AUC = 0.778, sensitivity = 0.633, specificity = 0.825 for the pathway level model) and demonstrated their pre-AD onset prediction potentials. Our study provides a proof-of-concept that it is possible to discriminate antecedent cognitive impairment in older adults before the onset of overt clinical symptoms using metabolomics. Our findings, if validated in future studies, could enable the earlier detection and intervention of cognitive impairment that may halt its progression. AU - Wang, J.* AU - Wei, R.* AU - Xie, G.* AU - Arnold, M. AU - Kueider-Paisley, A.* AU - Louie, G.* AU - Mahmoudian Dehkordi, S.* AU - Blach, C.* AU - Baillie, R.* AU - Han, X.* AU - de Jager, P.L.* AU - Bennett, D.A.* AU - Kaddurah-Daouk, R.* AU - Jia, W.* C1 - 59933 C2 - 49128 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Peripheral serum metabolomic profiles inform central cognitive impairment. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Reduced lung function is associated with overall and cardiovascular mortality. Chronic low grade systemic inflammation is linked to impaired lung function and cardiovascular outcomes. We assessed the association of lung function with overall 8-year mortality in 867 individuals of the Activity and Function in the Elderly study using confounder-adjusted Cox proportional hazards models (including gait speed and daily walking time as measures of physical function) without and with adjustment for inflammatory and cardiac markers. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) but not FVC was related to mortality after adjustment for physical function and other confounders. Additional adjustment for inflammatory and cardiac markers did not change the hazard ratios (HR) markedly, e.g. for a FEV1/FVC below 0.7 from 1.55 [95% confidence-interval (CI) 1.14-2.11] to 1.49 (95% CI 1.09-2.03). These independent associations were also observed in the apparently lung healthy subpopulation with even higher HRs up to 2.76 (95% CI 1.52-4.93). A measure of airflow limitation but not vital capacity was associated with overall mortality in this community-dwelling older population and in the subgroup classified as lung healthy. These associations were independent of adjustment for inflammatory and cardiac markers and support the role of airflow limitation as independent predictor of mortality in older adults. AU - Weinmayr, G.* AU - Schulz, H. AU - Klenk, J.* AU - Denkinger, M.* AU - Duran-Tauleria, E.* AU - Koenig, W.* AU - Dallmeier, D.* AU - Rothenbacher, D.* C1 - 59699 C2 - 48946 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Association of lung function with overall mortality is independent of inflammatory, cardiac, and functional biomarkers in older adults: The ActiFE-study. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Oligonucleotide-conjugated antibodies have gained importance for their use in protein diagnostics. The possibility to transfer the readout signal from the protein to the DNA level with an oligonucleotide-conjugated antibody increased the sensitivity of protein assays by orders of magnitude and enabled new multiplexing strategies. A bottleneck in the generation of larger oligonucleotide-conjugated antibody panels is the low conjugation yield between antibodies and oligonucleotides, as well as the lack of product purification methods. In this study, we combined a non-site-directed antibody conjugation technique using copper-free click chemistry with ion-exchange chromatography to obtain purified single and double oligonucleotide-conjugated antibodies. We optimized the click conjugation reaction of antibodies with oligonucleotides by evaluating crosslinker, reaction temperature, duration, oligonucleotide length, and secondary structure. As a result, we were able to achieve conjugation yields of 30% at a starting quantity as low as tens of nanograms of antibody, which makes the approach applicable for a wide variety of protein analytical assays. In contrast to previous non-site-directed conjugation methods, we also optimized the conjugation reaction for antibody specificity, confirmed by testing with knockout cell lines. The advantages of using single or double oligonucleotide-conjugated antibodies in regards to signal noise reduction are shown within immunofluorescence, proximity ligation assays, and single cell CITE-seq experiments. AU - Wiener, J. AU - Kokotek, D. AU - Rosowski, S. AU - Lickert, H. AU - Meier, M. C1 - 57971 C2 - 48202 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Preparation of single- and double-oligonucleotide antibody conjugates and their application for protein analytics. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The posttranslational modification ADP-ribosylation is involved in many cellular processes, with distinct roles for poly- and mono(ADP-ribosyl)ation (PAR- and MARylation, respectively). Reversibility of intracellular MARylation was demonstrated with the discovery of MACROD1, MACROD2 and TARG1, three macrodomain-containing enzymes capable of reversing MARylation of proteins and RNA. While the three enzymes have identical activities in vitro, their roles in cells are unclear and published data are partially contradictory, possibly due to a lack of validated reagents. We developed monoclonal antibodies to study these proteins and analysed their tissue distribution and intracellular localisation. MACROD1 is most prevalent in mitochondria of skeletal muscle, MACROD2 localises to nucleo- and cytoplasm and is found so far only in neuroblastoma cells, whereas the more ubiquitously expressed TARG1 is present in nucleoplasm, nucleolus and stress granules. Loss of MACROD1 or loss of TARG1 leads to disruption of mitochondrial or nucleolar morphology, respectively, hinting at their importance for these organelles. To start elucidating the underlying mechanisms, we have mapped their interactomes using BioID. The cellular localisation of interactors supports the mitochondrial, nucleolar and stress granule localisation of MACROD1 and TARG1, respectively. Gene ontology analysis suggests an involvement of MACROD1 and TARG1 in RNA metabolism in their respective compartments. The detailed description of the hydrolases' expression, localisation and interactome presented here provides a solid basis for future work addressing their physiological function in more detail. AU - Žaja, R.* AU - Aydin, G.* AU - Lippok, B.E.* AU - Feederle, R. AU - Lüscher, B.* AU - Feijs, K.L.H.* C1 - 59202 C2 - 48726 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Publishing Group PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - Gunderson's and Holling's adaptive cycle metaphor provides a qualitative description of the development of a dynamically evolving complex system. According to the metaphor, a complex system alternately passes through phases of stability and predictability and phases of reorganization and stochasticity. So far, there have been no attempts to quantify the underlying notions in a way which is independent of the concrete realization of the system. We propose a method which can be applied in a generic way to estimate a system's position within the adaptive cycle as well as to identify drivers of change. We demonstrate applicability and flexibility of our method by three different case studies: Analyzing data obtained from a simulation of a model of interaction of abstract genotypes, we show that our approach is able to capture the nature of these interactions. We then study European economies as systems of economic state variables to illustrate the ability of system comparison. Finally, we identify drivers of change in a plant ecosystem in the prairie-forest. We hereby confirm the conceptual dynamics of the adaptive cycle and thus underline its usability in understanding system dynamics. AU - zu Castell, W. AU - Schrenk, H. C1 - 60418 C2 - 49439 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Computing the adaptive cycle. JO - Sci. Rep. VL - 10 IS - 1 PB - Nature Research PY - 2020 SN - 2045-2322 ER - TY - JOUR AB - The present study evaluated the ability of the visceral adiposity index (VAI), the lipid accumulation product (LAP), and product of triglycerides and glucose (TyG), three novel, insulin resistance-related markers, to discriminate prediabetes/diabetes in the general German population. Altogether 2,045 Germans (31-72 years, 53.3% women) without known diabetes and a history of Myocardial Infarction (MI)/stroke from the Cooperative Health Research in the Region of Augsburg (KORA) F4 Study were eligible. The discriminatory accuracy of the markers for oral glucose tolerance test (OGTT)-defined prediabetes/diabetes according to the American Diabetes Association (ADA) criteria was assessed by the area under the receiver operating characteristic (ROC) curve (AUC). The Youden Index (YI) was used to determine optimal cut-off values, and a non-parametric ROC regression was used to examine whether the discriminatory accuracy varied by sex and age. 365 men (38.2%) and 257 women (23.6%) were newly diagnosed with prediabetes/diabetes. AUCs for TyG, LAP and VAI were 0.762 (95%CI 0.740-0.784), 0.743 (95% CI 0.720-0.765), and 0.687 (95%CI 0.662-0.712), respectively. The optimal cut-off values for the LAP and TyG were 56.70 and 8.75 in men, and 30.40 and 8.53 in women. In conclusion, TyG and LAP provide good discrimination of persons with prediabetes/diabetes. AU - Ahn, N.* AU - Baumeister, S.E.* AU - Amann, U.* AU - Rathmann, W.* AU - Peters, A. AU - Huth, C. AU - Thorand, B. AU - Meisinger, C. C1 - 56552 C2 - 47114 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Visceral adiposity index (VAI), lipid accumulation product (LAP), and product of triglycerides and glucose (TyG) to discriminate prediabetes and diabetes. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, consequently, their diagnosis, treatment, and prevention. To this end, omics data are integrated with other data types, e.g., clinical, phenotypic, and demographic parameters of categorical or continuous nature. We exemplify this data integration issue for a chronic kidney disease (CKD) study, comprising complex clinical, demographic, and one-dimensional H-1 nuclear magnetic resonance metabolic variables. Routine analysis screens for associations of single metabolic features with clinical parameters while accounting for confounders typically chosen by expert knowledge. This knowledge can be incomplete or unavailable. We introduce a framework for data integration that intrinsically adjusts for confounding variables. We give its mathematical and algorithmic foundation, provide a state-of-the-art implementation, and evaluate its performance by sanity checks and predictive performance assessment on independent test data. Particularly, we show that discovered associations remain significant after variable adjustment based on expert knowledge. In contrast, we illustrate that associations discovered in routine univariate screening approaches can be biased by incorrect or incomplete expert knowledge. Our data integration approach reveals important associations between CKD comorbidities and metabolites, including novel associations of the plasma metabolite trimethylamine-N-oxide with cardiac arrhythmia and infarction in CKD stage 3 patients. AU - Altenbuchinger, M.* AU - Zacharias, H.U. AU - Solbrig, S.* AU - Schäfer, A.* AU - Büyüközkan, M. AU - Schultheiß, U.T.* AU - Kotsis, F.* AU - Köttgen, A.* AU - Spang, R.* AU - Oefner, P.J.* AU - Krumsiek, J. AU - Gronwald, W.* C1 - 56988 C2 - 47390 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - A multi-source data integration approach reveals novel associations between metabolites and renal outcomes in the German Chronic Kidney Disease study. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Fluorescence imaging opens new possibilities for intraoperative guidance and early cancer detection, in particular when using agents that target specific disease features. Nevertheless, photon scattering in tissue degrades image quality and leads to ambiguity in fluorescence image interpretation and challenges clinical translation. We introduce the concept of capturing the spatially-dependent impulse response of an image and investigate Spatially Adaptive Impulse Response Correction (SAIRC), a method that is proposed for improving the accuracy and sensitivity achieved. Unlike classical methods that presume a homogeneous spatial distribution of optical properties in tissue, SAIRC explicitly measures the optical heterogeneity in tissues. This information allows, for the first time, the application of spatially-dependent deconvolution to correct the fluorescence images captured in relation to their modification by photon scatter. Using experimental measurements from phantoms and animals, we investigate the improvement in resolution and quantification over non-corrected images. We discuss how the proposed method is essential for maximizing the performance of fluorescence molecular imaging in the clinic. AU - Anastasopoulou, M. AU - Gorpas, D. AU - Koch, M. AU - Liapis, E. AU - Glasl, S. AU - Klemm, U. AU - Karlas, A. AU - Lasser, T.* AU - Ntziachristos, V. C1 - 57499 C2 - 47820 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Fluorescence imaging reversion using spatially variant deconvolution. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Non-alcoholic fatty-liver disease (NAFLD) is frequent in obese patients and represents a major risk factor for the development of diabetes and its complications. Bariatric surgery reverses the hepatic features of NAFLD. However, its mechanism of action remains elusive. We performed a comprehensive analysis of the mechanism leading to the improvement of NAFLD and insulin resistance in both obese rodents and humans following sleeve-gastrectomy (SG). SG improved insulin sensitivity and reduced hepatic and monocyte fat accumulation. Importantly, fat accumulation in monocytes was well comparable to that in hepatocytes, suggesting that Plin2 levels in monocytes might be a non-invasive marker for the diagnosis of NAFLD. Both in vitro and in vivo studies demonstrated an effective metabolic regeneration of liver function and insulin sensitivity. Specifically, SG improved NAFLD significantly by enhancing AMP-activated protein kinase (AMPK) phosphorylation and chaperone-mediated autophagy (CMA) that translate into the removal of Plin2 coating lipid droplets. This led to an increase in lipolysis and specific amelioration of hepatic insulin resistance. Elucidating the mechanism of impaired liver metabolism in obese subjects will help to design new strategies for the prevention and treatment of NAFLD. AU - Angelini, G.* AU - Gissey, L.C.* AU - Del Corpo, G.* AU - Giordano, C.* AU - Cerbelli, B.* AU - Severino, A.* AU - Manco, M.* AU - Basso, N.* AU - Birkenfeld, A.L. AU - Bornstein, S.R. AU - Genco, A.* AU - Mingrone, G.* AU - Casella, G.* C1 - 57397 C2 - 47762 TI - New insight into the mechanisms of ectopic fat deposition improvement after bariatric surgery. JO - Sci. Rep. VL - 9 IS - 1 PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - We recently introduced RAP (reduced adjoining protonation) labelling as an easy to implement and cost-effective strategy to yield selectively methyl protonated protein samples. We show here that even though the amount of H2O employed in the bacterial growth medium is rather low, the intensities obtained in MAS solid-state NMR H-1,C-13 correlation spectra are comparable to spectra obtained for samples in which alpha-ketoisovalerate was employed as precursor. In addition to correlations for Leu and Val residues, RAP labelled samples yield also resonances for all methyl containing side chains. The labelling scheme has been employed to quantify order parameters, together with the respective asymmetry parameters. We obtain a very good correlation between the order parameters measured using a GlcRAP (glucose carbon source) and a alpha-ketoisovalerate labelled sample. The labelling scheme holds the potential to be very useful for the collection of long-range distance restraints among side chain atoms. Experiments are demonstrated using RAP and alpha-ketoisovalerate labelled samples of the alpha-spectrin SH3 domain, and are applied to fibrils formed from the Alzheimer's disease A beta(1-40) peptide. AU - Asami, S.* AU - Reif, B. C1 - 57271 C2 - 47711 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Accessing methyl groups in proteins via 1H-detected MAS solid-state NMR spectroscopy employing random protonation. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The consideration of how a given technique affects results of experimental measurements is a must to achieve correct data interpretation. This might be challenging when it comes to measurements on biological systems, where it is unrealistic to have full control (e.g. through a software replica) of all steps in the measurement chain. In this work we address how the effectiveness of different radiation qualities in inducing biological damage can be assessed measuring DNA damage foci yields, only provided that artefacts related to the scoring technique are adequately considered. To this aim, we developed a unified stochastic modelling approach that, starting from radiation tracks, predicts both the induction, spatial distribution and complexity of DNA damage, and the experimental readout of foci when immunocytochemistry coupled to 2D fluorescence microscopy is used. The approach is used to interpret gamma-H2AX data for photon and neutron exposures. When foci are reconstructed in the whole cell nucleus, we obtain information on damage characteristics "behind" experimental observations, as the average damage content of a focus. We reproduce how the detection technique affects experimental findings, e.g. contributing to the saturation of foci yields scored at 30 minutes after exposure with increasing dose and to the lack of dose dependence for yields at 24 hours. AU - Barbieri, S.* AU - Babini, G.* AU - Morini, J.* AU - Friedland, W. AU - Buonanno, M.* AU - Grilj, V.* AU - Brenner, D.J.* AU - Ottolenghi, A.* AU - Baiocco, G.* C1 - 57022 C2 - 47493 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Predicting DNA damage foci and their experimental readout with 2D microscopy: A unified approach applied to photon and neutron exposures. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The patho-mechanism of somatic driver mutations in cancer usually involves transcription, but the proportion of mutations and wild-type alleles transcribed from DNA to RNA is largely unknown. We systematically compared the variant allele frequencies of recurrently mutated genes in DNA and RNA sequencing data of 246 acute myeloid leukaemia (AML) patients. We observed that 95% of all detected variants were transcribed while the rest were not detectable in RNA sequencing with a minimum read-depth cut-off (10x). Our analysis focusing on 11 genes harbouring recurring mutations demonstrated allelic imbalance (AI) in most patients. GATA2, RUNX1, TET2, SRSF2, IDH2, PTPN11, WT1, NPM1 and CEBPA showed significant AIs. While the effect size was small in general, GATA2 exhibited the largest allelic imbalance. By pooling heterogeneous data from three independent AML cohorts with paired DNA and RNA sequencing (N = 253), we could validate the preferential transcription of GATA2-mutated alleles. Differential expression analysis of the genes with significant AI showed no significant differential gene and isoform expression for the mutated genes, between mutated and wild-type patients. In conclusion, our analyses identified AI in nine out of eleven recurrently mutated genes. AI might be a common phenomenon in AML which potentially contributes to leukaemogenesis. AU - Batcha, A.M.N.* AU - Bamopoulos, S.A.* AU - Kerbs, P.* AU - Kumar, A.* AU - Jurinovic, V.* AU - Rothenberg-Thurley, M.* AU - Ksienzyk, B.* AU - Philippou-Massier, J.* AU - Krebs, S.* AU - Blum, H.* AU - Schneider, S.* AU - Konstandin, N.* AU - Bohlander, S.K.* AU - Heckman, C.* AU - Kontro, M.* AU - Hiddemann, W.* AU - Spiekermann, K.* AU - Braess, J.* AU - Metzeler, K.H.* AU - Greif, P.A.* AU - Mansmann, U.* AU - Herold, T. C1 - 56748 C2 - 47274 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Allelic imbalance of recurrently mutated genes in acute myeloid leukaemia. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Dual-specificity phosphatase 8 (Dusp8) acts as physiological inhibitor for the MAPKs Jnk, Erk and p38 which are involved in regulating multiple CNS processes. While Dusp8 expression levels are high in limbic areas such as the hippocampus, the functional role of Dusp8 in hippocampus morphology, MAPK-signaling, neurogenesis and apoptosis as well as in behavior are still unclear. It is of particular interest whether human carriers of a DUSP8 allelic variant show similar hippocampal alterations to mice. Addressing these questions using Dusp8WT and KO mouse littermates, we found that KOs suffered from mildly impaired spatial learning, increased locomotor activity and elevated anxiety. Cell proliferation, apoptosis and p38 and Jnk phosphorylation were unaffected, but phospho-Erk levels were higher in hippocampi of the KOs. Consistent with a decreased hippocampus size in Dusp8 KO mice, we found reduced volumes of the hippocampal subregions subiculum and CA4 in humans carrying the DUSP8 allelic variant SNP rs2334499:C > T. Overall, aberrations in morphology and behavior in Dusp8 KO mice and a decrease in hippocampal volume of SNP rs2334499:C > T carriers point to a novel, translationally relevant role of Dusp8 in hippocampus function that warrants further studies on the role of Dusp8 within the limbic network. AU - Baumann, P. AU - Schriever, S.C. AU - Kullmann, S. AU - Zimprich, A.* AU - Feuchtinger, A. AU - Amarie, O.V. AU - Peter, A. AU - Walch, A.K. AU - Gailus-Durner, V. AU - Fuchs, H. AU - Hrabě de Angelis, M. AU - Wurst, W. AU - Tschöp, M.H. AU - Heni, M. AU - Hölter, S.M. AU - Pfluger, P.T. C1 - 57699 C2 - 47857 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Dusp8 affects hippocampal size and behavior in mice and humans. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Previous studies have reported increased risks of myocardial infarction in association with elevated ambient particulate matter (PM) in the previous hour(s). However, whether PM can trigger mechanisms that act on this time scale is still unclear. We hypothesized that increases in PM are associated with rapid changes in measures of heart rate variability and repolarization. We used data from panel studies in Augsburg, Germany, and Rochester, New York, USA, and two controlled human exposure studies in Rochester. Data included ECG recordings from all four studies, controlled exposures to (concentrated) ultrafine particles (UFP; particles with an aerodynamic diameter < 100 nm) and ambient concentrations of UFP and fine PM (PM2.5, aerodynamic diameter < 2.5 mu m). Factor analysis identified three representative ECG parameters: standard deviation of NN-intervals (SDNN), root mean square of successive differences (RMSSD), and T-wave complexity. Associations between air pollutants and ECG parameters in the concurrent and previous six hours were estimated using additive mixed models adjusting for long-and short-term time trends, meteorology, and study visit number. We found decreases in SDNN in relation to increased exposures to UFP in the previous five hours in both of the panel studies (e. g. Augsburg study, lag 3 hours: -2.26%, 95% confidence interval [ CI]: -3.98% to -0.53%; Rochester panel study, lag 1 hour: -2.69%; 95% CI: -5.13% to -0.26%) and one of the two controlled human exposure studies (1-hour lag: -13.22%; 95% CI: -24.11% to -2.33%). Similarly, we observed consistent decreases in SDNN and RMSSD in association with elevated PM2.5 concentrations in the preceding six hours in both panel studies. We did not find consistent associations between particle metrics and T-wave complexity. This study provided consistent evidence that recent exposures to UFP and PM2.5 can induce acute pathophysiological responses. AU - Breitner-Busch, S. AU - Peters, A. AU - Zareba, W.* AU - Hampel, R. AU - Oakes, D.* AU - Wiltshire, J.* AU - Frampton, M.W.* AU - Hopke, P.K.* AU - Cyrys, J. AU - Utell, M.J.* AU - Kane, C.* AU - Schneider, A.E. AU - Rich, D.Q.* C1 - 55514 C2 - 46365 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Ambient and controlled exposures to particulate air pollution and acute changes in heart rate variability and repolarization. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - This study evaluates the association between indoor microbial diversity early in life and hyperactivity/inattention symptoms in children at ages 10 and 15 years.A random sample enriched with subjects with hyperactivity/inattention at age 15 years was selected from the German LISA birth cohort. Bedroom floor dust was collected at age 3 months and 4 bacterial and fungal diversity measures [number of observed operational taxonomic units (OTUs), Chao1, Shannon and Simpson indices] were calculated from Illumina MiSeq sequencing data. Hyperactivity/inattention was based on the Strengths and Difficulties Questionnaire at ages 10 and 15 (cut-off >= 7). Adjusted associations between 4 diversity measures in tertiles and hyperactivity/inattention were investigated with weighted and survey logistic regression models. We included 226 individuals with information on microbial diversity and hyperactivity/inattention. Early life bacterial diversity was inversely associated with hyperactivity/inattention at age 10 [bacterial OTUs (medium vs low: aOR = 0.4, 95%CI = (0.2-0.8)) and Chao1 (medium vs low: 0.3 (0.1-0.5); high vs low: 0.3 (0.2-0.6)], whereas fungal diversity was directly associated [Chao1 (high vs low: 2.1 (1.1-4.0)), Shannon (medium vs low: 2.8 (1.3-5.8)), and Simpson (medium vs low: 4.7 (2.4-9.3))]. At age 15, only Shannon index was significantly associated with hyperactivity/inattention [bacteria (medium vs low: 2.3 (1.2-4.2); fungi (high vs low: 0.5 (0.3-0.9))]. In conclusion, early life exposure to microbial diversity may play a role in the psychobehavioural development. We observe heterogeneity in the direction of the associations encouraging further longitudinal studies to deepen our understanding of the characteristics of the microbial community underlying the observed associations. AU - Casas, L.* AU - Karvonen, A.M.* AU - Kirjavainen, P.V.* AU - Täubel, M.* AU - Hyytiäinen, H.* AU - Jayaprakash, B.* AU - Lehmann, I.* AU - Standl, M. AU - Pekkanen, J.* AU - Heinrich, J. C1 - 57400 C2 - 47760 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Early life home microbiome and hyperactivity/inattention in schoolage children. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The functional roles of the Caudate nucleus (Cd) are well known. Selective Cd lesions can be found in neurological disorders. However, little is known about the dynamics of the behavioral changes during progressive Cd ablation. Current stereotactic radiosurgery technologies allow the progressive ablation of a brain region with limited adverse effects in surrounding normal tissues. This could be of high interest for the study of the modified behavioral functions in relation with the degree of impairment of the brain structures. Using hypofractionated stereotactic radiotherapy combined with synchrotron microbeam radiation, we investigated, during one year after irradiation, the effects of unilateral radio-ablation of the right Cd on the behavior of Yucatan minipigs. The right Cd was irradiated to a minimal dose of 35.5 Gy delivered in three fractions. MRI-based morphological brain integrity and behavioral functions, i.e. locomotion, motivation/hedonism were assessed. We detected a progressive radionecrosis leading to a quasi-total ablation one year after irradiation, with an additional alteration of surrounding areas. Transitory changes in the motivation/hedonism were firstly detected, then on locomotion, suggesting the influence of different compensatory mechanisms depending on the functions related to Cd and possibly some surrounding areas. We concluded that early behavioral changes related to eating functions are relevant markers for the early detection of ongoing lesions occurring in Cd-related neurological disorders. AU - Coquery, N.* AU - Adam, J.F.* AU - Nemoz, C.* AU - Janvier, R.* AU - Livingstone, J.* AU - Chauvin, A.* AU - Kefs, S.* AU - Guerineau, C.* AU - De Saint Jean, L.* AU - Ocadiz, A.* AU - Bouchet, A.* AU - Bartzsch, S. AU - Schültke, E.* AU - Siegbahn, A.* AU - Bräuer-Krisch, E.* AU - Lemasson, B.* AU - Barbier, E.L.* AU - Laissue, J.* AU - Balosso, J.* AU - Val-Laillet, D.* AU - Serduc, R.* C1 - 57371 C2 - 47767 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Locomotion and eating behavior changes in Yucatan minipigs after unilateral radio-induced ablation of the caudate nucleus. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The glucagon receptor (GCGR) is an emerging target in anti-diabetic therapy. Reliable biomarkers for in vivo activity on the GCGR, in the setting of dual glucagon-like peptide 1/glucagon (GLP-1/GCG) receptor agonism, are currently unavailable. Here, we investigated [Ga-68]Ga-DO3A-S01-GCG as a biomarker for GCGR occupancy in liver, the tissue with highest GCGR expression, in non-human primates (NHP) by PET. [Ga-68]Ga-DO3A-S01-GCG was evaluated by dynamic PET in NHPs by a dose escalation study design, where up to 67 mu g/kg DO3A-S01-GCG peptide mass was co-injected. The test-retest reproducibility of [Ga-68]Ga-DO3A-S01-GCG binding in liver was evaluated. Furthermore, we investigated the effect of pre-treatment with acylated glucagon agonist 1-GCG on [Ga-68]GaDO3A-S01-GCG binding in liver. [Ga-68]Ga-DO3A-S01-GCG bound to liver in vivo in a dose-dependent manner. Negligible peptide mass effect was observed for DO3A-S01-GCG doses <0.2 mu g/kg. In vivo K-d for [Ga-68]Ga-DO3A-S01-GCG corresponded to 0.7 mu g/kg, which indicates high potency. The test-retest reproducibility for [Ga-68]Ga-DO3A-S01-GCG binding in liver was 5.7 +/- 7.9%. Pre-treatment with 1-GCG, an acylated glucagon agonist, resulted in a GCGR occupancy of 61.5 +/- 9.1% in liver. Predicted human radiation dosimetry would allow for repeated annual [Ga-68]Ga-DO3A-S01-GCG PET examinations. In summary, PET radioligand [Ga-68]Ga-DO3A-S01-GCG is a quantitative biomarker of in vivo GCGR occupancy. AU - Eriksson, O.* AU - Velikyan, I.* AU - Haack, T.* AU - Bossart, M.* AU - Evers, A.* AU - Laitinen, I.* AU - Larsen, P.J.* AU - Plettenburg, O. AU - Takano, A.* AU - Halldin, C.* AU - Antoni, G.* AU - Johansson, L.* AU - Pierrou, S.* AU - Wagner, M.* C1 - 57147 C2 - 47573 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Assessment of glucagon receptor occupancy by Positron Emission Tomography in non-human primates. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Dysregulation of signaling networks controlling self-renewal and migration of developmental cell lineages is closely linked to the proliferative and invasive properties of tumors. Identification of such signaling pathways and their critical regulators is vital for successful design of effective targeted therapies against neoplastic tissue growth. The neurotrophin receptor (CD271/NGFR/p75NTR) is a key regulator of the melanocytic cell lineage through its ability to mediate cell growth, survival, and differentiation. Using clinical melanoma samples, normal melanocytes and global gene expression profiling we have investigated the role of CD271 in rewiring signal transduction networks of melanoma cells during neoplastic transformation. Our analysis demonstrates that depending on the cell fate of tumor initiation vs normal development, elevated levels of CD271 can serve as a switch between proliferation/survival and differentiation/cell death. Two divergent arms of neurotrophin signaling hold the balance between positive regulators of tumor growth controlled by E2F, MYC, SREBP1 and AKT3 pathways on the one hand, and differentiation, senescence, and apoptosis controlled by TRAF6/IRAK-dependent activation of AP1 and TP53 mediated processes on the other hand. A molecular network map revealed in this study uncovers CD271 as a context-specific molecular switch between normal development and malignant transformation. AU - Filipp, F.V. AU - Li, C.* AU - Boiko, A.D.* C1 - 56138 C2 - 46841 TI - CD271 is a molecular switch with divergent roles in melanoma and melanocyte development. JO - Sci. Rep. VL - 9 IS - 1 PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - This study aimed at estimating the prevalence in adults of complying with the aerobic physical activity (PA) recommendation through transportation-related walking and cycling. Furthermore, potential determinants of transportation-related PA recommendation compliance were investigated. 10,872 men and 13,144 women aged 18 years or older participated in the cross-sectional 'German Health Update 2014/15 - EHIS' in Germany. Transportation-related walking and cycling were assessed using the European Health Interview Survey-Physical Activity Questionnaire. Three outcome indicators were constructed: walking, cycling, and total active transportation (≥600 metabolic equivalent, MET-min/week). Associations were analyzed using multilevel regression analysis. Forty-two percent of men and 39% of women achieved ≥600 MET-min/week with total active transportation. The corresponding percentages for walking were 27% and 28% and for cycling 17% and 13%, respectively. Higher population density, older age, lower income, higher work-related and leisure-time PA, not being obese, and better self-perceived health were positively associated with transportation-related walking and cycling and total active transportation among both men and women. The promotion of walking and cycling among inactive people has great potential to increase PA in the general adult population and to comply with PA recommendations. Several correlates of active transportation were identified which should be considered when planning public health policies and interventions. AU - Finger, J.D.* AU - Varnaccia, G.* AU - Gabrys, L.* AU - Hoebel, J.* AU - Kroll, L.E.* AU - Krug, S.* AU - Manz, K.* AU - Baumeister, S. AU - Mensink, G.B.M.* AU - Lange, C.* AU - Leitzmann, M.F.* C1 - 57308 C2 - 47680 TI - Area-level and individual correlates of active transportation among adults in Germany: A population-based multilevel study. JO - Sci. Rep. VL - 9 IS - 1 PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Mutations within Leucine-rich repeat kinase 2 (LRRK2) are associated with late-onset Parkinson's disease. The physiological function of LRRK2 and molecular mechanism underlying the pathogenic role of LRRK2 mutations remain uncertain. Here, we investigated the role of LRRK2 in intracellular signal transduction. We find that deficiency of Lrrk2 in rodents affects insulin-dependent translocation of glucose transporter type 4 (GLUT4). This deficit is restored during aging by prolonged insulin-dependent activation of protein kinase B (PKB, Akt) and Akt substrate of 160 kDa (AS160), and is compensated by elevated basal expression of GLUT4 on the cell surface. Furthermore, we find a crucial role of Rab10 phosphorylation by LRRK2 for efficient insulin signal transduction. Translating our findings into human cell lines, we find comparable molecular alterations in fibroblasts from Parkinson's patients with the known pathogenic G2019S LRRK2 mutation. Our results highlight the role of LRRK2 in insulin-dependent signalling with potential therapeutic implications. AU - Funk, N.* AU - Munz, M.* AU - Ott, T.* AU - Brockmann, K.* AU - Wenninger-Weinzierl, A.* AU - Kühn, R.* AU - Vogt Weisenhorn, D.M. AU - Giesert, F. AU - Wurst, W. AU - Gasser, T.* AU - Biskup, S.* C1 - 55693 C2 - 46476 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - The Parkinson's disease-linked Leucine-rich repeat kinase 2 (LRRK2) is required for insulin-stimulated translocation of GLUT4. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - It is increasingly recognized that Alzheimer's disease (AD) exists before dementia is present and that shifts in amyloid beta occur long before clinical symptoms can be detected. Early detection of these molecular changes is a key aspect for the success of interventions aimed at slowing down rates of cognitive decline. Recent evidence indicates that of the two established methods for measuring amyloid, a decrease in cerebrospinal fluid (CSF) amyloid beta(1-42) (A beta(1-42)) may be an earlier indicator of Alzheimer's disease risk than measures of amyloid obtained from Positron Emission Tomography (PET). However, CSF collection is highly invasive and expensive. In contrast, blood collection is routinely performed, minimally invasive and cheap. In this work, we develop a blood-based signature that can provide a cheap and minimally invasive estimation of an individual's CSF amyloid status using a machine learning approach. We show that a Random Forest model derived from plasma analytes can accurately predict subjects as having abnormal (low) CSF A beta(1-42) levels indicative of AD risk (0.84 AUC, 0.78 sensitivity, and 0.73 specificity). Refinement of the modeling indicates that only APOE epsilon 4 carrier status and four plasma analytes (CGA, A beta(1-42), Eotaxin 3, APOE) are required to achieve a high level of accuracy. Furthermore, we show across an independent validation cohort that individuals with predicted abnormal CSF A beta(1-42) levels transitioned to an AD diagnosis over 120 months significantly faster than those with predicted normal CSF A beta(1-42) levels and that the resulting model also validates reasonably across PET A beta(1-42) status (0.78 AUC). This is the first study to show that a machine learning approach, using plasma protein levels, age and APOE epsilon 4 carrier status, is able to predict CSF A beta(1-42) status, the earliest risk indicator for AD, with high accuracy. AU - Goudey, B.* AU - Fung, B.J.* AU - Schieber, C.* AU - Faux, N.G.* AU - Alzheimer's Disease Neuroimaging Initiative (Kastenmüller, G. AU - Arnold, M.) C1 - 55690 C2 - 46479 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - A blood-based signature of cerebrospinal fluid Aβ1-42 status. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the association between several early life determinants and the gut microbiome composition in six-year-old children from the LISA birth cohort. A total number of 166 fecal samples were analyzed using 16S rRNA gene-based barcoding to assess bacterial diversity pattern. The bacterial profiles were investigated for their association with maternal smoking during pregnancy, mode of delivery, breastfeeding, antibiotic treatment between one and two years of age, gender and socioeconomic status (SES). While alpha and beta diversity of the infants' gut microbiome remained unaffected, amplicon sequence variants (ASVs) annotated to Firmicutes and Actinobacteria responded to early life determinants, mostly to feeding practice and antibiotics use. ASVs associated to Bacteriodetes remained unaffected. Our findings indicate that early life determinants could have a long-term sustainable effect on the gut microflora of six-year-old children, however, associations with early life determinates are weaker than reported for infants. AU - Gschwendtner, S. AU - Kang, H. AU - Thiering, E. AU - Kublik, S. AU - Fösel, B. AU - Schulz, H. AU - Krauss-Etschmann, S.* AU - Heinrich, J. AU - Schöler, A. AU - Schloter, M. AU - Standl, M. C1 - 56846 C2 - 47338 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Early life determinants induce sustainable changes in the gut microbiome of six-year-old children. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected. AU - Hammerl, V. AU - Kastl, E.-M. AU - Schloter, M. AU - Kublik, S. AU - Schmidt, H.* AU - Welzl, G. AU - Jentsch, A.* AU - Beierkuhnlein, C.* AU - Gschwendtner, S. C1 - 55541 C2 - 46398 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Childhood obesity prevalence is rising in countries worldwide. A variety of etiologic factors contribute to childhood obesity but little is known about underlying biochemical mechanisms. We performed an individual participant meta-analysis including 1,020 pre-pubertal children from three European studies and investigated the associations of 285 metabolites measured by LC/MS-MS with BMI z-score, height, weight, HOMA, and lipoprotein concentrations. Seventeen metabolites were significantly associated with BMI z-score. Sphingomyelin (SM) 32:2 showed the strongest association with BMI z-score (P=4.68 x 10(-23)) and was also closely related to weight, and less strongly to height and LDL, but not to HOMA. Mass spectrometric analyses identified SM 32:2 as myristic acid containing SM d18:2/14:0. Thirty-five metabolites were significantly associated to HOMA index. Alanine showed the strongest positive association with HOMA (P =9.77 x 10(-16)), while acylcarnitines and non-esterified fatty acids were negatively associated with HOMA. SM d18:2/14:0 is a powerful marker for molecular changes in childhood obesity. Tracing back the origin of SM 32:2 to dietary source in combination with genetic predisposition will path the way for early intervention programs. Metabolic profiling might facilitate risk prediction and personalized interventions in overweight children. AU - Hellmuth, C.* AU - Kirchberg, F.F.* AU - Brandt, S.* AU - Moß, A.* AU - Walter, V.* AU - Rothenbacher, D.* AU - Brenner, H.* AU - Grote, V.* AU - Gruszfeld, D.* AU - Socha, P.* AU - Closa-Monasterolo, R.* AU - Escribano, J.* AU - Luque, V.* AU - Verduci, E.* AU - Mariani, B.* AU - Langhendries, J.-P.* AU - Poncelet, P.* AU - Heinrich, J. AU - Lehmann, I.* AU - Standl, M. AU - Uhl, O.* AU - Koletzko, B.* AU - Thiering, E. AU - Wabitsch, M.* C1 - 55750 C2 - 46541 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - An individual participant data meta-analysis on metabolomics profiles for obesity and insulin resistance in European children. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Here we describe a unique microbial biotechnology for simultaneous bioremediation and biomining of twelve ionic metals overcoming the obstacles of multimetal toxicity to microbes. After a thorough search of key microorganisms in microbiomes of many sulfidic springs in Bavaria (Germany) over an area of 200 km(2), we found three new strains EH8, EH10 and EH11 of Mucor hiemalis physiologically compatible and capable of multimetal-remediation and enrichment. We combined the multimetal-resistance, hyper-accumulation and elicitation power of EH8, EH10 and EH11 to develop a novel biotechnology for simultaneous removal, fractionation and enrichment of metal ions. As a first step we showed the intracellular fixing and deposition of mercury as nanospheres in EH8's sporangiospores. Scanning Electron Microscopy-Energy-Dispersive X-Ray analysis revealed binding and precipitation of other applied metal ions as spherical nano-particles (similar to 50-100 nm) at the outer electro-negative cellwall-surface of EH8, EH10 and EH11 sporangiospores. Microbiomes, germinated spores and dead insoluble cellwalls of these strains removed >81-99% of applied Al, Cd, Co, Cr, Cu, Hg, Ni, Pb, U, and Zn simultaneously and furthermore enriched precious Ag, Au and Ti from water all within 48 h, demonstrating the potential of new biotechnologies for safe-guarding our environment from metal pollution and concentrating precious diluted, ionic metals. AU - Hoque, E. AU - Fritscher, J. C1 - 56586 C2 - 47092 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Multimetal bioremediation and biomining by a combination of new aquatic strains of Mucor hiemalis. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Human methytransferase like proteins (METTL) are part of a large protein family characterized by the presence of binding domains for S-adenosyl methionine, a co-substrate for methylation reactions. Despite the fact that members of this protein family were shown or predicted to be DNA, RNA or protein methyltransferases, most METTL proteins are still poorly characterized. Identification of complexes in which these potential enzymes act could help to understand their function(s) and substrate specificities. Here we systematically studied interacting partners of METTL protein family members in HeLa cells using label-free quantitative mass spectrometry. We found that, surprisingly, many of the METTL proteins appear to function outside of stable complexes whereas others including METTL7B, METTL8 and METTL9 have high-confidence interaction partners. Our study is the first systematic and comprehensive overview of the interactome of METTL protein family that can provide a crucial resource for further studies of these potential novel methyltransferases. AU - Ignatova, V.V. AU - Jansen, P.W.T.C.* AU - Baltissen, M.P.* AU - Vermeulen, M.* AU - Schneider, R. C1 - 55960 C2 - 46708 TI - The interactome of a family of potential methyltransferases in HeLa cells. JO - Sci. Rep. VL - 9 IS - 1 PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Exposure to chronic hypoxia results in pulmonary hypertension characterized by increased vascular resistance and pulmonary vascular remodeling, changes in functional parameters of the pulmonary vasculature, and right ventricular hypertrophy, which can eventually lead to right heart failure. The underlying mechanisms of hypoxia-induced pulmonary hypertension have still not been fully elucidated while no curative treatment is currently available. Commonly employed pre-clinical analytic methods are largely limited to invasive studies interfering with cardiac tissue or otherwise ex vivo functional studies and histopathology. In this work, we suggest volumetric optoacoustic tomography (VOT) for non-invasive assessment of heart function in response to chronic hypoxia. Mice exposed for 3 consecutive weeks to normoxia or chronic hypoxia were imaged in vivo with heart perfusion tracked by VOT using indocyanide green contrast agent at high temporal (100 Hz) and spatial (200 µm) resolutions in 3D. Unequivocal difference in the pulmonary transit time was revealed between the hypoxic and normoxic conditions concomitant with the presence of pulmonary vascular remodeling within hypoxic models. Furthermore, a beat-to-beat analysis of the volumetric image data enabled identifying and characterizing arrhythmic events in mice exposed to chronic hypoxia. The newly introduced non-invasive methodology for analysis of impaired pulmonary vasculature and heart function under chronic hypoxic exposure provides important inputs into development of early diagnosis and treatment strategies in pulmonary hypertension. AU - Ivankovic, I.* AU - Deán-Ben, X.L.* AU - Lin, H.-C. AU - Zhang, Z.* AU - Trautz, B.* AU - Petry, A.* AU - Görlach, A.* AU - Razansky, D. C1 - 56287 C2 - 46958 TI - Volumetric optoacoustic tomography enables non-invasive in vivo characterization of impaired heart function in hypoxic conditions. JO - Sci. Rep. VL - 9 IS - 1 PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The role of diet in type 1 diabetes development is poorly understood. Metabolites, which reflect dietary response, may help elucidate this role. We explored metabolomics and lipidomics differences between 352 cases of islet autoimmunity (IA) and controls in the TEDDY (The Environmental Determinants of Diabetes in theYoung) study. We created dietary patterns reflecting pre-IA metabolite differences between groups and examined their association with IA. Secondary outcomes included IA cases positive for multiple autoantibodies (mAb+). The association of 853 plasma metabolites with outcomes was tested at seroconversion to IA, just prior to seroconversion, and during infancy. Key compounds in enriched metabolite sets were used to create dietary patterns reflecting metabolite composition, which were then tested for association with outcomes in the nested case-control subset and the full TEDDY cohort. Unsaturated phosphatidylcholines, sphingomyelins, phosphatidylethanolamines, glucosylceramides, and phospholipid ethers in infancy were inversely associated with mAb+ risk, while dicarboxylic acids were associated with an increased risk. An infancy dietary pattern representing higher levels of unsaturated phosphatidylcholines and phospholipid ethers, and lower sphingomyelins was protective for mAb+ in the nested case-control study only. Characterization of this high-risk infant metabolomics profile may help shape the future of early diagnosis or prevention efforts. AU - Johnson, R.K.* AU - Vanderlinden, L.* AU - DeFelice, B.C.* AU - Kechris, K.* AU - Uusitalo, U.* AU - Fiehn, O.* AU - Sontag, M.* AU - Crume, T.* AU - Beyerlein, A. AU - Lernmark, Å.* AU - Toppari, J.* AU - Ziegler, A.-G. AU - She, J.X.* AU - Hagopian, W.* AU - Rewers, M.* AU - Akolkar, B.* AU - Krischer, J.* AU - Virtanen, S.M.* AU - Norris, J.M.* AU - Teddy Study Group* C1 - 57130 C2 - 47571 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Metabolite-related dietary patterns and the development of islet autoimmunity. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Therapeutic vaccination against chronic hepatitis B must overcome high viral antigen load and local regulatory mechanisms that promote immune-tolerance in the liver and curtail hepatitis B virus (HBV)-specific CD8 T cell immunity. Here, we report that therapeutic heterologous HBcore-protein-prime/Modified-Vaccinia-Virus-Ankara (MVA-HBcore) boost vaccination followed by CpG-application augmented vaccine-induced HBcAg-specific CD8 T cell-function in the liver. In HBV-transgenic as well as AAV-HBV-transduced mice with persistent high-level HBV-replication, the combination of therapeutic vaccination with subsequent CpG-application was synergistic to generate more potent HBV-specific CD8 T cell immunity that improved control of hepatocytes replicating HBV. AU - Kosinska, A. AU - Moeed, A.* AU - Kallin, N.* AU - Festag, J. AU - Su, J. AU - Steiger, K.* AU - Michel, M.L.* AU - Protzer, U. AU - Knolle, P.A.* C1 - 56655 C2 - 47219 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Synergy of therapeutic heterologous prime-boost hepatitis B vaccination with CpG-application to improve immune control of persistent HBV infection. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Climate change affects all seasons, but warming is more pronounced in winter than summer at mid-and high latitudes. Winter warming can have profound ecological effects, which are rarely compared to the effects of summer warming, and causal explanations are not well established. We compared mild aboveground infrared warming in winter to warming in summer in a semi-natural, cool-temperate grassland in Germany for four years. Aboveground plant biomass increased following winter warming (+18%) and was unaffected by summer warming. Winter warming affected the composition of the plant community more than summer warming, favoring productive species. Winter warming increased soil respiration more than summer warming. Prolonged growing seasons and changes in plant-community composition accounted for the increased aboveground biomass production. Winter warming stimulated ecological processes, despite causing frost damage to plant roots and microorganisms during an extremely cold period when warming reduced the thermal insulation provided by snow. Future warming beyond such intermittent frosts may therefore further increase the accelerating effects of winter warming on ecological processes. AU - Kreyling, J.* AU - Grant, K.* AU - Hammerl, V. AU - Arfin-Khan, M.A.S.* AU - Malyshev, A.V.* AU - Peñuelas, J.* AU - Pritsch, K. AU - Sardans, J.* AU - Schloter, M. AU - Schuerings, J.* AU - Jentsch, A.* AU - Beierkuhnlein, C.* C1 - 57125 C2 - 47551 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Winter warming is ecologically more relevant than summer warming in a cool-temperate grassland. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease where substantial heterogeneity in clinical presentation urgently requires a better stratification of patients for the development of drug trials and clinical care. In this study we explored stratification through a crowdsourcing approach, the DREAM Prize4Life ALS Stratification Challenge. Using data from > 10,000 patients from ALS clinical trials and 1479 patients from community-based patient registers, more than 30 teams developed new approaches for machine learning and clustering, outperforming the best current predictions of disease outcome. We propose a new method to integrate and analyze patient clusters across methods, showing a clear pattern of consistent and clinically relevant sub-groups of patients that also enabled the reliable classification of new patients. Our analyses reveal novel insights in ALS and describe for the first time the potential of a crowdsourcing to uncover hidden patient sub-populations, and to accelerate disease understanding and therapeutic development. AU - Kueffner, R.* AU - Zach, N.* AU - Bronfeld, M.* AU - Norel, R.* AU - Atassi, N.* AU - Balagurusamy, V.* AU - di Camillo, B.* AU - Chio, A.* AU - Cudkowicz, M.* AU - Dillenberger, D.* AU - Garcia-Garcia, J.* AU - Hardiman, O.* AU - Hoff, B.* AU - Knight, J.* AU - Leitner, M.L.* AU - Li, G.* AU - Mangravite, L.* AU - Norman, T.* AU - Wang, L.* AU - Alkallas, R.* AU - Anghel, C.* AU - Avril, J.* AU - Bacardit, J.* AU - Balser, B.* AU - Balser, J.* AU - Bar-Sinai, Y.* AU - Ben-David, N.* AU - Ben-Zion, E.* AU - Bliss, R.* AU - Cai, J.* AU - Chernyshev, A.* AU - Chiang, J.* AU - Chicco, D.* AU - Corriveau, B.A.N.* AU - Dai, J.* AU - Deshpande, Y.* AU - Desplats, E.* AU - Durgin, J.S.* AU - Espiritu, S.M.G.* AU - Fan, F.* AU - Fevrier, P.* AU - Fridley, B.L.* AU - Godzik, A.* AU - Golinska, A.* AU - Gordon, J.* AU - Graw, S.* AU - Guo, Y.* AU - Herpelinck, T.* AU - Hopkins, J.* AU - Huang, B.* AU - Jacobsen, J.* AU - Jahandideh, S.* AU - Jeon, J.* AU - Ji, W.* AU - Jung, K.* AU - Karanevich, A.* AU - Koestler, D.C.* AU - Kozak, M.* AU - Kurz, C.F. AU - Lalansingh, C.* AU - Larrieu, T.* AU - Lazzarini, N.* AU - Lerner, B.* AU - Lesinski, W.* AU - Liang, X.* AU - Lin, X.* AU - Lowe, J.* AU - Mackey, L.* AU - Meier, R.* AU - Min, W.* AU - Mnich, K.* AU - Nahmias, V.* AU - Noel-MacDonnell, J.* AU - O'Donnell, A.* AU - Paadre, S.* AU - Park, J.* AU - Polewko-Klim, A.* AU - Raghavan, R.* AU - Rudnicki, W.* AU - Saghapour, E.* AU - Salomond, J.* AU - Sankaran, K.* AU - Sendorek, D.* AU - Sharan, V.* AU - Shiah, Y.* AU - Sirois, J.* AU - Sumanaweera, D.N.* AU - Usset, J.* AU - Vang, Y.S.* AU - Vens, C.* AU - Wadden, D.* AU - Wang, D.* AU - Wong, W.C.* AU - Xie, X.* AU - Xu, Z.* AU - Yang, H.* AU - Yu, X.* AU - Zhang, H.* AU - Zhang, L.* AU - Zhang, S.* AU - Zhu, S.* AU - Xiao, J.* AU - Fang, W.* AU - Peng, J.* AU - Yang, C.* AU - Chang, H.* AU - Stolovitzky, G.* C1 - 55439 C2 - 46253 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Stratification of amyotrophic lateral sclerosis patients: A crowdsourcing approach. JO - Sci. Rep. VL - 9 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The original version of this Article contained an error in Affiliation 7, which was incorrectly given as ‘Research Unit Environmental Simulation, Helmholtz Centre Munich, Neuherberg, 85764, Germany’. The correct affiliation is listed below: Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Neuherberg, 85764, Germany This error has now been corrected in the HTML and PDF versions of this Article. AU - La Cono, V.* AU - Bortoluzzi, G.* AU - Messina, E.* AU - La Spada, G.* AU - Smedile, F.* AU - Giuliano, L.* AU - Borghini, M.* AU - Stumpp, C. AU - Schmitt-Kopplin, P. AU - Harir, M. AU - O'Neill, W.K.* AU - Hallsworth, J.E.* AU - Yakimov, M.* C1 - 56170 C2 - 46865 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Author Correction: The discovery of Lake Hephaestus, the youngest athalassohaline deep-sea formation on Earth (Scientific Reports, (2019), 9, 1, (1679), 10.1038/s41598-018-38444-z). JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Hydrated, magnesium-rich minerals and subglacial brines exist on the martian surface, so the habitability of high-Mg2+ environments on Earth has extraterrestrial (as well as terrestrial) implications. Here, we report the discovery of a MgCl2-dominated (4.72 M) brine lake on the floor of the Mediterranean Ridge that underlies a 3500-m water column, and name it Lake Hephaestus. Stable isotope analyses indicated that the Hephaestus brine is derived from interactions between ancient bishofite-enriched evaporites and subsurface fluids. Analyses of sediment pore waters indicated that the Hephaestus depression had contained the MgCl2 brine for a remarkably short period; only 700 years. Lake Hephaestus is, therefore, the youngest among currently known submarine athalassohaline brine lakes on Earth. Due to its biologically hostile properties (low water-activity and extreme chaotropicity), the Hephaestus brine is devoid of life. By contrast, the seawater-Hephaestus brine interface has been shown to act as refuge for extremely halophilic and magnesium-adapted stratified communities of microbes, even at MgCl2 concentrations that approach the water-activity limit for life (0.653). AU - la Cono, V.L.* AU - Bortoluzzi, G.* AU - Messina, E.* AU - La Spada, G.* AU - Smedile, F.* AU - Giuliano, L.* AU - Borghini, M.* AU - Stumpp, C. AU - Schmitt-Kopplin, P. AU - Harir, M. AU - O'Neill, W.K.* AU - Hallsworth, J.E.* AU - Yakimov, M.* C1 - 55449 C2 - 46361 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - The discovery of Lake Hephaestus, the youngest athalassohaline deep-sea formation on Earth. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Birth by Cesarean section increases the risk of developing type 1 diabetes later in life. We aimed to elucidate common regulatory processes observed after Cesarean section and the development of islet autoimmunity, which precedes type 1 diabetes, by investigating the transcriptome of blood cells in the developing immune system. To investigate Cesarean section effects, we analyzed longitudinal gene expression profiles from peripheral blood mononuclear cells taken at several time points from children with increased familial and genetic risk for type 1 diabetes. For islet autoimmunity, we compared gene expression differences between children after initiation of islet autoimmunity and age-matched children who did not develop islet autoantibodies. Finally, we compared both results to identify common regulatory patterns. We identified the pentose phosphate pathway and pyrimidine metabolism - both involved in nucleotide synthesis and cell proliferation - to be differentially expressed in children born by Cesarean section and after islet autoimmunity. Comparison of global gene expression signatures showed that transcriptomic changes were systematically and significantly correlated between Cesarean section and islet autoimmunity. Moreover, signatures of both Cesarean section and islet autoimmunity correlated with transcriptional changes observed during activation of isolated CD4+ T lymphocytes. In conclusion, we identified shared molecular changes relating to immune cell activation in children born by Cesarean section and children who developed autoimmunity. Our results serve as a starting point for further investigations on how a type 1 diabetes risk factor impacts the young immune system at a molecular level. AU - Laimighofer, M. AU - Lickert, R. AU - Fuerst, R. AU - Theis, F.J. AU - Winkler, C. AU - Bonifacio, E.* AU - Ziegler, A.-G. AU - Krumsiek, J. C1 - 55906 C2 - 46667 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity - indications of immune cell activation. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Niacin inhibits fatty acid flux from adipose tissue to liver, reduces hepatic triglyceride synthesis and increases hepatic lipid oxidation. Thus, niacin may have a role in the regulation of liver fat content in humans. We tested if dietary intake of niacin predicts change of liver fat content during a lifestyle intervention. To this end, we estimated the composition of diet from diaries of 202 healthy subjects at risk of type 2 diabetes undergoing lifestyle intervention comprising physical activity and diet counselling. Total-, subcutaneous- and visceral adipose tissue mass were measured by magnetic resonance (MR) tomography and liver fat content by H-1-MR spectroscopy at baseline and after 9 months of follow-up. Among fat compartments, liver fat content showed the largest decrease (-32%, p < 0.0001). High baseline niacin intake predicted a larger decrease of liver fat (p = 0.004). Subjects in the highest quartile of niacin intake at baseline also had the largest decrease of liver fat (1st: -10%; 2nd: -27%; 3rd: -35%; 4th: -37%). Among 58 subjects with nonalcoholic fatty liver disease (NAFLD) at baseline, NAFLD resolved in 23 subjects during the lifestyle intervention. For one standard deviation increase in niacin intake, the odds ratio for resolution of NAFLD was 1.77 (95% CI, 1.00-3.43). High dietary niacin intake may have a favorable effect on the reduction of liver fat during lifestyle intervention. AU - Linder, K. AU - Willmann, C. AU - Kantartzis, K. AU - Machann, J. AU - Schick, F. AU - Graf, M.* AU - Kümmerle, S.* AU - Häring, H.-U. AU - Fritsche, A. AU - Stefan, N. AU - Wagner, R. C1 - 55447 C2 - 46362 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Dietary niacin intake predicts the decrease of liver fat content during a lifestyle intervention. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Type 2 diabetes (T2D) affects the health of millions of people worldwide. The identification of genetic determinants associated with changes in glycemia over time might illuminate biological features that precede the development of T2D. Here we conducted a genome-wide association study of longitudinal fasting glucose changes in up to 13,807 non-diabetic individuals of European descent from nine cohorts. Fasting glucose change over time was defined as the slope of the line defined by multiple fasting glucose measurements obtained over up to 14 years of observation. We tested for associations of genetic variants with inverse-normal transformed fasting glucose change over time adjusting for age at baseline, sex, and principal components of genetic variation. We found no genome-wide significant association (P < 5 x 10(-8)) with fasting glucose change over time. Seven loci previously associated with T2D, fasting glucose or HbA1c were nominally (P < 0.05) associated with fasting glucose change over time. Limited power influences unambiguous interpretation, but these data suggest that genetic effects on fasting glucose change over time are likely to be small. A public version of the data provides a genomic resource to combine with future studies to evaluate shared genetic links with T2D and other metabolic risk traits. AU - Liu, C.T.* AU - Merino, J.* AU - Rybin, D.* AU - DiCorpo, D.* AU - Benke, K.S.* AU - Bragg-Gresham, J.L.* AU - Canouil, M.* AU - Corre, T.* AU - Grallert, H. AU - Isaacs, A.* AU - Kutalik, Z.* AU - Lahti, J.* AU - Marullo, L.* AU - Marzi, C. AU - Rasmussen-Torvik, L.J.* AU - Rocheleau, G.* AU - Rueedi, R.* AU - Scapoli, C.* AU - Verweij, N.* AU - Vogelzangs, N.* AU - Willems, S.M.* AU - Yengo, L.* AU - Bakker, S.J.L.* AU - Beilby, J.* AU - Hui, J.* AU - Kajantie, E.* AU - Müller-Nurasyid, M. AU - Rathmann, W.* AU - Balkau, B.* AU - Bergmann, S.* AU - Eriksson, J.G.* AU - Florez, J.C.* AU - Froguel, P.* AU - Harris, T.* AU - Hung, J.* AU - James, A.L.* AU - Kavousi, M.* AU - Miljkovic, I.* AU - Musk, A.W.* AU - Palmer, L.J.* AU - Peters, A. AU - Roussel, R.* AU - van der Harst, P.* AU - van Duijn, C.M.* AU - Vollenweider, P.* AU - Barroso, I.* AU - Prokopenko, I.* AU - Dupuis, J.* AU - Meigs, J.B.* AU - Bouatia-Naji, N.* C1 - 56562 C2 - 47082 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Genome-wide association study of change in fasting glucose over time in 13,807 non-diabetic European Ancestry Individuals. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Isolated human islets do not always meet the quality standards required for transplant survival and reliable functional in vitro studies. The formation of pseudoislets, i.e. the reaggregation of a defined number of islet cells after dissociation, improves insulin secretion. We present a simple method of pseudoislet formation from human islet cells and assess the transcriptome and function of isolated human islets and pseudoislets from the same organ donors. Following pseudoislet formation, insulin content/DNA and mRNA/RPS13 resembled that of islets. In pseudoislets, glucose-stimulated insulin secretion (GSIS) was significantly higher (8-13-fold) than in islets (2-4-fold). GSIS of pseudoislets was partly inhibited by the glucagon-like peptide-1 receptor (GLP-1R) antagonist exendin-9. The stimulatory effects of palmitate and forskolin at 12 mM glucose were also significantly higher in pseudoislets than in islets. Further analysis of pseudoislets revealed that regulation of secretion and insulin and glucagon content was maintained over a longer culture period (6-14 d). While adrenaline inhibited GSIS, adrenaline together with palmitate stimulated glucagon secretion 2-fold at low glucose, an effect suppressed by high glucose. Transcriptome analysis revealed that, unlike islets, pseudoislets were deprived of exocrine and endothelial cells. In conclusion, pseudoislet formation restores functional integrity of human islet cells and allows long-term in vitro testing. AU - Lorza-Gil, E. AU - Gerst, F. AU - Oquendo, M.B.* AU - Deschl, U.* AU - Häring, H.-U. AU - Beilmann, M.* AU - Ullrich, S. C1 - 56585 C2 - 47150 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Glucose, adrenaline and palmitate antagonistically regulate insulin and glucagon secretion in human pseudoislets. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - We analyzed the associations between whole blood microRNA profiles and the indices of glucose metabolism and impaired fasting glucose and examined whether the discovered microRNAs correlate with the expression of their mRNA targets. MicroRNA and gene expression profiling were performed for the Young Finns Study participants (n= 871). Glucose, insulin, and glycated hemoglobin (HbA1c) levels were measured, the insulin resistance index (HOMA2-IR) was calculated, and the glycemic status (normoglycemic [n = 534]/impaired fasting glucose [IFG] [n = 252]/type 2 diabetes [T2D] [n = 24]) determined. Levels of hsa-miR-144-5p, -122-5p, -148a-3p, -589-5p, and hsa-let-7a-5p associated with glycemic status. hsa-miR-144-5p and -148a-3p associated with glucose levels, while hsa-miR-144-5p, -122-5p, -184, and -339-3p associated with insulin levels and HOMA2-IR, and hsa-miR-148a-3p, -15b-3p, -93-3p, -146b-5p, -221-3p, -18a-3p, -642a-5p, and -181-2-3p associated with HbA1c levels. The targets of hsa-miR-146b-5p that correlated with its levels were enriched in inflammatory pathways, and the targets of hsa-miR-221-3p were enriched in insulin signaling and T2D pathways. These pathways showed indications of co-regulation by HbA1c-associated miRNAs. There were significant differences in the microRNA profiles associated with glucose, insulin, or HOMA-IR compared to those associated with HbA1c. The HbA1c-associated miRNAs also correlated with the expression of target mRNAs in pathways important to the development ofT2D. AU - Mononen, N.* AU - Lyytikäinen, L.P.* AU - Seppälä, I.* AU - Mishra, P.P.* AU - Juonala, M.* AU - Waldenberger, M. AU - Klopp, N.* AU - Illig, T. AU - Leiviskä, J.* AU - Loo, B.M.* AU - Laaksonen, R.* AU - Oksala, N.* AU - Kähönen, M.* AU - Hutri-Kähönen, N.* AU - Raitakari, O.* AU - Lehtimäki, T.* AU - Raitoharju, E.* C1 - 56380 C2 - 47046 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Whole blood microRNA levels associate with glycemic status and correlate with target mRNAs in pathways important to type 2 diabetes. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Oculocutaneous syndromes are often due to mutations in single genes. In some cases, mouse models for these diseases exist in spontaneously occurring mutations, or in mice resulting from forward mutatagenesis screens. Here we present novel genes that may be causative for oculocutaneous disease in humans, discovered as part of a genome-wide screen of knockout-mice in a targeted single-gene deletion project. The International Mouse Phenotyping Consortium (IMPC) database (data release 10.0) was interrogated for all mouse strains with integument abnormalities, which were then cross-referenced individually to identify knockouts with concomitant ocular abnormalities attributed to the same targeted gene deletion. The search yielded 307 knockout strains from unique genes with integument abnormalities, 226 of which have not been previously associated with oculocutaneous conditions. Of the 307 knockout strains with integument abnormalities, 52 were determined to have ocular changes attributed to the targeted deletion, 35 of which represent novel oculocutaneous genes. Some examples of various integument abnormalities are shown, as well as two examples of knockout strains with oculocutaneous phenotypes. Each of the novel genes provided here are potentially relevant to the pathophysiology of human integumentary, or oculocutaneous conditions, such as albinism, phakomatoses, or other multi-system syndromes. The novel genes reported here may implicate molecular pathways relevant to these human diseases and may contribute to the discovery of novel therapeutic targets. AU - Moore, B.A.* AU - Flenniken, A.M.* AU - Clary, D.* AU - Moshiri, A.S.* AU - Nutter, L.M.J.* AU - Berberovic, Z.* AU - Owen, C.* AU - Newbigging, S.* AU - Adissu, H.* AU - Eskandarian, M.* AU - McKerlie, C.* AU - International Mouse Phenotyping Consortium (Hrabě de Angelis, M.) AU - Tomasy, S.M.* AU - Lloyd, K.C.K.* AU - Murphy, C.J.* AU - Moshiri, A.* C1 - 56691 C2 - 47185 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function. JO - Sci. Rep. VL - 9 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Neutrophil serine proteases (NSPs), like proteinase 3 (PR3) and neutrophil elastase (NE) are implicated in ischemia-reperfusion responses after lung transplantation (LTx). Cathepsin C (CatC) acts as the key regulator of NSP maturation during biosynthesis. We hypothesized that CatC inhibitors would reduce vascular breakdown and inflammation during reperfusion in pretreated lung transplant recipients by blocking NSP maturation in the bone marrow. An orthotopic LTx model in mice was used to mimic the induction of an ischemia-reperfusion response after 18 h cold storage of the graft and LTx. Recipient mice were treated subcutaneously with a chemical CatC inhibitor (ICatC) for 10 days prior to LTx. We examined the effect of the ICatC treatment by measuring the gas exchange function of the left lung graft, protein content, neutrophil numbers and NSP activities in the bone marrow 4 h after reperfusion. Pre-operative ICatC treatment of the recipient mice improved early graft function and lead to the disappearance of active NSP protein in the transplanted lung. NSP activities were also substantially reduced in bone marrow neutrophils. Preemptive NSP reduction by CatC inhibition may prove to be a viable and effective approach to reduce immediate ischemia reperfusion responses after LTx. AU - Rehm, S.R.T. AU - Smirnova, N.F. AU - Morrone, C. AU - Götzfried, J. AU - Feuchtinger, A. AU - Pedersen, J.* AU - Korkmaz, B.* AU - Yildirim, A.Ö. AU - Jenne, D. C1 - 56540 C2 - 47085 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Premedication with a cathepsin C inhibitor alleviates early primary graft dysfunction in mouse recipients after lung transplantation. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The objective of the study was to identify associations of longitudinal trajectories of traditional cardiometabolic risk factors with abdominal and ectopic adipose tissue depots measured by magnetic resonance imaging (MRI). We measured total abdominal, visceral, and subcutaneous adipose tissue in liter and intrahepatic, intrapancreatic and renal sinus fat as fat fractions by MRI in 325 individuals free of cardiovascular disease at Exam 3 of a population-based cohort. We related these MRI measurements at Exam 3 to longitudinal risk profile trajectory clusters, based on risk factor measurements from Exam 3, Exam 2 (seven years prior to MRI) and Exam 1 (14 years prior to MRI). Based on the levels and longitudinal trajectories of several risk factors (blood pressure, lipid profile, anthropometric measurements, HbA1c), we identified three different trajectory clusters. These clusters displayed a graded association with all adipose tissue traits after adjustment for potential confounders (e.g. visceral adipose tissue: beta(ClusterII) = 1.30 l, 95%-CI:[0.84 l;1.75 l], beta(ClusterIII) = 3.32 l[2.74 l;3.90 l]; intrahepatic: Estimate(ClusterII) = 1.54[1.27,1.86], Estimate(ClusterIII) = 2.48[1.93,3.16]. Associations remained statistically significant after additional adjustment for the risk factor levels at Exam 1 or Exam 3, respectively. Trajectory clusters provided additional information in explaining variation in the different fat compartments beyond risk factor profiles obtained at individual exams. In conclusion, sustained high risk factor levels and unfavorable trajectories are associated with high levels of adipose tissue; however, the association with cardiometabolic risk factors varies substantially between different ectopic adipose tissues. Trajectory clusters, covering longitudinal risk profiles, provide additional information beyond single-point risk profiles. This emphasizes the need to incorporate longitudinal information in cardiometabolic risk estimation. AU - Rospleszcz, S. AU - Lorbeer, R.* AU - Storz, C.* AU - Schlett, C.L.* AU - Meisinger, C. AU - Thorand, B. AU - Rathmann, W.* AU - Bamberg, F.* AU - Lieb, W.* AU - Peters, A. C1 - 57369 C2 - 47735 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Association of longitudinal risk profile trajectory clusters with adipose tissue depots measured by magnetic resonance imaging. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The endocardium is the endothelial component of the vertebrate heart and plays a key role in heart development. Where, when, and how the endocardium segregates during embryogenesis have remained largely unknown, however. We now show that Nkx2-5(+) cardiac progenitor cells (CPCs) that express the Sry-type HMG box gene Sox17 from embryonic day (E) 7.5 to E8.5 specifically differentiate into the endocardium in mouse embryos. Although Sox17 is not essential or sufficient for endocardium fate, it can bias the fate of CPCs toward the endocardium. On the other hand, Sox17 expression in the endocardium is required for heart development. Deletion of Sox17 specifically in the mesoderm markedly impaired endocardium development with regard to cell proliferation and behavior. The proliferation of cardiomyocytes, ventricular trabeculation, and myocardium thickening were also impaired in a non-cell-autonomous manner in the Sox17 mutant, likely as a consequence of down-regulation of NOTCH signaling. An unknown signal, regulated by Sox17 and required for nurturing of the myocardium, is responsible for the reduction in NOTCH-related genes in the mutant embryos. Our results thus provide insight into differentiation of the endocardium and its role in heart development. AU - Saba, R.* AU - Kitajima, K.* AU - Rainbow, L.* AU - Engert, S. AU - Uemura, M.* AU - Ishida, H.* AU - Kokkinopoulos, I.* AU - Shintani, Y.* AU - Miyagawa, S.* AU - Kanai, Y.* AU - Kanai-Azuma, M.* AU - Koopman, P.* AU - Meno, C.* AU - Kenny, J.* AU - Lickert, H. AU - Saga, Y.* AU - Suzuki, K.* AU - Sawa, Y.* AU - Yashiro, K.* C1 - 56800 C2 - 47294 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Endocardium differentiation through Sox17 expression in endocardium precursor cells regulates heart development in mice. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - To-date, most proteomic studies aimed at discovering tissue-based cancer biomarkers have compared the quantity of selected proteins between case and control groups. However, proteins generally function in association with other proteins to form modules localized in particular subcellular compartments in specialized cell types and tissues. Sub-cellular mislocalization of proteins has in fact been detected as a key feature in a variety of cancer cells. Here, we describe a strategy for tissue-biomarker detection based on a mitochondria! fold enrichment (mtFE) score, which is sensitive to protein abundance changes as well as changes in subcellular distribution between mitochondria and cytosol. The mtFE score integrates protein abundance data from total cellular lysates and mitochondria-enriched fractions, and provides novel information for the classification of cancer samples that is not necessarily apparent from conventional abundance measurements alone. We apply this new strategy to a panel of wild-type and mutant mice with a liver-specific gene deletion of Liver receptor homolog 1 (Lrh-1(hep-/-)), with both lines containing control individuals as well as individuals with liver cancer induced by diethylnitrosamine (DEN). Lrh-1 gene deletion attenuates cancer cell metabolism in hepatocytes through mitochondria! glutamine processing. We show that proteome changes based on mtFE scores outperform protein abundance measurements in discriminating DEN-induced liver cancer from healthy liver tissue, and are uniquely robust against genetic perturbation. We validate the capacity of selected proteins with informative mtFE scores to indicate hepatic malignant changes in two independent mouse models of hepatocellular carcinoma (HCC), thus demonstrating the robustness of this new approach to biomarker research. Overall, the method provides a novel, sensitive approach to cancer biomarker discovery that considers contextual information of tested proteins. AU - Sajic, T.* AU - Ciuffa, R.* AU - Lemos, V.* AU - Xu, P.* AU - Leone, V. AU - Li, C.* AU - Williams, E.G.* AU - Makris, G.* AU - Banaei-Esfahani, A.* AU - Heikenwalder, M.* AU - Schoonjans, K.* AU - Aebersold, R.* C1 - 56003 C2 - 46738 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - A new class of protein biomarkers based on subcellular distribution: Application to a mouse liver cancer model. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - We aimed to investigate the association of smoking and physical exercise on ventricular function and structure, determined by cardiac magnetic resonance imaging (CMR), in subjects without known cardiovascular diseases. A total of 381 participants (median age 57 years) of the Cooperative Health Research in the Region of Augsburg (KORA) FF4 cohort underwent CMR. The participants' smoking and sporting habits were measured by a questionnaire. Physical inactivity was associated with a reduction of left ventricular ejection fraction (LV-EF), stroke volume, early diastolic peak filling rate and peak ejection rate of the left ventricle as well as right ventricular stroke volume. LV-EF was reduced in subjects with almost no physical activity compared to subjects with regular physical activity (68.4%, 95%CI 66.8-70.1% vs. 70.8%, 95%CI 69.2-72.3%, p < 0,05). Smokers had lower right ventricular end-diastolic volumes (80.6 ml/m(2), 95%CI 76.7-84.5 ml/m(2); never-smokers: 85.5 ml/m(2), 95%CI 82.6-88.3 ml/m(2); p < 0.05) but higher extracellular volume fractions (ECV) and fibrosis volumes (34.3 ml, 95%CI 32.5-36.0 ml, vs. 31.0 ml, 95%CI 29.6-32.3 ml, p < 0.01). We conclude that asymptomatic individuals without known cardiovascular diseases show differences in cardiac function and structure depending on their physical activity and smoking habits. This underlines the importance of prevention and health education. AU - Schafnitzel, A.* AU - Lorbeer, R.* AU - Bayerl, C.* AU - Patscheider, H.* AU - Auweter, S.D.* AU - Meisinger, C. AU - Heier, M. AU - Ertl-Wagner, B.* AU - Reiser, M.* AU - Peters, A. AU - Bamberg, F.* AU - Hetterich, H.* C1 - 57596 C2 - 47840 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Association of smoking and physical inactivity with MRI derived changes in cardiac function and structure in cardiovascular healthy subjects. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Mitochondria are key for cellular metabolism and signalling processes during viral infection. We report a methodology to analyse mitochondrial properties at the single-organelle level during viral infection using a recombinant adenovirus coding for a mitochondrial tracer protein for tagging and detection by multispectral flow cytometry. Resolution at the level of tagged individual mitochondria revealed changes in mitochondrial size, membrane potential and displayed a fragile phenotype during viral infection of cells. Thus, single-organelle and multi-parameter resolution allows to explore altered energy metabolism and antiviral defence by tagged mitochondria selectively in virus-infected cells and will be instrumental to identify viral immune escape and to develop and monitor novel mitochondrial-targeted therapies. AU - Schneider, A.* AU - Kurz, S.* AU - Manske, K.* AU - Janas, M.K.* AU - Heikenwälder, M.* AU - Misgeld, T.* AU - Aichler, M. AU - Weissmann, S.F.* AU - Zischka, H. AU - Knolle, P.* AU - Wohlleber, D.* C1 - 56296 C2 - 46969 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Single organelle analysis to characterize mitochondrial function and crosstalk during viral infection. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The determination of unique functions of GABARAP (gamma-aminobutyric acid type A receptor-associated protein), a member of the highly conserved protein family of mammalian autophagy-related 8 protein (mATG8), within diverse cellular processes remains challenging. Because available anti-GABARAP antibodies perform inadequate, especially within various microscopy-based applications, we aimed to develop an antibody that targets GABARAP but not its close orthologs. Following the latest recommendations for antibody validation including fluorescence protein tagging, genetic and orthogonal strategies, we characterized the resulting anti-GABARAP (8H5) antibody during confocal immunofluorescence imaging in-depth. We compared the antibody staining pattern with that obtained for fluorescence protein tagged GABARAP, GABARAPL1 or GABARAPL2 each ectopically expressed in GABARAP knockout cells. Furthermore, we imaged cells expressing all mATG8 family members at endogenous levels and checked GABARAP knockout cells for unspecific staining under fed or macroautophagy-inducing conditions. Finally, we simultaneously stained cells for endogenous GABARAP and the common autophagosomal marker LC3B. Summarized, the presented antibody shows high specificity for GABARAP without cross-reactivity to other mATG8 family members in immunofluorescence imaging making it a valuable tool for the identification of unique GABARAP functions. AU - Simons, I.M.* AU - Mohrlüder, J.* AU - Feederle, R. AU - Kremmer, E. AU - Zobel, T.* AU - Dobner, J.* AU - Bleffert, N.* AU - Hoffmann, S.* AU - Willbold, D.* C1 - 55328 C2 - 46303 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - The highly GABARAP specific rat monoclonal antibody 8H5 visualizes GABARAP in immunofluorescence imaging at endogenous levels. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - This Article contains typographical errors in the Acknowledgements section. “This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Projektnummer 190586431 – SFB 974, project B02 (D.W., I.M.S.), and project WE5343/1–1 (T.Z.), and by a grant from the Jürgen Manchot Foundation, Molecules of Infection Graduate School (MOI III) (D.W. and J.D.).” should read: “This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Projektnummer 267205415 – SFB 1208, project B02 (D.W., I.M.S.), and project WE5343/1–1 (T.Z.), and by a grant from the Jürgen Manchot Foundation, Molecules of Infection Graduate School (MOI III) (D.W. and J.D.).”. AU - Simons, I.M.* AU - Mohrlüder, J.* AU - Feederle, R. AU - Kremmer, E. AU - Zobel, T.* AU - Dobner, J.* AU - Bleffert, N.* AU - Hoffmann, S.* AU - Willbold, D.* C1 - 57650 C2 - 47915 TI - Author Correction: The highly GABARAP specific rat monoclonal antibody 8H5 visualizes GABARAP in immunofluorescence imaging at endogenous levels (Scientific Reports, (2019), 9, 1, (526), 10.1038/s41598-018-36717-1). JO - Sci. Rep. VL - 9 IS - 1 PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Null models for the effect of combination therapies are widely used to evaluate synergy and antagonism of drugs. Due to the relevance of null models, their suitability is continuously discussed. Here, we contribute to the discussion by investigating the properties of five null models. Our study includes the model proposed by David J. Hand, which we refer to as Hand model. The Hand model has been introduced almost 20 years ago but hardly was used and studied. We show that the Hand model generalizes the principle of dose equivalence compared to the Loewe model and resolves the ambiguity of the Tallarida model. This provides a solution to the persisting conflict about the compatibility of two essential model properties: the sham combination principle and the principle of dose equivalence. By embedding several null models into a common framework, we shed light in their biochemical validity and provide indications that the Hand model is biochemically most plausible. We illustrate the practical implications and differences between null models by examining differences of null models on published data. AU - Sinzger, M. AU - Vanhoefer, J. AU - Loos, C. AU - Hasenauer, J. C1 - 55641 C2 - 46451 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations. AU - Tennant, R.K.* AU - Lux, T. AU - Sambles, C.M.* AU - Kuhn, N.J.* AU - Petticrew, E.L.* AU - Oldfield, R.* AU - Parker, D.A.* AU - Hatton, J.* AU - Moore, K.A.* AU - Lee, R.* AU - Turney, C.S.M.* AU - Jones, R.T.* AU - Love, J.* C1 - 55483 C2 - 46352 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Palaeogenomics of the hydrocarbon producing microalga Botryococcus braunii. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Chronic obstructive pulmonary disease (COPD) is induced by cigarette smoking and characterized by inflammation of airway tissue. Since smokers with COPD have a higher risk of developing lung cancer than those without, we hypothesized that they carry more mutations in affected tissue. We called somatic mutations in airway brush samples from medium-coverage whole genome sequencing data from healthy never and ex-smokers (n = 8), as well as from ex-smokers with variable degrees of COPD (n = 4). Owing to the limited concordance of resulting calls between the applied tools we built a consensus, a strategy that was validated with high accuracy for cancer data. However, consensus calls showed little promise of representing true positives due to low mappability of corresponding sequence reads and high overlap with positions harbouring known genetic polymorphisms. A targeted re-sequencing approach suggested that only few mutations would survive stringent verification testing and that our data did not allow the inference of any difference in the mutational load of bronchial brush samples between former smoking COPD cases and controls. High polyclonality in airway brush samples renders medium-depth sequencing insufficient to provide the resolution to detect somatic mutations. Deep sequencing data of airway biopsies are needed to tackle the question. AU - Thun, G.A.* AU - Derdak, S.* AU - Castro-Giner, F.* AU - Apunte-Ramos, K.* AU - Águeda, L.* AU - Wjst, M. AU - Boland, A.* AU - Deleuze, J.F.* AU - Kolsum, U.* AU - Heiss-Neumann, M.S.* AU - Nowinski, A.* AU - Gorecka, D.* AU - Hohlfeld, J.M.* AU - Welte, T.* AU - Brightling, C.E.* AU - Parr, D.G.* AU - Prasse, A.* AU - Müller-Quernheim, J.* AU - Greulich, T.* AU - Stendardo, M.* AU - Boschetto, P.* AU - Barta, I.* AU - Döme, B.* AU - Gut, M.* AU - Singh, D.* AU - Ziegler-Heitbrock, L.* AU - Gut, I.G.* C1 - 57797 C2 - 47922 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - High degree of polyclonality hinders somatic mutation calling in lung brush samples of COPD cases and controls. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Patient-derived 3D cell culture systems are currently advancing cancer research since they potentiate the molecular analysis of tissue-like properties and drug response under well-defined conditions. However, our understanding of the relationship between the heterogeneity of morphological phenotypes and the underlying transcriptome is still limited. To address this issue, we here introduce "pheno-seq" to directly link visual features of 3D cell culture systems with profiling their transcriptome. As prototypic applications breast and colorectal cancer (CRC) spheroids were analyzed by pheno-seq. We identified characteristic gene expression signatures of epithelial-to-mesenchymal transition that are associated with invasive growth behavior of clonal breast cancer spheroids. Furthermore, we linked long-term proliferative capacity in a patient-derived model of CRC to a lowly abundant PROX1-positive cancer stem cell subtype. We anticipate that the ability to integrate transcriptome analysis and morphological patho-phenotypes of cancer cells will provide novel insight on the molecular origins of intratumor heterogeneity. AU - Tirier, S.M.* AU - Park, J.* AU - Preußer, F.* AU - Amrhein, L. AU - Gu, Z.* AU - Steiger, S.* AU - Mallm, J.P.* AU - Krieger, T.* AU - Waschow, M.* AU - Eismann, B.* AU - Gut, M.* AU - Gut, I.G.* AU - Rippe, K.* AU - Schlesner, M.* AU - Theis, F.J. AU - Fuchs, C. AU - Ball, C.R.* AU - Glimm, H.* AU - Conrad, C.* C1 - 56806 C2 - 47262 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Pheno-seq - linking visual features and gene expression in 3D cell culture systems. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Essential oils (EO) of several plant species have the potential to combat plant and fungal diseases. However, the effects of Achillea millefolium EO on the development of common bean (Phaseolus vulgaris L.), is still unknown. Moreover, its effect on N-2-fixing bacteria, and in general on soil properties has not been studied yet. A greenhouse trial was set up to evaluate both the influence that Achillea millefolium EO and the inoculation with three different Rhizobium strains have on the bean plant and on the chemical and microbiological properties of an agriculturally used Cambisol. Non-inoculated pots were used as control. Our findings showed a decrease in bacterial colony forming units due to EO application and an increase following the Rhizobium inoculation compared to the control. The EO application decreased soil basal respiration and activities of dehydrogenase, urease, beta-glucosidase and acid phosphatase. Such effects were stronger with higher oil concentrations. Moreover, the treatments combining Rhizobium inoculation with EO showed a positive effect on nodulation and plant height. Overall, the combined application of Achillea millefolium EO and rhizobia works as an efficient biocide that could be applied in organic agriculture without hampering the activity of nodule-forming N-fixing bacteria and the development of common bean. AU - Turan, V.* AU - Schröder, P. AU - Bilen, S.* AU - Insam, H.* AU - Fernández-Delgado Juárez, M.* C1 - 57237 C2 - 47626 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Co-inoculation effect of Rhizobium and Achillea millefolium L. oil extracts on growth of common bean (Phaseolus vulgaris L.) and soil microbial-chemical properties. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Telomere shortening has been associated with multiple age-related diseases such as cardiovascular disease, diabetes, and dementia. However, the biological mechanisms responsible for these associations remain largely unknown. In order to gain insight into the metabolic processes driving the association of leukocyte telomere length (LTL) with age-related diseases, we investigated the association between LTL and serum metabolite levels in 7,853 individuals from seven independent cohorts. LTL was determined by quantitative polymerase chain reaction and the levels of 131 serum metabolites were measured with mass spectrometry in biological samples from the same blood draw. With partial correlation analysis, we identified six metabolites that were significantly associated with LTL after adjustment for multiple testing: lysophosphatidylcholine acyl C17:0 (lysoPC a C17:0, p-value=7.1 x 10(-6)), methionine (p-value=9.2 x 10(-5)), tyrosine (p-value=2.1 x 10(-4)), phosphatidylcholine diacyl C32:1 (PC aa C32:1, p-value=2.4 x 10(-4)), hydroxypropionylcarnitine (C3-OH, p-value=2.6 x 10(-4)), and phosphatidylcholine acyl-alkyl C38:4 (PC ae C38:4, p-value=9.0 x 10(-4)). Pathway analysis showed that the three phosphatidylcholines and methionine are involved in homocysteine metabolism and we found supporting evidence for an association of lipid metabolism with LTL. In conclusion, we found longer LTL associated with higher levels of lysoPC a C17:0 and PC ae C38:4, and with lower levels of methionine, tyrosine, PC aa C32:1, and C3-OH. These metabolites have been implicated in inflammation, oxidative stress, homocysteine metabolism, and in cardiovascular disease and diabetes, two major drivers of morbidity and mortality. AU - van der Spek, A.* AU - Broer, L.* AU - Draisma, H.H.M.* AU - Pool, R.* AU - Albrecht, E. AU - Beekman, M.* AU - Mangino, M.* AU - Raag, M.* AU - Nyholt, D.R.* AU - Dharuri, H.K.* AU - Codd, V.* AU - Amin, N.* AU - de Geus, E.J.C.* AU - Deelen, J.* AU - Demirkan, A.* AU - Yet, I.* AU - Fischer, K.* AU - Haller, T.* AU - Henders, A.K.* AU - Isaacs, A.* AU - Medland, S.E.* AU - Montgomery, G.W.* AU - Mooijaart, S.P.* AU - Strauch, K. AU - Suchiman, H.E.D.* AU - Vaarhorst, A.A.M.* AU - van Heemst, D.* AU - Wang-Sattler, R. AU - Whitfield, J.B.* AU - Willemsen, G.* AU - Wright, M.J.* AU - Martin, N.G.* AU - Samani, N.J.* AU - Metspalu, A.* AU - Spector, T.D.* AU - Boomsma, D.I.* AU - van Duijn, C.M.* AU - Gieger, C. C1 - 56746 C2 - 47275 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Metabolomics reveals a link between homocysteine and lipid metabolism and leukocyte telomere length: The ENGAGE consortium. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - The proteasome is essential for the selective degradation of most cellular proteins and is fine-tuned according to cellular needs. Proteasome activators serve as building blocks to adjust protein turnover in cell growth and differentiation. Understanding the cellular function of proteasome activation in more detail offers a new strategy for therapeutic targeting of proteasomal protein breakdown in disease. The role of the proteasome activator PA200 in cell function and its regulation in disease is unknown. In this study, we investigated the function of PA200 in myofibroblast differentiation and fibrotic tissue remodeling. PA200 was upregulated in hyperplastic basal cells and myofibroblasts of fibrotic lungs from patients with idiopathic pulmonary fibrosis. Increased expression of PA200 and enhanced formation of PA200-proteasome complexes was also evident in experimental fibrosis of the lung and kidney in vivo and in activated primary human myofibroblasts of the lung in vitro. Transient silencing and overexpression revealed that PA200 functions as a negative regulator of myofibroblast differentiation of human but not mouse cells. Our data thus suggest an unexpected and important role for PA200 in adjusting myofibroblast activation in response to pro-fibrotic stimuli, which fails in idiopathic pulmonary fibrosis. AU - Welk, V. AU - Meul, T. AU - Lukas, C. AU - Kammerl, I.E. AU - Mulay, S.R.* AU - Schamberger, A.C. AU - Semren, N. AU - Fernandez, I.E. AU - Anders, H.J.* AU - Günther, A.* AU - Behr, J. AU - Eickelberg, O. AU - Korfei, M.* AU - Meiners, S. C1 - 57199 C2 - 47589 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Proteasome activator PA200 regulates myofibroblast differentiation. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Obesity is a progressive, chronic disease, which can be caused by long-term miscommunication between organs. It remains challenging to understand how chronic dysfunction in a particular tissue remotely impairs other organs to eventually imbalance organismal energy homeostasis. Here we introduce RNAi Pulse Induction (RiPI) mediated by short hairpin RNA (shRiPI) or double-stranded RNA (dsRiPI) to generate chronic, organ-specific gene knockdown in the adult Drosophila fat tissue. We show that organ-restricted RiPI targeting Stromal interaction molecule (Stim), an essential factor of store-operated calcium entry (SOCE), results in progressive fat accumulation in fly adipose tissue. Chronic SOCE-dependent adipose tissue dysfunction manifests in considerable changes of the fat cell transcriptome profile, and in resistance to the glucagon-like Adipokinetic hormone (Akh) signaling. Remotely, the adipose tissue dysfunction promotes hyperphagia likely via increased secretion of Akh from the neuroendocrine system. Collectively, our study presents a novel in vivo paradigm in the fly, which is widely applicable to model and functionally analyze inter-organ communication processes in chronic diseases. AU - Xu, Y. AU - Borcherding, A.F.* AU - Heier, C.* AU - Tian, G.* AU - Roeder, T.* AU - Kühnlein, R.P.* C1 - 56002 C2 - 46741 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Chronic dysfunction of Stromal interaction molecule by pulsed RNAi induction in fat tissue impairs organismal energy homeostasis in Drosophila. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Fructose has become a major constituent of our modern diet and is implicated as an underlying cause in the development of metabolic diseases. The fructose transporter GLUT5 (SLC2A5) is required for intestinal fructose absorption. GLUT5 expression is induced in the intestine and skeletal muscle of type 2 diabetes (T2D) patients and in certain cancers that are dependent on fructose metabolism, indicating that modulation of GLUT5 levels could have potential in the treatment of these diseases. Using an unbiased screen for transcriptional control of the human GLUT5 promoter we identified a strong and specific regulation by liver X receptor alpha (LXR alpha, NR1H3). Using promoter truncations and site-directed mutagenesis we identified a functional LXR response element (LXRE) in the human GLUT5 promoter, located at -385 bp relative to the transcriptional start site (TSS). Finally, mice treated with LXR agonist T0901317 showed an increase in Glut5 mRNA and protein levels in duodenum and adipose tissue, underscoring the in vivo relevance of its regulation by LXR. Together, our findings show that LXR alpha regulates GLUT5 in mice and humans. As a ligand-activated transcription factor, LXR alpha might provide novel pharmacologic strategies for the selective modulation of GLUT5 activity in the treatment of metabolic disease as well as cancer. AU - Zwarts, I.* AU - van Zutphen, T.* AU - Kruit, J.K.* AU - Liu, W.* AU - Oosterveer, M.H.* AU - Verkade, H.J.* AU - Uhlenhaut, N.H. AU - Jonker, J.W.* C1 - 56421 C2 - 47072 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Identification of the fructose transporter GLUT5 (SLC2A5) as a novel target of nuclear receptor LXR. JO - Sci. Rep. VL - 9 IS - 1 PB - Nature Publishing Group PY - 2019 SN - 2045-2322 ER - TY - JOUR AB - Glycogen synthase kinase 3 beta (GSK3 beta) is a ubiquitously expressed serine/threonine kinase involved in the regulation of various cellular functions, such as energy homoeostasis, cell growth and developmental processes. More recently, GSK3 beta has been identified as a part of a protein complex involved in the regulation of the CARMA1-BCL10-MALT1 complex (CBM complex) formation, which is a key signalling event upon antigen receptor engagement of B and T cells, required for the activation of the NF-kappa B and JNK pathways. However, conflicting reports have been published regarding the role of GSK3 beta for the activation of the NF-kappa B signalling pathways. Therefore, we aimed to determine the impact of GSK3 beta on the NF-kappa B signalling induced upon T cell activation. Blocking GSK3 beta by either pharmacologic inhibitors (SB216763 and SB415286) or by RNAi caused a reduced proteolysis of the MALT1 targets CYLD1, BCL10 and RelB as well as diminished I kappa B alpha degradation, NF-kappa B DNA binding and NF-kappa B activity. This negative effect on NF-kappa B appears to be due to a diminished CBM complex formation caused by a reduced BCL10 phosphorylation. Taken together, we provide here evidence for a novel regulatory mechanism by which GSK3 beta affects NF-kappa B signalling in activated T cells. AU - Abd-Ellah, A.* AU - Voogdt, C.* AU - Krappmann, D. AU - Möller, P.* AU - Marienfeld, R.B.* C1 - 52777 C2 - 44317 CY - London TI - GSK3β modulates NF-κB activation and RelB degradation through site-specific phosphorylation of BCL10. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Caries is associated with shifts of microbiota in dental biofilms and primarily driven by frequent sucrose consumption. Data on environmentally induced in vivo microbiota shifts are scarce therefore we investigated the influence of frequent sucrose consumption on the oral biofilm. Splint systems containing enamel slabs were worn for 3 x 7 days with 7-day intervals to obtain oral biofilm samples. After a three-month dietary change of sucking 10 g of sucrose per day in addition to the regular diet, biofilm was obtained again at the end of the second phase. The microbiota was analysed using Illumina MiSeq amplicon sequencing (v1-v2 region). In addition, roughness of the enamel surface was measured with laser scanning microscopy. The sucrose phase resulted in significant differences in beta-diversity and significantly decreased species richness. It was marked by a significant increase in abundance of streptococci, specifically Streptococcus gordonii, Streptococcus parasanguinis and Streptococcus sanguinis. Enamel surface roughness began to increase, reflecting initial impairment of dental enamel surface. The results showed that frequent sucrose consumption provoked compositional changes in the microbiota, leading to an increase of non-mutans streptococci, hence supporting the extended ecological plaque hypothesis and emphasizing the synergy of multiple bacterial species in the development of caries. AU - Anderson, A.C.* AU - Rothballer, M. AU - Altenburger, M.J.* AU - Woelber, J.P.* AU - Karygianni, L.* AU - Lagkouvardos, I.* AU - Hellwig, E.* AU - Al-Ahmad, A.* C1 - 54381 C2 - 45540 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Mycoparasites, e.g. fungi feeding on other fungi, are prominent within the genus Trichoderma and represent a promising alternative to chemical fungicides for plant disease control. We previously showed that the seven-transmembrane receptor Gprl regulates mycelia! growth and asexual development and governs mycoparasitism-related processes in Trichoderma atroviride. We now describe the identification of genes being targeted by Gpr1 under mycoparasitic conditions. The identified gene set includes a candidate, sfp2, encoding a protein of the fungal-specific Sur7 superfamily, whose upregulation in T. atroviride upon interaction with a fungal prey is dependent on Gpr1. Sur7 family proteins are typical residents of membrane microdomains such as the membrane compartment of Canl (MCC)/eisosome in yeast. We found that GFP-labeled Gpr1 and Sfp2 proteins show partly overlapping localization patterns in T. atroviride hyphae, which may point to shared functions and potential interaction during signal perception and endocytosis. Deletion of sfp2 caused heavily altered colony morphology, defects in polarized growth, cell wall integrity and endocytosis, and significantly reduced mycoparasitic activity, whereas sfp2 overexpression enhanced full overgrowth and killing of the prey. Transcriptional activation of a chitinase specific for hyphal growth and network formation and strong downregulation of chitin synthase-encoding genes were observed in Delta sfp2. Taken together, these findings imply crucial functions of Sfp2 in hyphal morphogenesis of T. atroviride and its interaction with prey fungi. AU - Atanasova, L.* AU - Gruber, S.* AU - Lichius, A.* AU - Radebner, T.* AU - Abendstein, L.* AU - Münsterkötter, M. AU - Stralis-Pavese, N.* AU - Łabaj, P.P.* AU - Kreil, D.P.* AU - Zeilinger, S.* C1 - 54184 C2 - 45319 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - The Gpr1-regulated Sur7 family protein Sfp2 is required for hyphal growth and cell wall stability in the mycoparasite Trichoderma atroviride. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The intellectual disability gene, Sox11, encodes for a critical neurodevelopmental transcription factor with functions in precursor survival, neuronal fate determination, migration and morphogenesis. The mechanisms regulating SOX11's activity remain largely unknown. Mass spectrometric analysis uncovered that SOX11 can be post-translationally modified by phosphorylation. Here, we report that phosphorylatable serines surrounding the high-mobility group box modulate SOX11's transcriptional activity. Through Mass Spectrometry (MS), co-immunoprecipitation assays and in vitro phosphorylation assays followed by MS we verified that protein kinase A (PKA) interacts with SOX11 and phosphorylates it on S133. In vivo replacement of SoxC factors in developing adult-generated hippocampal neurons with SOX11 S133 phospho-mutants indicated that phosphorylation on S133 modulates dendrite development of adult-born dentate granule neurons, while reporter assays suggested that S133 phosphorylation fine-tunes the activation of select target genes. These data provide novel insight into the control of the critical neurodevelopmental regulator SOX11 and imply SOX11 as a mediator of PKA-regulated neuronal development. AU - Balta, E.A.* AU - Schäffner, I.* AU - Wittmann, M.T.* AU - Sock, E.* AU - von Zweydorf, F.* AU - von Wittgenstein, J.* AU - Steib, K. AU - Heim, B.* AU - Kremmer, E. AU - Häberle, B.M.* AU - Ueffing, M.* AU - Lie, D.C.C.* AU - Gloeckner, C.J.* C1 - 54637 C2 - 45739 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Phosphorylation of the neurogenic transcription factor SOX11 on serine 133 modulates neuronal morphogenesis. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Using targeted NMR spectroscopy of 227 fasting serum metabolic traits, we searched for novel metabolic signatures of renal function in 926 type 2 diabetics (T2D) and 4838 non-diabetic individuals from four independent cohorts. We furthermore investigated longitudinal changes of metabolic measures and renal function and associations with other T2D microvascular complications. 142 traits correlated with glomerular filtration rate (eGFR) after adjusting for confounders and multiple testing: 59 in diabetics, 109 in non-diabetics with 26 overlapping. The amino acids glycine and phenylalanine and the energy metabolites citrate and glycerol were negatively associated with eGFR in all the cohorts, while alanine, valine and pyruvate depicted opposite association in diabetics (positive) and non-diabetics (negative). Moreover, in all cohorts, the triglyceride content of different lipoprotein subclasses showed a negative association with eGFR, while cholesterol, cholesterol esters (CE), and phospholipids in HDL were associated with better renal function. In contrast, phospholipids and CEs in LDL showed positive associations with eGFR only in T2D, while phospholipid content in HDL was positively associated with eGFR both cross-sectionally and longitudinally only in non-diabetics. In conclusion, we provide a wide list of kidney function-associated metabolic traits and identified novel metabolic differences between diabetic and non-diabetic kidney disease. AU - Barrios, C.* AU - Zierer, J. AU - Würtz, P.* AU - Haller, T.* AU - Metspalu, A.* AU - Gieger, C. AU - Thorand, B. AU - Meisinger, C. AU - Waldenberger, M. AU - Raitakari, O.* AU - Lehtimäki, T.* AU - Otero, S.* AU - Rodríguez, E.* AU - Pedro-Botet, J.* AU - Kähönen, M.* AU - Ala-Korpela, M.* AU - Kastenmüller, G. AU - Spector, T.D.* AU - Pascual, J.* AU - Menni, C.* C1 - 54530 C2 - 45653 TI - Circulating metabolic biomarkers of renal function in diabetic and non-diabetic populations. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Locally advanced head and neck squamous cell carcinomas (HNSCC) have limited prognosis due to frequent treatment failure. Currently, TNM-classification and human papillomavirus (HPV) infection are the sole clinical prognosticators of outcome. Tumor heterogeneity and stemness based on epithelial-mesenchymal-transition reportedly associate with therapy resistance. The capacity of epithelial marker EpCAM (EpEX), stemness regulator Sox2 and mesenchymal marker vimentin to predict clinical outcome of HSNCC patients was assessed upon immunohistochemistry staining in two cohorts of HNSCC patients treated with surgery and adjuvant radio (chemo) therapy (n = 94) and primary radio (chemo) therapy (n = 94), respectively. Prognostic values with respect to overall, disease-free and disease-specific survival were assessed in uni- and multivariate cox proportional hazard models to generate integrated risk scores. EpEX, Sox2 and vimentin displayed substantial inter- and intratumoral heterogeneity. EpEX(high) and Sox2(hi)(gh )predicted improved clinical outcome in the discovery cohort and in the HPV-negative sub-cohort. EpEX(high) and Sox2(high) were confirmed as prognosticators of clinical outcome in the validation cohort treated with definitive radio(chemo)therapy. Importantly, EpEX(high) identified patients with improved survival within the HPV-negative subgroup of the validation cohort. Hence, Sox2(high) and particularly EpEX(high) have potential as tools to predict clinical performance of HNSCC patients, foremost HPV-negative cases, in the frame of molecular-guided treatment decision-making. AU - Baumeister, P. AU - Hollmann, A.* AU - Kitz, J.* AU - Afthonidou, A.* AU - Simon, F.* AU - Shakhtour, J.* AU - Mack, B.* AU - Kranz, G.* AU - Libl, D.* AU - Leu, M.* AU - Schirmer, M.A.* AU - Canis, M.* AU - Belka, C. AU - Zitzelsberger, H. AU - Ganswindt, U. AU - Hess J. AU - Jakob, M.* AU - Unger, K. AU - Gires, O. C1 - 54469 C2 - 45592 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - High expression of EpCAM and Sox2 is a positive prognosticator of clinical outcome for head and neck carcinoma. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Epigenetic deregulation, such as the reduction of histone acetylation levels, is thought to be causally linked to various maladies associated with aging. Consequently, histone deacetylase inhibitors are suggested to serve as epigenetic therapy by increasing histone acetylation. However, previous work suggests that many non-histone proteins, including metabolic enzymes, are also acetylated and that post transitional modifications may impact their activity. Furthermore, deacetylase inhibitors were recently shown to impact the acetylation of a variety of proteins. By utilizing a novel technique to measure oxygen consumption rate from whole living tissue, we demonstrate that treatment of whole living fly heads by the HDAC/KDAC inhibitors sodium butyrate and Trichostatin A, induces a rapid and transient increase of oxygen consumption rate. In addition, our study indicates that the rate increase is markedly attenuated in midlife fly head tissue. Overall, our data suggest that HDAC/KDAC inhibitors may induce enhanced mitochondrial activity in a rapid manner. This observed metabolic boost provides further, but novel evidence, that treating various maladies with deacetylase inhibitors may be beneficial. AU - Becker, L. AU - Schmitt Nogueira, M.* AU - Klima, C.* AU - Hrabě de Angelis, M. AU - Peleg, S.* C1 - 53227 C2 - 44379 CY - London TI - Rapid and transient oxygen consumption increase following acute HDAC/KDAC inhibition in Drosophila tissue. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The autoimmune neurological disease, Multiple Sclerosis (MS), have increased at alarming rates in the Western society over the last few decades. While there are numerous efforts to develop novel treatment approaches, there is an unmet need to identify preventive strategies. We explored whether central nervous system (CNS) autoimmunity can be prevented through dietary manipulation using a spontaneous autoimmune encephalomyelitis mouse model. We report that the nutritional supplementation of non-fermentable fiber, common components of a vegetarian diet, in early adult life, prevents autoimmune disease. Dietary non-fermentable fiber alters the composition of the gut microbiota and metabolic profile with an increase in the abundance of long-chain fatty acids. Immune assays revealed that cecal extracts and a long chain fatty acid but not cecal lysates promoted autoimmune suppressive T(H)2 immune responses, demonstrating that non-fermentable fiber-induced metabolic changes account for the beneficial effects. Overall, these findings identify a non-invasive dietary strategy to prevent CNS autoimmunity and warrants a focus on nutritional approaches in human MS. AU - Berer, K.* AU - Martínez, I.* AU - Walker, A. AU - Kunkel, B.* AU - Schmitt-Kopplin, P. AU - Walter, J.* AU - Krishnamoorthy, G.* C1 - 53921 C2 - 45091 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Dietary non-fermentable fiber prevents autoimmune neurological disease by changing gut metabolic and immune status. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Recent studies suggested that postoperative hypoxia might trigger invasive tumor growth, resulting in diffuse/multifocal recurrence patterns. Aim of this study was to analyze distinct recurrence patterns and their association to postoperative infarct volume and outcome. 526 consecutive glioblastoma patients were analyzed, of which 129 met our inclusion criteria: initial tumor diagnosis, surgery, postoperative diffusion-weighted imaging and tumor recurrence during follow-up. Distinct patterns of contrast-enhancement at initial diagnosis and at first tumor recurrence (multifocal growth/progression, contact to dura/ventricle, ependymal spread, local/distant recurrence) were recorded by two blinded neuroradiologists. The association of radiological patterns to survival and postoperative infarct volume was analyzed by uni-/multivariate survival analyses and binary logistic regression analysis. With increasing postoperative infarct volume, patients were significantly more likely to develop multifocal recurrence, recurrence with contact to ventricle and contact to dura. Patients with multifocal recurrence (Hazard Ratio (HR) 1.99, P = 0.010) had significantly shorter OS, patients with recurrent tumor with contact to ventricle (HR 1.85, P = 0.036), ependymal spread (HR 2.97, P = 0.004) and distant recurrence (HR 1.75, P = 0.019) significantly shorter post-progression survival in multivariate analyses including well-established prognostic factors like age, Karnofsky Performance Score (KPS), therapy, extent of resection and patterns of primary tumors. Postoperative infarct volume might initiate hypoxia-mediated aggressive tumor growth resulting in multifocal and diffuse recurrence patterns and impaired survival. AU - Bette, S.* AU - Barz, M.* AU - Huber, T.* AU - Straube, C. AU - Schmidt-Graf, F.* AU - Combs, S.E. AU - Delbridge, C.* AU - Gerhardt, J.* AU - Zimmer, C.* AU - Meyer, B.* AU - Kirschke, J.S.* AU - Boeckh-Behrens, T.* AU - Wiestler, B.* AU - Gempt, J.* C1 - 53350 C2 - 44686 CY - London TI - Retrospective analysis of radiological recurrence patterns in glioblastoma, their prognostic value and association to postoperative infarct volume. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The serotonin neurotransmitter system is widespread in the brain and implicated in modulation of neuronal responses to other neurotransmitters. Among 14 serotonin receptor subtypes, 5-HT2cR plays a pivotal role in controlling neuronal network excitability. Serotonergic activity conveyed through receptor 5-HT2cR is regulated post-transcriptionally via two mechanisms, alternative splicing and A-to-I RNA editing. Brain-specific small nucleolar RNA SNORD115 harbours a phylogenetically conserved 18-nucleotide antisense element with perfect complementarity to the region of 5ht2c primary transcript that undergoes post-transcriptional changes. Previous 5ht2c minigene studies have implicated SNORD115 in fine-tuning of both post-transcriptional events. We monitored post-transcriptional changes of endogenous 5ht2c transcripts during neuronal differentiation. Both SNORD115 and 5ht2c were upregulated upon neuronal commitment. We detected increased 5ht2c alternative exon Vb inclusion already at the stage of neuronal progenitors, and more extensive A-to-I editing of non-targeted sites A and B compared to adjacent adenosines at sites E, C and D throughout differentiation. As the extent of editing is known to positively correlate with exon Vb usage while it reduces receptor functionality, our data support the model where SNORD115 directly promotes alternative exon inclusion without the requirement for conversion of key adenosines to inosines, thereby favouring production of full-length receptor isoforms with higher potency. AU - Bratkovič, T.* AU - Modic, M. AU - Camargo Ortega, G. AU - Drukker, M. AU - Rogelj, B.* C1 - 53303 C2 - 44572 CY - London TI - Neuronal differentiation induces SNORD115 expression and is accompanied by post-transcriptional changes of serotonin receptor 2c mRNA. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Macrodomains are conserved protein folds associated with ADP-ribose binding and turnover. ADP-ribosylation is a posttranslational modification catalyzed primarily by ARTD (aka PARP) enzymes in cells. ARTDs transfer either single or multiple ADP-ribose units to substrates, resulting in mono-or poly-ADP-ribosylation. TARG1/C6orf130 is a macrodomain protein that hydrolyzes mono-ADP-ribosylation and interacts with poly-ADP-ribose chains. Interactome analyses revealed that TARG1 binds strongly to ribosomes and proteins associated with rRNA processing and ribosomal assembly factors. TARG1 localized to transcriptionally active nucleoli, which occurred independently of ADP-ribose binding. TARG1 shuttled continuously between nucleoli and nucleoplasm. In response to DNA damage, which activates ARTD1/2 (PARP1/2) and promotes synthesis of poly-ADP-ribose chains, TARG1 re-localized to the nucleoplasm. This was dependent on the ability of TARG1 to bind to poly-ADP-ribose. These findings are consistent with the observed ability of TARG1 to competitively interact with RNA and PAR chains. We propose a nucleolar role of TARG1 in ribosome assembly or quality control that is stalled when TARG1 is re-located to sites of DNA damage. AU - Bütepage, M.* AU - Preisinger, C.* AU - von Kriegsheim, A.* AU - Scheufen, A.* AU - Lausberg, E.* AU - Li, J.* AU - Kappes, F.* AU - Feederle, R. AU - Ernst, S.W.* AU - Eckei, L.* AU - Krieg, S.M.* AU - Müller-Newen, G.* AU - Rossetti, G.* AU - Feijs, K.L.H.* AU - Verheugd, P.* AU - Lüscher, B.* C1 - 53462 C2 - 44731 TI - Nucleolar-nucleoplasmic shuttling of TARG1 and its control by DNA damage-induced poly-ADP-ribosylation and by nucleolar transcription. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Cells vary in their dynamic response to external stimuli, due to stochastic fluctuations and non-uniform progression through the cell cycle. Hence, single-cell studies are required to reveal the range of heterogeneity in their responses to defined perturbations, which provides detailed insight into signaling processes. Here, we present a time-lapse study using arrays of micro-trenches to monitor the timing of cell division and apoptosis in non-adherent cells at the single-cell level. By employing automated cell tracking and division detection, we precisely determine cell cycle duration and sister-cell correlations for hundreds of individual cells in parallel. As a model application we study the response of leukemia cells to the chemostatic drug vincristine as a function of cell cycle phase. The time-to-death after drug addition is found to depend both on drug concentration and cell cycle phase. The resulting timing and dose-response distributions were reproduced in control experiments using synchronized cell populations. Interestingly, in non-synchronized cells, the time-to-death intervals for sister cells appear to be correlated. Our study demonstrates the practical benefits of micro-trench arrays as a platform for high-throughput, single-cell time-lapse studies on cell cycle dependence, correlations and cell fate decisions in general. AU - Chatzopoulou, E.I.* AU - Raharja-Liu, P. AU - Murschhauser, A.* AU - Sekhavati, F.* AU - Buggenthin, F. AU - Vollmar, A.M.* AU - Marr, C. AU - Rädler, J.O.* C1 - 55040 C2 - 46064 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - A single-cell micro-trench platform for automatic monitoring of cell division and apoptosis after chemotherapeutic drug administration. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Prenatal exposure to tobacco smoke is a significant risk-factor for airway disease development. Furthermore, the high prevalence of pregnant smoking women requires the establishment of strategies for offspring lung protection. Therefore, we here aimed to understand the molecular mechanism of how prenatal smoke exposure affects fetal lung development. We used a mouse model recapitulating clinical findings of prenatally exposed children, where pregnant mice were exposed to smoke until c-section or spontaneous delivery, and offspring weight development and lung function was monitored. Additionally, we investigated pulmonary transcriptome changes in fetal lungs (GD18.5) by mRNA/miRNA arrays, network analyses and qPCR. The results demonstrated that prenatally exposed mice showed intrauterine and postnatal growth retardation, and impaired lung function. 1340 genes and 133 miRNAs were found to be significantly dysregulated by in utero smoke exposure, and we identified Insulin-like growth factor 1 (Igf1) as a top hierarchical node in a network analysis. Moreover, Igf1 mRNA was increased in female murine offspring and in prenatally exposed children. These findings suggest that prenatal smoking is associated with a dysregulation of several genes, including Igf1 in a sex-specific manner. Thus, our results could represent a novel link between smoke exposure, abberant lung development and impaired lung function. AU - Dehmel, S. AU - Nathan, P. AU - Bartel, S.* AU - El-Mehrie, N.* AU - Scherb, H. AU - Milger, K. AU - John-Schuster, G. AU - Yildirim, A.Ö. AU - Hyklema, M.* AU - Irmler, M. AU - Beckers, J. AU - Schaub, B. AU - Eickelberg, O.* AU - Krauss-Etschmann, S.* C1 - 53522 C2 - 44603 TI - Intrauterine smoke exposure deregulates lung function, pulmonary transcriptomes, and in particular insulin-like growth factor (IGF)-1 in a sex-specific manner. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - © 2018 The Author(s). Ultrasound-mediated transcranial images of the brain often suffer from acoustic distortions produced by the skull bone. In high-resolution optoacoustic microscopy, the skull-induced acoustic aberrations are known to impair image resolution and contrast, further skewing the location and intensity of the different absorbing structures. We present a virtual craniotomy deconvolution algorithm based on an ultrasound wave propagation model that corrects for the skull-induced distortions in optically-resolved optoacoustic transcranial microscopy data. The method takes advantage of the geometrical and spectral information of a pulse-echo ultrasound image of the skull simultaneously acquired by our multimodal imaging system. Transcranial mouse brain imaging experiments confirmed the ability to accurately account for the signal amplitude decay, temporal delay and pulse broadening introduced by the rodent's skull. Our study is the first to demonstrate skull-corrected transcranial optoacoustic imaging in vivo. AU - Estrada, H. AU - Huang, X. AU - Rebling, J. AU - Zwack, M. AU - Gottschalk, S. AU - Razansky, D. C1 - 52795 C2 - 44174 CY - London TI - Virtual craniotomy for high-resolution optoacoustic brain microscopy. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The formation of amyloid fibrils by human islet amyloid polypeptide protein (hIAPP) has been implicated in pancreas dysfunction and diabetes. However, efficient treatment options to reduce amyloid fibrils in vivo are still lacking. Therefore, we tested the effect of epigallocatechin gallate (EGCG) on fibril formation in vitro and in vivo. To determine the binding of hIAPP and EGCG, in vitro interaction studies were performed. To inhibit amyloid plaque formation in vivo, homozygous (tg/tg), hemizygous (wt/tg), and control mice (wt/wt) were treated with EGCG. EGCG bound to hIAPP in vitro and induced formation of amorphous aggregates instead of amyloid fibrils. Amyloid fibrils were detected in the pancreatic islets of tg/tg mice, which was associated with disrupted islet structure and diabetes. Although pancreatic amyloid fibrils could be detected in wt/tg mice, these animals were non-diabetic. EGCG application decreased amyloid fibril intensity in wt/tg mice, however it was ineffective in tg/tg animals. Our data indicate that EGCG inhibits amyloid fibril formation in vitro and reduces fibril intensity in non-diabetic wt/tg mice. These results demonstrate a possible in vivo effectiveness of EGCG on amyloid formation and suggest an early therapeutical application. AU - Frankó, A. AU - Rodriguez Camargo, D.C. AU - Böddrich, A.* AU - Garg, D.* AU - Rodriguez Camargo, A. AU - Rathkolb, B. AU - Janik, D. AU - Aichler, M. AU - Feuchtinger, A. AU - Neff, F. AU - Fuchs, H. AU - Wanker, E.E.* AU - Reif, B. AU - Häring, H.-U. AU - Peter, A. AU - Hrabě de Angelis, M. C1 - 52756 C2 - 44314 CY - London TI - Epigallocatechin gallate (EGCG) reduces the intensity of pancreatic amyloid fibrils in human islet amyloid polypeptide (hIAPP) transgenic mice. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - DNA double strand breaks (DSB) play a pivotal role for cellular damage, which is a hazard encountered in toxicology and radiation protection, but also exploited e.g. in eradicating tumors in radiation therapy. It is still debated whether and in how far clustering of such DNA lesions leads to an enhanced severity of induced damage. Here we investigate - using focused spots of ionizing radiation as damaging agent - the spatial extension of DNA lesion patterns causing cell inactivation. We find that clustering of DNA damage on both the nm and pm scale leads to enhanced inactivation compared to more homogeneous lesion distributions. A biophysical model interprets these observations in terms of enhanced DSB production and DSB interaction, respectively. We decompose the overall effects quantitatively into contributions from these lesion formation processes, concluding that both processes coexist and need to be considered for determining the resulting damage on the cellular level. AU - Friedrich, T.* AU - Ilicic, K. AU - Greubel, C.* AU - Girst, S.* AU - Reindl, J.* AU - Sammer, M.* AU - Schwarz, B.* AU - Siebenwirth, C.* AU - Walsh, D.W.M.* AU - Schmid, T.E. AU - Scholz, M.* AU - Dollinger, G.* C1 - 54640 C2 - 45734 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - DNA damage interactions on both nanometer and micrometer scale determine overall cellular damage. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Yellowstone National Park hydrothermal springs were investigated according to their organic geochemistry with a special focus on the Yellowstone hot spring dissolved organic matter (YDOM) that was solid-phase extracted. Here we show that YDOM has a unique chemodiversity that has not yet been observed anywhere else in aquatic surface environments and that Yellowstone hot springs are organic chemodiversity hot spots. Four main geochemically classified hot spring types (alkaline-chloride, mixed alkaline-chloride, acid-chloride-sulfate and travertine-precipitating) exhibited distinct organic molecular signatures that correlated remarkably well with the known inorganic geochemistry and manifested themselves in excitation emission matrix fluorescence, nuclear magnetic resonance, and ultrahigh resolution mass spectra.YDOM contained thousands of molecular formulas unique to Yellowstone of which 80% contained sulfur, even in low hydrogen sulfide containing alkaline-chloride springs. This unique YDOM reflects the extreme organic geochemistry present in the hydrothermal features of Yellowstone National Park. AU - Gonsior, M.* AU - Hertkorn, N. AU - Hinman, N.* AU - Dvorski, S. AU - Harir, M. AU - Cooper, W.J.* AU - Schmitt-Kopplin, P. C1 - 54379 C2 - 45539 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Yellowstone hot springs are organic chemodiversity hot spots. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - We describe the first dynamic and the first in vivo X-ray imaging studies successfully performed at a laser-undulator-based compact synchrotron light source. The X-ray properties of this source enable time-sequence propagation-based X-ray phase-contrast imaging. We focus here on non-invasive imaging for respiratory treatment development and physiological understanding. In small animals, we capture the regional delivery of respiratory treatment, and two measures of respiratory health that can reveal the effectiveness of a treatment; lung motion and mucociliary clearance. The results demonstrate the ability of this set-up to perform laboratory-based dynamic imaging, specifically in small animal models, and with the possibility of longitudinal studies. AU - Gradl, R.* AU - Dierolf, M.* AU - Guenther, B.* AU - Hehn, L.* AU - Möller, W. AU - Kutschke, D. AU - Yang, L. AU - Donnelley, M.* AU - Murrie, R.* AU - Erl, A. AU - Stöger, T. AU - Gleich, B.* AU - Achterhold, K.* AU - Schmid, O. AU - Pfeiffer, F.* AU - Morgan, K.S.* C1 - 53535 C2 - 44740 TI - In vivo dynamic phase-contrast X-ray Imaging using a compact light source. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Accurate in vivo localisation of minimal amounts of functionalised gold-nanoparticles, enabling e.g. early-tumour diagnostics and pharmacokinetic tracking studies, requires a precision imaging system offering very high sensitivity, temporal and spatial resolution, large depth penetration, and arbitrarily long serial measurements. X-ray fluorescence imaging could offer such capabilities; however, its utilisation for human-sized scales is hampered by a high intrinsic background level. Here we measure and model this anisotropic background and present a spatial filtering scheme for background reduction enabling the localisation of nanoparticle-amounts as reported from small-animal tumour models. As a basic application study towards precision pharmacokinetics, we demonstrate specific localisation to sites of disease by adapting gold-nanoparticles with small targeting ligands in murine spinal cord injury models, at record sensitivity levels using sub-mm resolution. Both studies contribute to the future use of molecularly-targeted gold-nanoparticles as next-generation clinical diagnostic and pharmacokinetic tools. AU - Grüner, F.* AU - Blumendorf, F.* AU - Schmutzler, O.* AU - Staufer, T.* AU - Bradbury, M.* AU - Wiesner, U.* AU - Rosentreter, T. AU - Loers, G.* AU - Lutz, D.* AU - Richter, B.* AU - Fischer, M.* AU - Schulz, F.* AU - Steiner, S.* AU - Warmer, M.* AU - Burkhardt, A.* AU - Meents, A.* AU - Kupinski, M.A.* AU - Hoeschen, C.* C1 - 54753 C2 - 45790 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Localising functionalised gold-nanoparticles in murine spinal cords by X-ray fluorescence imaging and background-reduction through spatial filtering for human-sized objects. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - In hyper-IgE syndromes (HIES), a group of primary immunodeficiencies clinically overlapping with atopic dermatitis, early diagnosis is crucial to initiate appropriate therapy and prevent irreversible complications. Identification of underlying gene defects such as in DOCKS and STAT3 and corresponding molecular testing has improved diagnosis.Yet, in a child and her newborn sibling with HIES phenotype molecular diagnosis was misleading. Extensive analyses driven by the clinical phenotype identified an intronic homozygous DOCKS variant c.4626 76A > G creating a novel splice site as disease-causing. While the affected newborn carrying the homozygous variant had no expression of DOCK8 protein, in the index patient molecular diagnosis was compromised due to expression of altered and wildtype DOCKS transcripts and DOCK8 protein as well as defective STAT3 signaling. Sanger sequencing of lymphocyte subsets revealed that somatic alterations and reversions revoked the predominance of the novel over the canonical splice site in the index patient explaining DOCK8 protein expression, whereas defective STAT3 responses in the index patient were explained by a T cell phenotype skewed towards central and effector memory T cells. Hence, somatic alterations and skewed immune cell phenotypes due to selective pressure may compromise molecular diagnosis and need to be considered with unexpected clinical and molecular findings. AU - Hagl, B. AU - Spielberger, B.D. AU - Thoene, S.* AU - Bonnal, S.* AU - Mertes, C.* AU - Winter, C.* AU - Nijman, I.J.* AU - Verduin, S.* AU - Eberherr, A.C. AU - Puel, A.* AU - Schindler, D.* AU - Ruland, J.* AU - Meitinger, T. AU - Gagneur, J.* AU - Orange, J.S.* AU - van Gijn, M.E.* AU - Renner, E.D. C1 - 54739 C2 - 45804 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Somatic alterations compromised molecular diagnosis of DOCK8 hyper-IgE syndrome caused by a novel intronic splice site mutation. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The aim of this study was to evaluate the feasibility of early stage imaging of acute lung inflammation in mice using grating-based X-ray dark-field imaging in vivo. Acute lung inflammation was induced in mice by orotracheal instillation of porcine pancreatic elastase. Control mice received orotracheal instillation of PBS. Mice were imaged immediately before and 1 day after the application of elastase or PBS to assess acute changes in pulmonary structure due to lung inflammation. Subsequently, 6 mice from each group were sacrificed and their lungs were lavaged and explanted for histological analysis. A further 7, 14 and 21 days later the remaining mice were imaged again. All images were acquired with a prototype grating-based small-animal scanner to generate dark-field and transmission radiographs. Lavage confirmed that mice in the experimental group had developed acute lung inflammation one day after administration of elastase. Acute lung inflammation was visible as a striking decrease in signal intensity of the pulmonary parenchyma on dark-field images at day 1. Quantitative analysis confirmed that dark-field signal intensity at day 1 was significantly lower than signal intensities measured at the remaining timepoints, confirming that acute lung inflammation can be depicted in vivo with dark-field radiography. AU - Hellbach, K.* AU - Meinel, F.G.* AU - Conlon, T.M. AU - Willer, K.* AU - Yaroshenko, A.* AU - Velroyen, A.* AU - Braunagel, M.* AU - Auweter, S.* AU - Reiser, M.F.* AU - Eickelberg, O. AU - Pfeiffer, F.* AU - Yildirim, A.Ö. C1 - 53035 C2 - 44377 CY - London TI - X-ray dark-field imaging to depict acute lung inflammation in mice. JO - Sci. Rep. VL - 8 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Reactions between sugars and amino acids in the Maillard reaction produce a multitude of compounds through interconnected chemical pathways. The course of the pathways changes depending on the nature of the amino acids and sugars as well as the processing conditions (e.g. temperature, water activity). Some partial pathways have been elucidated using labelled precursors but the process is very time intensive. Here, we use rapid, non-targeted analysis with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to deliver the molecular formulae and ion intensities of the compounds generated from reaction of four amino acids with ribose (10 h at 100 degrees C) to study the effect of amino acid side chains on the reaction pathways. Using van Krevelen diagrams, known chemical changes during the reaction (e.g. dehydration or decarboxylation) can be studied. Comparison of the data from the four amino acids studied, showed a common pathway, which involved 73 Maillard reaction products (MRPs) where the differences were due only to the nature of the amino acid side chain. From the more than 1400 different molecular formulae found, pathways unique to the amino acids were also identified and the order of reactivity was lysine >cysteine >isoleucine approximate to glycine. While unequivocal identification of the compounds cannot be achieved with FT-ICR-MS, applying known chemical transformations found in the Maillard reaction, not only identifies new and known pathways, but also integrates the MRPs into a general Maillard reaction scheme that better represents the totality of the Maillard reaction. AU - Hemmler, D. AU - Roullier-Gall, C. AU - Marshall, J.W.* AU - Rychlik, M.* AU - Taylor, A.J.* AU - Schmitt-Kopplin, P. C1 - 54787 C2 - 45857 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Insights into the chemistry of non-enzymatic browning reactions in different ribose-amino acid model systems. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Mutations in mitochondrial DNA (mtDNA) lead to heteroplasmy, i.e., the intracellular coexistence of wild-type and mutant mtDNA strands, which impact a wide spectrum of diseases but also physiological processes, including endurance exercise performance in athletes. However, the phenotypic consequences of limited levels of naturally arising heteroplasmy have not been experimentally studied to date. We hence generated a conplastic mouse strain carrying the mitochondrial genome of an AKR/J mouse strain (B6-mt) in a C57BL/6 J nuclear genomic background, leading to >20% heteroplasmy in the origin of light-strand DNA replication (OriL). These conplastic mice demonstrate a shorter lifespan as well as dysregulation of multiple metabolic pathways, culminating in impaired glucose metabolism, compared to that of wild-type C57BL/6 J mice carrying lower levels of heteroplasmy. Our results indicate that physiologically relevant differences in mtDNA heteroplasmy levels at a single, functionally important site impair the metabolic health and lifespan in mice. AU - Hirose, M.* AU - Schilf, P.* AU - Gupta, Y.* AU - Zarse, K.* AU - Künstner, A.* AU - Fähnrich, A.* AU - Busch, H.* AU - Yin, J.* AU - Wright, M.N.* AU - Ziegler, A.* AU - Vallier, M.* AU - Belheouane, M.* AU - Baine, J.F.* AU - Tautz, D.* AU - Johann, K.* AU - Oelkrug, R.* AU - Mittag, J.* AU - Lehnert, H.* AU - Othmann, A.* AU - Jöhren, O.* AU - Schwaninger, M.* AU - Prehn, C. AU - Adamski, J. AU - Shima, K.* AU - Rupp, J.* AU - Häsler, R.* AU - Fuellen, G.* AU - Köhling, R.* AU - Ristow, M.* AU - Ibrahim, S.M.* C1 - 53391 C2 - 44551 TI - Low-level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice. JO - Sci. Rep. VL - 8 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Measuring mitochondrial respiration in cultured cells is a valuable tool to investigate the influence of physiological and disease-related factors on cellular metabolism; however, the details of the experimental workflow greatly influence the informative value of the results. Working with primary cells and cell types capable of differentiation can be particularly challenging. We present a streamlined workflow optimised for investigation of primary human skeletal muscle cells. We applied the workflow to differentiated and undifferentiated cells and we investigated the effect of TGF beta 1 treatment. Differentiation of myoblasts to myotubes increased mitochondrial respiration and abundance of mitochondrial enzymes and mitochondrial marker proteins. Differentiation also induced qualitative changes in mitochondrial protein composition and respiration. TGF beta 1 reduced complex IV protein MTCO1 abundance in both myoblasts and myotubes. In myoblasts, spare electron transport system (ETS) capacity was reduced due to a reduction in maximal oxygen consumption. In TGF beta 1-treated myotubes, the reduction in spare ETS capacity is mainly a consequence of increased oxidative phosphorylation capacity and complex III protein UQCRC2. Taken together, our data shows that it is important to monitor muscle cell differentiation when mitochondrial function is studied. Our workflow is not only sensitive enough to detect physiological-sized differences, but also adequate to form mechanistic hypotheses. AU - Hoffmann, C.* AU - Höckele, S. AU - Kappler, L.* AU - Hrabě de Angelis, M. AU - Häring, H.-U. AU - Weigert, C. C1 - 52810 C2 - 44320 CY - London TI - The effect of differentiation and TGFβ on mitochondrial respiration and mitochondrial enzyme abundance in cultured primary human skeletal muscle cells. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - We introduce a contrast mechanism for visualizing blood vessels based on radiofrequency-induced second harmonic acoustic (RISHA) signals sensing blood conductivity. We develop a novel imaging system using commonly available inexpensive components, and demonstrate in vivo RISHA visualization of blood vessels based on low-power quasi-continuous radiofrequency excitation of tissue at frequencies of a few MHz. We show how the novel approach also implicitly enables radiofrequency-induced passive ultrasound imaging and can be readily applied to non-invasive imaging of blood vessels ex vivo and in vivo. We discuss the implications of non-invasive conductivity measurements in the context of biomedical applications. AU - Huang, Y. AU - Kellnberger, S. AU - Sergiadis, G. AU - Ntziachristos, V. C1 - 54589 C2 - 45690 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Blood vessel imaging using radiofrequency-induced second harmonic acoustic response. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - MicroRNAs (miRNAs) play an important role in the regulation of gene expression. The binding to target messenger RNAs (mRNAs) results in mRNA cleavage or inhibition of the translational machinery leading to decreased protein levels. Various signalling pathways, including apoptosis are modulated by miRNAs. Here, we investigated the role of miR-744-5p in apoptosis signalling in ovarian cancer cell lines. MiR-744-5p expression was reduced in the cancer cell lines independent of the host gene MAP2K4. Overexpression of miR-744-5p activated the intrinsic apoptotic pathway in SKOV3, OVCAR3 and Cisplatin resistant (A2780-cis) and non-resistant A2780 cells leading to cell death. Notably, miR-744-5p overexpression together with Carboplatin treatment led to at least additive pro-apoptotic effects. Investigation of the apoptotic signalling pathways mediated by miR-744-5p revealed that its elevated expression directly downregulated mRNA and protein expression of nuclear factor I X (NFIX) and heterogeneous nuclear ribonucleoprotein C (HNRNPC). HNRNPC caused diminished miR-21 expression and AKT phosphorylation, while NFIX decreased Bcl2 levels, leading to the detected pro-apoptotic effects. Finally, Kaplan-Meier-Plots showed a prolonged median disease-free survival in ovarian serous cystadenocarcinoma patients with high miR-744 expression. AU - Kleemann, M.* AU - Schneider, H.* AU - Unger, K. AU - Sander, P.* AU - Schneider, E.M.* AU - Fischer-Posovszky, P.* AU - Handrick, R.* AU - Otte, K.* C1 - 53653 C2 - 44934 CY - 1752 N St Nw, Washington, Dc 20036-2904 Usa TI - MiR-744-5p inducing cell death by directly targeting HNRNPC and NFIX in ovarian cancer cells. JO - Sci. Rep. VL - 8 IS - 1 PB - Amer Soc Microbiology PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Regular exercise elicits advantageous metabolic adaptations in skeletal muscle, such as improved insulin sensitivity. However, the underpinning molecular mechanisms and the effect of diet on muscle exercise training benefits are unclear. We therefore characterized the skeletal muscle proteome following exercise training (ET) in mice fed chow or high-fat diet (HFD). ET increased exercise performance, lowered body-weight, decreased fat mass and improved muscle insulin action in chow-and HFD-fed mice. At the molecular level, ET regulated 170 muscle proteins in chow-fed mice, but only 29 proteins in HFD-fed mice. HFD per se altered 56 proteins, most of which were regulated in a similar direction by ET. To identify proteins that might have particular health-related bearing on skeletal muscle metabolism, we filtered for differentially regulated proteins in response to ET and HFD. This yielded 15 proteins, including the major urinary protein 1 (MUP1), which was the protein most decreased after HFD, but increased with ET. The ET-induced Mup1 expression was absent in mouse muscle lacking functional AMPK. MUP1 also potentiated insulin-stimulated GLUT4 translocation in cultured muscle cells. Collectively, we provide a resource of ET-regulated proteins in insulin-sensitive and insulin-resistant skeletal muscle. The identification of MUP1 as a diet-, ET-and AMPK-regulated skeletal muscle protein that improves insulin sensitivity in muscle cells demonstrates the usefulness of these data. AU - Kleinert, M. AU - Parker, B.L.* AU - Jensen, T.E.* AU - Raun, S.H.* AU - Pham, P. AU - Han, X.* AU - James, D.E.* AU - Richter, E.A.* AU - Sylow, L.* C1 - 53958 C2 - 45141 TI - Quantitative proteomic characterization of cellular pathways associated with altered insulin sensitivity in skeletal muscle following high-fat diet feeding and exercise training. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Disruption of metabolic homeostasis is an important factor in many diseases. Various metabolites have been linked to higher risk of morbidity and all-cause mortality using metabolomics in large population-based cohorts. In these studies, baseline metabolite levels were compared across subjects to identify associations with health outcomes, implying the existence of ‘healthy’ concentration ranges that are equally applicable to all individuals. Here, we focused on intra-individual changes in metabolite levels over time and their link to mortality, potentially allowing more personalized risk assessment. We analysed targeted metabolomics data for 134 blood metabolites from 1409 participants in the population-based CARLA cohort at baseline and after four years. Metabotypes of the majority of participants (59%) were extremely stable over time indicated by high correlation between the subjects’ metabolite profiles at the two time points. Metabotype instability and, in particular, decrease of valine were associated with higher risk of all-cause mortality in 7.9 years of follow-up (hazard ratio (HR) = 1.5(95%CI = 1.0–2.3) and 0.2(95%CI = 0.1–0.3)) after multifactorial adjustment. Excluding deaths that occurred in the first year after metabolite profiling showed similar results (HR = 1.8(95%CI = 1.1–2.8)). Lower metabotype stability was also associated with incident cardiovascular disease (OR = 1.2(95%CI = 1.0–1.3)). Therefore, changes in the personal metabotype might be a valuable indicator of pre-clinical disease. AU - Lacruz, M.E.* AU - Kluttig, A.* AU - Tiller, D.* AU - Medenwald, D.* AU - Giegling, I.* AU - Rujescu, D.* AU - Prehn, C. AU - Adamski, J. AU - Greiser, K.H.* AU - Kastenmüller, G. C1 - 53733 C2 - 44953 CY - Po Box 211, 1000 Ae Amsterdam, Netherlands TI - Instability of personal human metabotype is linked to all-cause mortality. JO - Sci. Rep. VL - 8 IS - 1 PB - Elsevier Science Bv PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The food-related behavior of functional dyspepsia has been attracting more interest of late. This pilot study aims to provide evidence of the physiological, emotional, and attentional aspects of food processing in functional dyspepsia patients. The study was performed in 15 functional dyspepsia patients and 17 healthy controls after a standard breakfast. We measured autonomic nervous system activity using skin conductance response and heart rate variability, emotional response using facial electromyography, and visual attention using eyetracking during the visual stimuli of food/non-food images. In comparison to healthy controls, functional dyspepsia patients showed a greater craving for food, a decreased intake of food, more dyspeptic symptoms, lower pleasantness rating of food images (particularly of high fat), decreased low frequency/high frequency ratio of heart rate variability, and suppressed total processing time of food images. There were no significant differences of skin conductance response and facial electromyography data between groups. The results suggest that high level cognitive functions rather than autonomic and emotional mechanisms are more liable to function differently in functional dyspepsia patients. Abnormal dietary behavior, reduced subjective rating of pleasantness and visual attention to food should be considered as important pathophysiological characteristics in functional dyspepsia. AU - Lee, I.* AU - Preissl, H. AU - Giel, K.E.* AU - Schag, K.* AU - Enck, P.* C1 - 52844 C2 - 44293 CY - London TI - Attentional and physiological processing of food images in functional dyspepsia patients: A pilot study. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The Langendorff-perfused heart technique has become the model of choice for multiparametric optical mapping of cardiac function and electrophysiology. However, photon scattering in tissues represents a significant drawback of the optical imaging approach, fundamentally limiting its mapping capacity to the heart surface. This work presents the first implementation of the optoacoustic approach for 4D imaging of the entire beating isolated mouse heart. The method combines optical excitation and acoustic detection to simultaneously render rich optical contrast and high spatio-temporal resolution at centimeter-scale depths. We demonstrate volumetric imaging of deeply located cardiac features, including the interventricular septum, chordae tendineae, and papillary muscles while further tracking the heart beat cycle and the motion of the pulmonary, mitral, and tricuspid valves in real time. The technique possesses a powerful combination between high imaging depth, fast volumetric imaging speed, functional and molecular imaging capacities not available with other imaging modalities currently used in cardiac research. AU - Lin, H.-C. AU - Dean-Ben, X.L. AU - Reiss, M. AU - Schöttle, V.* AU - Wahl-Schott, C.A.* AU - Efimov, I.R.* AU - Razansky, D. C1 - 54378 C2 - 45538 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Ultrafast volumetric optoacoustic imaging of whole isolated beating mouse heart. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Genetically modified mice models suggest an important role for G-protein-coupled receptor kinase 5 (GRK5) in the pathophysiology of obesity and related disorders. We investigated whether single nucleotide polymorphisms (SNPs) in the gene encoding GRK5 affect cardiometabolic traits in humans. We genotyped 3 common SNPs in intron 1 (rs1980030, rs10466210, rs9325562) and one SNP in intron 3 (rs10886471) of GRK5 in 2332 subjects at risk for type 2 diabetes. Total- and visceral fat mass were measured by magnetic resonance (MR) tomography and liver fat content by 1H-MR spectroscopy. Insulin secretion and sensitivity were estimated during an OGTT and measured during the euglycemic, hyperinsulinemic clamp (n = 498). Carriers of the minor allele of rs10466210 and rs1980030 had higher total- and LDL-cholesterol levels (p = 0.0018 and p = 0.0031, respectively, for rs10466210; p = 0.0035 and p = 0.0081, respectively, for rs1980030), independently of gender, age, BMI and lipid-lowering drugs. The effects of rs10466210 withstood Bonferroni correction. Similar associations were observed with apolipoprotein B levels (p = 0.0034 and p = 0.0122, respectively). Carriers of the minor allele of rs10466210 additionally displayed a trend for higher intima-media thickness of the carotid artery (p = 0.075). GRK5 may represent a novel target for strategies aiming at lowering LDL-cholesterol levels and at modifying cardiovascular risk. AU - Lutz, S.Z. AU - Falcenberg, M.* AU - Machicao, F. AU - Peter, A. AU - Kächele, M. AU - Randrianarisoa, E. AU - Lehn-Stefan, A. AU - Wagner, R. AU - Machann, J. AU - Schick, F. AU - Heni, M. AU - Ullrich, A.* AU - Fritsche, A. AU - Stefan, N. AU - Häring, H.-U. AU - Staiger, H. AU - Kantartzis, K. C1 - 53584 C2 - 44694 TI - Single nucleotide polymorphisms in the G-protein coupled receptor kinase 5 (GRK5) gene are associated with plasma LDL-cholesterol levels in humans. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Diabetes mellitus is a group of disorders characterized by prolonged high levels of circulating blood glucose. Type 1 diabetes is caused by decreased insulin production in the pancreas whereas type 2 diabetes may develop due to obesity and lack of exercise; it begins with insulin resistance whereby cells fail to respond properly to insulin and it may also progress to decreased insulin levels. The brain is an important target for insulin, and there is great interest in understanding how diabetes affects the brain. In addition to the direct effects of insulin on the brain, diabetes may also impact the brain through modulation of the inflammatory system. Here we investigate how perturbation of circulating insulin levels affects the expression of Hes3, a transcription factor expressed in neural stem and progenitor cells that is involved in tissue regeneration. Our data show that streptozotocin-induced beta-cell damage, high fat diet, as well as metformin, a common type 2 diabetes medication, regulate Hes3 levels in the brain. This work suggests that Hes3 is a valuable biomarker helping to monitor the state of endogenous neural stem and progenitor cells in the context of diabetes mellitus. AU - Nikolakopoulou, P.* AU - Chatzigeorgiou, A.* AU - Kourtzelis, I.* AU - Toutouna, L.* AU - Masjkur, J.* AU - Arps-Forker, C.* AU - Poser, S.W.* AU - Rozman, J. AU - Rathkolb, B. AU - Aguilar-Pimentel, J.A. AU - German Mouse Clinic Consortium* AU - Wolf, E.* AU - Klingenspor, M.* AU - Ollert, M.* AU - Schmidt-Weber, C.B. AU - Fuchs, H. AU - Gailus-Durner, V. AU - Hrabě de Angelis, M. AU - Tsata, V.* AU - Sebastian Monasor, L.* AU - Troullinaki, M.* AU - Witt, A.* AU - Anastasiou, V. AU - Chrousos, G.* AU - Yi, C.-X.* AU - García-Cáceres, C. AU - Tschöp, M.H. AU - Bornstein, S.R.* AU - Androutsellis-Theotokis, A.* AU - German Mouse Clinic Consortium (Garrett, L. AU - Hölter, S.M. AU - Zimprich, A. AU - Wurst, W. AU - Amarie, O.V. AU - Graw, J. AU - Neff, F.) C1 - 54023 C2 - 45199 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Streptozotocin-induced beta-cell damage, high fat diet, and metformin administration regulate Hes3 expression in the adult mouse brain. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Mechanisms of injury and repair in alveolar epithelial cells (AECs) are critically involved in the progression of various lung diseases including idiopathic pulmonary fibrosis (IPF). Homeobox only protein x (HOPX) contributes to the formation of distal lung during development. In adult lung, alveolar epithelial type (AT) I cells express HOPX and lineage-labeled Hopx+ cells give rise to both ATI and ATII cells after pneumonectomy. However, the cell function of HOPX-expressing cells in adult fibrotic lung diseases has not been investigated. In this study, we have established a flow cytometry-based method to evaluate HOPX-expressing cells in the lung. HOPX expression in cultured ATII cells increased over culture time, which was accompanied by a decrease of proSP-C, an ATII marker. Moreover, HOPX expression was increased in AECs from bleomycin-instilled mouse lungs in vivo. Small interfering RNA-based knockdown of Hopx resulted in suppressing ATII-ATI trans-differentiation and activating cellular proliferation in vitro. In IPF lungs, HOPX expression was decreased in whole lungs and significantly correlated to a decline in lung function and progression of IPF. In conclusion, HOPX is upregulated during early alveolar injury and repair process in the lung. Decreased HOPX expression might contribute to failed regenerative processes in end-stage IPF lungs. AU - Ota, C. AU - Ng-Blichfeldt, J.P.* AU - Korfei, M.* AU - Alsafadi, H.N. AU - Lehmann, M. AU - Skronska-Wasek, W. AU - De Santis, M. AU - Guenther, A.* AU - Wagner, D.E. AU - Königshoff, M. C1 - 54199 C2 - 45339 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Dynamic expression of HOPX in alveolar epithelial cells reflects injury and repair during the progression of pulmonary fibrosis. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - High-frequency oscillatory ventilation (HFOV) is a commonly used therapy applied to neonates requiring ventilatory support during their first weeks of life. Despite its wide application, the underlying gas exchange mechanisms promoting the success of HVOF in neonatal care are not fully understood until today. In this work, a highly resolved computational lung model, derived from Magnetic Resonance Imaging (MRI) and Infant Lung Function Testing (ILFT), is used to reveal the reason for highly efficient gas exchange during HFOV, in the preterm infant. In total we detected six mechanisms that facilitate gas exchange during HFOV: (i) turbulent vortices in large airways; (ii) asymmetric in-and expiratory flow profiles; (iii) radial mixing in main bronchi; (iv) laminar flow in higher generations of the respiratory tract; (v) pendelluft; (vi) direct ventilation of central alveoli. The illustration of six specific gas transport phenomena during HFOV in preterm infants advances general knowledge on protective ventilation in neonatal care and can support decisions on various modes of ventilatory therapy at high frequencies. AU - Roth, C.J.* AU - Förster, K. AU - Hilgendorff, A. AU - Ertl-Wagner, B.* AU - Wall, W.A.* AU - Flemmer, A.W.* C1 - 54243 C2 - 45401 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Gas exchange mechanisms in preterm infants on HFOV - a computational approach. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Epithelial cell adhesion molecule EpCAM is expressed in pluripotent embryonic stem cells (ESC) in vitro, but is repressed in differentiated cells, except epithelia and carcinomas. Molecular functions of EpCAM, possibly imposing such repression, were primarily studied in malignant cells and might not apply to non-pathologic differentiation. Here, we comprehensively describe timing and rationale for EpCAM regulation in early murine gastrulation and ESC differentiation using single cell RNA-sequencing datasets, in vivo and in vitro models including CRISPR-Cas9-engineered ESC-mutants. We demonstrate expression of EpCAM in inner cell mass, epiblast, primitive/visceral endoderm, and strict repression in the most primitive, nascent Flk1+ mesoderm progenitors at E7.0. Selective expression of EpCAM was confirmed at mid-gestation and perinatal stages. The rationale for strict patterning was studied in ESC differentiation. Gain/loss-of-function demonstrated supportive functions of EpCAM in achieving full pluripotency and guided endodermal differentiation, but repressive functions in mesodermal differentiation as exemplified with cardiomyocyte formation. We further identified embryonic Ras (ERas) as novel EpCAM interactor of EpCAM and an EpCAM/ERas/AKT axis that is instrumental in differentiation regulation. Hence, spatiotemporal patterning of EpCAM at the onset of gastrulation, resulting in early segregation of interdependent EpCAM+ endodermal and EpCAM-/vimentin+ mesodermal clusters represents a novel regulatory feature during ESC differentiation. AU - Sarrach, S.* AU - Huang, Y.* AU - Niedermeyer, S.* AU - Hachmeister, M.* AU - Fischer, L.* AU - Gille, S.* AU - Pan, M.* AU - Mack, B.* AU - Kranz, G.* AU - Libl, D.* AU - Merl-Pham, J. AU - Hauck, S.M. AU - Paoluzzi Tomada, E.* AU - Kieslinger, M. AU - Jeremias, I. AU - Scialdone, A. AU - Gires, O.* C1 - 52842 C2 - 44386 CY - London TI - Spatiotemporal patterning of EpCAM is important for murine embryonic endo-And mesodermal differentiation. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - System x c - was recently described as the most upstream node in a novel form of regulated necrotic cell death, called ferroptosis. In this context, the small molecule erastin was reported to target and inhibit system x c - , leading to cysteine starvation, glutathione depletion and consequently ferroptotic cell death. Although the inhibitory effect of erastin towards system x c - is well-documented, nothing is known about its mechanism of action. Therefore, we sought to interrogate in more detail the underlying mechanism of erastin's pro-ferroptotic effects. When comparing with some well-known inhibitors of system x c - , erastin was the most efficient inhibitor acting at low micromolar concentrations. Notably, only a very short exposure of cells with low erastin concentrations was sufficient to cause a strong and persistent inhibition of system x c - , causing glutathione depletion. These inhibitory effects towards system x c - did not involve cysteine modifications of the transporter. More importantly, short exposure of tumor cells with erastin strongly potentiated the cytotoxic effects of cisplatin to efficiently eradicate tumor cells. Hence, our data suggests that only a very short pre-treatment of erastin suffices to synergize with cisplatin to efficiently induce cancer cell death, findings that might guide us in the design of novel cancer treatment paradigms. AU - Sato, M.* AU - Kusumi, R.* AU - Hamashima, S.* AU - Kobayashi, S.* AU - Sasaki, S.* AU - Komiyama, Y.* AU - Izumikawa, T.* AU - Conrad, M. AU - Bannai, S.* AU - Sato, H.* C1 - 52750 C2 - 44326 CY - London TI - The ferroptosis inducer erastin irreversibly inhibits system xc- and synergizes with cisplatin to increase cisplatin's cytotoxicity in cancer cells. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - While many studies have demonstrated that canonical NF-κB signaling is a central pathway in lung tumorigenesis, the role of non-canonical NF-κB signaling in lung cancer remains undefined. We observed frequent nuclear accumulation of the non-canonical NF-κB component p100/p52 in human lung adenocarcinoma. To investigate the impact of non-canonical NF-κB signaling on lung carcinogenesis, we employed transgenic mice with doxycycline-inducible expression of p52 in airway epithelial cells. p52 over-expression led to increased tumor number and progression after injection of the carcinogen urethane. Gene expression analysis of lungs from transgenic mice combined with in vitro studies suggested that p52 promotes proliferation of lung epithelial cells through regulation of cell cycle-associated genes. Using gene expression and patient information from The Cancer Genome Atlas (TCGA) database, we found that expression of p52-associated genes was increased in lung adenocarcinomas and correlated with reduced survival, even in early stage disease. Analysis of p52-associated gene expression in additional human lung adenocarcinoma datasets corroborated these findings. Together, these studies implicate the non-canonical NF-κB component p52 in lung carcinogenesis and suggest modulation of p52 activity and/or downstream mediators as new therapeutic targets. AU - Saxon, J.A.* AU - Yu, H.* AU - Polosukhin, V.V.* AU - Stathopoulos, G.T. AU - Gleaves, L.A.* AU - McLoed, A.G.* AU - Massion, P.P.* AU - Yull, F.E.* AU - Zhao, Z.* AU - Blackwell, T.S.* C1 - 53660 C2 - 44784 TI - P52 expression enhances lung cancer progression. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The GTP-binding protein septin 7 is involved in various cellular processes, including cytoskeleton organization, migration and the regulation of cell shape. Septin 7 function in lymphocytes, however, is poorly characterized. Since the intracellular signaling role of septin 7 is dependent on its interaction network, interaction proteomics was applied to attain novel knowledge about septin 7 function in hematopoietic cells. Our previous finding of decreased septin 7 expression in blood-derived lymphocytes in ERU, a spontaneous animal model for autoimmune uveitis in man, extended the role of septin 7 to a potential key player in autoimmunity. Here, we revealed novel insights into septin 7 function by identification of DOCK8 as an interaction partner in primary blood-derived lymphocytes. Since DOCK8 is associated with important immune functions, our finding of significantly decreased DOCK8 expression and altered DOCK8 interaction network in ERU might explain changes in immune response and shows the contribution of DOCK8 in pathomechanisms of spontaneous autoimmune diseases. Moreover, our analyses revealed insights in DOCK8 function, by identifying the signal transducer ILK as a DOCK8 interactor in lymphocytes. Our finding of the enhanced enrichment of ILK in ERU cases indicates a deviant influence of DOCK8 on inter-and intracellular signaling in autoimmune disease. AU - Schauer, M.* AU - Kleinwort, K.J.H.* AU - Degroote, R.L.* AU - Wiedemann, C.* AU - Kremmer, E. AU - Hauck, S.M. AU - Deeg, C.A.* C1 - 54145 C2 - 45367 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Hymenoptera venom allergy can cause severe anaphylaxis in untreated patients. Polistes dominula is an important elicitor of venom allergy in Southern Europe as well as in the United States. Due to its increased spreading to more moderate climate zones, Polistes venom allergy is likely to gain importance also in these areas. So far, only few allergens of Polistes dominula venom were identified as basis for component-resolved diagnostics. Therefore, this study aimed to broaden the available panel of important Polistes venom allergens. The 100 kDa allergen Pol d 3 was identified by mass spectrometry and found to be a dipeptidyl peptidase IV. Recombinantly produced Pol d 3 exhibited sIgE-reactivity with approximately 66% of Polistes venom-sensitized patients. Moreover, its clinical relevance was supported by the potent activation of basophils from allergic patients. Cross-reactivity with the dipeptidyl peptidases IV from honeybee and yellow jacket venom suggests the presence of exclusive as well as conserved IgE epitopes. The obtained data suggest a pivotal role of Pol d 3 as sensitizing component of Polistes venom, thus supporting its status as a major allergen of clinical relevance. Therefore, Pol d 3 might become a key element for proper diagnosis of Polistes venom allergy. AU - Schiener, M. AU - Hilger, C.* AU - Eberlein, B.* AU - Pascal, M.* AU - Kuehn, A.* AU - Revets, D.* AU - Planchon, S.* AU - Pietsch, G.* AU - Serrano, P.* AU - Moreno-Aguilar, C.* AU - de la Roca, F.* AU - Biedermann, T.* AU - Darsow, U.* AU - Schmidt-Weber, C.B. AU - Ollert, M.* AU - Blank, S. C1 - 52778 C2 - 44249 CY - London TI - The high molecular weight dipeptidyl peptidase IV Pol d 3 is a major allergen of Polistes dominula venom. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Although the impact of dietary patterns on human serum metabolites has been examined, the fasting effect on the metabolic profile has not yet been considered. The aim of this cross-sectional study is to investigate the influence of fasting regarding the association between dietary patterns, reflected by macro- and micronutrient intake, and human serum metabolites in a population-based cohort. A total 1197 non-diabetic German adults aged 45 to 83 years, who participated in baseline of the CARLA study 2002-2006 and had metabolite quantification were selected for this study. Macro- and micronutrient intakes were estimated from a food frequency questionnaire (FFQ). Concentrations of 134 serum metabolites were measured by targeted metabolomics AbsoluteIDQ p150 Kit. The association of dietary patterns with serum metabolites was calculated by means of linear regression and the influence of the fasting status was considered by including interaction terms with each macro- and micronutrient. Higher self-reported intake of alcohol and lower self-reported intake of organic acids were associated with higher concentrations of acylcarnitines and phosphatidylcholines. Mainly the associations between dietary patterns and acylcarnitines and hexose were altered after including interaction terms, suggesting effect modification by fasting status. No effect from fasting time was seen for amino acids and saturated, mono- and polyunsaturated phosphatidylcholines. AU - Sedlmeier, A.* AU - Kluttig, A.* AU - Giegling, I.* AU - Prehn, C. AU - Adamski, J. AU - Kastenmüller, G. AU - Lacruz, M.E.* C1 - 54138 C2 - 45272 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - The human metabolic profile reflects macro- and micronutrient intake distinctly according to fasting time. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The human uptake transporter NaCT is important for human brain development, brain function and energy metabolism and mediates the uptake of citrate and other intermediates of the tricarboxylic acid cycle from blood into neurons and hepatocytes. Mutations in the SLC13A5 gene encoding NaCT are associated with epileptic encephalopathy. To gain more insights into the transport mechanisms we analyzed the functional consequences of mutations in the SLC13A5 gene on NaCT-mediated transport function. Using HEK293 cells expressing wild-type and eight mutated NaCT proteins, we investigated the mRNA and protein amount as well as the protein localization of all NaCT variants. Furthermore, the impact on NaCT-mediated citrate uptake was measured. In addition, a structural model of the transport pore was generated to rationalize the consequences of the mutations on a structural basis. We demonstrated that all proteins were synthesized with an identical molecular weight as the wild-type transporter but several mutations (NaCTp.G219R, -p.G219E, -p.T227M, -p.L420P and -p.L488P) lead to a complete loss of NaCT-mediated citrate transport. This loss of transport activity can be explained on the basis of the developed structural model. This model may help in the further elucidation of the transport mechanism of this important uptake transporter. AU - Selch, S.* AU - Chafai, A.* AU - Sticht, H.* AU - Birkenfeld, A.L. AU - Fromm, M.F.* AU - Koenig, J.* C1 - 54104 C2 - 45309 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Analysis of naturally occurring mutations in the human uptake transporter NaCT important for bone and brain development and energy metabolism. JO - Sci. Rep. VL - 8 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Age-associated deterioration of cellular physiology leads to pathological conditions. The ability to detect premature aging could provide a window for preventive therapies against age-related diseases. However, the techniques for determining cellular age are limited, as they rely on a limited set of histological markers and lack predictive power. Here, we implement GERAS (GEnetic Reference for Age of Single-cell), a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displays greater than 90% accuracy in classifying the chronological stage of zebrafish and human pancreatic cells. The framework demonstrates robustness against biological and technical noise, as evaluated by its performance on independent samplings of single-cells. Additionally, GERAS determines the impact of differences in calorie intake and BMI on the aging of zebrafish and human pancreatic cells, respectively. We further harness the classification ability of GERAS to identify molecular factors that are potentially associated with the aging of beta-cells. We show that one of these factors, junba, is necessary to maintain the proliferative state of juvenile beta-cells. Our results showcase the applicability of a machine learning framework to classify the chronological stage of heterogeneous cell populations, while enabling detection of candidate genes associated with aging. AU - Singh, S.P.* AU - Janjuha, S. AU - Chaudhuri, S.* AU - Reinhardt, S.* AU - Kränkel, A.* AU - Dietz, S.* AU - Eugster, A.* AU - Bilgin, H.* AU - Korkmaz, S.* AU - Zararsız, G.* AU - Ninov, N. AU - Reid, J.E.* C1 - 54817 C2 - 45853 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Machine learning based classification of cells into chronological stages using single-cell transcriptomics. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Accelerometers objectively monitor physical activity, and ongoing research suggests they can also detect patterns of body movement. However, different types of signal (uniaxial, captured by older studies, vs. the newer triaxial) and or/device (validated Actigraph used by older studies, vs. others) may lead to incomparability of results from different time periods. Standardization is desirable. We establish whether uniaxial signals adequately monitor routine activity, and whether triaxial accelerometry can detect sport-specific variations in movement pattern. 1402 adolescents wore triaxial Actigraphs (GT3X) for one week and diaried sport. Uni- and triaxial counts per minute were compared across the week and between over 30 different sports. Across the whole recording period 95% of variance in triaxial counts was explained by the vertical axis (5th percentile for R2, 91%). Sport made up a small fraction of daily routine, but differences were visible: even when total acceleration was comparable, little was vertical in horizontal movements, such as ice skating (uniaxial counts 41% of triaxial) compared to complex movements (taekwondo, 55%) or ambulation (soccer, 69%). Triaxial accelerometry captured differences in movement pattern between sports, but so little time was spent in sport that, across the whole day, uni- and triaxial signals correlated closely. This indicates that, with certain limitations, uniaxial accelerometric measures of routine activity from older studies can be feasibly compared to triaxial measures from newer studies. Comparison of new studies based on raw accelerations to older studies based on proprietary devices and measures (epochs, counts) will require additional efforts which are not addressed in this paper. AU - Smith, M. AU - Horsch, A.* AU - Standl, M. AU - Heinrich, J. AU - Schulz, H. C1 - 54501 C2 - 45589 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Uni- and triaxial accelerometric signals agree during daily routine, but show differences between sports. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The hypothalamic neurohormone oxytocin decreases food intake via largely unexplored mechanisms. We investigated the central nervous mediation of oxytocin's hypophagic effect in comparison to its impact on the processing of generalized rewards. Fifteen fasted normal-weight, young men received intranasal oxytocin (24 IU) or placebo before functional magnetic resonance imaging (fMRI) measurements of brain activity during exposure to food stimuli and a monetary incentive delay task (MID). Subsequently, ad-libitum breakfast intake was assessed. Oxytocin compared to placebo increased activity in the ventromedial prefrontal cortex, supplementary motor area, anterior cingulate, and ventrolateral prefrontal cortices in response to high-vs. low-calorie food images in the fasted state, and reduced calorie intake by 12%. During anticipation of monetary rewards, oxytocin compared to placebo augmented striatal, orbitofrontal and insular activity without altering MID performance. We conclude that during the anticipation of generalized rewards, oxytocin stimulates dopaminergic reward-processing circuits. In contrast, oxytocin restrains food intake by enhancing the activity of brain regions that exert cognitive control, while concomitantly increasing the activity of structures that process food reward value. This pattern points towards a specific role of oxytocin in the regulation of eating behaviour in humans that might be of relevance for potential clinical applications. AU - Spetter, M.S.* AU - Feld, G.B.* AU - Thienel, M.* AU - Preissl, H. AU - Hege, M.A. AU - Hallschmid, M. C1 - 53032 C2 - 44376 CY - London TI - Oxytocin curbs calorie intake via food-specific increases in the activity of brain areas that process reward and establish cognitive control. JO - Sci. Rep. VL - 8 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - The number of pregnancies complicated by gestational diabetes (GDM) is increasing worldwide. To identify novel characteristics of GDM, we studied miRNA profiles of maternal and fetal whole blood cells (WBCs) from GDM and normal glucose tolerant (NGT) pregnant women matched for body mass index and maternal age. After adjustment for maternal weight gain and pregnancy week, we identified 29 mature micro-RNAs (miRNAs) up-regulated in GDM, one of which, i.e., miRNA-340, was validated by qPCR. mRNA and protein expression of PAIP1, a miRNA-340 target gene, was found down-regulated in GDM women, accordingly. In lymphocytes derived from the mothers' blood and treated in vitro, insulin increased and glucose reduced miRNA-340 expression. In fetal cord blood samples, no associations of miRNA-340 with maternal GDM were observed. Our results provide evidence for insulin-induced epigenetic, i.e., miRNA-dependent, programming of maternal WBCs in GDM. AU - Stirm, L. AU - Huypens, P. AU - Sass, S. AU - Batra, R. AU - Fritsche, L. AU - Brucker, S.* AU - Abele, H.* AU - Hennige, A.M. AU - Theis, F.J. AU - Beckers, J. AU - Hrabě de Angelis, M. AU - Fritsche, A. AU - Häring, H.-U. AU - Staiger, H. C1 - 52845 C2 - 44298 CY - London TI - Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - Fatty liver (FL) disease is the most common type of chronic liver disease. We hypothesized that liver's response to the process where large droplets of triglyceride fat accumulate in liver cells is reflected also in gene pathway expression in blood. Peripheral blood genome wide gene expression analysis and ultrasonic imaging of liver were performed for 1,650 participants (316 individuals with FL and 1,334 controls) of the Young Finns Study. Gene set enrichment analysis (GSEA) was performed for the expression data. Fourteen gene sets were upregulated (false discovery rate, FDR < 0.05) in subjects with FL. These pathways related to extracellular matrix (ECM) turnover, immune response regulation, prothrombotic state and neural tissues. After adjustment for known risk factors and biomarkers of FL, we found i) integrin A4B1 signaling, ii) leukocyte transendothelial migration, iii) CD40/CD40L and iv) netrin-1 signaling pathways to be upregulated in individuals with FL (nominal p < 0.05). From these all but not ii) remained significantly upregulated when analyzing only subjects without history of heavy alcohol use. In conclusion, FL was associated with blood gene sets of ECM turnover, inflammatory response, immune system activation and prothrombotic state. These may form a systemic link between FL and the development of cardiovascular diseases. AU - Taipale, T.* AU - Seppälä, I.* AU - Raitoharju, E.* AU - Mononen, N.* AU - Lyytikäinen, L.-P.* AU - Illig, T.* AU - Waldenberger, M. AU - Juonala, M.* AU - Hutri-Kähönen, N.* AU - Oksala, N.* AU - Kähönen, M.* AU - Raitakari, O.* AU - Lehtimäki, T.* C1 - 53914 C2 - 45043 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England SP - 10358 TI - Fatty liver is associated with blood pathways of inflammatory response, immune system activation and prothrombotic state in Young Finns Study. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - In prior studies, stroke incidence has mainly shown either declining time trends or stable rates in high-income countries. Changes could partially be linked to trends in classic cardiovascular disease (CVD) risk factors. In the present study, we analyzed the incidence of stroke in parallel with the prevalence of CVD risk factors over time in a German population. Data from three independent population-based MONICA/KORA Augsburg surveys conducted in 1989/90 (S2), 1994/95 (S3), and 1999/2001 (S4) were used to calculate age-standardized incidence rates (IR) of first-ever stroke over eight years from each baseline survey. Furthermore, the age-standardized prevalence rates of CVD risk factors were analyzed for these surveys. Changes in IR or prevalence were considered significantly different if their 95% confidence intervals (CI) did not overlap. The age-standardized IR of stroke showed no significant time trend (S2: IR = 203.4 per 100,000 person-years; CI 176.4-233.4, S3: IR = 225.6; 197.1-257.0, S4: IR = 209.9; CI 182.4-240.3). In agreement, the prevalence of the CVD risk factors was quite stable over time, showing divergent, but mostly non-significant changes. However, due to the aging Western societies and the longer survival time of stroke patients, the total number of stroke patients in the population will increase even with a stable IR. AU - Thiele, I. AU - Linseisen, J. AU - Heier, M. AU - Holle, R. AU - Kirchberger, I.* AU - Peters, A. AU - Thorand, B. AU - Meisinger, C. C1 - 54131 C2 - 45298 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England TI - Time trends in stroke incidence and in prevalence of risk factors in Southern Germany, 1989 to 2008/09. JO - Sci. Rep. VL - 8 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - By N-ethyl-N-nitrosourea (ENU) mutagenesis, we generated the mutant mouse line TUB6 that is characterised by severe combined immunodeficiency (SCID) and systemic sterile autoinflammation in homozygotes, and a selective T cell defect in heterozygotes. The causative missense point mutation results in the single amino acid exchange G170W in multicatalytic endopeptidase complex subunit-1 (MECL-1), the β2i-subunit of the immuno- and thymoproteasome. Yeast mutagenesis and crystallographic data suggest that the severe TUB6-phenotype compared to the MECL-1 knockout mouse is caused by structural changes in the C-terminal appendage of β2i that prevent the biogenesis of immuno- and thymoproteasomes. Proteasomes are essential for cell survival, and defective proteasome assembly causes selective death of cells expressing the mutant MECL-1, leading to the severe immunological phenotype. In contrast to the immunosubunits β1i (LMP2) and β5i (LMP7), mutations in the gene encoding MECL-1 have not yet been assigned to human disorders. The TUB6 mutant mouse line exemplifies the involvement of MECL-1 in immunopathogenesis and provides the first mouse model for primary immuno- and thymoproteasome-associated immunodeficiency that may also be relevant in humans. AU - Treise, I. AU - Huber, E.M.* AU - Klein-Rodewald, T. AU - Heinemeyer, W.* AU - Grassmann, S.A.* AU - Basler, M.* AU - Adler, T. AU - Rathkolb, B. AU - Helming, L.* AU - Andres, C.* AU - Klaften, M. AU - Landbrecht, C.* AU - Wieland, T. AU - Strom, T.M. AU - McCoy, K.D.* AU - Macpherson, A.J.* AU - Wolf, E.* AU - Groettrup, M.* AU - Ollert, M.* AU - Neff, F. AU - Gailus-Durner, V. AU - Fuchs, H. AU - Hrabě de Angelis, M. AU - Groll, M.* AU - Busch, D.H.* C1 - 53400 C2 - 44553 TI - Defective immuno- and thymoproteasome assembly causes severe immunodeficiency. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - TAR DNA-binding protein 43 (TDP-43) is a key player in neurodegenerative diseases including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Accumulation of TDP-43 is associated with neuronal death in the brain. How increased and disease-causing mutant forms of TDP-43 induce cell death remains unclear. Here we addressed the role of TDP-43 during neural development and show that reduced TDP-43 causes defects in neural stem/progenitor cell proliferation but not cell death. However, overexpression of wild type and TDP-43A315Tproteins induce p53-dependent apoptosis of neural stem/progenitors and human induced pluripotent cell (iPS)-derived immature cortical neurons. We show that TDP-43 induces expression of the proapoptotic BH3-only genes Bbc3 and Bax, and that p53 inhibition rescues TDP-43 induced cell death of embryonic mouse, and human cortical neurons, including those derived from TDP-43G298SALS patient iPS cells. Hence, an increase in wild type and mutant TDP-43 induces p53-dependent cell death in neural progenitors developing neurons and this can be rescued. These findings may have important implications for accumulated or mutant TDP-43 induced neurodegenerative diseases. AU - Vogt, M.A.* AU - Ehsaei, Z.* AU - Knuckles, P.* AU - Higginbottom, A.* AU - Helmbrecht, M.S. AU - Kunath, T.* AU - Eggan, K.* AU - Williams, L.A.* AU - Shaw, P.J.* AU - Wurst, W. AU - Floss, T. AU - Huber, A.B. AU - Taylor, V.* C1 - 53579 C2 - 44805 TI - TDP-43 induces p53-mediated cell death of cortical progenitors and immature neurons. JO - Sci. Rep. VL - 8 IS - 1 PY - 2018 SN - 2045-2322 ER - TY - JOUR AB - We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken. AU - Akmatov, M.F.* AU - Koch, N.* AU - Vital, M.* AU - Ahrens, W.* AU - Flesch-Janys, D.* AU - Fricke, J.* AU - Gatzemeier, A.* AU - Greiser, H.* AU - Günther, K.* AU - Illig, T. AU - Kaaks, R.* AU - Krone, B.* AU - Kühn-Steven, A. AU - Linseisen, J. AU - Meisinger, C. AU - Michels, K.* AU - Moebus, S.* AU - Nieters, A.* AU - Obi, N.* AU - Schultze, A.* AU - Six-Merker, J. AU - Pieper, D.H.* AU - Pessler, F.* C1 - 51112 C2 - 42685 CY - London TI - Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The pancreatic beta-cells control glucose homeostasis by secreting insulin in response to nutrient intake. The number of beta-cells is under tight metabolic control, as this number increases with higher nutrient intake. However, the signaling pathways matching nutrition with beta-cell mass plasticity remain poorly defined. By applying pharmacological and genetic manipulations, we show that reactive oxygen species (ROS) regulate dose-dependently beta-cell proliferation in vivo and in vitro. In particular, reducing ROS levels in beta-cells blocks their proliferation in response to nutrients. Using a non-invasive genetic sensor of intracellular hydrogen peroxide (H2O2), we reveal that glucose can directly increase the levels of H2O2. Furthermore, a moderate increase in H2O2 levels can stimulate beta-cell proliferation. Interestingly, while high H2O2 levels are inhibitory to beta-cell proliferation, they expand beta-cell mass in vivo by inducing rapid beta-cell neogenesis. Our study thus reveals a ROS-level-dependent mechanism linking nutrients with beta-cell mass plasticity. Hence, given the requirement of ROS for beta-cell mass expansion, antioxidant therapies should be applied with caution in diabetes. AU - Alfar, E.A. AU - Kirova, D.* AU - Konantz, J.* AU - Birke, S.* AU - Mansfeld, J.* AU - Ninov, N. C1 - 51473 C2 - 43150 CY - London TI - Distinct levels of reactive oxygen species coordinate metabolic activity with beta-cell mass plasticity. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Recognizing that insights into the modulation of sleep duration can emerge by exploring the functional relationships among genes, we used this strategy to explore the genome-wide association results for this trait. We detected two major signalling pathways (ion channels and the ERBB signalling family of tyrosine kinases) that could be replicated across independent GWA studies meta-analyses. To investigate the significance of these pathways for sleep modulation, we performed transcriptome analyses of short sleeping flies' heads (knockdown for the ABCC9 gene homolog; dSur). We found significant alterations in gene-expression in the short sleeping knockdowns versus controls flies, which correspond to pathways associated with sleep duration in our human studies. Most notably, the expression of Rho and EGFR (members of the ERBB signalling pathway) genes was down- and up-regulated, respectively, consistently with the established role of these genes for sleep consolidation in Drosophila. Using a disease multifactorial interaction network, we showed that many of the genes of the pathways indicated to be relevant for sleep duration had functional evidence of their involvement with sleep regulation, circadian rhythms, insulin secretion, gluconeogenesis and lipogenesis. AU - Allebrandt, K.V.* AU - Teder-Laving, M.* AU - Cusumano, P.* AU - Frishman, G. AU - Levandovski, R.* AU - Ruepp, A. AU - Hidalgo, M.P.L.* AU - Costa, R.* AU - Metspalu, A.* AU - Roenneberg, T.* AU - De Pittà, C.* C1 - 51481 C2 - 43260 CY - London TI - Identifying pathways modulating sleep duration: From genomics to transcriptomics. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Asthma is highly prevalent, but current therapies cannot influence the chronic course of the disease. It is thus important to understand underlying early molecular events. In this study, we aimed to use microRNAs (miRNAs) - which are critical regulators of signaling cascades - to identify so far uncharacterized asthma pathogenesis pathways. Therefore, deregulation of miRNAs was assessed in whole lungs from mice with ovalbumin (OVA)-induced allergic airway inflammation (AAI). In silico predicted target genes were confirmed in reporter assays and in house-dust-mite (HDM) induced AAI and primary human bronchial epithelial cells (NHBE) cultured at the air-liquid interface. We identified and validated the transcription factor cAMP-responsive element binding protein (Creb1) and its transcriptional co-activators (Crtc1-3) as targets of miR-17, miR-144, and miR-21. Sec14-like 3 (Sec14l3) - a putative target of Creb1 - was down-regulated in both asthma models and in NHBE cells upon IL13 treatment, while it's expression correlated with ciliated cell development and decreased along with increasing goblet cell metaplasia. Finally, we propose that Creb1/Crtc1-3 and Sec14l3 could be important for early responses of the bronchial epithelium to Th2-stimuli. This study shows that miRNA profiles can be used to identify novel targets that would be overlooked in mRNA based strategies. AU - Bartel, S. AU - Schulz, N. AU - Alessandrini, F. AU - Schamberger, A.C. AU - Pagel, P.* AU - Theis, F.J. AU - Milger, K. AU - Nößner, E. AU - Stick, S.M.* AU - Kicic, A.* AU - Eickelberg, O. AU - Freishtat, R.J.* AU - Krauss-Etschmann, S. C1 - 50901 C2 - 42993 CY - London TI - Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Existing clinical intravascular imaging modalities are not capable of accurate detection of critical plaque pathophysiology in the coronary arteries. This study reports the first intravascular catheter combining intravascular ultrasound (IVUS) with multispectral fluorescence lifetime imaging (FLIm) that enables label-free simultaneous assessment of morpho logical and biochemical features of coronary vessels in vivo. A 3.7 Fr catheter with a fiber-optic channel was constructed based on a 40 MHz clinical IVUS catheter. The ability to safely acquire co-registered FLIm-IVUS data in vivo using Dextran40 solution flushing was demonstrated in swine coronary arteries. FLIm parameters from the arterial wall were consistent with the emission of fluorophores present in healthy arterial wall (collagen, elastin). Additionally, structural and biochemical features from atherosclerotic lesions were acquired in ex vivo human coronary samples and corroborated with histological findings. Current results show that FLIm parameters linked to the amount of structural proteins (e.g. collagen, elastin) and lipids (e.g. foam cells, extracellular lipids) in the first 200 μm of the intima provide important biochemical information that can supplement IVUS data for a comprehensive assessment of plaques pathophysiology. The unique FLIm-IVUS system evaluated here has the potential to provide a comprehensive insight into atherosclerotic lesion formation, diagnostics and response to therapy. AU - Bec, J.* AU - Phipps, J.E.* AU - Gorpas, D. AU - Ma, D.* AU - Fatakdawala, H.* AU - Margulies, K.B.* AU - Southard, J.A.* AU - Marcu, L.* C1 - 51767 C2 - 43483 TI - In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Two-component systems are crucial for signal perception and modulation of bacterial behavior. Nevertheless, to date, very few ligands have been identified that directly interact with histidine kinases. The histidine kinase/response regulator system YehU/YehT of Escherichia coli is part of a nutrient-sensing network. Here we demonstrate that this system senses the onset of nutrient limitation in amino acid rich media and responds to extracellular pyruvate. Binding of radiolabeled pyruvate was found for full-length YehU in right-side-out membrane vesicles as well as for a truncated, membrane-integrated variant, confirming that YehU is a high-affinity receptor for extracellular pyruvate. Therefore we propose to rename YehU/YehT as BtsS/BtsR, after "Brenztraubensäure", the name given to pyruvic acid when it was first synthesized. The function of BtsS/BtsR was also assessed in a clinically relevant uropathogenic E. coli strain. Quantitative transcriptional analysis revealed BtsS/BtsR importance during acute and chronic urinary-tract infections. AU - Behr, S.* AU - Kristoficova, I.* AU - Witting, M. AU - Breland, E.J.* AU - Eberly, A.R.* AU - Sachs, C.* AU - Schmitt-Kopplin, P. AU - Hadjifrangiskou, M.* AU - Jung, K.* C1 - 51082 C2 - 43062 TI - Identification of a high-affinity pyruvate receptor in escherichia coli. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Cyclooxygenase-2 inhibitors (coxibs) are characterized by multiple molecular off-target effects and increased coronary artery disease (CAD) risk. Here, we systematically explored common variants of genes representing molecular targets of coxibs for association with CAD. Given a broad spectrum of pleiotropic effects of coxibs, our intention was to narrow potential mechanisms affecting CAD risk as we hypothesized that the affected genes may also display genomic signals of coronary disease risk. A Drug Gene Interaction Database search identified 47 gene products to be affected by coxibs. We traced association signals in 200-kb regions surrounding these genes in 84,813 CAD cases and 202,543 controls. Based on a threshold of 1 x 10(-5) (Bonferroni correction for 3131 haplotype blocks), four gene loci yielded significant associations. The lead SNPs were rs7270354 (MMP9), rs4888383 (BCAR1), rs6905288 (VEGFA1), and rs556321 (CACNA1E). By additional genotyping, rs7270354 at MMP9 and rs4888383 at BCAR1 also reached the established GWAS threshold for genome-wide significance. The findings demonstrate overlap of genes affected by coxibs and those mediating CAD risk and points to further mechanisms, which are potentially responsible for coxib-associated CAD risk. The novel approach furthermore suggests that genetic studies may be useful to explore the clinical relevance of off-target drug effects. AU - Braenne, I.* AU - Willenborg, C.* AU - Tragante, V.* AU - Kessler, T.* AU - Zeng, L.* AU - Reiz, B.* AU - Kleinecke, M.* AU - von Ameln, S.* AU - Willer, C.J.* AU - Laakso, M.* AU - Wild, P.S.* AU - Zeller, T.* AU - Wallentin, L.* AU - Franks, P.W.* AU - Salomaa, V.* AU - Dehghan, A.* AU - Meitinger, T. AU - Samani, N.J.* AU - Asselbergs, F.W.* AU - Erdmann, J.* AU - Schunkert, H.* C1 - 51866 C2 - 43540 CY - London TI - A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454–pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH–CLSM). Pyrosequencing showed a relative dominance of Gammaproteobacteria within the sponge microbiota. Five of the ten most abundant OTUs were closely related to risk group 2 (RG2) species, previously detected in the BE and kitchen microbiome. Regular cleaning of sponges, indicated by their users, significantly affected the microbiome structure. Two of the ten dominant OTUs, closely related to the RG2-species Chryseobacterium hominis and Moraxella osloensis, showed significantly greater proportions in regularly sanitized sponges, thereby questioning such sanitation methods in a long term perspective. FISH–CLSM showed an ubiquitous distribution of bacteria within the sponge tissue, concentrating in internal cavities and on sponge surfaces, where biofilm–like structures occurred. Image analysis showed local densities of up to 5.4 * 1010 cells per cm3, and confirmed the dominance of Gammaproteobacteria. Our study stresses and visualizes the role of kitchen sponges as microbiological hot spots in the BE, with the capability to collect and spread bacteria with a probable pathogenic potential. AU - Cardinale, M.* AU - Kaiser, D.* AU - Lueders, T. AU - Schnell, S.* AU - Egert, M.* C1 - 51548 C2 - 43189 CY - London TI - Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Mutations in the Leucine-rich repeat kinase 2 gene (LRRK2) are associated with familial Parkinson's disease (PD). LRRK2 protein contains several functional domains, including protein-protein interaction domains at its N- and C-termini. In this study, we analyzed the functional features attributed to LRRK2 by its N- and C-terminal domains. We combined TIRF microscopy and synaptopHluorin assay to visualize synaptic vesicle trafficking. We found that N- and C-terminal domains have opposite impact on synaptic vesicle dynamics. Biochemical analysis demonstrated that different proteins are bound at the two extremities, namely β3-Cav2.1 at N-terminus part and β-Actin and Synapsin I at C-terminus domain. A sequence variant (G2385R) harboured within the C-terminal WD40 domain increases the risk for PD. Complementary biochemical and imaging approaches revealed that the G2385R variant alters strength and quality of LRRK2 interactions and increases fusion of synaptic vesicles. Our data suggest that the G2385R variant behaves like a loss-of-function mutation that mimics activity-driven events. Impaired scaffolding capabilities of mutant LRRK2 resulting in perturbed vesicular trafficking may arise as a common pathophysiological denominator through which different LRRK2 pathological mutations cause disease. AU - Carrion, M.D.P.* AU - Marsicano, S.* AU - Daniele, F.* AU - Marte, A.* AU - Pischedda, F.* AU - Cairano, E.D.* AU - Piovesana, E.* AU - von Zweydorf, F.* AU - Kremmer, E. AU - Gloeckner, C.J.* AU - Onofri, F.* AU - Perego, C.* AU - Piccoli, G.* C1 - 51528 C2 - 43282 CY - London TI - The LRRK2 G2385R variant is a partial loss-of-function mutation that affects synaptic vesicle trafficking through altered protein interactions. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Fluorescence microscopy is rapidly turning into nanoscopy. Among the various nanoscopy methods, the STED/RESOLFT super-resolution family has recently been expanded to image even large fields of view within a few seconds. This advance relies on using light patterns featuring substantial arrays of intensity minima for discerning features by switching their fluorophores between 'on' and 'off' states of fluorescence. Here we show that splitting the light with a grating and recombining it in the focal plane of the objective lens renders arrays of minima with wavelength-independent periodicity. This colour-independent creation of periodic patterns facilitates coaligned on- and off-switching and readout with combinations chosen from a range of wavelengths. Applying up to three such periodic patterns on the switchable fluorescent proteins Dreiklang and rsCherryRev1.4, we demonstrate highly parallelized, multicolour RESOLFT nanoscopy in living cells for ~100 × 100 μm(2) fields of view. Individual keratin filaments were rendered at a FWHM of ~60-80 nm, with effective resolution for the filaments of ~80-100 nm. We discuss the impact of novel image reconstruction algorithms featuring background elimination by spatial bandpass filtering, as well as strategies that incorporate complete image formation models. AU - Chmyrov, A. AU - Leutenegger, M.* AU - Grotjohann, T.* AU - Schönle, A.* AU - Keller-Findeisen, J.* AU - Kastrup, L.* AU - Jakobs, S.* AU - Donnert, G.* AU - Sahl, S.J.* AU - Hell, S.W.* C1 - 50977 C2 - 42557 TI - Achromatic light patterning and improved image reconstruction for parallelized RESOLFT nanoscopy. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The heat shock response is characterized by the transcriptional activation of both hsp genes and noncoding and repeated satellite III DNA sequences located at pericentric heterochromatin. Both events are under the control of Heat Shock Factor I (HSF1). Here we show that under heat shock, HSF1 recruits major cellular acetyltransferases, GCN5, TIP60 and p300 to pericentric heterochromatin leading to a targeted hyperacetylation of pericentric chromatin. Redistribution of histone acetylation toward pericentric region in turn directs the recruitment of Bromodomain and Extra-Terminal (BET) proteins BRD2, BRD3, BRD4, which are required for satellite III transcription by RNAP II. Altogether we uncover here a critical role for HSF1 in stressed cells relying on the restricted use of histone acetylation signaling over pericentric heterochromatin (HC). AU - Col, E.* AU - Hoghoughi, N.* AU - Dufour, S.* AU - Penin, J.* AU - Koskas, S.* AU - Faure, V.* AU - Ouzounova, M.* AU - Hernandez-Vargash, H.* AU - Reynoird, N.* AU - Daujat, S.* AU - Folco, E.J.* AU - Vigneron, M.* AU - Schneider, R. AU - Verdel, A.* AU - Khochbin, S.* AU - Herceg, Z.* AU - Caron, C.* AU - Vourc'h, C.* C1 - 51601 C2 - 43346 CY - London TI - Bromodomain factors of BET family are new essential actors of pericentric heterochromatin transcriptional activation in response to heat shock. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Airborne pollen and fungal spores are monitored mainly in highly populated, urban environments, for allergy prevention purposes. However, their sources can frequently be located outside cities' fringes with more vegetation. So as to shed light to this paradox, we investigated the diversity and abundance of airborne pollen and fungal spores at various environmental regimes. We monitored pollen and spores using an aircraft and a car, at elevations from sea level to 2,000 m above ground, in the region of Thesssaloniki, Greece. We found a total of 24 pollen types and more than 15 spore types. Pollen and spores were detected throughout the elevational transect. Lower elevations exhibited higher pollen concentrations in only half of plant taxa and higher fungal spore concentrations in only Ustilago. Pinaceae and Quercus pollen were the most abundant recorded by airplane (>54% of the total). Poaceae pollen were the most abundant via car measurements (>77% of the total). Cladosporium and Alternaria spores were the most abundant in all cases (aircraft: >69% and >17%, car: >45% and >27%, respectively). We conclude that pollen and fungal spores can be diverse and abundant even outside the main source area, evidently because of long-distance transport incidents. AU - Damialis, A. AU - Kaimakamis, E.* AU - Konoglou, M.* AU - Akritidis, I.* AU - Traidl-Hoffmann, C. AU - Gioulekas, D.* C1 - 50732 C2 - 42478 TI - Estimating the abundance of airborne pollen and fungal spores at variable elevations using an aircraft: How high can they fly? JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Optical microscopy remains a fundamental tool for modern biological discovery owing to its excellent spatial resolution and versatile contrast in visualizing cellular and sub-cellular structures. Yet, the time domain is paramount for the observation of biological dynamics in living systems. Commonly, acquisition of microscopy data involves scanning of a spherically-or cylindrically-focused light beam across the imaged volume, which significantly limits temporal resolution in 3D. Additional complications arise from intense light scattering of biological tissues, further restraining the effective penetration depth and field of view of optical microscopy techniques. To overcome these limitations, we devised a fast optoacoustic micro-tomography (OMT) approach based on simultaneous acquisition of 3D image data with a high-density hemispherical ultrasound array having effective detection bandwidth beyond 25 MHz. We demonstrate fast three-dimensional imaging of freely-swimming zebrafish larvae, achieving 3D imaging speed of 100 volumes per second with isotropic spatial resolution approaching the dimensions of large cells across a field of view exceeding 50mm(3). As opposed to other microscopy techniques based on optical contrast, OMT resolves optical absorption acoustically using unfocused light excitation. Thus, no penetration barriers are imposed by light scattering in deep tissues, suggesting it as a powerful approach for multi-scale functional and molecular imaging applications. AU - Dean-Ben, X.L. AU - López-Schier, H. AU - Razansky, D. C1 - 51653 C2 - 43512 CY - London TI - Optoacoustic micro-tomography at 100 volumes per second. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The bromodomain protein Brd4 is an epigenetic reader and plays a critical role in the development and maintenance of leukemia. Brd4 binds to acetylated histone tails and activates transcription by recruiting the positive elongation factor P-TEFb. Small molecule inhibitor JQ1 competitively binds the bromodomains of Brd4 and displaces the protein from acetylated histones. However, it remains unclear whether genes targeted by JQ1 are mainly regulated by Brd4 or by other bromodomain proteins such as Brd2 and Brd3. Here, we describe anti-proliferative dominant-negative Brd4 mutants that compete with the function of distinct Brd4 domains. We used these Brd4 mutants to compare the Brd4-specific transcriptome with the transcriptome of JQ1-treated cells. We found that most JQ1-regulated genes are also regulated by dominant-negative Brd4 mutants, including the mutant that competes with the P-TEFb recruitment function of Brd4. Importantly, JQ1 and dominant-negative Brd4 mutants regulated the same set of target genes of c-Myc, a key regulator of the JQ1 response in leukemia cells. Our results suggest that Brd4 mediates most of the anti-cancer effects of JQ1 and that the major function of Brd4 in this process is the recruitment of P-TEFb. In summary, our studies define the molecular targets of JQ1 in more detail. AU - Decker, T.-M. AU - Kluge, M.* AU - Krebs, S.* AU - Shah, N. AU - Blum, H.* AU - Friedel, C.C.* AU - Eick, D. C1 - 51106 C2 - 42667 CY - London TI - Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The mechanisms how environmental compounds influence the human immune system are unknown. The environmentally sensitive transcription factor aryl hydrocarbon receptor (AHR) has immune-modulating functions and responds to small molecules. Cytochrome P4501 enzymes (CYP1) act downstream of the AHR and metabolize small molecules. However, it is currently unknown whether CYP1 activity is relevant for immune modulation. We studied the interdependence of CYP1 and AHR in human primary immune cells using pharmacological methods. CYP1 inhibition increased the expression levels of the stem cell factor receptor (c-Kit) and interleukin (IL)-22 but decreased IL-17. Single cell analyses showed that CYP1 inhibition especially promoted CD4(+) helper T (Th) cells that co-express c-Kit and IL-22 simultaneously. The addition of an AHR antagonist reversed all these effects. In addition to T cells, we screened other human immune cells for CYP and found cell-specific fingerprints, suggesting that similar mechanisms are present in multiple immune cells. We describe a feedback loop yet unknown in human immune cells where CYP1 inhibition resulted in an altered AHR-dependent immune response. This mechanism relates CYP1-dependent metabolism of environmental small molecules to human immunity. AU - Effner, R. AU - Hiller, J. AU - Eyerich, S. AU - Traidl-Hoffmann, C. AU - Brockow, K.* AU - Triggiani, M.* AU - Behrendt, H. AU - Schmidt-Weber, C.B. AU - Buters, J.T.M. C1 - 50681 C2 - 42825 TI - Cytochrome P450s in human immune cells regulate IL-22 and c-Kit via an AHR feedback loop. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Paladin (Pald1, mKIAA1274 or x99384) was identified in screens for vascular-specific genes and is a putative phosphatase. Paladin has also been proposed to be involved in various biological processes such as insulin signaling, innate immunity and neural crest migration. To determine the role of paladin we have now characterized the Pald1 knock-out mouse in a broad array of behavioral, physiological and biochemical tests. Here, we show that female, but not male, Pald1 heterozygous and homozygous knock-out mice display an emphysema-like histology with increased alveolar air spaces and impaired lung function with an obstructive phenotype. In contrast to many other tissues where Pald1 is restricted to the vascular compartment, Pald1 is expressed in both the epithelial and mesenchymal compartments of the postnatal lung. However, in Pald1 knock-out females, there is a specific increase in apoptosis and proliferation of endothelial cells, but not in non-endothelial cells. This results in a transient reduction of endothelial cells in the maturing lung. Our data suggests that Pald1 is required during lung vascular development and for normal function of the developing and adult lung in a sex-specific manner. To our knowledge, this is the first report of a sex-specific effect on endothelial cell apoptosis. AU - Egaña, I.* AU - Kaito, H.* AU - Nitzsche, A.* AU - Becker, L. AU - Ballester-Lopez, C. AU - Niaudet, C.* AU - Petkova, M.* AU - Liu, W.* AU - Vandlandewijck, M.* AU - Vernaleken, A. AU - Klopstock, T.* AU - Fuchs, H. AU - Gailus-Durner, V. AU - Hrabě de Angelis, M. AU - Rask-Andersen, H.* AU - Johansson, H.J.* AU - Lehtiö, J.* AU - He, L.* AU - Yildirim, A.Ö. AU - Hellström, M.* AU - German Mouse Clinic Consortium (Aguilar-Pimentel, J.A. AU - Ollert, M. AU - Schmidt-Weber, C.B. AU - Amarie, O.V. AU - Graw, J. AU - Beckers, J. AU - Garrett, L. AU - Hölter, S.M. AU - Zimprich, A. AU - Wurst, W. AU - Moreth, K. AU - Bekeredjian, R.* AU - Neff, F. AU - Calzada-Wack, J. AU - Rácz, I. AU - Zimmer, A. AU - Rathkolb, B. AU - Wolf, E. AU - Rozman, J. AU - Klingenspor, M. AU - Stöger, T. AU - Eickelberg, O. AU - Treise, I. AU - Busch, D.H. AU - Östereicher, M.A. AU - Steinkamp, R. AU - Lengger, C. AU - Maier, H. AU - Stoeger, C. AU - Leuchtenberger, S.) C1 - 52320 C2 - 43867 CY - London TI - Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Chronic venous disease (CVD) is a multifactorial condition representing one of the most common disorders among populations of Western countries. The heritability of about 17% suggests genetic risk factors in CVD etiology. However, so far the genetic causes are unknown. We undertook the hitherto first genome-wide association study (GWAS) for CVD, analyzing more than 1.93 M SNPs in 4,942 German individuals, followed by replication in two independent German data sets. The combined analysis of discovery and replication stages (2,269 cases and 7,765 controls) yielded robust associations within the two genes EFEMP1 and KCNH8 (rs17278665, rs727139 with P < 5 × 10(-8)), and suggestive association within gene SKAP2 (rs2030136 with P < 5 × 10(-7)). Association signals of rs17278665 and rs727139 reside in regions of low linkage disequilibrium containing no other genes. Data from the ENCODE and Roadmap Epigenomics projects show that tissue specific marks overlap with the variants. SNPs rs17278665 and rs2030136 are known eQTLs. Our study demonstrates that GWAS are a valuable tool to study the genetic component of CVD. With our approach, we identified two novel genome-wide significant susceptibility loci for this common disease. Particularly, the extracellular matrix glycoprotein EFEMP1 is promising for future functional studies due to its antagonistic role in vessel development and angiogenesis. AU - Ellinghaus, E.* AU - Ellinghaus, D.* AU - Krusche, P.* AU - Greiner, A.* AU - Schreiber, C.* AU - Nikolaus, S.* AU - Gieger, C. AU - Strauch, K. AU - Lieb, W.* AU - Rosenstiel, P.* AU - Frings, N.* AU - Fiebig, A.* AU - Schreiber, S.* AU - Franke, A.* C1 - 50855 C2 - 42620 CY - London TI - Genome-wide association analysis for chronic venous disease identifies EFEMP1 and KCNH8 as susceptibility loci. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The T-cell protein tyrosine phosphatase (TCPTP) pathway consists of signaling events mediated by TCPTP. Mutations and genetic variants of some genes in the TCPTP pathway are associated with lung cancer risk and survival. In the present study, we first investigated associations of 5,162 single nucleotide polymorphisms (SNPs) in 43 genes of this TCPTP pathway with lung cancer risk by using summary data of six published genome-wide association studies (GWAS) of 12,160 cases and 16,838 controls. We identified 11 independent SNPs in eight genes after correction for multiple comparisons by a false discovery rate <0.20. Then, we performed in silico functional analyses for these 11 SNPs by eQTL analysis, two of which, PTPN2 SNPs rs2847297 and rs2847282, were chosen as tagSNPs. We further included two additional GWAS datasets of Harvard University (984 cases and 970 controls) and deCODE (1,319 cases and 26,380 controls), and the overall effects of these two SNPs among all eight GWAS studies remained significant (OR = 0.95, 95% CI = 0.92-0.98, and P = 0.004 for rs2847297; OR = 0.95, 95% CI = 0.92-0.99, and P = 0.009 for rs2847282). In conclusion, the PTPN2 rs2847297 and rs2847282 may be potential susceptible loci for lung cancer risk. AU - Feng, Y.* AU - Wang, Y.* AU - Liu, H.* AU - Liu, Z.* AU - Mills, C.* AU - Han, Y.* AU - Hung, R.J.* AU - Brhane, Y.* AU - McLaughlin, J.* AU - Brennan, P.* AU - Bickeboeller, H.* AU - Rosenberger, A.* AU - Houlston, R.S.* AU - Caporaso, N.E.* AU - Teresa Landi, M.* AU - Brüske, I. AU - Risch, A.* AU - Ye, Y.* AU - Wu, X.* AU - Christiani, D.C.* AU - Amos, C.I.* AU - Wei, Q.* C1 - 50922 C2 - 42689 CY - London TI - Genetic variants of PTPN2 are associated with lung cancer risk: A re-analysis of eight GWASs in the TRICL-ILCCO consortium. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - We compared gene expression in low and high-grade intraepithelial dysplastic polyps from pigs carrying an APC 1311 truncating mutation orthologous to human APC 1309 , analysing whole samples and microdissected dysplastic epithelium. Gene set enrichment analysis revealed differential expression of gene sets similar to human normal mucosa versus T1 stage polyps. Transcriptome analysis of whole samples revealed many differentially-expressed genes reflecting immune infiltration. Analysis of microdissected dysplastic epithelium was markedly different and showed increased expression in high-grade intraepithelial neoplasia of several genes known to be involved in human CRC; and revealed possible new roles for GBP6 and PLXND1. The pig model thus facilitates analysis of CRC pathogenesis. AU - Flisikowska, T.* AU - Stachowiak, M.* AU - Xu, H.* AU - Wagner, A.* AU - Hernandez-Caceres, A.* AU - Wurmser, C.* AU - Perleberg, C.* AU - Pausch, H.* AU - Perkowska, A.* AU - Fischer, K.* AU - Frishman, D. AU - Fries, R.* AU - Switonski, M.* AU - Kind, A.* AU - Saur, D.* AU - Schnieke, A.* AU - Flisikowski, K.* C1 - 51672 C2 - 43389 CY - London TI - Porcine familial adenomatous polyposis model enables systematic analysis of early events in adenoma progression. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Track structures and resulting DNA damage in human cells have been simulated for hydrogen, helium, carbon, nitrogen, oxygen and neon ions with 0.25-256 MeV/u energy. The needed ion interaction cross sections have been scaled from those of hydrogen; Barkas scaling formula has been refined, extending its applicability down to about 10 keV/u, and validated against established stopping power data. Linear energy transfer (LET) has been scored from energy deposits in a cell nucleus; for very low-energy ions, it has been defined locally within thin slabs. The simulations show that protons and helium ions induce more DNA damage than heavier ions do at the same LET. With increasing LET, less DNA strand breaks are formed per unit dose, but due to their clustering the yields of double-strand breaks (DSB) increase, up to saturation around 300 keV/μm. Also individual DSB tend to cluster; DSB clusters peak around 500 keV/μm, while DSB multiplicities per cluster steadily increase with LET. Remarkably similar to patterns known from cell survival studies, LET-dependencies with pronounced maxima around 100-200 keV/μm occur on nanometre scale for sites that contain one or more DSB, and on micrometre scale for megabasepair-sized DNA fragments. AU - Friedland, W. AU - Schmitt, E. AU - Kundrát, P. AU - Dingfelder, M.* AU - Baiocco, G.* AU - Barbieri, S.* AU - Ottolenghi, A.* C1 - 50797 C2 - 42547 SP - 45161 TI - Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - CD8(+) T cells directed against beta cell autoantigens are considered relevant for the pathogenesis of type 1 diabetes. Using single cell T cell receptor sequencing of CD8(+) T cells specific for the IGRP265-273 epitope, we examined whether there was expansion of clonotypes and sharing of T cell receptor chains in autoreactive CD8(+) T cell repertoires. HLA-A*0201 positive type 1 diabetes patients (n = 19) and controls (n = 18) were analysed. TCR α- and β-chain sequences of 418 patient-derived IGRP265-273-multimer(+) CD8(+) T cells representing 48 clonotypes were obtained. Expanded populations of IGRP265-273-specific CD8(+) T cells with dominant clonotypes that had TCR α-chains shared across patients were observed. The SGGSNYKLTF motif corresponding to TRAJ53 was contained in 384 (91.9%) cells, and in 20 (41.7%) patient-derived clonotypes. TRAJ53 together with TRAV29/DV5 was found in 15 (31.3%) clonotypes. Using next generation TCR α-chain sequencing, we found enrichment of one of these TCR α-chains in the memory CD8(+) T cells of patients as compared to healthy controls. CD8(+) T cell clones bearing the enriched motifs mediated antigen-specific target cell lysis. We provide the first evidence for restriction of T cell receptor motifs in the alpha chain of human CD8(+) T cells with specificity to a beta cell antigen. AU - Fuchs, Y.F. AU - Eugster, A.* AU - Dietz, S. AU - Sebelefsky, C. AU - Kühn, D.* AU - Wilhelm, C.* AU - Lindner, A. AU - Gavrisan, A.* AU - Knoop, J. AU - Dahl, A.* AU - Ziegler, A.-G. AU - Bonifacio, E. C1 - 50727 C2 - 42865 TI - CD8+ T cells specific for the islet autoantigen IGRP are restricted in their T cell receptor chain usage. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The tumour suppressor gene (Rb1) is necessary for the maintenance of telomere integrity in osteoblastic cells. We now show that the compaction of telomeric chromatin and the appropriate histone modifications of telomeric DNA are both dependent upon Rb1-mediated transcription of the telomere-derived long non-coding RNA TERRA. Expression of TERRA was reduced in Rb1 haploinsufficient cells, and further decreased by shRNA-mediated reduction of residual Rb1 expression. Restoration of Rb1 levels through lentiviral transduction was sufficient to reestablish both transcription of TERRA and condensation of telomeric chromatin. The human chromosome 15q TERRA promoter contains predicted retinoblastoma control elements, and was able to confer Rb1-dependent transcription upon a promoterless reporter gene. Chromatin immunoprecipitation revealed preferential binding of phosphorylated over non-phosphorylated Rb1 at the TERRA promoter. As Rb1-deficient cells show increased genomic instability we suggest that this novel non-canonical action of Rb1 may contribute to the tumour suppressive actions of Rb1. AU - Gonzalez-Vasconcellos, I.* AU - Schneider, R. AU - Anastasov, N. AU - Alonso-Rodriguez, S.* AU - Sanli-Bonazzi, B. AU - Fernández, J.L.* AU - Atkinson, M.J. C1 - 50514 C2 - 42450 CY - London SP - 42056 TI - The Rb1 tumour suppressor gene modifies telomeric chromatin architecture by regulating TERRA expression. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10(-8) previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, which were missed by our previous analyses. Among those, the 10 identified novel genes are part of pathways of kidney development, carbohydrate metabolism, cardiac septum development and glucose metabolism. These results highlight the utility of re-imputing from denser reference panels, until whole-genome sequencing becomes feasible in large samples. AU - Gorski, M.* AU - van der Most, P.J.* AU - Teumer, A.* AU - Chu, A.Y.* AU - Li, M.* AU - Mijatovic, V.* AU - Nolte, I.M.* AU - Cocca, M.* AU - Taliun, D.* AU - Gomez, F.* AU - Li, Y.* AU - Tayo, B.O.* AU - Tin, A.* AU - Feitosa, M.F.* AU - Aspelund, T.* AU - Attia, J.* AU - Biffar, R.* AU - Bochud, M.* AU - Boerwinkle, E.* AU - Borecki, I.* AU - Bottinger, E.P.* AU - Chen, M.H.* AU - Chouraki, V.* AU - Ciullo, M.* AU - Coresh, J.* AU - Cornelis, M.C.* AU - Curhan, G.C.* AU - d'Adamo, A.P.* AU - Dehghan, A.* AU - Dengler, L.* AU - Ding, J.* AU - Eiriksdottir, G.* AU - Endlich, K.* AU - Enroth, S.* AU - Esko, T.* AU - Franco, O.H.* AU - Gasparini, P.* AU - Gieger, C. AU - Girotto, G.* AU - Gottesman, O.* AU - Gudnason, V.* AU - Gyllensten, U.* AU - Hancock, S.J.* AU - Harris, T.B.* AU - Helmer, C.* AU - Höllerer, S.* AU - Hofer, E.* AU - Hofman, A.* AU - Holliday, E.G.* AU - Homuth, G.* AU - Hu, F.B.* AU - Huth, C. AU - Hutri-Kähönen, N.* AU - Hwang, S.J.* AU - Imboden, M.* AU - Johansson, Å* AU - Kähönen, M.* AU - König, W.* AU - Kramer, H.* AU - Krämer, B.K.* AU - Kumar, A.* AU - Kutalik, Z.* AU - Lambert, J.C.* AU - Launer, L.J.* AU - Lehtimäki, T.* AU - de Borst, M.H.* AU - Navis, G.* AU - Swertz, M.A.* AU - Liu, Y.* AU - Lohman, K.* AU - Loos, R.J.F.* AU - Lu, Y.* AU - Lyytikäinen, L.-P.* AU - McEvoy, M.A.* AU - Meisinger, C. AU - Meitinger, T. AU - Metspalu, A.* AU - Metzger, M.* AU - Mihailov, E.* AU - Mitchell, P.* AU - Nauck, M.* AU - Oldehinkel, A.J.* AU - Olden, M.* AU - Wjh Penninx, B.* AU - Pistis, G.* AU - Pramstaller, P.P.* AU - Probst-Hensch, N.* AU - Raitakari, O.T.* AU - Rettig, R.* AU - Ridker, P.M.* AU - Rivadeneira, F.* AU - Robino, A.* AU - Rosas, S.E.* AU - Ruderfer, D.* AU - Ruggiero, D.* AU - Saba, Y.* AU - Sala, C.* AU - Schmidt, H.* AU - Schmidt, R.* AU - Scott, R.J.* AU - Sedaghat, S.* AU - Smith, A.V.* AU - Sorice, R.* AU - Stengel, B.* AU - Stracke, S.* AU - Strauch, K. AU - Toniolo, D.* AU - Uitterlinden, A.G.* AU - Ulivi, S.* AU - Viikari, J.S.* AU - Völker, U.* AU - Vollenweider, P.* AU - Völzke, H.* AU - Vuckovic, D.* AU - Waldenberger, M. AU - Jin Wang, J.* AU - Yang, Q.* AU - Chasman, D.I.* AU - Tromp, G.* AU - Snieder, H.* AU - Heid, I.M.* AU - Fox, C.S.* AU - Köttgen, A.* AU - Pattaro, C.* AU - Böger, C.A.* AU - Fuchsberger, C.* C1 - 51014 C2 - 42704 TI - 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - We demonstrate the applicability of propagation-based X-ray phase-contrast imaging at a laser-assisted compact light source with known phantoms and the lungs and airways of a mouse. The Munich Compact Light Source provides a quasi-monochromatic beam with partial spatial coherence, and high flux relative to other non-synchrotron sources (up to 10(10) ph/s). In our study we observe significant edge-enhancement and quantitative phase-retrieval is successfully performed on the known phantom. Furthermore the images of a small animal show the potential for live bio-imaging research studies that capture biological function using short exposures. AU - Gradl, R.* AU - Dierolf, M.* AU - Hehn, L.* AU - Günther, B.* AU - Yildirim, A.Ö. AU - Gleich, B.* AU - Achterhold, K.* AU - Pfeiffer, F.* AU - Morgan, K.S.* C1 - 51492 C2 - 43261 CY - London TI - Propagation-based phase-contrast x-ray imaging at a compact light source. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Concentrations of (239)Pu, (240)Pu, and (241)Am, and atomic ratio of (240)Pu/(239)Pu in freshly fallen snow on Mt. Zugspitze collected in 2014, 2015 and 2016 were determined by accelerator mass spectrometry (AMS). For the sub-femtogram (10(-15) g) - level of Pu and Am analysis, a chemical separation procedure combined with AMS was improved and an excellent overall efficiency of about 10(-4) was achieved. The concentration of (239)Pu ranges from 75 ± 13 ag/kg to 2823 ± 84 ag/kg, of (240)Pu from 20.6 ± 5.2 to 601 ± 21 ag/kg, and of (241)Am was found in the range of 16.7 ± 5.0-218.8 ± 8.9 ag/kg. Atomic ratios of (240)Pu/(239)Pu for most samples are comparable to the fallout in middle Europe. One exceptional sample shows a higher Pu concentration. High airborne dust concentration, wind directions, high Cs concentrations and the activity ratio of (239+240)Pu/(137)Cs lead to the conclusion that the sample was influenced by Pu in Saharan dust transported to Mt. Zugspitze. AU - Gückel, K. AU - Shinonaga, T. AU - Christl, M.* AU - Tschiersch, J. C1 - 51945 C2 - 43534 CY - London TI - Scavenged 239Pu, 240Pu, and 241Am from snowfalls in the atmosphere settling on Mt. Zugspitze in 2014, 2015 and 2016. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Early identification of patients at risk of developing diabetic nephropathy is essential. Elevated serum concentrations of soluble urokinase receptor (suPAR) associate with diabetes mellitus and predict onset and loss of renal function in chronic kidney disease. We hypothesize, that suPAR may be an early risk indicator for diabetic nephropathy, preceding microalbuminuria. The relationship of baseline suPAR and incident microalbuminuria was assessed in a prospective long-term cohort of subjects at increased risk for type 2 diabetes (TULIP, n = 258). Association with albuminuria at later stages of disease was studied in a cross-sectional cohort with manifest type 2 diabetes (ICEPHA, n = 266). A higher baseline suPAR was associated with an increased risk of new-onset microalbuminuria in subjects at risk for type 2 diabetes (hazard ratio 5.3 (95% CI 1.1-25.2, p = 0.03) for the highest vs. lowest suPAR quartile). The proportion of subjects with prediabetes at the end of observation was higher in subjects with new-onset microalbuminuria. suPAR consistently correlated with albuminuria in a separate cohort with manifest type 2 diabetes. Elevated baseline suPAR concentrations independently associate with new-onset microalbuminuria in subjects at increased risk of developing type 2 diabetes. suPAR may hence allow for earlier risk stratification than microalbuminuria. AU - Guthoff, M. AU - Wagner, R. AU - Randrianarisoa, E. AU - Hatziagelaki, E.* AU - Peter, A. AU - Häring, H.-U. AU - Fritsche, A. AU - Heyne, N. C1 - 52824 C2 - 44188 TI - Soluble urokinase receptor (suPAR) predicts microalbuminuria in patients at risk for type 2 diabetes mellitus. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The metabolic phenotype of a cancer cell is determined by its genetic makeup and microenvironment, which dynamically modulates the tumor landscape. The endothelial cells provide both a promoting and protective microenvironment - a niche for cancer cells. Although metabolic alterations associated with cancer and its progression have been fairly defined, there is a significant gap in our understanding of cancer metabolism in context of its microenvironment. We deployed an in vitro co-culture system based on direct contact of cancer cells with endothelial cells (E4 + EC), mimicking the tumor microenvironment. Metabolism of colon (HTC15 and HTC116) and ovarian (OVCAR3 and SKOV3) cancer cell lines was profiled with non-targeted metabolic approaches at different time points in the first 48 hours after co-culture was established. We found significant, coherent and non-cell line specific changes in fatty acids, glycerophospholipids and carbohydrates over time, induced by endothelial cell contact. The metabolic patterns pinpoint alterations in hexosamine biosynthetic pathway, glycosylation and lipid metabolism as crucial for cancer - endothelial cells interaction. We demonstrated that "Warburg effect" is not modulated in the initial stage of nesting of cancer cell in the endothelial niche. Our study provides novel insight into cancer cell metabolism in the context of the endothelial microenvironment. AU - Halama, A.* AU - Guerrouahen, B.S.* AU - Pasquier, J.* AU - Satheesh, N.J.* AU - Suhre, K. AU - Rafii, A.* C1 - 50300 C2 - 42428 CY - London TI - Nesting of colon and ovarian cancer cells in the endothelial niche is associated with alterations in glycan and lipid metabolism. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - NMR spectroscopy is a powerful technique to study ribonucleic acids (RNAs) which are key players in a plethora of cellular processes. Although the NMR toolbox for structural studies of RNAs expanded during the last decades, they often remain challenging. Here, we show that solvent paramagnetic relaxation enhancements (sPRE) induced by the soluble, paramagnetic compound Gd(DTPA-BMA) provide a quantitative measure for RNA solvent accessibility and encode distance-to-surface information that correlates well with RNA structure and improves accuracy and convergence of RNA structure determination. Moreover, we show that sPRE data can be easily obtained for RNAs with any isotope labeling scheme and is advantageous regarding sample preparation, stability and recovery. sPRE data show a large dynamic range and reflect the global fold of the RNA suggesting that they are well suited to identify interaction surfaces, to score structural models and as restraints in RNA structure determination. AU - Hartlmüller, C. AU - Günther, J. AU - Wolter, A.C.* AU - Wöhnert, J.* AU - Sattler, M. AU - Madl, T. C1 - 51602 C2 - 43347 CY - London TI - RNA structure refinement using NMR solvent accessibility data. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - In order to better understand the underpinnings of attention-deficit/hyperactivity disorder (ADHD), we targeted the relationship of attentional, cognitive control and motivational processes with DNA methylation patterns of 60 candidate genes in boys at early school age. Participants (6 to 8 years; N = 82) were selected from a German longitudinal cohort (FRANCES). ADHD-related behaviour was assessed via maternal ratings. Performance and event-related potential measures (inter alia Cue-P3 and Nogo-P3), which were recorded in a motivational go/nogo task, indicated diminished attentional orienting, reduced inhibitory response control and a larger motivational effect on performance in ADHD already at this relatively young age. Methylation patterns were analysed in buccal cell DNA with the Illumina HumanMethylation 450K array. For CpG sites at genes of the dopaminergic (COMT, ANKK1) and the neurotrophic (BDNF, NGFR) system, associations with the Nogo-P3 as well as ADHD symptom severity were found suggesting that these systems are involved in response control deficits in ADHD. Methylation effects related to both functional aspects and ADHD behaviour were also observed for DPP10 and TPH2. Epigenetic mechanisms may play a role in ADHD-associated deficits but findings need to be replicated in larger samples and are limited by the fact that only peripheral methylation could be considered. AU - Heinrich, H.* AU - Grunitz, J.* AU - Stonawski, V.* AU - Frey, S.* AU - Wahl, S. AU - Albrecht, B.* AU - Goecke, T.W.* AU - Beckmann, M.W.* AU - Kornhuber, J.* AU - Fasching, P.A.* AU - Moll, G.H.* AU - Eichler, A.* C1 - 51457 C2 - 43238 TI - Attention, cognitive control and motivation in ADHD: Linking event-related brain potentials and DNA methylation patterns in boys at early school age. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The aim of this study was to evaluate whether diagnosing pulmonary fibrosis with projection radiography can be improved by using X-ray dark-field radiograms. Pulmonary X-ray transmission and dark-field images of C57Bl/6N mice, either treated with bleomycin to induce pulmonary fibrosis or PBS to serve as controls, were acquired with a prototype grating-based small-animal scanner. Two blinded readers, both experienced radiologists and familiar with dark-field imaging, had to assess dark-field and transmission images for the absence or presence of fibrosis. Furthermore readers were asked to grade their stage of diagnostic confidence. Histological evaluation of the lungs served as the standard of reference in this study. Both readers showed a notably higher diagnostic confidence when analyzing the dark-field radiographs (p< 0.001). Diagnostic accuracy improved significantly when evaluating the lungs in dark-field images alone (p = 0.02) or in combination with transmission images (p = 0.01) compared to sole analysis of absorption images. Interreader agreement improved from good when assessing only transmission images to excellent when analyzing dark-field images alone or in combination with transmission images. Adding dark-field images to conventional transmission images in a murine model of pulmonary fibrosis leads to an improved diagnosis of this disease on chest radiographs. AU - Hellbach, K.* AU - Yaroshenko, A.* AU - Willer, K.* AU - Conlon, T.M. AU - Braunagel, M.B.* AU - Auweter, S.* AU - Yildirim, A.Ö. AU - Eickelberg, O. AU - Pfeiffer, F.* AU - Reiser, M.F.* AU - Meinel, F.G.* C1 - 52929 C2 - 44250 CY - London TI - X-ray dark-field radiography facilitates the diagnosis of pulmonary fibrosis in a mouse model. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - In this study, we monitored the thermal formation of early ribose-glycine Maillard reaction products over time by ion cyclotron resonance mass spectrometry. Here, we considered sugar decomposition (caramelization) apart from compounds that could only be produced in the presence of the amino acid. More than 300 intermediates as a result of the two initial reactants were found after ten hours (100 °C) to participate in the interplay of the Maillard reaction cascade. Despite the large numerical variety the majority of intermediates follow simple and repetitive reaction patterns. Dehydration, carbonyl cleavage, and redox reactions turned out to have a large impact on the diversity the Maillard reaction causes. Although the Amadori breakdown is considered as the main Maillard reaction pathway, other reactive intermediates, often of higher molecular weight than the Amadori rearrangement product, contribute to a large extent to the multitude of intermediates we observed. AU - Hemmler, D. AU - Roullier-Gall, C. AU - Marshall, J.W.* AU - Rychlik, M. AU - Taylor, A.J.* AU - Schmitt-Kopplin, P. C1 - 51412 C2 - 43230 CY - London TI - Evolution of complex ,maillard chemical reactions, resolved in time. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Using oral contraceptives has been implicated in the aetiology of stress-related disorders like depression. Here, we followed the hypothesis that oral contraceptives deregulate the HPA-axis by elevating circulating cortisol levels. We report for a sample of 233 pre-menopausal women increased circulating cortisol levels in those using oral contraceptives. For women taking oral contraceptives, we observed alterations in circulating phospholipid levels and elevated triglycerides and found evidence for increased glucocorticoid signalling as the transcript levels of the glucocorticoid-regulated genes DDIT4 and FKBP5 were increased in whole blood. The effects were statistically mediated by cortisol. The associations of oral contraceptives with higher FKBP5 mRNA and altered phospholipid levels were modified by rs1360780, a genetic variance implicated in psychiatric diseases. Accordingly, the methylation pattern of FKBP5 intron 7 was altered in women taking oral contraceptives depending on the rs1360780 genotype. Moreover, oral contraceptives modified the association of circulating cortisol with depressive symptoms, potentially explaining conflicting results in the literature. Finally, women taking oral contraceptives displayed smaller hippocampal volumes than non-using women. In conclusion, the integrative analyses of different types of physiological data provided converging evidence indicating that oral contraceptives may cause effects analogous to chronic psychological stressors regarding the regulation of the HPA axis. AU - Hertel, J.* AU - König, J.* AU - Homuth, G.* AU - Van der Auwera, S.* AU - Wittfeld, K.* AU - Pietzner, M.* AU - Kacprowski, T.* AU - Pfeiffer, L. AU - Kretschmer, A. AU - Waldenberger, M. AU - Kastenmüller, G. AU - Artati, A. AU - Suhre, K. AU - Adamski, J. AU - Langner, S.* AU - Völker, U.* AU - Völzke, H.* AU - Nauck, M.* AU - Friedrich, N.* AU - Grabe, H.J.* C1 - 52231 C2 - 43863 CY - London TI - Evidence for stress-like alterations in the HPA-Axis in women taking oral contraceptives. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - α-synuclein-induced neurotoxicity is a core pathogenic event in neurodegenerative synucleinopathies such as Parkinson's disease, dementia with Lewy bodies, or multiple system atrophy. There is currently no disease-modifying therapy available for these diseases. We screened 1,600 FDA-approved drugs for their efficacy to protect LUHMES cells from degeneration induced by wild-type α-synuclein and identified dipyridamole, a non-selective phosphodiesterase inhibitor, as top hit. Systematic analysis of other phosphodiesterase inhibitors identified a specific phosphodiesterase 1 inhibitor as most potent to rescue from α-synuclein toxicity. Protection was mediated by an increase of cGMP and associated with the reduction of a specific α-synuclein oligomeric species. RNA interference experiments confirmed PDE1A and to a smaller extent PDE1C as molecular targets accounting for the protective efficacy. PDE1 inhibition also rescued dopaminergic neurons from wild-type α-synuclein induced degeneration in the substantia nigra of mice. In conclusion, this work identifies inhibition of PDE1A in particular as promising target for neuroprotective treatment of synucleinopathies. AU - Höllerhage, M.* AU - Moebius, C.* AU - Melms, J.* AU - Chiu, W.H.* AU - Goebel, J.N.* AU - Chakroun, T.* AU - Koeglsperger, T.* AU - Oertel, W.H. AU - Rösler, T.W.* AU - Bickle, M.* AU - Höglinger, G.U.* C1 - 51970 C2 - 43627 TI - Protective efficacy of phosphodiesterase-1 inhibition against alpha-synuclein toxicity revealed by compound screening in LUHMES cells. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Antibody light chain amyloidosis is a rare disease caused by fibril formation of secreted immunoglobulin light chains (LCs). The huge variety of antibody sequences puts a serious challenge to drug discovery. The green tea polyphenol epigallocatechin-3-gallate (EGCG) is known to interfere with fibril formation in general. Here we present solution-and solid-state NMR studies as well as MD simulations to characterise the interaction of EGCG with LC variable domains. We identified two distinct EGCG binding sites, both of which include a proline as an important recognition element. The binding sites were confirmed by site-directed mutagenesis and solid-state NMR analysis. The EGCG-induced protein complexes are unstructured. We propose a general mechanistic model for EGCG binding to a conserved site in LCs. We find that EGCG reacts selectively with amyloidogenic mutants. This makes this compound a promising lead structure, that can handle the immense sequence variability of antibody LCs. AU - Hora, M. AU - Carballo-Pacheco, M.* AU - Weber, B.* AU - Morris, V.K.* AU - Wittkopf, A.* AU - Buchner, J.* AU - Strodel, B.* AU - Reif, B. C1 - 50487 C2 - 42500 CY - London TI - Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Estimation of physical activity using 24 h-accelerometry requires detection of accelerometer non-wear time (NWT). It is common practice to define NWT as periods >60 minutes of consecutive zero-accelerations, but this algorithm was originally developed for waking hours only and its applicability to 24 h-accelerometry is unclear. We investigated sensitivity and specificity of different algorithms to detect NWT in 24 h-accelerometry compared to diary in 47 ActivE and 559 KORA participants. NWT was determined with algorithms >60, >90, >120, >150, or >180 minutes of consecutive zero-counts. Overall, 9.1% (ActivE) and 15.4% (KORA) of reported NWT was >60 minutes. Sensitivity and specificity were lowest for the 60-min algorithm in ActivE (0.72 and 0.00) and KORA (0.64 and 0.08), and highest for the 180-min algorithm in ActivE (0.88 and 0.92) and for the 120-min algorithm in KORA (0.76 and 0.74). Nevertheless, when applying these last two algorithms, the overlap of accelerometry with any diary based NWT minutes was around 20% only. In conclusion, only a small proportion of NWT is >60 minutes. The 60-min algorithm is less suitable for NWT detection in 24 h-accelerometry because of low sensitivity, specificity, and small overlap with reported NWT minutes. Longer algorithms perform better but detect lower proportions of reported NWT. AU - Jaeschke, L.* AU - Luzak, A. AU - Steinbrecher, A.* AU - Jeran, S.* AU - Ferland, M. AU - Linkohr, B. AU - Schulz, H. AU - Pischon, T.* C1 - 51179 C2 - 42879 TI - 24 h-accelerometry in epidemiological studies: Automated detection of non-wear time in comparison to diary information. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Diabetes-associated metabolites may aid the identification of new risk variants for type 2 diabetes. Using targeted metabolomics within a subsample of the German EPIC-Potsdam study (n = 2500), we tested previously published SNPs for their association with diabetes-associated metabolites and conducted an additional exploratory analysis using data from the exome chip including replication within 2,692 individuals from the German KORA F4 study. We identified a total of 16 loci associated with diabetes-related metabolite traits, including one novel association between rs499974 (MOGAT2) and a diacyl-phosphatidylcholine ratio (PC aa C40:5/PC aa C38:5). Gene-based tests on all exome chip variants revealed associations between GFRAL and PC aa C42:1/PC aa C42:0, BIN1 and SM (OH) C22:2/SM C18:0 and TFRC and SM (OH) C22:2/SM C16:1). Selecting variants for gene-based tests based on functional annotation identified one additional association between OR51Q1 and hexoses. Among single genetic variants consistently associated with diabetes-related metabolites, two (rs174550 (FADS1), rs3204953 (REV3L)) were significantly associated with type 2 diabetes in large-scale meta-analysis for type 2 diabetes. In conclusion, we identified a novel metabolite locus in single variant analyses and four genes within gene-based tests and confirmed two previously known mGWAS loci which might be relevant for the risk of type 2 diabetes. AU - Jäger, S.* AU - Wahl, S. AU - Kröger, J.* AU - Sharma, S. AU - Hoffmann, P.* AU - Floegel, A.* AU - Pischon, T.* AU - Prehn, C. AU - Adamski, J. AU - Müller-Nurasyid, M. AU - Waldenberger, M. AU - Strauch, K. AU - Peters, A. AU - Gieger, C. AU - Suhre, K.* AU - Grallert, H. AU - Boeing, H.* AU - Schulze, M.B.* AU - Meidtner, K.* C1 - 51567 C2 - 43251 CY - London TI - Genetic variants including markers from the exome chip and metabolite traits of type 2 diabetes. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - For long-lived forest tree species, the understanding of intraspecific variation among populations and their response to water availability can reveal their ability to cope with and adapt to climate change. Dissipation of excess excitation energy, mediated by photoprotective isoprenoids, is an important defense mechanism against drought and high light when photosynthesis is hampered. We used 50-year-old Douglas-fir trees of four provenances at two common garden experiments to characterize provenance-specific variation in photosynthesis and photoprotective mechanisms mediated by essential and non-essential isoprenoids in response to soil water availability and solar radiation. All provenances revealed uniform photoprotective responses to high solar radiation, including increased de-epoxidation of photoprotective xanthophyll cycle pigments and enhanced emission of volatile monoterpenes. In contrast, we observed differences between provenances in response to drought, where provenances sustaining higher CO2 assimilation rates also revealed increased water-use efficiency, carotenoid-chlorophyll ratios, pools of xanthophyll cycle pigments, β-carotene and stored monoterpenes. Our results demonstrate that local adaptation to contrasting habitats affected chlorophyll-carotenoid ratios, pool sizes of photoprotective xanthophylls, β-carotene, and stored volatile isoprenoids. We conclude that intraspecific variation in isoprenoid-mediated photoprotective mechanisms contributes to the adaptive potential of Douglas-fir provenances to climate change. AU - Junker, L.V.* AU - Kleiber, A.* AU - Jansen, K.* AU - Wildhagen, H.* AU - Hess, M.* AU - Kayler, Z.* AU - Kammerer, B.* AU - Schnitzler, J.-P. AU - Kreuzwieser, J.* AU - Gessler, A.* AU - Ensminger, J.* C1 - 50334 C2 - 42099 CY - London TI - Variation in short-term and long-term responses of photosynthesis and isoprenoid-mediated photoprotection to soil water availability in four Douglas-fir provenances. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The human growth hormone (hGH) minigene used for transgene stabilization in mice has been recently identified to be locally expressed in the tissues where transgenes are active and associated with phenotypic alterations. Here we extend these findings by analyzing the effect of the hGH minigene in TgC6hp55 transgenic mice which express the human TNFR1 under the control of the mesenchymal cell-specific CollagenVI promoter. These mice displayed a fully penetrant phenotype characterized by growth enhancement accompanied by perturbations in metabolic, skeletal, histological and other physiological parameters. Notably, this phenotype was independent of TNF-TNFR1 signaling since the genetic ablation of either Tnf or Tradd did not rescue the phenotype. Further analyses showed that the hGH minigene was expressed in several tissues, also leading to increased hGH protein levels in the serum. Pharmacological blockade of GH signaling prevented the development of the phenotype. Our results indicate that the unplanned expression of the hGH minigene in CollagenVI expressing mesenchymal cells can lead through local and/or systemic mechanisms to enhanced somatic growth followed by a plethora of primary and/or secondary effects such as hyperphagia, hypermetabolism, disturbed glucose homeostasis, altered hematological parameters, increased bone formation and lipid accumulation in metabolically critical tissues. AU - Kaklamanos, A.* AU - Rozman, J. AU - Roulis, M.* AU - Karagianni, N.* AU - Armaka, M.* AU - Wu, M. AU - Brachthäuser, L. AU - Calzada-Wack, J. AU - Horsch, M. AU - Beckers, J. AU - Rathkolb, B. AU - Adler, T. AU - Neff, F. AU - Wolf, E.* AU - Gailus-Durner, V. AU - Fuchs, H. AU - Hrabě de Angelis, M. AU - Kollias, G.* C1 - 51198 C2 - 42777 CY - London TI - Extensive phenotypic characterization of a new transgenic mouse reveals pleiotropic perturbations in physiology due to mesenchymal hGH minigene expression. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Aquacultures are of great economic importance worldwide but pollute pristine headwater streams, lakes, and estuaries. However, there are no in-depth studies of the consequences of aquacultures on dissolved organic matter (DOM) composition and structure. We performed a detailed molecular level characterization of aquaculture DOM quality and its bacterial degradation using four salmon aquacultures in Chile. Fluorescence measurements, ultrahigh-resolution mass spectrometry, and nuclear magnetic resonance spectroscopy of the DOM revealed specific and extensive molecular alterations caused by aquacultures. Aquacultures released large quantities of readily bioavailable metabolites (primarily carbohydrates and peptides/proteins, and lipids), causing the organic matter downstream of all the investigated aquacultures to deviate strongly from the highly processed, polydisperse and molecularly heterogeneous DOM found in pristine rivers. However, the upstream individual catchment DOM signatures remained distinguishable at the downstream sites. The benthic algal biovolume decreased and the bacterial biovolume and production increased downstream of the aquacultures, shifting stream ecosystems to a more heterotrophic state and thus impairing the ecosystem health. The bacterial DOM degradation rates explain the attenuation of aquaculture DOM within the subsequent stream reaches. This knowledge may aid the development of improved waste processing facilities and may help to define emission thresholds to protect sensitive stream ecosystems. AU - Kamjunke, N.* AU - Nimptsch, J.* AU - Harir, M. AU - Herzsprung, P.* AU - Schmitt-Kopplin, P. AU - Neu, T.R.* AU - Graeber, D.* AU - Osorio, S.* AU - Valenzuela, J.* AU - Carlos Reyes, J.* AU - Woelfl, S.* AU - Hertkorn, N. C1 - 50621 C2 - 42650 TI - Land-based salmon aquacultures change the quality and bacterial degradation of riverine dissolved organic matter. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Riboswitches are bacterial RNA elements that regulate gene expression in response to metabolite or ion abundance and are considered as potential drug targets. In recent years a number of methods to find non-natural riboswitch ligands have been described. Here we report a high-throughput in vivo screening system that allows identifying OFF-riboswitch modulators in a 384 well bioluminescence assay format. We use a reverse reporter gene setup in Bacillus subtilis, consisting of a primary screening assay, a secondary assay as well as counter assays to detect compounds in a library of 1,280 molecules that act on the guanine-responsive xpt riboswitch from B. anthracis. With this in vivo high-throughput approach we identified several hit compounds and could validate the impact of one of them on riboswitch-mediated gene regulation, albeit this might not be due to direct binding to the riboswitch. However, our data demonstrate the capability of our screening assay for bigger high-throughput screening campaigns. Furthermore, the screening system described here can not only be generally employed to detect non-natural ligands or compounds influencing riboswitches acting as genetic OFF switches, but it can also be used to investigate natural ligands of orphan OFF-riboswitches. AU - Kirchner, M.* AU - Schorpp, K.K. AU - Hadian, K. AU - Schneider, S.* C1 - 51714 C2 - 43470 CY - London TI - An in vivo high-throughput screening for riboswitch ligands using a reverse reporter gene system. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - © 2017 The Author(s).Brain insulin sensitivity is an important link between metabolism and cognitive dysfunction. Intranasal insulin is a promising tool to investigate central insulin action in humans. We evaluated the acute effects of 160 U intranasal insulin on resting-state brain functional connectivity in healthy young adults. Twenty-five lean and twenty-two overweight and obese participants underwent functional magnetic resonance imaging, on two separate days, before and after intranasal insulin or placebo application. Insulin compared to placebo administration resulted in increased functional connectivity between the prefrontal regions of the default-mode network and the hippocampus as well as the hypothalamus. The change in hippocampal functional connectivity significantly correlated with visceral adipose tissue and the change in subjective feeling of hunger after intranasal insulin. Mediation analysis revealed that the intranasal insulin induced hippocampal functional connectivity increase served as a mediator, suppressing the relationship between visceral adipose tissue and hunger. The insulin-induced hypothalamic functional connectivity change showed a significant interaction with peripheral insulin sensitivity. Only participants with high peripheral insulin sensitivity showed a boost in hypothalamic functional connectivity. Hence, brain insulin action may regulate eating behavior and facilitate weight loss by modifying brain functional connectivity within and between cognitive and homeostatic brain regions. AU - Kullmann, S. AU - Heni, M. AU - Veit, R. AU - Scheffler, K.* AU - Machann, J. AU - Häring, H.-U. AU - Fritsche, A.* AU - Preissl, H. C1 - 51166 C2 - 42967 CY - London TI - Intranasal insulin enhances brain functional connectivity mediating the relationship between adiposity and subjective feeling of hunger. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Radiomics applies machine learning algorithms to quantitative imaging data to characterise the tumour phenotype and predict clinical outcome. For the development of radiomics risk models, a variety of different algorithms is available and it is not clear which one gives optimal results. Therefore, we assessed the performance of 11 machine learning algorithms combined with 12 feature selection methods by the concordance index (C-Index), to predict loco-regional tumour control (LRC) and overall survival for patients with head and neck squamous cell carcinoma. The considered algorithms are able to deal with continuous time-To-event survival data. Feature selection and model building were performed on a multicentre cohort (213 patients) and validated using an independent cohort (80 patients). We found several combinations of machine learning algorithms and feature selection methods which achieve similar results, e.g., MSR-RF: C-Index = 0.71 and BT-COX: C-Index = 0.70 in combination with Spearman feature selection. Using the best performing models, patients were stratified into groups of low and high risk of recurrence. Significant differences in LRC were obtained between both groups on the validation cohort. Based on the presented analysis, we identified a subset of algorithms which should be considered in future radiomics studies to develop stable and clinically relevant predictive models for time-To-event endpoints. AU - Leger, S.* AU - Zwanenburg, A.* AU - Pilz, K.* AU - Lohaus, F.* AU - Linge, A.* AU - Zöphel, K.* AU - Kotzerke, J.* AU - Schreiber, A.* AU - Tinhofer, I.* AU - Budach, V.* AU - Sak, A.* AU - Stuschke, M.* AU - Balermpas, P.* AU - Rödel, C.* AU - Ganswindt, U. AU - Belka, C. AU - Pigorsch, S.* AU - Combs, S.E. AU - Mönnich, D.* AU - Zips, D.* AU - Krause, M.* AU - Baumann, M.* AU - Troost, E.G.C.* AU - Löck, S.* AU - Richter, C.* C1 - 52224 C2 - 43814 TI - A comparative study of machine learning methods for time-to-event survival data for radiomics risk modelling. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - We conducted a genome-wide association study (GWAS) of anorexia nervosa (AN) using a stringently defined phenotype. Analysis of phenotypic variability led to the identification of a specific genetic risk factor that approached genome-wide significance (rs929626 in EBF1 (Early B-Cell Factor 1); P = 2.04 × 10-7; OR = 0.7; 95% confidence interval (CI) = 0.61-0.8) with independent replication (P = 0.04), suggesting a variant-mediated dysregulation of leptin signaling may play a role in AN. Multiple SNPs in LD with the variant support the nominal association. This demonstrates that although the clinical and etiologic heterogeneity of AN is universally recognized, further careful sub-typing of cases may provide more precise genomic signals. In this study, through a refinement of the phenotype spectrum of AN, we present a replicable GWAS signal that is nominally associated with AN, highlighting a potentially important candidate locus for further investigation. AU - Li, D.* AU - Chang, X.* AU - Connolly, J.J.* AU - Tian, L.* AU - Liu, Y.* AU - Bhoj, E.J.* AU - Robinson, N.* AU - Abrams, D.J.* AU - Li, Y.R.* AU - Bradfield, J.P.* AU - Kim, C.E.* AU - Li, J.* AU - Wang, F.* AU - Snyder, J.* AU - Lemma, M.* AU - Hou, C.* AU - Wei, Z.* AU - Guo, Y.* AU - Qiu, H.* AU - Mentch, F.D.* AU - Thomas, K.A.* AU - Chiavacci, R.M.* AU - Cone, R.D.* AU - Li, B.* AU - Sleiman, P.A.* AU - Hakonarson, H.* AU - Perica, V.B.* AU - Franklin, C.S.* AU - Floyd, J.A.B.* AU - Thornton, L.M.* AU - Huckins, L.M.* AU - Southam, L.* AU - Rayner, N.W.* AU - Tachmazidou, I.* AU - Schmidt, U.* AU - Tozzi, F.* AU - Kiezebrink, K.* AU - Hebebrand, J.* AU - Gorwood, P.* AU - Adan, R.A.H.* AU - Kas, M.J.H.* AU - Favaro, A.* AU - Santonastaso, P.* AU - Fernánde-Aranda, F.* AU - Gratacòs, M.* AU - Rybakowski, F.* AU - Dmitrzak-Weglarz, M.* AU - Kaprio, J.* AU - Keski-Rahkonen, A.* AU - Raevuori-Helkamaa, A.* AU - Furth, E.F.V.* AU - Slof-Opt Landt, M.C.T.* AU - Hudson, J.I.* AU - Reichborn-Kjennerud, T.* AU - Knudsen, G.P.S.* AU - Monteleone, P.* AU - Karwautz, A.* AU - Eating Disorders Working Group of the Psychiatric Genomics Consortium (Wichmann, H.-E.) AU - Schork, N.J.* AU - Ando, T.* AU - Inoko, H.* AU - Esko, T.* AU - Fischer, K.* AU - Männik, K.* AU - Metspalu, A.* AU - Baker, J.H.* AU - DeSocio, J.E.* AU - Hilliard, C.E.* AU - O'Toole, J.K.* AU - Pantel, J.* AU - Szatkiewicz, J.P.* AU - Zerwas, S.* AU - Davis, O.S.P.* AU - Helder, S.* AU - Bühren, K.* AU - Burghardt, R.* AU - de Zwaan, M.* C1 - 51461 C2 - 43171 TI - A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Organ transplantation remains the most effective treatment for patients with late stage organ failure. Transgenic pigs provide an alternative organ donor source to the limited availability of human organs. However, cellular rejection still remains to be the obstacle for xenotransplantation. Superior to other methods, antigen-specific regulatory T cells (Treg) alleviate cellular rejection with fewer side effects. Here we demonstrate the use of a fast method to provide tolerogenic dendritic cells (tolDC) that can be used to generate effective porcine-specific Treg cells (PSTreg). TolDC were produced within three days from human monocytes in medium supplemented with anti-inflammatory cytokines. Treg were generated from naïve CD4+ T cells and induced to become PSTreg by cocultivation with porcine-antigen-loaded tolDC. Results s/howed that PSTreg exhibited the expected phenotype, CD4+CD25+CD127low/- Foxp3+, and a more activated phenotype. The specificity of PSTreg was demonstrated by suppression of effector T cell (Teff) activation markers of different stages and inhibition of Teff cell proliferation. TolDC and PSTreg exhibited high expression of IL-10 and TGF-β1 at both protein and RNA levels, and PSTreg also highly expressed IL-35 at RNA levels. Upon restimulation, PSTreg retained the activated phenotype and specificity. Taken together, the newly developed procedure allows efficient generation of highly suppressive PSTreg. AU - Li, M.* AU - Eckl, J. AU - Geiger, C. AU - Schendel, D.J. AU - Pohla, H. C1 - 51453 C2 - 43236 CY - London TI - A novel and effective method to generate human porcine-specific regulatory T cells with high expression of IL-10, TGF-β1 and IL-35. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Previous studies identified APOBEC deaminases as enzymes targeting hepatitis B virus (HBV) DNA in the nucleus thus affecting its persistence. Interferon (IFN)-α treated chimpanzees and hepatitis C patients showed elevated APOBEC expression. We thus hypothesized that the responses to IFN-α treatment of chronic hepatitis B (CHB) patients is influenced by IFN-induced base excision repair (BER). CHB-treatment naïve patients, patients treated with PEGylated IFN-α, and patients with sequential treatment of Entecavior and PEGylated IFN-α were recruited. Blood and liver biopsy samples were collected before treatment and at treatment endpoint. BER genes were assessed by quantitative RT-PCR. BER gene expression levels and IFN treatment responses were correlated in patient liver biopsies. APOBEC3A,-B,-C,-D/E, and-G mRNA levels were up-regulated in IFN-treated patients. APOBEC3A expression was significantly higher in IFN-responders than in non-responders. BER genes NEIL3 was down-regulated in IFN-treated pa tients. APOBEC3 and BER gene expression at treatment endpoints partially correlated with the corresponding absolute DNA level or degree of HBsAg and HBV DNA decline. Our study suggests that the expression of APOBEC3A positively correlates with IFN-treatment responses in CHB patients, while NEIL3 shows negative correlation. These genes may involve to IFN mediated viral suppression and serve as biomarkers for CHB disease management. AU - Li, Y.* AU - Xia, Y. AU - Han, M.* AU - Chen, G.* AU - Zhang, D.* AU - Thasler, W.E.* AU - Protzer, U. AU - Ning, Q.* C1 - 52115 C2 - 43760 CY - London TI - IFN-α-mediated base excision repair pathway correlates with antiviral response against hepatitis B virus infection. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Conventional circulating tumor cell (CTC) detection strategies rely on cell surface marker EpCAM and intracellular cytokeratins (CKs) for isolation and identification, respectively. Application of such methods is considerably limited by inherent heterogeneous and dynamic expression or absence of EpCAM and/or CKs in CTCs. Here, we report a novel strategy, integrating antigen-independent subtraction enrichment and immunostaining-FISH (SE-iFISH), to detect a variety of aneuploid circulating rare cells (CRCs), including CTCs and circulating tumor endothelial cells (CECs). Enriched CRCs, maintained at high viability and suitable for primary tumor cell culture, are comprehensively characterized by in situ co-examination of chromosome aneuploidy by FISH and immunostaining of multiple biomarkers displayed in diverse fluorescence channels. We described and quantified for the first time the existence of individual aneuploid CD31 + CECs and co-existence of "fusion clusters" of endothelial-epithelial aneuploid tumor cells among enriched non-hematopoietic CRCs. Hence, SE-iFISH is feasible for efficient co-detection and in situ phenotypic and karyotypic characterization as well as quantification of various CRCs, allowing for their classification into diverse subtypes upon biomarker expression and chromosome ploidy. Enhanced SE-iFISH technology, assisted by the Metafer-iFISH automated CRC imaging system, provides a platform for the analysis of potential contributions of each subtype of CRCs to distinct clinical outcome. AU - Lin, P.P.* AU - Gires, O. AU - Wang, D.D.* AU - Li, L.* AU - Wang, H.* C1 - 51793 C2 - 43477 CY - London TI - Comprehensive in situ co-detection of aneuploid circulating endothelial and tumor cells. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Bioactive peptides play critical roles in regulating many biological processes. Recently, natural short peptides biomarkers are drawing significant attention and are considered as "hidden treasure" of drug candidates. High resolution and high mass accuracy provided by mass spectrometry (MS)-based untargeted metabolomics would enable the rapid detection and wide coverage of the low-molecular-weight peptidome. However, translating unknown masses (<1 500 Da) into putative peptides is often limited due to the lack of automatic data processing tools and to the limit of peptide databases. The web server OligoNet responds to this challenge by attempting to decompose each individual mass into a combination of amino acids out of metabolomics datasets. It provides an additional network-based data interpretation named "Peptide degradation network" (PDN), which unravels interesting relations between annotated peptides and generates potential functional patterns. The ab initio PDN built from yeast metabolic profiling data shows a great similarity with well-known metabolic networks, and could aid biological interpretation. OligoNet allows also an easy evaluation and interpretation of annotated peptides in systems biology, and is freely accessible at https://daniellyz200608105.shinyapps.io/OligoNet/ . AU - Liu, Y.* AU - Forcisi, S. AU - Lucio, M. AU - Harir, M. AU - Bahut, F.* AU - Deleris-Bou, M.* AU - Krieger-Weber, S.* AU - Gougeon, R.D.* AU - Alexandre, H.* AU - Schmitt-Kopplin, P. C1 - 51902 C2 - 43561 CY - London TI - Digging into the low molecular weight peptidome with the OligoNet web server. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Apolipoprotein A-IV (apoA-IV) has been observed to be associated with lipids, kidney function, adiposity- and diabetes-related parameters. To assess the causal relationship of apoA-IV with these phenotypes, we conducted bidirectional Mendelian randomization (MR) analyses using publicly available summary-level datasets from GWAS consortia on apoA-IV concentrations (n = 13,813), kidney function (estimated glomerular filtration rate (eGFR), n = 133,413), lipid traits (HDL cholesterol, LDL cholesterol, triglycerides, n = 188,577), adiposity-related traits (body-mass-index (n = 322,206), waist-hip-ratio (n = 210,088)) and fasting glucose (n = 133,010). Main analyses consisted in inverse-variance weighted and multivariable MR, whereas MR-Egger regression and weighted median estimation were used as sensitivity analyses. We found that eGFR is likely to be causal on apoA-IV concentrations (53 SNPs; causal effect estimate per 1-SD increase in eGFR = -0.39; 95% CI = [-0.54, -0.24]; p-value = 2.4e-07). Triglyceride concentrations were also causally associated with apoA-IV concentrations (40 SNPs; causal effect estimate per 1-SD increase in triglycerides = -0.06; 95% CI = [-0.08, -0.04] ; p-value = 4.8e-07), independently of HDL-C and LDL-C concentrations (causal effect estimate from multivariable MR = -0.06; 95% CI = [-0.10, -0.02]; p-value = 0.0014). Evaluating the inverse direction of causality revealed a possible causal association of apoA-IV on HDL-cholesterol (2 SNPs; causal effect estimate per one percent increase in apoA-IV = -0.40; 95% CI = [-0.60, -0.21] ; p-value = 5.5e-05). AU - Mack, S.* AU - Coassin, S.* AU - Vaucher, J.* AU - Kronenberg, F.* AU - Lamina, C.* AU - Rueedi, R.* AU - Yousri, N.A.* AU - Seppälä, I.* AU - ApoA-IV-GWAS Constortium (Gieger, C.) AU - Schönherr, S.* AU - Forer, L.* AU - Erhart, G.* AU - Kollerits, B.* AU - Marques-Vidal, P.* AU - ApoA-IV-GWAS Constortium (Müller-Nurasyid, M.) AU - Waeber, G.* AU - Bergmann, S.* AU - Dähnhardt, D.* AU - Stöckl, A.* AU - Kiechl, S.* AU - Raitakari, O.T.* AU - Kähönen, M.* AU - Willeit, J.* AU - Kedenko, L.* AU - Paulweber, B.* AU - ApoA-IV-GWAS Constortium (Peters, A.) AU - ApoA-IV-GWAS Constortium (Meitinger, T.) AU - ApoA-IV-GWAS Constortium (Strauch, K.) AU - Lehtimäki, T.* AU - Hunt, S.C.* AU - Vollenweider, P.* C1 - 51766 C2 - 43376 TI - Evaluating the causal relation of ApoA-IV with disease-related traits - A bidirectional two-sample mendelian randomization study. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Omega-3 fatty acids may influence human physiological parameters in part by affecting the gut microbiome. The aim of this study was to investigate the links between omega-3 fatty acids, gut microbiome diversity and composition and faecal metabolomic profiles in middle aged and elderly women. We analysed data from 876 twins with 16S microbiome data and DHA, total omega-3, and other circulating fatty acids. Estimated food intake of omega-3 fatty acids were obtained from food frequency questionnaires. Both total omega-3and DHA serum levels were significantly correlated with microbiome alpha diversity (Shannon index) after adjusting for confounders (DHA Beta(SE) = 0.13(0.04), P = 0.0006 total omega-3: 0.13(0.04), P = 0.001). These associations remained significant after adjusting for dietary fibre intake. We found even stronger associations between DHA and 38 operational taxonomic units (OTUs), the strongest ones being with OTUs from the Lachnospiraceae family (Beta(SE) = 0.13(0.03), P = 8 × 10 -7 ). Some of the associations with gut bacterial OTUs appear to be mediated by the abundance of the faecal metabolite N-carbamylglutamate. Our data indicate a link between omega-3 circulating levels/intake and microbiome composition independent of dietary fibre intake, particularly with bacteria of the Lachnospiraceae family. These data suggest the potential use of omega-3 supplementation to improve the microbiome composition. AU - Menni, C.* AU - Zierer, J. AU - Pallister, T.* AU - Jackson, M.A.* AU - Long, T.C.* AU - Mohney, R.P.* AU - Steves, C.J.* AU - Spector, T.D.* AU - Valdes, A.M.* C1 - 51971 C2 - 43638 CY - London TI - Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Liver cells communicate with the extracellular environment to take up nutrients via endocytosis. Iron uptake is essential for metabolic activities and cell homeostasis. Here, we investigated the role of the endocytic system for maintaining iron homeostasis. We specifically depleted the small GTPase Rab5 in the mouse liver, causing a transient loss of the entire endo-lysosomal system. Strikingly, endosome depletion led to a fast reduction of hepatic iron levels, which was preceded by an increased abundance of the iron exporter ferroportin. Compensatory changes in livers of Rab5-depleted mice include increased expression of transferrin receptor 1 as well as reduced expression of the iron-regulatory hormone hepcidin. Serum iron indices (serum iron, free iron binding capacity and total iron binding capacity) in Rab5-KD mice were increased, consistent with an elevated splenic and hepatic iron export. Our data emphasize the critical importance of the endosomal compartments in hepatocytes to maintain hepatic and systemic iron homeostasis in vivo. The short time period (between day four and five) upon which these changes occur underscore the fast dynamics of the liver iron pool. AU - Metzendorf, C.* AU - Zeigerer, A. AU - Seifert, S.* AU - Sparla, R.* AU - Najafi, B. AU - Canonne-Hergaux, F.* AU - Zerial, M.* AU - Muckenthaler, M.U.* C1 - 51462 C2 - 43504 CY - London TI - Acute loss of the hepatic endo-lysosomal system in vivo causes compensatory changes in iron homeostasis. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The chemokine receptor CXCR5 is primarily expressed on B cells and Tfh cells and facilitates their migration towards B cell follicles. In the present study we investigated the role of the CXCL13/CXCR5 axis in the pathogenesis of rheumatoid arthritis (RA) and specifically addressed the impact of CXCR5-mediated T and B cell migration in this disease. Employing collagen-induced arthritis (CIA) we identify CXCR5 as an absolutely essential factor for the induction of inflammatory autoimmune arthritis. Cxcr5-deficient mice and mice selectively lacking Cxcr5 on T cells were completely resistant to CIA, showed impaired germinal center responses and failed to mount an IgG1 antibody response to collagen II. Selective ablation of CXCR5 expression in B cells also led to suppression of CIA owing to diminished GC responses in secondary lymphoid organs (SLO) and impaired anti-collagen II antibody production. Chimeric mice harboring Cxcr5-proficient and Cxcr5-deficient immune cells revealed SLO and not the synovial tissue as the compartment where CXCR5-mediated cell migration induces autoimmune inflammation in arthritis. Thus our data demonstrate that CXCR5-mediated co-localization of Tfh cells and B cells in SLOs is absolutely essential for the induction of RA and identify CXCR5 and Tfh cells as promising therapeutic targets for the treatment of RA. AU - Moschovakis, G.L.* AU - Bubke, A.* AU - Friedrichsen, M.* AU - Falk, C.S.* AU - Feederle, R. AU - Förster, R.* C1 - 51742 C2 - 43458 CY - London TI - T cell specific Cxcr5 deficiency prevents rheumatoid arthritis. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of a self-labeling protein to insulin allows for the quantification of age-distinct insulin granule pools in pancreatic beta cells by a combination of super resolution and transmission electron microscopy on Tokuyasu cryosections. In contrast to fluorescent proteins like GFP organic dyes covalently bound to self-labeling proteins retain their fluorescence also in epoxy resin following high pressure freezing and freeze substitution, or remarkably even after strong chemical fixation. This enables for the assessment of age-defined granule morphology and degradation. Finally, we demonstrate that this CLEM protocol is highly versatile, being suitable for single and dual fluorescent labeling and detection of different proteins with optimal ultrastructure preservation and contrast. AU - Müller, A. AU - Neukam, M. AU - Ivanova, A. AU - Sönmez, A. AU - Münster, C. AU - Kretschmar, S.* AU - Kalaidzidis, Y.* AU - Kurth, T.* AU - Verbavatz, J.-M.* AU - Solimena, M. C1 - 50467 C2 - 42297 CY - London TI - A global approach for quantitative super resolution and electron microscopy on cryo and epoxy sections using self-labeling protein tags. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Radiation is a highly efficient therapy in squamous head and neck carcinoma (HNSCC) treatment. However, local recurrence and metastasis are common complications. Recent evidence shows that cancer-cell-derived exosomes modify tumour cell movement and metastasis. In this study, we link radiation-induced changes of exosomes to their ability to promote migration of recipient HNSCC cells. We demonstrate that exosomes isolated from irradiated donor cells boost the motility of the HNSCC cells BHY and FaDu. Molecular data identified enhanced AKT-signalling, manifested through increased phospho-mTOR, phospho-rpS6 and MMP2/9 protease activity, as underlying mechanism. AKT-inhibition blocked the pro-migratory action, suggesting AKT-signalling as key player in exosome-mediated migration. Proteomic analysis of exosomes isolated from irradiated and non-irradiated BHY donor cells identified 39 up- and 36 downregulated proteins. In line with the observed pro-migratory effect of exosomes isolated from irradiated cells protein function analysis assigned the deregulated exosomal proteins to cell motility and AKT-signalling. Together, our findings demonstrate that exosomes derived from irradiated HNSCC cells confer a migratory phenotype to recipient cancer cells. This is possibly due to radiation-regulated exosomal proteins that increase AKT-signalling. We conclude that exosomes may act as driver of HNSCC progression during radiotherapy and are therefore attractive targets to improve radiation therapy strategies. AU - Mutschelknaus, L. AU - Azimzadeh, O. AU - Heider, T. AU - Winkler, K. AU - Vetter, M.* AU - Kell, R. AU - Tapio, S. AU - Merl-Pham, J. AU - Huber, S.M.* AU - Edalat, L.* AU - Radulović, V. AU - Anastasov, N. AU - Atkinson, M.J. AU - Mörtl, S. C1 - 52021 C2 - 43649 CY - London TI - Radiation alters the cargo of exosomes released from squamous head and neck cancer cells to promote migration of recipient cells. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Magnetic cell sorting provides a valuable complementary mechanism to fluorescent techniques, especially if its parameters can be fine-tuned. In addition, there has recently been growing interest in studying naturally occurring magnetic cells and genetic engineering of cells to render them magnetic in order to control molecular processes via magnetic fields. For such approaches, contamination-free magnetic separation is an essential capability. We here present a robust and tunable microfluidic sorting system in which magnetic gradients of up to 1700 T/m can be applied to cells flowing through a sorting channel by reversible magnetization of ferrofluids. Visual control of the sorting process allowed us to optimize sorting efficiencies for a large range of sizes and magnetic moments of cells. Using automated quantification based on imaging of fluorescent markers, we showed that macrophages containing phagocytosed magnetic nanoparticles, with cellular magnetic dipole moments on the order of 10 fAm(2), could be sorted with an efficiency of 90 +/- 1%. Furthermore, we successfully sorted intrinsically magnetic magnetotactic bacteria with magnetic moments of 0.1 fAm(2). In distinction to column-based magnetic sorting devices, microfluidic systems can prevent sample contact with superparamagnetic material. This ensures contamination-free separation of naturally occurring or bioengineered magnetic cells and is essential for downstream characterization of their properties. AU - Myklatun, A. AU - Cappetta, M. AU - Winklhofer, M.* AU - Ntziachristos, V. AU - Westmeyer, G.G.* C1 - 51649 C2 - 43298 CY - London TI - Microfluidic sorting of intrinsically magnetic cells under visual control. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) expression is transiently elevated following low dose irradiation typically encountered in the workplace and from natural sources. This long non-coding RNA recruits epigenetic silencers for cis-acting repression of its neighbouring Methionine adenosyltransferase 2A gene. It now emerges that PARTICLE operates as a trans-acting mediator of DNA and histone lysine methylation. Chromatin immunoprecipitation sequencing (ChIP-seq) and immunological evidence established elevated PARTICLE expression linked to increased histone 3 lysine 27 trimethylation. Live-imaging of dbroccoli-PARTICLE revealing its dynamic association with DNA methyltransferase 1 was confirmed by flow cytometry, immunoprecipitation and direct competitive binding interaction through electrophoretic mobility shift assay. Acting as a regulatory docking platform, the long non-coding RNA PARTICLE serves to interlink epigenetic modification machineries and represents a compelling innovative component necessary for gene silencing on a global scale. AU - O'Leary, V.B. AU - Hain, S. AU - Maugg, D. AU - Smida, J. AU - Azimzadeh, O. AU - Tapio, S. AU - Ovsepian, S.V. AU - Atkinson, M.J. C1 - 51110 C2 - 42986 CY - London TI - Long non-coding RNA PARTICLE bridges histone and DNA methylation. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The long non-coding RNA PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) partakes in triple helix (triplex) formation, is transiently elevated following low dose irradiation and regulates transcription of its neighbouring gene - Methionine adenosyltransferase 2A. It now emerges that PARTICLE triplex sites are predicted in many different genes across all human chromosomes. In silico analysis identified additional regions for PARTICLE triplexes at >1600 genomic locations. Multiple PARTICLE triplexes are clustered predominantly within the human and mouse tumor suppressor WW Domain Containing Oxidoreductase (WWOX) gene. Surface plasmon resonance diffraction and electrophoretic mobility shift assays were consistent with PARTICLE triplex formation within human WWOX with high resolution imaging demonstrating its enrichment at this locus on chromosome 16. PARTICLE knockdown and over-expression resulted in inverse changes in WWOX transcripts levels with siRNA interference eliminating PARTICLEs elevated transcription to irradiation. The evidence for a second functional site of PARTICLE triplex formation at WWOX suggests that PARTICLE may form triplex-mediated interactions at multiple positions in the human genome including remote loci. These findings provide a mechanistic explanation for the ability of lncRNAs to regulate the expression of numerous genes distributed across the genome. AU - O'Leary, V.B. AU - Smida, J. AU - Buske, F.A.* AU - Carrascosa, L.G.* AU - Azimzadeh, O. AU - Maugg, D. AU - Hain, S. AU - Tapio, S. AU - Heidenreich, W.F. AU - Kerr, J.* AU - Trau, M.* AU - Ovsepian, S.V. AU - Atkinson, M.J. C1 - 51679 C2 - 43333 CY - London TI - PARTICLE triplexes cluster in the tumor suppressor WWOX and may extend throughout the human genome. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Monocytes are actively recruited at sites of chronic inflammation. However, molecular factors involved in this process are not fully elucidated. Here, we show that cytokine IL-4 which is implicated in the development of chronic inflammatory disease atopic dermatitis (AD) induces expression of transcription factor FoxQ1 in human monocytes and macrophages. FoxQ1 mRNA levels were elevated in monocytes of AD patients compared to healthy donors. Overexpression of FoxQ1 in RAW 264.7 monocytic cells facilitated their migration towards MCP-1 and was associated with decreased expression of migration-regulating genes (claudin 11 and plexin C1). Furthermore, FoxQ1 overexpression in RAW cells accelerated TNFα secretion after LPS challenge. Overall, our results indicate that FoxQ1 stimulates monocyte motility, increases pro-inflammatory potential, and directs monocyte migration towards MCP-1 that is crucial for monocyte influx into inflammatory sites. This mechanism could contribute to the pathogenesis of chronic inflammatory disorders such as AD. AU - Ovsiy, I.* AU - Riabov, V.* AU - Manousaridis, I.* AU - Michel, J.* AU - Moganti, K.* AU - Yin, S.* AU - Liu, T.* AU - Sticht, C.* AU - Kremmer, E. AU - Harmsen, M.C.* AU - Goerdt, S.* AU - Gratchev, A.* AU - Kzhyshkowska, J.* C1 - 52480 C2 - 44006 CY - London TI - IL-4 driven transcription factor FoxQ1 is expressed by monocytes in atopic dermatitis and stimulates monocyte migration. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Photothermal therapy and ablation are commonplace medical procedures employed for treatment of tumors, vascular and brain abnormalities as well as other disorders that require selective destruction of tissues. Yet, accurate mapping of the dynamic temperature field distribution in the treated region represents an unmet clinical need, strongly affecting the clinical outcome of these interventions. We introduce a fast three-dimensional temperature mapping method based on real-time optoacoustic sensing of the treated region coupled with a thermal-diffusion-based model of heat distribution in tissues. Deviations of the optoacoustic temperature readings provided at 40  ms intervals remained below 10% in tissue-mimicking phantom experiments for temperature elevations above 3 °C, as validated by simultaneous thermocouple measurements. Performance of the new method to dynamically estimate the volumetric temperature distribution was further showcased in post-mortem mouse imaging experiments. The newly discovered capacity to non-invasively measure the temperature map in an entire treated volume with both high spatial and temporal resolutions holds potential for improving safety and efficacy of light-based therapeutic interventions. AU - Oyaga Landa, F.J. AU - Dean-Ben, X.L. AU - Sroka, R.* AU - Razansky, D. C1 - 51781 C2 - 43390 CY - London TI - Volumetric optoacoustic temperature mapping in photothermal therapy. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Reduced gut microbiome diversity is associated with multiple disorders including metabolic syndrome (MetS) features, though metabolomic markers have not been investigated. Our objective was to identify blood metabolite markers of gut microbiome diversity, and explore their relationship with dietary intake and MetS. We examined associations between Shannon diversity and 292 metabolites profiled by the untargeted metabolomics provider Metabolon Inc. in 1529 females from TwinsUK using linear regressions adjusting for confounders and multiple testing (Bonferroni: P < 1.71 × 10 -4 ). We replicated the top results in an independent sample of 420 individuals as well as discordant identical twin pairs and explored associations with self-reported intakes of 20 food groups. Longitudinal changes in circulating levels of the top metabolite, were examined for their association with food intake at baseline and with MetS at endpoint. Five metabolites were associated with microbiome diversity and replicated in the independent sample. Higher intakes of fruit and whole grains were associated with higher levels of hippurate cross-sectionally and longitudinally. An increasing hippurate trend was associated with reduced odds of having MetS (OR: 0.795[0.082]; P = 0.026). These data add further weight to the key role of the microbiome as a potential mediator of the impact of dietary intake on metabolic status and health. AU - Pallister, T.* AU - Jackson, M.A.* AU - Martin, T.C.* AU - Zierer, J. AU - Jennings, A.* AU - Mohney, R.P.* AU - MacGregor, A.* AU - Steves, C.J.* AU - Cassidy, A.* AU - Spector, T.D.* AU - Menni, C.* C1 - 52235 C2 - 43810 CY - London TI - Hippurate as a metabolomic marker of gut microbiome diversity: Modulation by diet and relationship to metabolic syndrome. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - mRNA splicing is an important mechanism to regulate mRNA expression. Abnormal regulation of this process may lead to lung cancer. Here, we investigated the associations of 11,966 single-nucleotide polymorphisms (SNPs) in 206 mRNA splicing-related genes with lung cancer risk by using the summary data from six published genome-wide association studies (GWASs) of Transdisciplinary Research in Cancer of the Lung (TRICL) (12,160 cases and 16,838 controls) and another two lung cancer GWASs of Harvard University (984 cases and 970 controls) and deCODE (1,319 cases and 26,380 controls). We found that a total of 12 significant SNPs with false discovery rate (FDR) ≤0.05 were mapped to one novel gene PRPF6 and two previously reported genes (DHX16 and LSM2) that were also confirmed in this study. The six novel SNPs in PRPF6 were in high linkage disequilibrium and associated with PRPF6 mRNA expression in lymphoblastoid cells from 373 Europeans in the 1000 Genomes Project. Taken together, our studies shed new light on the role of mRNA splicing genes in the development of lung cancer. AU - Pan, Y.* AU - Liu, H.* AU - Wang, Y.* AU - Kang, X.* AU - Liu, Z.* AU - Owzar, K.* AU - Han, Y.* AU - Su, L.* AU - Wei, Y.* AU - Hung, R.J.* AU - Brhane, Y.* AU - McLaughlin, J.* AU - Brennan, P.* AU - Bickeböller, H.* AU - Rosenberger, A.* AU - Houlston, R.S.* AU - Caporaso, N.* AU - Teresa Landi, M.* AU - Heinrich, J. AU - Risch, A.* AU - Wu, X.* AU - Ye, Y.* AU - Christiani, D.C.* AU - Amos, C.I.* AU - Wei, Q.* C1 - 50729 C2 - 42570 TI - Associations between genetic variants in mRNA splicing-related genes and risk of lung cancer: A pathway-based analysis from published GWASs. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The role of androgens in metabolism with respect to sex-specific disease associations is poorly understood. Therefore, we aimed to provide molecular signatures in plasma and urine of androgen action in a sex-specific manner using state-of-the-art metabolomics techniques. Our study population consisted of 430 men and 343 women, aged 20-80 years, who were recruited for the cross-sectional population-based Study of Health in Pomerania (SHIP-TREND), Germany. We used linear regression models to identify associations between testosterone, androstenedione and dehydroepiandrosterone-sulfate (DHEAS) as well as sex hormone-binding globulin and plasma or urine metabolites measured by mass spectrometry. The analyses revealed major sex-specific differences in androgen-associated metabolites, particularly for levels of urate, lipids and metabolic surrogates of lifestyle factors, like cotinine or piperine. In women, in particular in the postmenopausal state, androgens showed a greater impact on the metabolome than in men (especially DHEAS and lipids were highly related in women). We observed a novel association of androstenedione on the metabolism of biogenic amines and only a small sex-overlap of associations within steroid metabolism. The present study yields new insights in the interaction between androgens and metabolism, especially about their implication in female metabolism. AU - Piontek, U.* AU - Wallaschofski, H.* AU - Kastenmüller, G. AU - Suhre, K. AU - Völzke, H.* AU - Do, K.T. AU - Artati, A. AU - Nauck, M.* AU - Adamski, J. AU - Friedrich, N.* AU - Pietzner, M.* C1 - 51180 C2 - 42775 CY - London TI - Sex-specific metabolic profiles of androgens and its main binding protein SHBG in a middle aged population without diabetes. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Brown adipocytes are important in regulating non-shivering thermogenesis, whole body glucose and lipid homeostasis. Increasing evidence supports an important role of metabolites as well as macro-and micronutrients in brown adipocyte differentiation and function. Calcium is one of the most abundant ions in the body regulating multiple cellular processes. We observed that increasing extracellular calcium concentration during brown adipocyte differentiation blocks lipid accumulation and suppresses induction of major adipogenic transcription factors such as PPAR gamma and C/EBP alpha. In contrast, the depletion of calcium in the medium enhances adipogenesis and expression of brown adipocyte selective genes, such as UCP1. Mechanistically, we show that elevated extracellular calcium inhibits C/EBP beta activity through hyperactivation of ERK, a process that is independent of intracellular calcium levels and reversibly halts differentiation. Moreover, increased extracellular calcium solely after the induction phase of differentiation specifically suppresses gene expression of UCP1, PRDM16 and PGC1-alpha. Notably, depleting extracellular calcium provokes opposite effects. Together, we show that modulating extracellular calcium concentration controls brown adipocyte differentiation and thermogenic gene expression, highlighting the importance of tissue microenvironment on brown adipocyte heterogeneity and function. AU - Pramme-Steinwachs, I. AU - Jastroch, M. AU - Ussar, S. C1 - 51827 C2 - 43387 CY - London TI - Extracellular calcium modulates brown adipocyte differentiation and identity. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker. Furthermore, cultivation-based approaches were used to obtain isolates of the major taxa to study their ecophysiology. The endophytic microbiome from P. pinaster trees differed significantly between the two sampling sites. Main bacterial OTUs belonged to the Proteobacteria (39% (site M) - 97% (site A)), and Firmicutes (0.70% (site A) - 44% (site M)). However, consequences of the invasion with the pathogen were comparable. Interestingly diversity of wood endophytic bacteria increased with the severity of the diseases, with highest diversity levels observed in in the most affected trees. Our results suggest that in the first stages of the disease, the defence mechanisms of plants are repressed by the pathogen, resulting in a colonization of the wood interior by soil microorganisms. AU - Proença, D.N.* AU - Francisco, R.* AU - Kublik, S. AU - Schöler, A. AU - Vestergaard, G. AU - Schloter, M. AU - Morais, P.V.* C1 - 51389 C2 - 43202 CY - London TI - The microbiome of endophytic, wood colonizing bacteria from pine trees as affected by pine wilt disease. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Type II diabetes (T2D) is characterized by diminished insulin production and resistance of cells to insulin. Among others, endoplasmic reticulum (ER) stress is a principal factor contributing to T2D and induces a shift towards a more reducing cellular environment. At the same time, peripheral insulin resistance triggers the over-production of regulatory hormones such as insulin and human islet amyloid polypeptide (hIAPP). We show that the differential aggregation of reduced and oxidized hIAPP assists to maintain the redox equilibrium by restoring redox equivalents. Aggregation thus induces redox balancing which can assist initially to counteract ER stress. Failure of the protein degradation machinery might finally result in β-cell disruption and cell death. We further present a structural characterization of hIAPP in solution, demonstrating that the N-terminus of the oxidized peptide has a high propensity to form an α-helical structure which is lacking in the reduced state of hIAPP. In healthy cells, this residual structure prevents the conversion into amyloidogenic aggregates. AU - Rodriguez Camargo, D.C. AU - Tripsianes, K.* AU - Buday, K. AU - Frankó, A. AU - Göbl, C. AU - Hartlmüller, C.* AU - Sarkar, R. AU - Aichler, M. AU - Mettenleiter, G. AU - Schulz, M. AU - Böddrich, A.* AU - Erck, C.* AU - Martens, H.* AU - Walch, A.K. AU - Madl, T. AU - Wanker, E.E.* AU - Conrad, M. AU - Hrabě de Angelis, M. AU - Reif, B. C1 - 50706 C2 - 42448 TI - The redox environment triggers conformational changes and aggregation of hIAPP in Type II Diabetes. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Adiposity and obesity result from the interaction of genetic variation and environmental factors from very early in life, possibly mediated by epigenetic processes. Few Epigenome-Wide-Association-Studies have identified DNA-methylation (DNAm) signatures associated with BMI and body composition in children. Body composition by Bio-Impedance-Analysis and genome-wide DNAm in whole blood were assessed in 374 pre-school children from four European countries. Associations were tested by linear regression adjusted for sex, age, centre, education, 6 WBC-proportions according to Houseman and 30 principal components derived from control probes. Specific DNAm variants were identified to be associated with BMI (212), fat-mass (230), fat-free-mass (120), fat-mass-index (24) and fat-free-mass-index (15). Probes in genes SNED1(IRE-BP1), KLHL6, WDR51A(POC1A), CYTH4-ELFN2, CFLAR, PRDM14, SOS1, ZNF643(ZFP69B), ST6GAL1, C3orf70, CILP2, MLLT4 and ncRNA LOC101929268 remained significantly associated after Bonferroni-correction of P-values. We provide novel evidence linking DNAm with (i) altered lipid and glucose metabolism, (ii) diabetes and (iii) body size and composition in children. Both common and specific epigenetic signatures among measures were also revealed. The causal direction with phenotypic measures and stability of DNAm variants throughout the life course remains unclear and longitudinal analysis in other populations is required. These findings give support for potential epigenetic programming of body composition and obesity. AU - Rzehak, P.* AU - Covic, M.* AU - Saffery, R.* AU - Reischl, E. AU - Wahl, S. AU - Grote, V.* AU - Weber, M.* AU - Xhonneux, A.* AU - Langhendries, J.P.* AU - Ferre, N.* AU - Closa-Monasterolo, R.* AU - Escribano, J.* AU - Verduci, E.* AU - Riva, E.* AU - Socha, P.* AU - Gruszfeld, D.* AU - Koletzko, B.* C1 - 52241 C2 - 43876 TI - DNA-methylation and body composition in preschool children: Epigenome-wide-analysis in the European Childhood Obesity Project (CHOP)-Study. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Accounting for about 1.5 million deaths annually, lung cancer is the prevailing cause of cancer deaths worldwide, mostly associated with long-term smoking effects. Numerous small-animal studies are performed currently in order to better understand the pathogenesis of the disease and to develop treatment strategies. Within this letter, we propose to exploit X-ray dark-field imaging as a novel diagnostic tool for the detection of lung cancer on projection radiographs. Here, we demonstrate in living mice bearing lung tumors, that X-ray dark-field radiography provides significantly improved lung tumor detection rates without increasing the number of false-positives, especially in the case of small and superimposed nodules, when compared to conventional absorption-based imaging. While this method still needs to be adapted to larger mammals and finally humans, the technique presented here can already serve as a valuable tool in evaluating novel lung cancer therapies, tested in mice and other small animal models. AU - Scherer, K.* AU - Yaroshenko, A.* AU - Bölükbas, D.A. AU - Gromann, L.B.* AU - Hellbach, K.* AU - Meinel, F.G.* AU - Braunagel, M.* AU - Berg, J.V.* AU - Eickelberg, O. AU - Reiser, M.F.* AU - Pfeiffer, F.* AU - Meiners, S. AU - Herzen, J.* C1 - 50799 C2 - 42887 TI - X-ray dark-field radiography - in-vivo diagnosis of lung cancer in mice. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC. However, the molecular details for its interaction with DNA have remained elusive. Here, we present the crystal structure of the CadC DNA-binding domain (DBD) and show that it adopts a winged helix-turn-helix fold. The interaction with the cadBA promoter site Cad1 is studied by using nuclear magnetic resonance (NMR) spectroscopy, biophysical methods and functional assays and reveals a preference for AT-rich regions. By mutational analysis we identify amino acids within the CadC DBD that are crucial for DNA-binding and functional activity. Experimentally derived structural models of the CadC-DNA complex indicate that the CadC DBD employs mainly non-sequence-specific over a few specific contacts. Our data provide molecular insights into the CadC-DNA interaction and suggest how CadC dimerization may provide high-affinity binding to the Cad1 promoter. AU - Schlundt, A. AU - Buchner, S.* AU - Janowski, R. AU - Heydenreich, T.* AU - Heermann, R.* AU - Lassak, J.* AU - Geerlof, A. AU - Stehle, R. AU - Niessing, D. AU - Jung, K.* AU - Sattler, M. C1 - 50972 C2 - 43034 CY - London TI - Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Raster-scan optoacoustic mesoscopy (RSOM), also termed photoacoustic mesoscopy, offers novel insights into vascular morphology and pathophysiological biomarkers of skin inflammation in vivo at depths unattainable by other optical imaging methods. Using ultra-wideband detection and focused ultrasound transducers, RSOM can achieve axial resolution of 4 micron and lateral resolution of 20 micron to depths of several millimeters. However, motion effects may deteriorate performance and reduce the effective resolution. To provide high-quality optoacoustic images in clinical measurements, we developed a motion correction algorithm for RSOM. The algorithm is based on observing disruptions of the ultrasound wave front generated by the vertical movement of the melanin layer at the skin surface. From the disrupted skin surface, a smooth synthetic surface is generated, and the offset between the two surfaces is used to correct for the relative position of the ultrasound detector. We test the algorithm in measurements of healthy and psoriatic human skin and achieve effective resolution up to 5-fold higher than before correction. We discuss the performance of the correction algorithm and its implications in the context of multispectral mesoscopy. AU - Schwarz, M. AU - Garzorz-Stark, N.* AU - Eyerich, K.* AU - Aguirre Bueno, J. AU - Ntziachristos, V. C1 - 51834 C2 - 43377 CY - London TI - Motion correction in optoacoustic mesoscopy. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Using a non-targeted metabolomics platform, we recently identified C-mannosyltryptophan and pseudouridine as non-traditional kidney function markers. The aims of this study were to obtain absolute concentrations of both metabolites in blood and urine from individuals with and without CKD to provide reference ranges and to assess their fractional excretions (FE), and to assess the agreement with their non-targeted counterparts. In individuals without/with CKD, mean plasma and urine concentrations for C-mannosyltryptophan were 0.26/0.72 μmol/L and 3.39/4.30 μmol/mmol creatinine, respectively. The respective concentrations for pseudouridine were 2.89/5.67 μmol/L and 39.7/33.9 μmol/mmol creatinine. Median (25 th , 75 th percentiles) FEs were 70.8% (65.6%, 77.8%) for C-mannosyltryptophan and 76.0% (68.6%, 82.4%) for pseudouridine, indicating partial net reabsorption. Association analyses validated reported associations between single metabolites and eGFR. Targeted measurements of both metabolites agreed well with the non-targeted measurements, especially in urine. Agreement for composite nephrological measures FE and urinary metabolite-to-creatinine ratio was lower, but could be improved by replacing non-targeted creatinine measurements with a standard clinical creatinine test. In summary, targeted quantification and additional characterization in relevant populations are necessary steps in the translation of non-traditional biomarkers in nephrology from non-targeted discovery to clinical application. AU - Sekula, P.* AU - Dettmer, K.* AU - Vogl, F.C.* AU - Gronwald, W.* AU - Ellmann, L.* AU - Mohney, R.P.* AU - Eckardt, K.U.* AU - Suhre, K.* AU - Kastenmüller, G. AU - Oefner, P.J.* AU - Köttgen, A.* C1 - 52568 C2 - 44078 CY - London TI - From discovery to translation: Characterization of c-mannosyltryptophan and pseudouridine as markers of kidney function. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Observational studies on smoking and risk of hay fever and asthma have shown inconsistent results. However, observational studies may be biased by confounding and reverse causation. Mendelian randomization uses genetic variants as markers of exposures to examine causal effects. We examined the causal effect of smoking on hay fever and asthma by using the smoking-associated single nucleotide polymorphism (SNP) rs16969968/rs1051730. We included 231,020 participants from 22 population-based studies. Observational analyses showed that current vs never smokers had lower risk of hay fever (odds ratio (OR) = 0·68, 95% confidence interval (CI): 0·61, 0·76; P < 0·001) and allergic sensitization (OR = 0·74, 95% CI: 0·64, 0·86; P < 0·001), but similar asthma risk (OR = 1·00, 95% CI: 0·91, 1·09; P = 0·967). Mendelian randomization analyses in current smokers showed a slightly lower risk of hay fever (OR = 0·958, 95% CI: 0·920, 0·998; P = 0·041), a lower risk of allergic sensitization (OR = 0·92, 95% CI: 0·84, 1·02; P = 0·117), but higher risk of asthma (OR = 1·06, 95% CI: 1·01, 1·11; P = 0·020) per smoking-increasing allele. Our results suggest that smoking may be causally related to a higher risk of asthma and a slightly lower risk of hay fever. However, the adverse events associated with smoking limit its clinical significance. AU - Skaaby, T.* AU - Taylor, A.E.* AU - Jacobsen, R.K.* AU - Paternoster, L.* AU - Thuesen, B.H.* AU - Ahluwalia, T.S.* AU - Larsen, S.C.* AU - Zhou, A.* AU - Wong, A.* AU - Gabrielsen, M.E.* AU - Bjørngaard, J.H.* AU - Flexeder, C. AU - Männistö, S.* AU - Hardy, R.* AU - Kuh, D.* AU - Barry, S.J.* AU - Tang Møllehave, L.* AU - Cerqueira, C.* AU - Friedrich, N.* AU - Bonten, T.N.* AU - Noordam, R.* AU - Mook-Kanamori, D.O.* AU - Taube, C.* AU - Jessen, L.E.* AU - McConnachie, A.* AU - Sattar, N.* AU - Upton, M.N.* AU - McSharry, C.* AU - Bønnelykke, K.* AU - Bisgaard, H.* AU - Schulz, H. AU - Strauch, K. AU - Meitinger, T. AU - Peters, A. AU - Grallert, H. AU - Nohr, E.A.* AU - Kivimaki, M.* AU - Kumari, M.* AU - Völker, U.* AU - Nauck, M.* AU - Völzke, H.* AU - Power, C.* AU - Hyppönen, E.* AU - Hansen, T.* AU - Jørgensen, T.* AU - Pedersen, O.* AU - Salomaa, V.* AU - Grarup, N.* AU - Langhammer, A.* AU - Romundstad, P.R.* AU - Skorpen, F.* AU - Kaprio, J.* AU - R Munafò, M.* AU - Linneberg, A.* C1 - 51178 C2 - 42881 TI - Investigating the causal effect of smoking on hay fever and asthma: A Mendelian randomization meta-analysis in the CARTA consortium. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Cardiovascular diseases due to atherosclerosis are the leading cause of death globally. We aimed to investigate the potentially altered gene and pathway expression in advanced peripheral atherosclerotic plaques in comparison to healthy control arteries. Gene expression analysis was performed (Illumina HumanHT-12 version 3 Expression BeadChip) for 68 advanced atherosclerotic plaques (15 aortic, 29 carotid and 24 femoral plaques) and 28 controls (left internal thoracic artery (LITA)) from Tampere Vascular Study. Dysregulation of individual genes was compared to healthy controls and between plaques from different arterial beds and Ingenuity pathway analysis was conducted on genes with a fold change (FC) > ±1.5 and false discovery rate (FDR) < 0.05. 787 genes were significantly differentially expressed in atherosclerotic plaques. The most up-regulated genes were osteopontin and multiple MMPs, and the most down-regulated were cell death-inducing DFFA-like effector C and A (CIDEC, CIDEA) and apolipoprotein D (FC > 20). 156 pathways were differentially expressed in atherosclerotic plaques, mostly inflammation-related, especially related with leukocyte trafficking and signaling. In artery specific plaque analysis 50.4% of canonical pathways and 41.2% GO terms differentially expressed were in common for all three arterial beds. Our results confirm the inflammatory nature of advanced atherosclerosis and show novel pathway differences between different arterial beds. AU - Sulkava, M.* AU - Raitoharju, E.* AU - Levula, M.* AU - Seppälä, I.* AU - Lyytikäinen, L.-P.* AU - Mennander, A.* AU - Järvinen, O.* AU - Zeitlin, R.* AU - Salenius, J.P.* AU - Illig, T. AU - Klopp, N. AU - Mononen, N.* AU - Laaksonen, R.* AU - Kähönen, M.* AU - Oksala, N.* AU - Lehtimäki, T.* C1 - 50485 C2 - 42356 CY - London TI - Differentially expressed genes and canonical pathway expression in human atherosclerotic plaques-Tampere Vascular Study. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Ascending thoracic aortic aneurysm (ATAA) is a multifactorial disease with a strong inflammatory component. Surgery is often required to prevent aortic rupture and dissection. We performed gene expression analysis (Illumina HumanHT-12 version 3 Expression BeadChip) for 32 samples from ATAA (26 without/6 with dissection), and 28 left internal thoracic arteries (controls) collected in Tampere Vascular study. We compared expression profiles and conducted pathway analysis using Ingenuity Pathway Analysis (IPA) to reveal differences between ATAA and a healthy artery wall. Almost 5000 genes were differentially expressed in ATAA samples compared to controls. The most downregulated gene was homeobox (HOX) A5 (fold change, FC = -25.3) and upregulated cadherin-2 (FC = 12.6). Several other HOX genes were also found downregulated (FCs between -25.3 and -1.5, FDR < 0.05). 43, mostly inflammatory, canonical pathways in ATAA were found to be significantly (p < 0.05, FDR < 0.05) differentially expressed. The results remained essentially the same when the 6 dissected ATAA samples were excluded from the analysis. We show for the first time on genome level that ATAA is an inflammatory process, revealing a more detailed molecular pathway level pathogenesis. We propose HOX genes as potentially important players in maintaining aortic integrity, altered expression of which might be important in the pathobiology of ATAA. AU - Sulkava, M.* AU - Raitoharju, E.* AU - Mennander, A.* AU - Levula, M.* AU - Seppälä, I.* AU - Lyytikäinen, L.-P.* AU - Järvinen, O.* AU - Illig, T. AU - Klopp, N. AU - Mononen, N.* AU - Laaksonen, R.* AU - Kähönen, M.* AU - Oksala, N.* AU - Lehtimäki, T.* C1 - 52009 C2 - 43647 CY - London TI - Differentially expressed genes and canonical pathways in the ascending thoracic aortic aneurysm - The Tampere Vascular Study. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Restless Legs Syndrome (RLS) is a genetically complex neurological disorder in which overlapping genetic risk factors may contribute to the diversity and heterogeneity of the symptoms. The main goal of the study was to investigate, through analysis of heart rate variability (HRV), whether in RLS patients the MEIS1 polymorphism at risk influences the sympathovagal regulation in different sleep stages. Sixty-four RLS patients with periodic leg movement index above 15 per hour, and 38 controls underwent one night of video-polysomnographic recording. HRV in the frequency- and time- domains was analyzed during nighttime sleep. All RLS patients were genotyped, and homozygotes for rs2300478 in the MEIS1 locus were used for further analysis. Comparison of the sympathovagal pattern of RLS patients to control subjects did not show significant differences after adjustments for confounding factors in frequency-domain analyses, but showed an increased variability during N2 and N3 stages in time-domain analyses in RLS patients. Sorting of RLS patients according to MEIS1 polymorphism reconfirmed the association between MEIS1 and PLMS, and showed a significant increased sympathovagal balance during N3 stage in those homozygotes for the risk allele. RLS patients should be considered differently depending on MEIS1 genotype, some being potentially at risk for cardiovascular disorders. AU - Thireau, J.* AU - Farah, C.* AU - Molinari, N.* AU - Bouilloux, F.* AU - Torreilles, L.* AU - Winkelmann, J. AU - Scholz, S.* AU - Richard, S.* AU - Dauvilliers, Y.* AU - Marmigère, F.* C1 - 50969 C2 - 43030 CY - London TI - MEIS1 variant as a determinant of autonomic imbalance in Restless Legs Syndrome. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Renal sinus fat (RSF) is a perivascular fat compartment located around renal arteries. In this in vitro and in vivo study we hypothesized that the hepatokine fetuin-A may impair renal function in non alcoholic fatty liver disease (NAFLD) by altering inflammatory signalling in RSF. To study effects of the crosstalk between fetuin-A, RSF and kidney, human renal sinus fat cells (RSFC) were isolated and cocultured with human endothelial cells (EC) or podocytes (PO). RSFC caused downregulation of proinflammatory and upregulation of regenerative factors in cocultured EC and PO, indicating a protective influence of RFSC. However, fetuin-A inverted these benign effects of RSFC from an anti- to a proinflammatory status. RSF was quantified by magnetic resonance imaging and liver fat content by 1H-MR spectroscopy in 449 individuals at risk for type 2 diabetes. Impaired renal function was determined via urinary albumin/creatinine-ratio (uACR). RSF did not correlate with uACR in subjects without NAFLD (n = 212, p = 0.94), but correlated positively in subjects with NAFLD (n = 105, p = 0.0005). Estimated glomerular filtration rate (eGRF) was inversely correlated with RSF, suggesting lower eGFR for subjects with higher RSF (r = 0.24, p < 0.0001). In conclusion, our data suggest that in the presence of NAFLD elevated fetuin-A levels may impair renal function by RSF-induced proinflammatory signalling in glomerular cells. AU - Wagner, R. AU - Machann, J. AU - Guthoff, M.* AU - Nawroth, P.P.* AU - Nadalin, S.* AU - Saleem, M.A.* AU - Heyne, N.* AU - Koenigsrainer, A.* AU - Fend, F.* AU - Schick, F. AU - Fritsche, A. AU - Stefan, N. AU - Häring, H.-U. AU - Schleicher, E. AU - Siegel-Axel, D. C1 - 51267 C2 - 42956 TI - The protective effect of human renal sinus fat on glomerular cells is reversed by the hepatokine fetuin-A. JO - Sci. Rep. VL - 7 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Variation in FTO is the most important common genetic determinant of body weight. Altered energy metabolism could underlie this association. We hypothesized that higher circulating glucose or triglycerides can amplify the FTO impact on BMI. In 2671 subjects of the TUEF study, we investigated the interaction effect of fasting glucose and triglyceride levels with rs9939609 in FTO on BMI. We analysed the same interaction effect by longitudinally utilizing mixed effect models in the prospective Whitehall II study. In TUEF, we detected an interaction effect between fasting glucose and fasting triglycerides with rs9939609 on BMI (p = 0.0005 and p = 5 × 10(-7), respectively). The effect size of one risk allele was 1.4 ± 0.3 vs. 2.2 ± 0.44 kg/m² in persons with fasting glucose levels below and above the median, respectively. Fasting triglycerides above the median increased the per-allele effect from 1.4 ± 0.3 to 1.7 ± 0.4 kg/m(2). In the Whitehall II study, body weight increased by 2.96 ± 6.5 kg during a follow-up of 13.5 ± 4.6 yrs. Baseline fasting glucose and rs9939609 interacted on weight change (p = 0.009). Higher fasting glucose levels may amplify obesity-risk in FTO carriers and lead to an exaggerated weight gain over time. Since weight gain perpetuates metabolic alterations, this interplay may trigger a vicious circle that leads to obesity and diabetes. AU - Wagner, R. AU - Tabák,* AU - Fehlert, E. AU - Fritsche, L. AU - Jaghutriz, B.A. AU - Bánhegyi, R.J.* AU - Schmid, S.M.* AU - Staiger, H. AU - Machicao, F. AU - Peter, A. AU - Häring, H.-U. AU - Fritsche, A. AU - Heni, M. C1 - 52351 C2 - 43923 CY - London TI - Excessive fuel availability amplifies the FTO-mediated obesity risk: Results from the TUEF and Whitehall II studies. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The gut microbiota generates a huge pool of unknown metabolites, and their identification and characterization is a key challenge in metabolomics. However, there are still gaps on the studies of gut microbiota and their chemical structures. In this investigation, an unusual class of bacterial sulfonolipids (SLs) is detected in mouse cecum, which was originally found in environmental microbes. We have performed a detailed molecular level characterization of this class of lipids by combining high-resolution mass spectrometry and liquid chromatography analysis. Eighteen SLs that differ in their capnoid and fatty acid chain compositions were identified. The SL called "sulfobacin B" was isolated, characterized, and was significantly increased in mice fed with high-fat diets. To reveal bacterial producers of SLs, metagenome analysis was acquired and only two bacterial genera, i.e., Alistipes and Odoribacter, were revealed to be responsible for their production. This knowledge enables explaining a part of the molecular complexity introduced by microbes to the mammalian gastrointestinal tract and can be used as chemotaxonomic evidence in gut microbiota. AU - Walker, A. AU - Pfitzner, B. AU - Harir, M. AU - Schaubeck, M.* AU - Calasan, J.* AU - Heinzmann, S.S. AU - Turaev, D.* AU - Rattei, T.* AU - Endesfelder, D. AU - zu Castell, W. AU - Haller, D.* AU - Schmid, M. AU - Hartmann, A. AU - Schmitt-Kopplin, P. C1 - 51842 C2 - 43491 CY - London TI - Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - The reliance of all cell types on the mitochondrial function for survival makes mitochondria an interesting target when trying to understand their role in the cellular response to ionizing radiation. By harnessing highly focused carbon ions and protons using microbeams, we have performed in situ live cell imaging of the targeted irradiation of individual mitochondria stained with Tetramethyl rhodamine ethyl ester (TMRE), a cationic fluorophore which accumulates electrophoretically in polarized mitochondria. Targeted irradiation with both carbon ions and protons down to beam spots of <1 μm induced a near instant loss of mitochondrial TMRE fluorescence signal in the targeted area. The loss of TMRE after targeted irradiation represents a radiation induced change in mitochondrial membrane potential. This is the first time such mitochondrial responses have been documented in situ after targeted microbeam irradiation. The methods developed and the results obtained have the ability to shed new light on not just mitochondria's response to radiation but to further elucidate a putative mechanism of radiation induced depolarization and mitochondrial response. AU - Walsh, D.W.M.* AU - Siebenwirth, C.* AU - Greubel, C.* AU - Ilicic, K.* AU - Reindl, J.* AU - Girst, S.* AU - Muggiolu, G.* AU - Simon, M.* AU - Barberet, P.* AU - Seznec, H.* AU - Zischka, H. AU - Multhoff, G.* AU - Schmid, T.E.* AU - Dollinger, G.* C1 - 50988 C2 - 43032 CY - London TI - Live cell imaging of mitochondria following targeted irradiation in situ reveals rapid and highly localized loss of membrane potential. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above-and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting. Our data indicates a significant influence of season and site on bacterial community structure. We showed that during the wet season soil organic matter, pH and salinity strongly influence bacterial community composition, whereas during the dry period bacterial diversity was mainly driven by the shortage of water at all sites. Consequently diversity was lowest during dry season at dunes close to the shore, whereas during the wet season the higher water content and the reduced salinity at the dunes which are more at the inland induced an increase in diversity, which illustrates the pronounced dynamics of microbial communities in soil over a season mainly at inland dunes. AU - Wasserstrom, H.* AU - Kublik, S. AU - Wasserstrom, R.* AU - Schulz, S. AU - Schloter, M. AU - Steinberger, Y.* C1 - 50350 C2 - 42387 CY - London TI - Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland. JO - Sci. Rep. VL - 7 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - It is unclear whether genetic markers interact with risk factors to influence atrial fibrillation (AF) risk. We performed genome-wide interaction analyses between genetic variants and age, sex, hypertension, and body mass index in the AFGen Consortium. Study-specific results were combined using meta-analysis (88,383 individuals of European descent, including 7,292 with AF). Variants with nominal interaction associations in the discovery analysis were tested for association in four independent studies (131,441 individuals, including 5,722 with AF). In the discovery analysis, the AF risk associated with the minor rs6817105 allele (at the PITX2 locus) was greater among subjects ≤ 65 years of age than among those > 65 years (interaction p-value = 4.0 × 10(-5)). The interaction p-value exceeded genome-wide significance in combined discovery and replication analyses (interaction p-value = 1.7 × 10(-8)). We observed one genome-wide significant interaction with body mass index and several suggestive interactions with age, sex, and body mass index in the discovery analysis. However, none was replicated in the independent sample. Our findings suggest that the pathogenesis of AF may differ according to age in individuals of European descent, but we did not observe evidence of statistically significant genetic interactions with sex, body mass index, or hypertension on AF risk. AU - Weng, L.C.* AU - Lunetta, K.L.* AU - Müller-Nurasyid, M. AU - Smith, A.V.* AU - Thériault, S.* AU - Weeke, P.E.* AU - Barnard, J.* AU - Bis, J.C.* AU - Lyytikäinen, L.-P.* AU - Kleber, M.E.* AU - Martinsson, A.* AU - Lin, H.J.* AU - Rienstra, M.* AU - Trompet, S.* AU - Krijthe, B.P.* AU - Dörr, M.* AU - Klarin, D.* AU - Chasman, D.I.* AU - Sinner, M.F.* AU - Waldenberger, M. AU - Launer, L.J.* AU - Harris, T.B.* AU - Soliman, E.Z.* AU - Alonso, A.* AU - Paré, G.* AU - Teixeira, P.L.* AU - Denny, J.C.* AU - Shoemaker, M.B.* AU - van Wagoner, D.R.* AU - Smith, J.D.* AU - Psaty, B.M.* AU - Sotoodehnia, N.* AU - Taylor, K.D.* AU - Kähönen, M.* AU - Nikus, K.* AU - Delgado, G.E.* AU - Melander, O.* AU - Engström, G.* AU - Yao, J.* AU - Guo, X.* AU - Christophersen, I.E.* AU - Ellinor, P.T.* AU - Geelhoed, B.* AU - Verweij, N.* AU - Macfarlane, P.W.* AU - Ford, I.* AU - Heeringa, J.* AU - Franco, O.H.* AU - Uitterlinden, A.G.* AU - Völker, U.* AU - Teumer, A.* AU - Rose, L.M.* AU - Kääb, S.* AU - Gudnason, V.* AU - Arking, D.E.* AU - Conen, D.* AU - Roden, D.M.* AU - Chung, M.K.* AU - Heckbert, S.R.* AU - Benjamin, E.J.* AU - Lehtimäki, T.* AU - März, W.* AU - Smith, J.G.* AU - Rotter, J.I.* AU - van der Harst, P.* AU - Jukema, J.W.* AU - Stricker, B.H.* AU - Felix, S.B.* AU - Albert, C.M.* AU - Lubitz, S.A.* C1 - 51966 C2 - 43544 TI - Genetic interactions with age, sex, body mass index, and hypertension in relation to atrial fibrillation: The AFGen Consortium. JO - Sci. Rep. VL - 7 IS - 1 PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - MAS solid-state NMR is capable of determining structures of protonated solid proteins using proton-detected experiments. These experiments are performed at MAS rotation frequency of around 110 kHz, employing 0.5 mg of material. Here, we compare (1)H, (13)C correlation spectra obtained from protonated and deuterated microcrystalline proteins at MAS rotation frequency of 111 kHz, and show that the spectral quality obtained from deuterated samples is superior to those acquired using protonated samples in terms of resolution and sensitivity. In comparison to protonated samples, spectra obtained from deuterated samples yield a gain in resolution on the order of 3 and 2 in the proton and carbon dimensions, respectively. Additionally, the spectrum from the deuterated sample yields approximately 2-3 times more sensitivity compared to the spectrum of a protonated sample. This gain could be further increased by a factor of 2 by making use of stereospecific precursors for biosynthesis. Although the overall resolution and sensitivity of (1)H, (13)C correlation spectra obtained using protonated solid samples with rotation frequencies on the order of 110 kHz is high, the spectral quality is still poor when compared to the deuterated samples. We believe that experiments involving large protein complexes in which sensitivity is limiting will benefit from the application of deuteration schemes. AU - Xue, K. AU - Sarkar, R. AU - Motz, C.* AU - Asami, S.* AU - Camargo, D.C.R.* AU - Decker, V.* AU - Wegner, S.* AU - Tosner, Z.* AU - Reif, B. C1 - 51694 C2 - 43414 CY - London TI - Limits of resolution and sensitivity of proton detected MAS solid-state NMR experiments at 111 kHz in deuterated and protonated proteins. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Netrin-1 (Ntn1) emanating from the ventral midline has been thought to act as a long-range diffusible chemoattractant for commissural axons (CAs). However, CAs still grow towards the midline in the absence of the floor plate (FP), a glial structure occupying the midline. Here, using genetically loss-of-function approaches in mice, we show that Ntn1 derived from the ventricular zone (VZ), but not the FP, is crucial for CA guidance in the mouse hindbrain. During the period of CA growth, Ntn1 is expressed in the ventral two-thirds of the VZ, in addition to the FP. Remarkably, deletion of Ntn1 from the VZ and even from the dorsal VZ highly disrupts CA guidance to the midline, whereas the deletion from the FP has little impact on it. We also show that the severities of CA guidance defects found in the Ntn1 conditional mutants were irrelevant to their FP long-range chemoattractive activities. Our results are incompatible with the prevailing view that Ntn1 is an FP-derived long-range diffusible chemoattractant for CAs, but suggest a novel mechanism that VZ-derived Ntn1 directs CAs to the ventral midline by its local actions. AU - Yamauchi, K.* AU - Yamazaki, M.* AU - Abe, M.* AU - Sakimura, K.* AU - Lickert, H. AU - Kawasaki, T.* AU - Murakami, F.* AU - Hirata, T.* C1 - 51950 C2 - 43602 CY - London TI - Netrin-1 derived from the ventricular zone, but not the floor plate, directs hindbrain commissural axons to the ventral midline. JO - Sci. Rep. VL - 7 IS - 1 PB - Nature Publishing Group PY - 2017 SN - 2045-2322 ER - TY - JOUR AB - Viral infections are associated with autoimmunity in type 1 diabetes. Here, we asked whether this association could be explained by variations in host immune response to a putative type 1 etiological factor, namely coxsackie B viruses (CVB). Heterogeneous antibody responses were observed against CVB capsid proteins. Heterogeneity was largely defined by different binding to VP1 or VP2. Antibody responses that were anti-VP2 competent but anti-VP1 deficient were unable to neutralize CVB, and were characteristic of children who developed early insulin-targeting autoimmunity, suggesting an impaired ability to clear CVB in early childhood. In contrast, children who developed a GAD-targeting autoimmunity had robust VP1 and VP2 antibody responses to CVB. We further found that 20% of memory CD4(+) T cells responding to the GAD65247-266 peptide share identical T cell receptors to T cells responding to the CVB4 p2C30-51 peptide, thereby providing direct evidence for the potential of molecular mimicry as a mechanism for GAD autoimmunity. Here, we highlight functional immune response differences between children who develop insulin-targeting and GAD-targeting autoimmunity, and suggest that children who lose B cell tolerance to insulin within the first years of life have a paradoxical impaired ability to mount humoral immune responses to coxsackie viruses. AU - Ashton, M.P.* AU - Eugster, A.* AU - Walther, D.* AU - Daehling, N.* AU - Riethausen, S. AU - Kuehn, D.* AU - Klingel, K.* AU - Beyerlein, A. AU - Zillmer, S. AU - Ziegler, A.-G. AU - Bonifacio, E. C1 - 49454 C2 - 32233 CY - London TI - Incomplete immune response to coxsackie B viruses associates with early autoimmunity against insulin. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Metabolomic analyses in epidemiological studies have demonstrated a strong sexual dimorphism for most metabolites. Cross-sex hormone treatment (CSH) in transgender individuals enables the study of metabolites in a cross-gender setting. Targeted metabolomic profiling of serum of fasting transmen and transwomen at baseline and following 12 months of CSH (N = 20/group) was performed. Changes in 186 serum metabolites and metabolite ratios were determined by targeted metabolomics analysis based on ESI-LC-MS/MS. RandomForest (RF) analysis was applied to detect metabolites of highest interest for grouping of transwomen and transmen before and after initiation of CSH. Principal component analysis (PCA) was performed to check whether group differentiation was achievable according to these variables and to see if changes in metabolite levels could be explained by a priori gender differences. PCA predicted grouping of individuals-determined by the citrulline/arginine-ratio and the amino acids lysine, alanine and asymmetric dimethylarginine - in addition to the expected grouping due to changes in sex steroids and body composition. The fact that most of the investigated metabolites did, however, not change, indicates that the majority of sex dependent differences in metabolites reported in the literature before may primarily not be attributable to sex hormones but to other gender-differences. AU - Auer, M.K.* AU - Cecil, A. AU - Roepke, Y.* AU - Bultynck, C.* AU - Pas, C.* AU - Fuss, J.* AU - Prehn, C. AU - Wang-Sattler, R. AU - Adamski, J. AU - Stalla, G.K.* AU - T'sjoen, G.* C1 - 49896 C2 - 41908 CY - London TI - 12-months metabolic changes among gender dysphoric individuals under cross-sex hormone treatment: A targeted metabolomics study. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data. AU - Baiocco, G.* AU - Barbieri, S.* AU - Babini, G.* AU - Morini, J.* AU - Alloni, D.* AU - Friedland, W. AU - Kundrát, P. AU - Schmitt, E. AU - Puchalska, M.* AU - Sihver, L.* AU - Ottolenghi, A.* C1 - 49541 C2 - 40767 CY - London TI - The origin of neutron biological effectiveness as a function of energy. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - PC4 is an abundant single-strand DNA binding protein that has been implicated in transcription and DNA repair. Here, we show that PC4 is involved in the cellular DNA damage response. To elucidate the role, we used the DT40 chicken B cell model, which produces clustered DNA lesions at Ig loci via the action of activation-induced deaminase. Our results help resolve key aspects of immunoglobulin diversification and suggest an essential role of PC4 in repair pathway choice. We show that PC4 ablation in gene conversion (GC)-active cells significantly disrupts GC but has little to no effect on targeted homologous recombination. In agreement, the global double-strand break repair response, as measured by γH2AX foci analysis, is unperturbed 16 hours post irradiation. In cells with the pseudo-genes removed (GC inactive), PC4 ablation reduced the overall mutation rate while simultaneously increasing the transversion mutation ratio. By tagging the N-terminus of PC4, gene conversion and somatic hypermutation are all but abolished even when native non-tagged PC4 is present, indicating a dominant negative effect. Our data point to a very early and deterministic role for PC4 in DNA repair pathway re-routing. AU - Caldwell, R.B. AU - Braselmann, H. AU - Schoetz, U.* AU - Heuer, S. AU - Scherthan, H.* AU - Zitzelsberger, H. C1 - 49000 C2 - 41558 CY - London TI - Positive Cofactor 4 (PC4) is critical for DNA repair pathway re-routing in DT40 cells. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Horizontal gene transfer (HGT) drives the evolution of recipient organism particularly if it provides a novel function which enhances the fitness or its adaption to the environment. Virus-host co-evolution is attractive for studying co-evolutionary processes, since viruses strictly replicate inside of the host cells and thus their evolution is inexorably tangled with host biology. HGT, as a mechanism of co-evolution between human and viruses, has been widely documented, however, the roles HGT play during the interaction between human and viruses are still in their infancy. In this study, we performed a comprehensive analysis on the genes horizontally transferred between viruses and their corresponding human hosts. Our study suggests that the HGT genes in human are predominantly enriched in immune related GO terms while viral HGT genes are tend to be encoded by viruses which promote the invasion of immune system of hosts. Based on our results, it gives us a hint about the evolution trajectory of HGT events. Overall, our study suggests that the HGT between human and viruses are highly relevant to immune interaction and probably reshaped the arm race between hosts and viruses. AU - Chen, D.S.* AU - Wu, Y.Q.* AU - Zhang, W. AU - Jiang, S.J.* AU - Chen, S.Z.* C1 - 48778 C2 - 41319 TI - Horizontal gene transfer events reshape the global landscape of arm race between viruses and homo sapiens. JO - Sci. Rep. VL - 6 PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Tansy plants (Tanacetum vulgare L.) exhibit high chemical variation, particularly in mono- and sesquiterpenes that are stored in specialised glands on the plant surface. In the present work we investigated the effects of terpene chemotypes on Metopeurum fuscoviride, an aphid species specialised on tansy, and their tending ants, at the field scale. Previous studies have chemotyped tansy by assessing dominant compounds; here we propose a method of chemotyping using all volatile compounds that are likely emitted from the storage glands. The analysis is based on two extraction methods: GC-MS analysis of leaf hexane extracts and SBSE analysis of headspace emissions. In an initial screening we identified the subset of compounds present in both chemical patterns, labelled as 'compounds likely emitted from storage'. In a large field survey we could show that the putative chemotypic emission pattern from storage pools significantly affected the early aphid colonisation of tansy. Moreover, the statistical analyses revealed that minor compounds exerted a stronger influence on aphid and tending-ant presence than dominant compounds. Overall we demonstrated that within the enormous chemotypic variation of terpenes in tansy plants, chemical signatures of volatile terpenes can be related to the occurrence of insects on individual plants in the field. AU - Clancy, M.V. AU - Zytynska, S.E.* AU - Senft, M.* AU - Weisser, W.W.* AU - Schnitzler, J.-P. C1 - 50075 C2 - 42106 CY - London TI - Chemotypic variation in terpenes emitted from storage pools influences early aphid colonisation on tansy. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - High abundance proteins like protease inhibitors of plasma display a multitude of interactions in natural environments. Quantitative analysis of such interactions in vivo is essential to study diseases, but have not been forthcoming, as most methods cannot be directly applied in a complex biological environment. Here, we report a quantitative microscale thermophoresis assay capable of deciphering functional deviations from in vitro inhibition data by combining concentration and affinity measurements. We obtained stable measurement signals for the substrate-like interaction of the disease relevant inhibitor α-1-antitrypsin (AAT) Z-variant with catalytically inactive elastase. The signal differentiates between healthy and sick AAT-deficient individuals suggesting that affinity between AAT and elastase is strongly modulated by so-far overlooked additional binding partners from the plasma. AU - Dau, T. AU - Edeleva, E.V.* AU - Seidel, S.A.* AU - Stockley, R.A.* AU - Braun, D.* AU - Jenne, D. C1 - 49725 C2 - 40891 CY - London TI - Quantitative analysis of protease recognition by inhibitors in plasma using microscale thermophoresis. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - p63 is a close homologue of p53 and, together with p73, is grouped into the p53 family of transcription factors. p63 is known to be involved in the induction of controlled apoptosis important for differentiation processes, germ line integrity and development. Despite its high homology to p53, especially within the DNA binding domain (DBD), p63-DBD does not show cooperative DNA binding properties and is significantly more stable against thermal and chemical denaturation. Here, we determined the solution structure of p63-DBD and show that it is markedly less dynamic than p53-DBD. In addition, we also investigate the effect of a double salt bridge present in p53-DBD, but not in p63-DBD on the cooperative binding behavior and specificity to various DNA sites. Restoration of the salt bridges in p63-DBD by mutagenesis leads to enhanced binding affinity to p53-specific, but not p63-specific response elements. Furthermore, we show that p63-DBD is capable of binding to anti-apoptotic BclxL via its DNA binding interface, a feature that has only been shown for p53 so far. These data suggest that all p53 family members - despite alterations in the specificity and binding affinity - are capable of activating pro-apoptotic pathways in a tissue specific manner. AU - Enthart, A.* AU - Klein, C.* AU - Dehner, A.* AU - Coles, M.* AU - Gemmecker, G.* AU - Kessler, H.* AU - Hagn, F. C1 - 48670 C2 - 41253 CY - London TI - Solution structure and binding specificity of the p63 DNA binding domain. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Myopia, currently at epidemic levels in East Asia, is a leading cause of untreatable visual impairment. Genome-wide association studies (GWAS) in adults have identified 39 loci associated with refractive error and myopia. Here, the age-of-onset of association between genetic variants at these 39 loci and refractive error was investigated in 5200 children assessed longitudinally across ages 7-15 years, along with gene-environment interactions involving the major environmental risk-factors, nearwork and time outdoors. Specific variants could be categorized as showing evidence of: (a) early-onset effects remaining stable through childhood, (b) early-onset effects that progressed further with increasing age, or (c) onset later in childhood (N = 10, 5 and 11 variants, respectively). A genetic risk score (GRS) for all 39 variants explained 0.6% (P = 6.6E-08) and 2.3% (P = 6.9E-21) of the variance in refractive error at ages 7 and 15, respectively, supporting increased effects from these genetic variants at older ages. Replication in multi-ancestry samples (combined N = 5599) yielded evidence of childhood onset for 6 of 12 variants present in both Asians and Europeans. There was no indication that variant or GRS effects altered depending on time outdoors, however 5 variants showed nominal evidence of interactions with nearwork (top variant, rs7829127 in ZMAT4; P = 6.3E-04). AU - Fan, Q.* AU - Guo, X.* AU - Tideman, J.W.L.* AU - Williams, K.M.* AU - Yazar, S.* AU - Hosseini, S.M.* AU - Howe, L.D.* AU - Pourcain, B.S.* AU - Evans, D.M* AU - Timpson, N.J.* AU - McMahon, G.* AU - Hysi, P.G.* AU - Krapohl, E.* AU - Wang, Y.X.* AU - Jonas, J.B.* AU - Baird, P.N.* AU - Wang, J.J.* AU - Cheng, C.Y.* AU - Teo, Y.Y.* AU - Wong, T.Y.* AU - Ding, X.* AU - Wojciechowski, R.* AU - Young, T.L.* AU - Pärssinen, O.* AU - Oexle, K.* AU - Pfeiffer, N.* AU - Bailey-Wilson, J.E.* AU - Paterson, A.D.* AU - Klaver, C.C.W.* AU - Plomin, R.* AU - Hammond, C.J.* AU - He, M.* AU - Saw, S.M.* AU - Guggenheim, J.A.* AU - Meguro, A.* AU - Wright, A.F.* AU - Hewitt, A.W.* AU - Young, A.L.* AU - Veluchamy, A.B.* AU - Metspalu, A.* AU - The CREAM Consortium (Döring, A. AU - Gieger, C. AU - Ried, J.S.) AU - Khawaja, A.P.* AU - Klein, B.E.* AU - St Pourcain, B.* AU - Fleck, B.* AU - Hayward, C.* AU - Williams, C.* AU - Delcourt, C.* AU - Pang, C.P.* AU - Khor, C.C.* AU - Simpson, C.L.* AU - van Duijn, C.M.* AU - Mackey, D.A.* AU - Stambolian, D.* AU - Chew, E.* AU - Tai, E.S.* AU - Mihailov, E.* AU - Smith, G.D.* AU - Biino, G.* AU - Campbell, H.* AU - Rudan, I.* AU - Seppälä, I.* AU - Kaprio, J.* AU - Wilson, J.F.* AU - Craig, J.E.* C1 - 49471 C2 - 30578 TI - Childhood gene-environment interactions and age-dependent effects of genetic variants associated with refractive error and myopia: The CREAM Consortium. JO - Sci. Rep. VL - 6 PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts. AU - Ferreira, P.G.* AU - Oti, M.* AU - Barann, M.* AU - Wieland, T. AU - Ezquina, S.* AU - Friedländer, M.R.* AU - Rivas, M.A.* AU - Esteve-Codina, A.* AU - Rosenstiel, P.* AU - Strom, T.M. AU - Lappalainen, T.* AU - Guigo, R.* AU - Sammeth, M.* C1 - 49466 C2 - 30549 CY - London SP - 32406 TI - Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Hypothalamic astrocytes can respond to metabolic signals, such as leptin and insulin, to modulate adjacent neuronal circuits and systemic metabolism. Ghrelin regulates appetite, adiposity and glucose metabolism, but little is known regarding the response of astrocytes to this orexigenic hormone. We have used both in vivo and in vitro approaches to demonstrate that acylated ghrelin (acyl-ghrelin) rapidly stimulates glutamate transporter expression and glutamate uptake by astrocytes. Moreover, acyl-ghrelin rapidly reduces glucose transporter (GLUT) 2 levels and glucose uptake by these glial cells. Glutamine synthetase and lactate dehydrogenase decrease, while glycogen phosphorylase and lactate transporters increase in response to acyl-ghrelin, suggesting a change in glutamate and glucose metabolism, as well as glycogen storage by astrocytes. These effects are partially mediated through ghrelin receptor 1A (GHSR-1A) as astrocytes do not respond equally to desacyl-ghrelin, an isoform that does not activate GHSR-1A. Moreover, primary astrocyte cultures from GHSR-1A knock-out mice do not change glutamate transporter or GLUT2 levels in response to acyl-ghrelin. Our results indicate that acyl-ghrelin may mediate part of its metabolic actions through modulation of hypothalamic astrocytes and that this effect could involve astrocyte mediated changes in local glucose and glutamate metabolism that alter the signals/nutrients reaching neighboring neurons. AU - Fuente-Martin, E. AU - García-Cáceres, C. AU - Argente-Arizon, P.* AU - Díaz, F.* AU - Granado, M.* AU - Freire-Regatillo, A.* AU - Castro-Gonzalez, D.* AU - Ceballos, M.L.* AU - Frago, L.M.* AU - Dickson, S.L.* AU - Argente, J.* AU - Chowen, J.A.* C1 - 48448 C2 - 41622 CY - London TI - Ghrelin regulates glucose and glutamate transporters in hypothalamic astrocytes. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - In response to cold or β3-adrenoreceptor stimulation brown adipose tissue (BAT) promotes non-shivering thermogenesis, leading to energy dissipation. BAT has long been thought to be absent or scarce in adult humans. The recent discovery of thermogenic brite/beige adipocytes has opened the way to development of novel innovative strategies to combat overweight/obesity and associated diseases. Thus it is of great interest to identify regulatory factors that govern the brite adipogenic program. Here, we carried out global microRNA (miRNA) expression profiling on human adipocytes to identify miRNAs that are regulated upon the conversion from white to brite adipocytes. Among the miRNAs that were differentially expressed, we found that Let-7i-5p was down regulated in brite adipocytes. A detailed analysis of the Let-7i-5p levels showed an inverse expression of UCP1 in murine and human brite adipocytes both in vivo and in vitro. Functional studies with Let-7i-5p mimic in human brite adipocytes in vitro revealed a decrease in the expression of UCP1 and in the oxygen consumption rate. Moreover, the Let-7i-5p mimic when injected into murine sub-cutaneous white adipose tissue inhibited partially β3-adrenergic activation of the browning process. These results suggest that the miRNAs Let-7i-5p participates in the recruitment and the function of brite adipocytes. AU - Giroud, M.* AU - Karbiener, M.* AU - Pisani, D.F.* AU - Ghandour, R.A.* AU - Beranger, G.E.* AU - Niemi, T.* AU - Taittonen, M.* AU - Nuutila, P.* AU - Virtanen, K.A.* AU - Langin, D.* AU - Scheideler, M. AU - Amri, E.Z.* C1 - 49029 C2 - 41549 CY - London TI - Let-7i-5p represses brite adipocyte function in mice and humans. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Dynamic phosphorylation of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 heptad-repeats in the C-terminal domain (CTD) of the large subunit coordinates progression of RNA polymerase (Pol) II through the transcription cycle. Here, we describe an M phase-specific form of Pol II phosphorylated at Thr4, but not at Tyr1, Ser2, Ser5, and Ser7 residues. Thr4 phosphorylated Pol II binds to centrosomes and midbody and interacts with the Thr4-specific Polo-like kinase 1. Binding of Pol II to centrosomes does not require the CTD but may involve subunits of the non-canonical R2TP-Prefoldin-like complex, which bind to and co-localize with Pol II at centrosomes. CTD Thr4 mutants, but not Ser2 and Ser5 mutants, display severe mitosis and cytokinesis defects characterized by multipolar spindles and polyploid cells. We conclude that proper M phase progression of cells requires binding of Pol II to centrosomes to facilitate regulation of mitosis and cytokinesis in a CTD Thr4-P dependent manner. AU - Hintermair, C. AU - Voß, K. AU - Forne, I.* AU - Heidemann, M. AU - Flatley, A. AU - Kremmer, E. AU - Imhof, A.* AU - Eick, D. C1 - 48765 C2 - 41323 CY - London TI - Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Intracellular lipid pools are highly dynamic and tissue-specific. Physical exercise is a strong physiologic modulator of lipid metabolism, but most studies focus on changes induced by long-term training. To assess the acute effects of endurance exercise, mice were subjected to one hour of treadmill running, and (13)C16-palmitate was applied to trace fatty acid incorporation in soleus and gastrocnemius muscle and liver. The amounts of carnitine, FFA, lysophospholipids and diacylglycerol and the post-exercise increase in acetylcarnitine were pronouncedly higher in soleus than in gastrocnemius. In the liver, exercise increased the content of lysophospholipids, plasmalogens and carnitine as well as transcript levels of the carnitine transporter. (13)C16-palmitate was detectable in several lipid and acylcarnitine species, with pronounced levels of tracer-derived palmitoylcarnitine in both muscles and a strikingly high incorporation into triacylglycerol and phosphatidylcholine in the liver. These data illustrate the high lipid storing activity of the liver immediately after exercise whereas in muscle, fatty acids are directed towards oxidation. The observed muscle-specific differences accentuate the need for single-muscle analyses as well as careful consideration of the particular muscle employed when studying lipid metabolism in mice. In addition, our results reveal that lysophospholipids and plasmalogens, potential lipid signalling molecules, are acutely regulated by physical exercise. AU - Hoene, M.* AU - Li, J.* AU - Li, Y.* AU - Runge, H.* AU - Zhao, X.* AU - Häring, H.-U. AU - Lehmann, R. AU - Xu, G.* AU - Weigert, C. C1 - 48002 C2 - 39834 CY - London TI - Muscle and liver-specific alterations in lipid and acylcarnitine metabolism after a single bout of exercise in mice. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - We describe the generation of a set of plasmid vector tools that allow the rapid generation of complex-interacting stable transgenes in immortalized and primary cells. Of particular importance is inclusion of a mechanism to monitor the activation status of regulatory pathways via a reporter cassette (using Gaussia Luciferase), with control of additional transgene expression through doxycycline de-repression. The resulting vectors can be used to assess regulatory pathway activation and are well suited for regulatory pathway crosstalk studies. The system incorporates MultiSite-Gateway cloning for the rapid generation of vectors allowing flexible choice of promoters and transgenes, and Sleeping Beauty transposase technology for efficient incorporation of multiple transgenes in into host cell DNA. The vectors and a library of compatible Gateway Entry clones are available from the non-profit plasmid repository Addgene. AU - Jäckel, C.* AU - Nogueira, M.S.* AU - Ehni, N.* AU - Kraus, C.* AU - Ranke, J.* AU - Dohmann, M.* AU - Nößner, E. AU - Nelson, P.J.* C1 - 49746 C2 - 40924 CY - London TI - A vector platform for the rapid and efficient engineering of stable complex transgenes. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Trafficking of the G protein-coupled receptor (GPCR) Smoothened (Smo) to the primary cilium (PC) is a potential target to inhibit oncogenic Hh pathway activation in a large number of tumors. One drawback is the appearance of Smo mutations that resist drug treatment, which is a common reason for cancer treatment failure. Here, we undertook a high content screen with compounds in preclinical or clinical development and identified ten small molecules that prevent constitutive active mutant SmoM2 transport into PC for subsequent Hh pathway activation. Eight of the ten small molecules act through direct interference with the G protein-coupled receptor associated sorting protein 2 (Gprasp2)-SmoM2 ciliary targeting complex, whereas one antagonist of ionotropic receptors prevents intracellular trafficking of Smo to the PC. Together, these findings identify several compounds with the potential to treat drug-resistant SmoM2-driven cancer forms, but also reveal off-target effects of established drugs in the clinics. AU - Jung, B. AU - Messias, A.C. AU - Schorpp, K.K. AU - Geerlof, A. AU - Schneider, G.* AU - Saur, D.* AU - Hadian, K. AU - Sattler, M. AU - Wanker, E.E.* AU - Hasenöder, S. AU - Lickert, H. C1 - 48041 C2 - 39866 CY - London TI - Novel small molecules targeting ciliary transport of smoothened and oncogenic Hedgehog pathway activation. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Subcellular lipidomics is a novel field of research that requires the careful combination of several pre-analytical and analytical steps. To define a reliable strategy for mitochondrial lipid profiling, we performed a systematic comparison of different mitochondria isolation procedures by western blot analyses and comprehensive high-resolution lipidomics. Using liver-derived HepG2 cells, we compared three common mitochondria isolation methods, differential centrifugation (DC), ultracentrifugation (UC) and a magnetic bead-assisted method (MACS). In total, 397 lipid species, including 32 cardiolipins, could be quantified in only 100 μg (by protein) of purified mitochondria. Mitochondria isolated by UC showed the highest enrichment in the mitochondria-specific cardiolipins as well as their precursors, phosphatidylglycerols. Mitochondrial fractions obtained by the commonly used DC and the more recent MACS method contained substantial contaminations by other organelles. Employing these isolation methods when performing lipidomics analyses from cell culture mitochondria may lead to inaccurate results. To conclude, we present a protocol how to obtain reliable mitochondria-specific lipid profiles from cell culture samples and show that quality controls are indispensable when performing mitochondria lipidomics. AU - Kappler, L.* AU - Li, J.* AU - Häring, H.-U. AU - Weigert, C. AU - Lehmann, R. AU - Xu, G.* AU - Hoene, M.* C1 - 48009 C2 - 39841 CY - London TI - Purity matters: A workflow for the valid high-resolution lipid profiling of mitochondria from cell culture samples. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Ions provide a more advantageous dose distribution than photons for external beam radiotherapy, due to their so-called inverse depth dose deposition and, in particular a characteristic dose maximum at their end-of-range (Bragg peak). The favorable physical interaction properties enable selective treatment of tumors while sparing surrounding healthy tissue, but optimal clinical use requires accurate monitoring of Bragg peak positioning inside tissue. We introduce ionoacoustic tomography based on detection of ion induced ultrasound waves as a technique to provide feedback on the ion beam profile. We demonstrate for 20 MeV protons that ion range imaging is possible with submillimeter accuracy and can be combined with clinical ultrasound and optoacoustic tomography of similar precision. Our results indicate a simple and direct possibility to correlate, in-vivo and in real-time, the conventional ultrasound echo of the tumor region with ionoacoustic tomography. Combined with optoacoustic tomography it offers a well suited pre-clinical imaging system. AU - Kellnberger, S. AU - Assmann, W.* AU - Lehrack, S.* AU - Reinhardt, S.* AU - Thirolf, P.* AU - Queirós, D. AU - Sergiadis, G.* AU - Dollinger, G.* AU - Parodi, K.* AU - Ntziachristos, V. C1 - 49036 C2 - 41562 CY - London TI - Ionoacoustic tomography of the proton Bragg peak in combination with ultrasound and optoacoustic imaging. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease. IPF is characterized by epithelial cell injury and reprogramming, increases in (myo)fibroblasts, and altered deposition of extracellular matrix. The Wnt1-inducible signaling protein 1 (WISP1) is involved in impaired epithelial-mesenchymal crosstalk in pulmonary fibrosis. Here, we aimed to further investigate WISP1 regulation and function in primary human lung fibroblasts (phLFs). We demonstrate that WISP1 is directly upregulated by Transforming growth factor β1 (TGFβ1) and Tumor necrosis factor α (TNFα) in phLFs, using a luciferase-based reporter system. WISP1 mRNA and protein secretion increased in a time-and concentration-dependent manner by TGFβ1 and TNFα in phLFs, as analysed by qPCR and ELISA, respectively. Notably, WISP1 is required for TGFβ1-and TNFα-dependent induction of interleukin 6 (IL-6), a mechanism that is conserved in IPF phLFs. The siRNA-mediated WISP1 knockdown led to a significant IL-6 reduction after TGFβ1 or TNFα stimulation. Furthermore, siRNA-mediated downregulation or antibody-mediated neutralization of WISP1 reduced phLFs proliferation, a process that was in part rescued by IL-6. Taken together, these results strongly indicate that WISP1-induced IL-6 expression contributes to the pro-proliferative effect on fibroblasts, which is likely orchestrated by a variety of profibrotic mediators, including Wnts, TGFβ1 and TNFα. AU - Klee, S. AU - Lehmann, M. AU - Wagner, D.E. AU - Baarsma, H.A. AU - Königshoff, M. C1 - 47957 C2 - 39830 CY - London TI - WISP1 mediates IL-6-dependent proliferation in primary human lung fibroblasts. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Detailed mechanistic modelling has been performed of the intercellular signalling cascade between precancerous cells and their normal neighbours that leads to a selective removal of the precancerous cells by apoptosis. Two interconnected signalling pathways that were identified experimentally have been modelled, explicitly accounting for temporal and spatial effects. The model predicts highly non-linear behaviour of the signalling. Importantly, under certain conditions, enhanced release of primary signals by precancerous cells renders the signalling ineffective. This counter-intuitive behaviour arises due to spatial aspects of the underlying signalling scheme: Increased primary signalling by precancerous cells does, upon reaction with factors derived from normal cells, produce higher yields of apoptosis-triggering molecules. However, the apoptosis-triggering signals are formed farther from the precancerous cells, so that these are attacked less efficiently. Spatial effects thus may represent a novel analogue of negative feedback mechanisms. AU - Kundrát, P. AU - Friedland, W. C1 - 49527 C2 - 40783 SP - 33214 TI - Enhanced release of primary signals may render intercellular signalling ineffective due to spatial aspects. JO - Sci. Rep. VL - 6 PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - X-ray computed tomography of small animals and their organs is an essential tool in basic and preclinical biomedical research. In both phase-contrast and absorption tomography high spatial resolution and short exposure times are of key importance. However, the observable spatial resolutions and achievable exposure times are presently limited by system parameters rather than more fundamental constraints like, e.g., dose. Here we demonstrate laboratory tomography with few-ten μm spatial resolution and few-minute exposure time at an acceptable dose for small-animal imaging, both with absorption contrast and phase contrast. The method relies on a magnifying imaging scheme in combination with a high-power small-spot liquid-metal-jet electron-impact source. The tomographic imaging is demonstrated on intact mouse, phantoms and excised lungs, both healthy and with pulmonary emphysema. AU - Larsson, D.H.* AU - Vågberg, W.* AU - Yaroshenko, A.* AU - Yildirim, A.Ö. AU - Hertz, H.M.* C1 - 50186 C2 - 42226 CY - London TI - High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Atrial fibrillation (AF) is a heritable disease that affects more than thirty million individuals worldwide. Extensive efforts have been devoted to the study of genetic determinants of AF. The objective of our study is to examine the effect of gene-gene interaction on AF susceptibility. We performed a large-scale association analysis of gene-gene interactions with AF in 8,173 AF cases, and 65,237 AF-free referents collected from 15 studies for discovery. We examined putative interactions between genome-wide SNPs and 17 known AF-related SNPs. The top interactions were then tested for association in an independent cohort for replication, which included more than 2,363 AF cases and 114,746 AF-free referents. One interaction, between rs7164883 at the HCN4 locus and rs4980345 at the SLC28A1 locus, was found to be significantly associated with AF in the discovery cohorts (interaction OR = 1.44, 95% CI: 1.27-1.65, P = 4.3 × 10-8). Eight additional gene-gene interactions were also marginally significant (P < 5 × 10-7). However, none of the top interactions were replicated. In summary, we did not find significant interactions that were associated with AF susceptibility. Future increases in sample size and denser genotyping might facilitate the identification of gene-gene interactions associated with AF. AU - Lin, H.* AU - Müller-Nurasyid, M. AU - Smith, A.V.* AU - Arking, D.E.* AU - Barnard, J.* AU - Bartz, T.M.* AU - Lunetta, K.L.* AU - Lohman, K.* AU - Kleber, M.E.* AU - Lubitz, S.A.* AU - Geelhoed, B.* AU - Trompet, S.* AU - Niemeijer, M.N.* AU - Kacprowski, T.* AU - Chasman, D.I.* AU - Klarin, D.* AU - Sinner, M.F.* AU - Waldenberger, M. AU - Meitinger, T. AU - Harris, T.B.* AU - Launer, L.J.* AU - Soliman, E.Z.* AU - Chen, L.Y.* AU - Smith, J.D.* AU - van Wagoner, D.R.* AU - Rotter, J.I.* AU - Psaty, B.M.* AU - Xie, Z.* AU - Hendricks, A.E.* AU - Ding, J.* AU - Delgado, G.E.* AU - Verweij, N.* AU - van der Harst, P.* AU - Macfarlane, P.W.* AU - Ford, I.* AU - Hofman, A.* AU - Uitterlinden, A.* AU - Heeringa, J.* AU - Franco, O.H.* AU - Kors, J.A.* AU - Weiss, S.* AU - Völzke, H.* AU - Rose, L.M.* AU - Natarajan, P.* AU - Kathiresan, S.* AU - Kääb, S.* AU - Gudnason, V.* AU - Alonso, A.* AU - Chung, M.K.* AU - Heckbert, S.R.* AU - Benjamin, E.J.* AU - Liu, Y.* AU - Marz, W.* AU - Rienstra, M.* AU - Jukema, J.W.* AU - Stricker, B.H.* AU - Dörr, M.* AU - Albert, C.M.* AU - Ellinor, P.T.* C1 - 49944 C2 - 41922 CY - London TI - Gene-gene interaction analyses for atrial fibrillation. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Determination of ovarian status and follicle monitoring are common methods of diagnosing female infertility. We evaluated the suitability of selective plane illumination microscopy (SPIM) for the study of ovarian follicles. The large field of view and fast acquisition speed of our SPIM system enables rendering of volumetric image stacks from intact whole porcine ovarian follicles, clearly visualizing follicular features including follicle volume and average diameter (70 μm–2.5 mm), their spherical asymmetry parameters, size of developing cumulus oophorus complexes (40 μm–110 μm), and follicular wall thickness (90 μm–120 μm). Follicles at all developmental stages were identified. A distribution of the theca thickness was measured for each follicle, and a relationship between these distributions and the stages of follicular development was discerned. The ability of the system to non-destructively generate sub-cellular resolution 3D images of developing follicles, with excellent image contrast and high throughput capacity compared to conventional histology, suggests that it can be used to monitor follicular development and identify structural abnormalities indicative of ovarian ailments. Accurate folliculometric measurements provided by SPIM images can immensely help the understanding of ovarian physiology and provide important information for the proper management of ovarian diseases. AU - Lin, H.-C. AU - Dutta, R.* AU - Mandal, S. AU - Kind, A.* AU - Schnieke, A.* AU - Razansky, D. C1 - 49964 C2 - 41992 CY - London TI - Advancing ovarian folliculometry with selective plane illumination microscopy JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Cancer was hypothesized to be driven by cancer stem cells (CSCs), but the metabolic determinants of CSC-like phenotype still remain elusive. Here, we present that hexosamine biosynthetic pathway (HBP) at least in part rescues cancer cell fate with inactivation of glycolysis. Firstly, metabolomic analysis profiled cellular metabolome in CSCs of hepatocellular carcinoma using CD133 cell-surface marker. The metabolic signatures of CD133-positive subpopulation compared to CD133-negative cells highlighted HBP as one of the distinct metabolic pathways, prompting us to uncover the role of HBP in maintenance of CSC-like phenotype. To address this, CSC-like phenotypes and cell survival were investigated in cancer cells under low glucose conditions. As a result, HBP inhibitor azaserine reduced CD133-positive subpopulation and CD133 expression under high glucose condition. Furthermore, treatment of N-Acetylglucosamine in part restores CD133-positive subpopulation when either 2.5 mM glucose in culture media or glycolytic inhibitor 2-deoxy-D-glucose in HCC cell lines was applied, enhancing CD133 expression as well as promoting cancer cell survival. Together, HBP might be a key metabolic determinant in the functions of hepatic CSC marker CD133. AU - Lin, S.H.* AU - Liu, T.* AU - Ming, X.* AU - Tang, Z.* AU - Fu, L.* AU - Schmitt-Kopplin, P. AU - Kanawati, B. AU - Guan, X.Y.* AU - Cai, Z.* C1 - 47981 C2 - 39823 CY - London TI - Regulatory role of hexosamine biosynthetic pathway on hepatic cancer stem cell marker CD133 under low glucose conditions. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - miRNA dysregulation is a hallmark of many neurodegenerative disorders, including those involving the retina. Up-regulation of miR-1/133 and miR-142, and down-regulation of miR-183/96/182 has been described in the RHO-P347S mouse retina, a model for a common form of inherited blindness. High-throughput LC-MS/MS was employed to analyse the protein expression of predicted targets for these miRNAs in RHO-P347S mouse retinas; 133 potential target genes were identified. Pathway over-representation analysis suggests G-protein signaling/visual transduction, and synaptic transmission for miR-1, and transmembrane transport, cell-adhesion, signal transduction and apoptosis for miR-183/96/182 as regulated functions in retina. Validation of miRNA-target mRNA interactions for miR-1, miR-96/182 and miR-96 targeting Ctbp2, Rac1 and Slc6a9, respectively, was demonstrated in vitro. In vivo interaction of miR-183/96/182 and Rac1 mRNA in retina was confirmed using miR-CATCH. Additional miRNAs (including miR-103-3p, miR-9-5p) were both predicted to target Rac1 mRNA and enriched by Rac1-miR-CATCH. Other Rac1-miR-CATCH-enriched miRNAs (including miR-125a/b-5p, miR-378a-3p) were not predicted to target Rac1. Furthermore, levels of ~25% of the retinal Rac1 interactors were determined by LC-MS/MS; expression of Rap1gds1 and Cav1 was elevated. Our data suggest significant utilisation of miRNA-based regulation in retina. Possibly more than 30 miRNAs interact with Rac1 in retina, targeting both UTRs and coding regions. AU - Palfi, A.* AU - Hokamp, K.* AU - Hauck, S.M. AU - Vencken, S.* AU - Millington-Ward, S.* AU - Chadderton, N.* AU - Carrigan, M.* AU - Körtvely, E.* AU - Greene, C.M.* AU - Kenna, P.F.* AU - Farrar, G.J.* C1 - 49272 C2 - 41766 CY - London TI - microRNA regulatory circuits in a mouse model of inherited retinal degeneration. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Recently thioredoxin reductase 1 (TrxR1), encoded by Txnrd1, was suggested to modulate glucose and lipid metabolism in mice. Here we discovered that TrxR1 suppresses insulin responsiveness, anabolic metabolism and adipocyte differentiation. Immortalized mouse embryonic fibroblasts (MEFs) lacking Txnrd1 (Txnrd1(-/-)) displayed increased metabolic flux, glycogen storage, lipogenesis and adipogenesis. This phenotype coincided with upregulated PPARγ expression, promotion of mitotic clonal expansion and downregulation of p27 and p53. Enhanced Akt activation also contributed to augmented adipogenesis and insulin sensitivity. Knockdown of TXNRD1 transcripts accelerated adipocyte differentiation also in human primary preadipocytes. Furthermore, TXNRD1 transcript levels in subcutaneous adipose tissue from 56 women were inversely associated with insulin sensitivity in vivo and lipogenesis in their isolated adipocytes. These results suggest that TrxR1 suppresses anabolic metabolism and adipogenesis by inhibition of intracellular signaling pathways downstream of insulin stimulation. AU - Peng, X.* AU - Giménez-Cassina, A.* AU - Petrus, P.* AU - Conrad, M. AU - Rydén, M.* AU - Arner, E.S.J.* C1 - 48902 C2 - 41475 CY - London TI - Thioredoxin reductase 1 suppresses adipocyte differentiation and insulin responsiveness. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - MicroRNAs are involved in disease development and may be utilized as biomarkers. We investigated the association of blood miRNA levels and a) fatty liver (FL), b) lipoprotein and lipid pathways involved in liver lipid accumulation and c) levels of predicted mRNA targets in general population based cohort. Blood microRNA profiling (TaqMan OpenArray), genome-wide gene expression arrays and nuclear magnetic resonance metabolomics were performed for Young Finns Study participants aged 34-49 years (n = 871). Liver fat status was assessed ultrasonographically. Levels of hsa-miR-122-5p and -885-5p were up-regulated in individuals with FL (fold change (FC) = 1.55, p = 1.36 ∗ 10-14 and FC = 1.25, p = 4.86 ∗ 10-4, respectively). In regression model adjusted with age, sex and BMI, hsa-miR-122-5p and -885-5p predicted FL (OR = 2.07, p = 1.29 ∗ 10-8 and OR = 1.41, p = 0.002, respectively). Together hsa-miR-122-5p and -885-5p slightly improved the detection of FL beyond established risk factors. These miRNAs may be associated with FL formation through the regulation of lipoprotein metabolism as hsa-miR-122-5p levels associated with small VLDL, IDL, and large LDL lipoprotein subclass components, while hsa-miR-885-5p levels associated inversely with XL HDL cholesterol levels. Hsa-miR-885-5p levels correlated inversely with oxysterol-binding protein 2 (OSBPL2) expression (r = -0.143, p = 1.00 ∗ 10-4) and suppressing the expression of this lipid receptor and sterol transporter could link hsa-miR-885-5p with HDL cholesterol levels. AU - Raitoharju, E.* AU - Seppälä, I.* AU - Lyytikäinen, L.-P.* AU - Viikari, J.* AU - Ala-Korpela, M.* AU - Soininen, P.* AU - Kangas, A.J.* AU - Waldenberger, M. AU - Klopp, N.* AU - Illig, T. AU - Leiviskä, J.* AU - Loo, B.M.* AU - Oksala, N.* AU - Kähönen, M.* AU - Hutri-Kähönen, N.* AU - Laaksonen, R.* AU - Raitakari, O.* AU - Lehtimäki, T.* C1 - 50149 C2 - 31883 CY - London TI - Blood hsa-MIR-122-5p and hsa-MIR-885-5p levels associate with fatty liver and related lipoprotein metabolism - The Young Finns Study. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Circulating trimethylamine N-Oxide (TMAO) levels predict cardiovascular disease (CVD), possibly by impacting on cholesterol metabolism and oxidative stress. Because hepatic TMAO production is regulated by insulin signalling and it is unclear whether and to what extent circulating TMAO levels associate with CVD risk, independently of insulin resistance and its important determinants fatty liver and visceral obesity, we have now addressed this question in 220 subjects who participated in the Tübingen Lifestyle Intervention Program. Visceral fat mass (r = 0.40, p < 0.0001), liver fat content (r = 0.23, p = 0.0005) and TMAO levels (r = 0.26, p < 0.0001) associated positively, and insulin sensitivity associated negatively (r = -0.18, p = 0.009) with carotid intima-media thickness (cIMT). Higher TMAO levels (std.-Beta 0.11, p = 0.03) predicted increased cIMT, independently of age, sex and visceral fat mass. While during the lifestyle intervention most cardiovascular risk parameters improved, mean TMAO levels did not change (p = 0.18). However, cIMT decreased significantly (p = 0.0056) only in subjects in the tertile with the largest decrease of TMAO levels (>20%). We provide novel information that increased serum TMAO levels associate with increased cIMT, independently of established cardiovascular risk markers, including insulin resistance, visceral obesity and fatty liver. Furthermore, the decrease of cIMT during a lifestyle intervention may be related to the decrease of TMAO levels. AU - Randrianarisoa, E. AU - Lehn-Stefan, A. AU - Wang, X. AU - Hoene, M. AU - Peter, A. AU - Heinzmann, S.S. AU - Zhao, X.* AU - Königsrainer, I.* AU - Königsrainer, A.* AU - Balletshofer, B.* AU - Machann, J. AU - Schick, F. AU - Fritsche, A. AU - Häring, H.-U. AU - Xu, G.* AU - Lehmann, R. AU - Stefan, N. C1 - 48753 C2 - 41410 CY - London TI - Relationship of serum trimethylamine n-oxide (TMAO) levels with early atherosclerosis in humans. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Novel therapeutic options are urgently needed to improve global treatment of virus infections. Herbal products with confirmed clinical safety features are attractive starting material for the identification of new antiviral activities. Here we demonstrate that Cistus incanus (Ci) herbal products inhibit human immunodeficiency virus (HIV) infections in vitro. Ci extract inhibited clinical HIV-1 and HIV-2 isolates, and, importantly, a virus isolate with multiple drug resistances, confirming broad anti-HIV activity. Antiviral activity was highly selective for virus particles, preventing primary attachment of the virus to the cell surface and viral envelope proteins from binding to heparin. Bioassay-guided fractionation indicated that Ci extract contains numerous antiviral compounds and therefore has favorably low propensity to induce virus resistance. Indeed, no resistant viruses emerged during 24 weeks of continuous propagation of the virus in the presence of Ci extracts. Finally, Ci extracts also inhibited infection by virus particles pseudotyped with Ebola and Marburg virus envelope proteins, indicating that antiviral activity of Ci extract extends to emerging viral pathogens. These results demonstrate that Ci extracts show potent and broad in vitro antiviral activity against viruses that cause life-threatening diseases in humans and are promising sources of agents that target virus particles. AU - Rebensburg, S. AU - Helfer, M. AU - Schneider, M. AU - Koppensteiner, H. AU - Eberle, J.* AU - Schindler, M. AU - Gürtler, L.* AU - Brack-Werner, R. C1 - 47808 C2 - 39499 CY - London TI - Potent in vitro antiviral activity of Cistus incanus extract against HIV and Filoviruses targets viral envelope proteins. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Protein phosphatase 2A (PP2A) is one of the most abundant serine-threonine phosphatases in mammalian cells. PP2A is a hetero-trimeric holoenzyme participating in a variety of physiological processes whose deregulation is often associated to cancer. The specificity and activity of this phosphatase is tightly modulated by a family of regulatory B subunits that dock the catalytic subunit to the substrates. Here we characterize a novel and unconventional molecular mechanism controlling the activity of the tumor suppressor PP2A. By applying a mass spectrometry-based interactomics approach, we identified novel PP2A interacting proteins. Unexpectedly we found that a significant number of RAB proteins associate with the PP2A scaffold subunit (PPP2R1A), but not with the catalytic subunit (PPP2CA). Such interactions occur in vitro and in vivo in specific subcellular compartments. Notably we demonstrated that one of these RAB proteins, RAB9, competes with the catalytic subunit PPP2CA in binding to PPP2R1A. This competitive association has an important role in controlling the PP2A catalytic activity, which is compromised in several solid tumors and leukemias. AU - Sacco, F.* AU - Mattioni, A.* AU - Boldt, K.H.W.* AU - Panni, S.* AU - Santonico, E.* AU - Castagnoli, L.* AU - Ueffing, M. AU - Cesareni, G.* C1 - 49535 C2 - 30636 CY - London TI - A subset of RAB proteins modulates PP2A phosphatase activity. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Aberrant antioxidant activity and excessive deposition of extracellular matrix (ECM) are hallmarks of interstitial lung diseases (ILD). It is known that oxidative stress alters the ECM, but extracellular antioxidant defence mechanisms in ILD are incompletely understood. Here, we extracted abundance and detergent solubility of extracellular antioxidant enzymes from a proteomic dataset of bleomycin-induced lung fibrosis in mice and assessed regulation and distribution of glutathione peroxidase 3 (GPX3) in murine and human lung fibrosis. Superoxide dismutase 3 (Sod3), Gpx3, and Gpx activity were increased in mouse BALF during bleomycin-induced lung fibrosis. In lung tissue homogenates, Gpx3, but not Sod3, was upregulated and detergent solubility profiling indicated that Gpx3 associated with ECM proteins. Immunofluorescence analysis showed that Gpx3 was expressed by bronchial epithelial cells and interstitial fibroblasts and localized to the basement membrane and interstitial ECM in lung tissue. As to human ILD samples, BALF of some patients contained high levels of GPX3, and GPX3 was upregulated in lung homogenates from IPF patients. GPX3 expression in primary human bronchial epithelial cells and lung fibroblasts was downregulated by TNF-α, but more variably regulated by TGF-β1 and menadione. In conclusion, the antioxidant enzyme GPX3 localizes to lung ECM and is variably upregulated in ILD. AU - Schamberger, A.C. AU - Schiller, H. B. AU - Fernandez, I.E. AU - Sterclova, M.* AU - Heinzelmann, K. AU - Hennen, E. AU - Hatz, R.A.* AU - Behr, J.* AU - Vasakova, M.* AU - Mann, M.* AU - Eickelberg, O. AU - Staab-Weijnitz, C.A. C1 - 49135 C2 - 41624 CY - London TI - Glutathione peroxidase 3 localizes to the epithelial lining fluid and the extracellular matrix in interstitial lung disease. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - The International Knockout Mouse Consortium (IKMC) has produced a genome-wide collection of 15,000 isogenic targeting vectors for conditional mutagenesis in C57BL/6N mice. Although most of the vectors have been used successfully in murine embryonic stem (ES) cells, there remain a set of nearly two thousand genes that have failed to target even after several attempts. Recent attention has turned to the use of new genome editing technology for the generation of mutant alleles in mice. Here, we demonstrate how Cas9-assisted targeting can be combined with the IKMC targeting vector resource to generate conditional alleles in genes that have previously eluded targeting using conventional methods. AU - Schick, J. AU - Seisenberger, C. AU - Beig, J. AU - Bürger, A. AU - Iyer, V.* AU - Maier, V. AU - Perera, S.* AU - Rosen, B.* AU - Skarnes, W.C.* AU - Wurst, W. C1 - 49359 C2 - 41777 CY - London TI - CRISPR-Cas9 enables conditional mutagenesis of challenging loci. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - The human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), which are associated with a variety of diseases including tumors, produce various small noncoding RNAs (sncRNAs) such as microRNAs (miRNAs). Like all herpesviruses, they show two stages in their life cycle: lytic replication and latency. During latency, hardly any viral proteins are expressed to avoid recognition by the immune system. Thus, sncRNAs might be exploited since they are less likely to be recognized. Specifically, it has been proposed that sncRNAs might contribute to the maintenance of latency. This has already been shown in vitro, but the respective evidence in vivo is very limited. A natural model system to explore this question in vivo is infection of mice with murine gammaherpesvirus 68 (MHV-68). We used this model to analyze a MHV-68 mutant lacking the expression of all miRNAs. In the absence of the miRNAs, we observed a higher viral genomic load during late latency in the spleens of mice. We propose that this is due to a disturbed regulation of the latent-to-lytic switch, altering the balance between latent and lytic infection. Hence, we provide for the first time evidence that gammaherpesvirus sncRNAs contribute to the maintenance of latency in vivo. AU - Steer, B. AU - Strehle, M. AU - Sattler, C. AU - Bund, D. AU - Flach, B. AU - Stöger, T. AU - Haas, J.G.* AU - Adler, H. C1 - 49331 C2 - 41753 CY - London TI - The small noncoding RNAs (sncRNAs) of murine gammaherpesvirus 68 (MHV-68) are involved in regulating the latent-to-lytic switch in vivo. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. We show that C-terminally truncated Redβ, whilst still able to promote annealing and nucleoprotein filament formation, is unable to mediate homologous recombination. Mutations of the C-terminal domain were evaluated using both single- and double stranded (ss and ds) substrates in recombination assays. Mutations of critical amino acids affected either dsDNA recombination or both ssDNA and dsDNA recombination indicating two separable functions, one of which is critical for dsDNA recombination and the second for recombination per se. As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. Because the nucleoprotein filament formed with C-terminally truncated Redβ has altered properties, the second C-terminal function could be due to an interaction required for functional filaments. Alternatively the second C-terminal function could indicate a requirement for a Redβ-host factor interaction. These data further advance the model for Red recombination and the proposition that Redβ and RAD52 SSAPs share ancestral and mechanistic roots. AU - Subramaniam, S.* AU - Erler, A.* AU - Fu, J.* AU - Kranz, A.* AU - Tang, J.* AU - Gopalswamy, M. AU - Ramakrishnan, S.* AU - Keller, A.* AU - Grundmeier, G.* AU - Müller, D.* AU - Sattler, M. AU - Stewart, A.F.* C1 - 49691 C2 - 31202 CY - London SP - 34525 TI - DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter-molecular interactions. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - A total of 15 SNPs within complement genes and present on the ImmunoChip were analyzed in The Environmental Determinants of Diabetes in the Young (TEDDY) study. A total of 5474 subjects were followed from three months of age until islet autoimmunity (IA: n = 413) and the subsequent onset of type 1 diabetes (n = 115) for a median of 73 months (IQR 54-91). Three SNPs within ITGAM were nominally associated (p < 0.05) with IA: rs1143678 [Hazard ratio; HR 0.80; 95% CI 0.66-0.98; p = 0.032], rs1143683 [HR 0.80; 95% CI 0.65-0.98; p = 0.030] and rs4597342 [HR 1.16; 95% CI 1.01-1.32; p = 0.041]. When type 1 diabetes was the outcome, in DR3/4 subjects, there was nominal significance for two SNPs: rs17615 in CD21 [HR 1.52; 95% CI 1.05-2.20; p = 0.025] and rs4844573 in C4BPA [HR 0.63; 95% CI 0.43-0.92; p = 0.017]. Among DR4/4 subjects, rs2230199 in C3 was significantly associated [HR 3.20; 95% CI 1.75-5.85; p = 0.0002, uncorrected] a significance that withstood Bonferroni correction since it was less than 0.000833 (0.05/60) in the HLA-specific analyses. SNPs within the complement genes may contribute to IA, the first step to type 1 diabetes, with at least one SNP in C3 significantly associated with clinically diagnosed type 1 diabetes. AU - Törn, C.* AU - Liu, X.* AU - Hagopian, W.* AU - Lernmark, A.* AU - Simell, O.* AU - Rewers, M.* AU - Ziegler, A.-G. AU - Schatz, D.* AU - Akolkar, B.* AU - Onengut-Gumuscu, S.* AU - Chen, W.M.* AU - Toppari, J.* AU - Mykkänen, J.* AU - Ilonen, J.* AU - Rich, S.S.* AU - She, J.X.* AU - Sharma, A.* AU - Steck, A.* AU - Krischer, J.* AU - TEDDY Study Group (Hummel, M. AU - Hummel, S. AU - Knopff, A. AU - Peplow, C. AU - Roth, R. AU - Stock, J. AU - Strauss, E. AU - Warncke, K. AU - Winkler, C.) C1 - 48832 C2 - 41443 CY - London TI - Complement gene variants in relation to autoantibodies to beta cell specific antigens and type 1 diabetes in the TEDDY study. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - The IκB kinase (IKK) complex acts as the gatekeeper of canonical NF-κB signaling, thereby regulating immunity, inflammation and cancer. It consists of the catalytic subunits IKKα and IKKβ and the regulatory subunit NEMO/IKKγ. Here, we show that the ubiquitin binding domain (UBAN) in NEMO is essential for IKK/NF-κB activation in response to TNFα, but not IL-1β stimulation. By screening a natural compound library we identified an anthraquinone derivative that acts as an inhibitor of NEMO-ubiquitin binding (iNUB). Using biochemical and NMR experiments we demonstrate that iNUB binds to NEMOUBAN and competes for interaction with methionine-1-linked linear ubiquitin chains. iNUB inhibited NF-κB activation upon UBAN-dependent TNFα and TCR/CD28, but not UBAN-independent IL-1β stimulation. Moreover, iNUB was selectively killing lymphoma cells that are addicted to chronic B-cell receptor triggered IKK/NF-κB activation. Thus, iNUB disrupts the NEMO-ubiquitin protein-protein interaction interface and thereby inhibits physiological and pathological NF-κB signaling. AU - Vincendeau, M. AU - Hadian, K. AU - Messias, A.C. AU - Brenke, J.K. AU - Halander, J. AU - Griesbach, R.A. AU - Greczmiel, U. AU - Bertossi, A. AU - Stehle, R. AU - Nagel, D. AU - Demski, K. AU - Velvarska, H. AU - Niessing, D. AU - Geerlof, A. AU - Sattler, M. AU - Krappmann, D. C1 - 47656 C2 - 40652 TI - Inhibition of canonical NF-κB signaling by a small molecule targeting NEMO-ubiquitin interaction. JO - Sci. Rep. VL - 6 PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Alternaria alternata is one of the most studied fungi to date because of its impact on human life - from plant pathogenicity to allergenicity. However, its sesquiterpene emissions have not been systematically explored. Alternaria regularly co-occurs with Fusarium fungi, which are common plant pathogens, on withering plants. We analyzed the diversity and determined the absolute quantities of volatile organic compounds (VOCs) in the headspace above mycelial cultures of A. alternata and Fusarium oxysporum under different conditions (nutrient rich and poor, single cultures and co-cultivation) and at different mycelial ages. Using stir bar sorptive extraction and gas chromatography-mass spectrometry, we observed A. alternata to strongly emit sesquiterpenes, particularly during the early growth stages, while emissions from F. oxysporum consistently remained comparatively low. The emission profile characterizing A. alternata comprised over 20 sesquiterpenes with few effects from nutrient quality and age on the overall emission profile. Co-cultivation with F. oxysporum resulted in reduced amounts of VOCs emitted from A. alternata although its profile remained similar. Both fungi showed distinct emission profiles, rendering them suitable biomarkers for growth-detection of their phylotype in ambient air. The study highlights the importance of thorough and quantitative evaluations of fungal emissions of volatile infochemicals such as sesquiterpenes. AU - Weikl, F. AU - Ghirardo, A. AU - Schnitzler, J.-P. AU - Pritsch, K. C1 - 47986 C2 - 39800 CY - London TI - Sesquiterpene emissions from Alternaria alternata and Fusarium oxysporum: Effects of age, nutrient availability, and co-cultivation. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Monocytes are key players in atherosclerotic. Human monocytes display a considerable heterogeneity and at least three subsets can be distinguished. While the role of monocyte subset heterogeneity has already been well investigated in coronary artery disease (CAD), the knowledge about monocytes and their heterogeneity in peripheral artery occlusive disease (PAOD) still is limited. Therefore, we aimed to investigate monocyte subset heterogeneity in patients with PAOD. Peripheral blood was obtained from 143 patients suffering from PAOD (Rutherford stage I to VI) and three monocyte subsets were identified by flow cytometry: CD14(++)CD16(-) classical monocytes, CD14(+)CD1(6++) non-classical monocytes and CD14(++)CD16(+) intermediate monocytes. Additionally the expression of distinct surface markers (CD106, CD162 and myeloperoxidase MPO) was analyzed. Proportions of CD14(++)CD16(+) intermediate monocyte levels were significantly increased in advanced stages of PAOD, while classical and non-classical monocytes displayed no such trend. Moreover, CD162 and MPO expression increased significantly in intermediate monocyte subsets in advanced disease stages. Likewise, increased CD162 and MPO expression was noted in CD14(++)CD16(-) classical monocytes. These data suggest substantial dynamics in monocyte subset distributions and phenotypes in different stages of PAOD, which can either serve as biomarkers or as potential therapeutic targets to decrease the inflammatory burden in advanced stages of atherosclerosis. AU - Wildgruber, M.* AU - Aschenbrenner, T.* AU - Wendorff, H.* AU - Czubba, M.* AU - Glinzer, A.* AU - Haller, B.* AU - Schiemann, M. AU - Zimmermann, A.* AU - Berger, H.* AU - Eckstein, H.H.* AU - Meier, R.* AU - Wohlgemuth, W.A.* AU - Libby, P.* AU - Zernecke, A.* C1 - 50228 C2 - 42232 CY - London TI - The "Intermediate" CD14++CD16+ monocyte subset increases in severe peripheral artery disease in humans. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Herein we present the synthesis of a novel type of peptidomimetics composed of repeating diaminopropionic acid residues modified with structurally diverse heterobifunctional polyethylene glycol chains (abbreviated as DAPEG). Based on the developed compounds, a library of fluorogenic substrates was synthesized. Further library deconvolution towards human neutrophil serine protease 4 (NSP4) yielded highly sensitive and selective internally quenched peptidomimetic substrates. In silico analysis of the obtained peptidomimetics revealed the presence of an interaction network with distant subsites located on the enzyme surface. AU - Wysocka, M.* AU - Gruba, N.* AU - Grzywa, R.* AU - Giełdoń, A.* AU - Bąchor, R.* AU - Brzozowski, K.* AU - Sienczyk, M.* AU - Jenne, D. AU - Szewczuk, Z.* AU - Rolka, K.* AU - Lesner, A.* C1 - 48075 C2 - 39883 CY - London TI - PEGylated substrates of NSP4 protease: A tool to study protease specificity. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Mechanical ventilation (MV) and supplementation of oxygen-enriched gas, often needed in postnatal resuscitation procedures, are known to be main risk factors for impaired pulmonary development in the preterm and term neonates. Unfortunately, current imaging modalities lack in sensitivity for the detection of early stage lung injury. The present study reports a new imaging approach for diagnosis and staging of early lung injury induced by MV and hyperoxia in neonatal mice. The imaging method is based on the Talbot-Lau x-ray grating interferometry that makes it possible to quantify the x-ray small-angle scattering on the air-tissue interfaces. This so-called dark-field signal revealed increasing loss of x-ray small-angle scattering when comparing images of neonatal mice undergoing hyperoxia and MV-O2 with animals kept at room air. The changes in the dark field correlated well with histologic findings and provided superior differentiation than conventional x-ray imaging and lung function testing. The results suggest that x-ray dark-field radiography is a sensitive tool for assessing structural changes in the developing lung. In the future, with further technical developments x-ray dark-field imaging could be an important tool for earlier diagnosis and sensitive monitoring of lung injury in neonates requiring postnatal oxygen or ventilator therapy. AU - Yaroshenko, A.* AU - Pritzke, T. AU - Koschlig, M. AU - Kamgari, N. AU - Willer, K.* AU - Gromann, L.* AU - Auweter, S.* AU - Hellbach, K.* AU - Reiser, M.* AU - Eickelberg, O. AU - Pfeiffer, F.* AU - Hilgendorff, A. C1 - 48390 C2 - 41024 CY - London TI - Visualization of neonatal lung injury associated with mechanical ventilation using X-ray dark-field radiography. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Lung cancer etiology is multifactorial, and growing evidence has indicated that long non-coding RNAs (lncRNAs) are important players in lung carcinogenesis. We performed a large-scale meta-analysis of 690,564 SNPs in 15,531 autosomal lncRNAs by using datasets from six previously published genome-wide association studies (GWASs) from the Transdisciplinary Research in Cancer of the Lung (TRICL) consortium in populations of European ancestry. Previously unreported significant SNPs (P value < 1 × 10-7) were further validated in two additional independent lung cancer GWAS datasets from Harvard University and deCODE. In the final meta-analysis of all eight GWAS datasets with 17,153 cases and 239,337 controls, a novel risk SNP rs114020893 in the lncRNA NEXN-AS1 region at 1p31.1 remained statistically significant (odds ratio = 1.17; 95% confidence interval = 1.11-1.24; P = 8.31 × 10-9). In further in silico analysis, rs114020893 was predicted to change the secondary structure of the lncRNA. Our finding indicates that SNP rs114020893 of NEXN-AS1 at 1p31.1 may contribute to lung cancer susceptibility. AU - Yuan, H.M.* AU - Liu, H.* AU - Liu, Z.* AU - Owzar, K.* AU - Han, Y.* AU - Su, L.* AU - Wei, Y.* AU - Hung, R.J.* AU - McLaughlin, J.* AU - Brhane, Y.* AU - Brennan, P.* AU - Bickeboeller, H.* AU - Rosenberger, A.* AU - Houlston, R.S.* AU - Caporaso, N.* AU - Landi, M.T.* AU - Heinrich, J. AU - Risch, A.* AU - Christiani, D.C.* AU - Gümüå, Z.H.* AU - Klein, R.J.* AU - Amos, C.I.* AU - Wei, Q.* C1 - 49736 C2 - 40925 CY - London TI - A novel genetic variant in long non-coding RNA gene NEXN-AS1 is associated with risk of lung cancer. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Although association studies have unveiled numerous correlations of biochemical markers with age and age-related diseases, we still lack an understanding of their mutual dependencies. To find molecular pathways that underlie age-related diseases as well as their comorbidities, we integrated aging markers from four different high-throughput omics datasets, namely epigenomics, transcriptomics, glycomics and metabolomics, with a comprehensive set of disease phenotypes from 510 participants of the TwinsUK cohort. We used graphical random forests to assess conditional dependencies between omics markers and phenotypes while eliminating mediated associations. Applying this novel approach for multi-omics data integration yields a model consisting of seven modules that represent distinct aspects of aging. These modules are connected by hubs that potentially trigger comorbidities of age-related diseases. As an example, we identified urate as one of these key players mediating the comorbidity of renal disease with body composition and obesity. Body composition variables are in turn associated with inflammatory IgG markers, mediated by the expression of the hormone oxytocin. Thus, oxytocin potentially contributes to the development of chronic low-grade inflammation, which often accompanies obesity. Our multi-omics graphical model demonstrates the interconnectivity of age-related diseases and highlights molecular markers of the aging process that might drive disease comorbidities. AU - Zierer, J. AU - Pallister, T.* AU - Tsai, P.C.* AU - Krumsiek, J. AU - Bell, J.T.* AU - Lauc, G.* AU - Spector, T.D.* AU - Menni, C.* AU - Kastenmüller, G. C1 - 50058 C2 - 42102 CY - London TI - Exploring the molecular basis of age-related disease comorbidities using a multi-omics graphical model. JO - Sci. Rep. VL - 6 PB - Nature Publishing Group PY - 2016 SN - 2045-2322 ER - TY - JOUR AB - Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection. AU - de Vega, J.J.* AU - Ayling, S.* AU - Hegarty, M.* AU - Kudrna, D.* AU - Goicoechea, J.L.* AU - Ergon, A.* AU - Rognli, O.A.* AU - Jones, C.* AU - Swain, M.* AU - Geurts, R.* AU - Lang, C.* AU - Mayer, K.F.X. AU - Rössner, S. AU - Yates, S.* AU - Webb, K.J.* AU - Donnison, I.S.* AU - Oldroyd, G.E.* AU - Wing, R.A.* AU - Caccamo, M.* AU - Powell, W.* AU - Abberton, M.T.* AU - Skøt, L.* C1 - 47452 C2 - 39336 TI - Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. JO - Sci. Rep. VL - 5 PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Functional imaging of mouse models of cardiac health and disease provides a major contribution to our fundamental understanding of the mammalian heart. However, imaging murine hearts presents significant challenges due to their small size and rapid heart rate. Here we demonstrate the feasibility of high-frame-rate, noninvasive optoacoustic imaging of the murine heart. The temporal resolution of 50 three-dimensional frames per second provides functional information at important phases of the cardiac cycle without the use of gating or other motion-reduction methods. Differentiation of the blood oxygenation state in the heart chambers was enabled by exploiting the wavelength dependence of optoacoustic signals. Real-time volumetric tracking of blood perfusion in the cardiac chambers was also evaluated using indocyanine green. Taken together, the newly-discovered capacities offer a unique tool set for in-vivo structural and functional imaging of the whole heart with high spatio-temporal resolution in all three dimensions. AU - Dean-Ben, X.L. AU - Ford, S.J. AU - Razansky, D. C1 - 45673 C2 - 37413 CY - London TI - High-frame rate four dimensional optoacoustic tomography enables visualization of cardiovascular dynamics and mouse heart perfusion. JO - Sci. Rep. VL - 5 PB - Nature Publishing Group PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - The gut microbiota has been linked to metabolic diseases. However, information on the microbiome of young adults at risk for type 2 diabetes (T2D) is lacking. The aim of this cross-sectional analysis was to investigate whether insulin resistant women with previous gestational diabetes (pGDM), a high risk group for T2D, differ in their stool microbiota from women after a normoglycemic pregnancy (controls). Bacterial communities were analyzed by high-throughput 16S rRNA gene sequencing using fecal samples from 42 pGDM and 35 control subjects 3-16 months after delivery. Clinical characterization included a 5-point OGTT, anthropometrics, clinical chemistry markers and a food frequency questionnaire. Women with a Prevotellaceae-dominated intestinal microbiome were overrepresented in the pGDM group (p < 0.0001). Additionally, the relative abundance of the phylum Firmicutes was significantly lower in women pGDM (median 48.5 vs. 56.8%; p = 0.013). Taxa richness (alpha diversity) was similar between the two groups and with correction for multiple testing we observed no significant differences on lower taxonomic levels. These results suggest that distinctive features of the intestinal microbiota are already present in young adults at risk for T2D and that further investigations of a potential pathophysiological role of gut bacteria in early T2D development are warranted. AU - Fugmann, M. AU - Breier, M. AU - Rottenkolber, M.* AU - Banning, F. AU - Ferrari, U. AU - Sacco, V. AU - Grallert, H. AU - Parhofer, K.G.* AU - Seissler, J. AU - Clavel, T.* AU - Lechner, A. C1 - 46587 C2 - 37696 CY - London TI - The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes. JO - Sci. Rep. VL - 5 PB - Nature Publishing Group PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome. AU - Garg, D. AU - Skouloubris, S.* AU - Briffotaux, J.* AU - Myllykallio, H.* AU - Wade, R.C.* C1 - 47519 C2 - 40639 TI - Conservation and role of electrostatics in thymidylate synthase. JO - Sci. Rep. VL - 5 PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Protein phosphatase 5 is involved in the regulation of kinases and transcription factors. The dephosphorylation activity is modulated by the molecular chaperone Hsp90, which binds to the TPR-domain of protein phosphatase 5. This interaction is dependent on the C-terminal MEEVD motif of Hsp90. We show that C-terminal Hsp90 fragments differ in their regulation of the phosphatase activity hinting to a more complex interaction. Also hydrodynamic parameters from analytical ultracentrifugation and small-angle X-ray scattering data suggest a compact structure for the Hsp90-protein phosphatase 5 complexes. Using crosslinking experiments coupled with mass spectrometric analysis and structural modelling we identify sites, which link the middle/C-terminal domain interface of C. elegans Hsp90 to the phosphatase domain of the corresponding kinase. Studying the relevance of the domains of Hsp90 for turnover of native substrates we find that ternary complexes with the glucocorticoid receptor (GR) are cooperatively formed by full-length Hsp90 and PPH-5. Our data suggest that the direct stimulation of the phosphatase activity by C-terminal Hsp90 fragments leads to increased dephosphorylation rates. These are further modulated by the binding of clients to the N-terminal and middle domain of Hsp90 and their presentation to the phosphatase within the phosphatase-Hsp90 complex. AU - Haslbeck, V.* AU - Eckl, J.M.* AU - Drazic, A.* AU - Rutz, D.A.* AU - Lorenz, O.R.* AU - Zimmermann, K.* AU - Kriehuber, T.* AU - Lindemann, C.* AU - Madl, T. AU - Richter, K.* C1 - 47457 C2 - 40540 TI - The activity of protein phosphatase 5 towards native clients is modulated by the middle- and C-terminal domains of Hsp90. JO - Sci. Rep. VL - 5 PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - There is growing interest in genetically expressed reporters for in vivo studies of bacterial colonization in the context of infectious disease research, studies of the bacterial microbiome or cancer imaging and treatment. To empower non-invasive high-resolution bacterial tracking with deep tissue penetration, we herein use the genetically controlled biosynthesis of the deep-purple pigment Violacein as a photobleaching-resistant chromophore label for in vivo optoacoustic (photoacoustic) imaging in the near-infrared range. We demonstrate that Violacein-producing bacteria can be imaged with high contrast-to-noise in strongly vascularized xenografted murine tumors and further observe that Violacein shows anti-tumoral activity. Our experiments thus identify Violacein as a robust bacterial label for non-invasive optoacoustic imaging with high potential for basic research and future theranostic applications in bacterial tumor targeting. AU - Jiang, Y. AU - Sigmund, F. AU - Reber, J. AU - Dean-Ben, X.L. AU - Glasl, S. AU - Kneipp, M. AU - Estrada, H. AU - Razansky, D. AU - Ntziachristos, V. AU - Westmeyer, G.G. C1 - 45354 C2 - 37305 CY - London TI - Violacein as a genetically-controlled, enzymatically amplified and photobleaching-resistant chromophore for optoacoustic bacterial imaging. JO - Sci. Rep. VL - 5 PB - Nature Publishing Group PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Impaired immune function contributes to the development of chronic obstructive pulmonary disease (COPD). Disease progression is further exacerbated by pathogen infections due to impaired immune responses. Elimination of infected cells is achieved by cytotoxic CD8(+)  T cells that are activated by MHC I-mediated presentation of pathogen-derived antigenic peptides. The immunoproteasome, a specialized form of the proteasome, improves generation of antigenic peptides for MHC I presentation thereby facilitating anti-viral immune responses. However, immunoproteasome function in the lung has not been investigated in detail yet. In this study, we comprehensively characterized the function of immunoproteasomes in the human and murine lung. Parenchymal cells of the lung express low constitutive levels of immunoproteasomes, while they are highly and specifically expressed in alveolar macrophages. Immunoproteasome expression is not altered in whole lung tissue of COPD patients. Novel activity-based probes and native gel analysis revealed that immunoproteasome activities are specifically and rapidly induced by IFNγ treatment in respiratory cells in vitro and by virus infection of the lung in mice. Our results suggest that the lung is potentially capable of mounting an immunoproteasome-mediated efficient adaptive immune response to intracellular infections. AU - Keller, I.E. AU - Vosyka, O. AU - Takenaka, S. AU - Kloß, A.* AU - Dahlmann, B.* AU - Willems, L.I.* AU - Verdoes, M.* AU - Overkleeft, H.S.* AU - Marcos, E.* AU - Adnot, S.* AU - Hauck, S.M. AU - Ruppert, C.* AU - Günther, A.* AU - Herold, S.* AU - Ohno, S. AU - Adler, H. AU - Eickelberg, O. AU - Meiners, S. C1 - 44885 C2 - 37175 CY - London TI - Regulation of immunoproteasome function in the lung. JO - Sci. Rep. VL - 5 PB - Nature Publishing Group PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Genome-wide association studies (GWAS) have successfully identified a number of common single-nucleotide polymorphisms (SNPs) influencing glioma risk. While these SNPs only explain a small proportion of the genetic risk it is unclear how much is left to be detected by other, yet to be identified, common SNPs. Therefore, we applied Genome-Wide Complex Trait Analysis (GCTA) to three GWAS datasets totalling 3,373 cases and 4,571 controls and performed a meta-analysis to estimate the heritability of glioma. Our results identify heritability estimates of 25% (95% CI: 20-31%, P = 1.15 × 10-17) for all forms of glioma - 26% (95% CI: 17-35%, P = 1.05 × 10-8) for glioblastoma multiforme (GBM) and 25% (95% CI: 17-32%, P = 1.26 × 10-10) for non-GBM tumors. This is a substantial increase from the genetic variance identified by the currently identified GWAS risk loci (∼6% of common heritability), indicating that most of the heritable risk attributable to common genetic variants remains to be identified. AU - Kinnersley, B.* AU - Mitchell, J.S.* AU - Gousias, K.* AU - Schramm, J.* AU - Idbaih, A.* AU - Labussière, M.* AU - Marie, Y.* AU - Rahimian, A.* AU - Wichmann, H.-E. AU - Schreiber, S.* AU - Hoang-Xuan, K.* AU - Delattre, J.Y.* AU - Nöthen, M.M.* AU - Mokhtari, K.* AU - Lathrop, M* AU - Bondy, M.* AU - Simon, M.* AU - Houlston, R.S.* C1 - 47526 C2 - 40646 TI - Quantifying the heritability of glioma using genome-wide complex trait analysis. JO - Sci. Rep. VL - 5 PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - The invasion of activated fibroblasts represents a key pathomechanism in fibrotic diseases, carcinogenesis and metastasis. Invading fibroblasts contribute to fibrotic extracellular matrix (ECM) formation and the initiation, progression, or resistance of cancer. To construct transcriptome-wide signatures of fibroblast invasion, we used a multiplex phenotypic 3D invasion assay using lung fibroblasts. Microarray-based gene expression profiles of invading and non-invading fibroblasts demonstrated that 1,049 genes were differentially regulated (>1.5-fold). Unbiased pathway analysis (Ingenuity) identified significant enrichment for the functional clusters 'invasion of cells', 'idiopathic pulmonary fibrosis', and 'metastasis'. Matrix metalloprotease 13 (MMP13), transforming growth factor (TGF)-β1, Caveolin (Cav) 1, Phosphatase and Tensin Homolog (Pten), and secreted frizzled-related protein (Sfrp) 1 were among the highest regulated genes, confirmed by qRT-PCR and Western Blotting. We next performed in silico analysis (Ingenuity Pathway Analysis) to predict mediators that induced fibroblast invasion. Of these, TGFβ1, epidermal growth factor (EGF), fibroblast growth factor (FGF) 2, and platelet-derived growth factor (PDGF)-BB were tested in our 3D invasion assay and found to significantly induce invasion, thus validating the transcriptome profile. Accordingly, our transcriptomic invasion signature describes the invading fibroblast phenotype in unprecedented detail and provides a tool for future functional studies of cell invasion and therapeutic modulation thereof using complex phenotypic assays. AU - Oehrle, B. AU - Burgstaller, G. AU - Irmler, M. AU - Dehmel, S. AU - Grün, J. AU - Hwang, T. AU - Krauss-Etschmann, S. AU - Beckers, J. AU - Meiners, S. AU - Eickelberg, O. C1 - 46535 C2 - 37623 CY - London TI - Validated prediction of pro-invasive growth factors using a transcriptome-wide invasion signature derived from a complex 3D invasion assay. JO - Sci. Rep. VL - 5 PB - Nature Publishing Group PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - The differentiated human airway epithelium consists of different cell types forming a polarized and pseudostratified epithelium. This is dramatically altered in chronic obstructive pulmonary disease (COPD), characterized by basal and goblet cell hyperplasia, and squamous cell metaplasia. The effect of cigarette smoke on human bronchial epithelial cell (HBEC) differentiation remains to be elucidated. We analysed whether cigarette smoke extract (CSE) affected primary (p)HBEC differentiation and function. pHBEC were differentiated at the air-liquid interface (ALI) and differentiation was quantified after 7, 14, 21, or 28 days by assessing acetylated tubulin, CC10, or MUC5AC for ciliated, Clara, or goblet cells, respectively. Exposure of differentiating pHBEC to CSE impaired epithelial barrier formation, as assessed by resistance measurements (TEER). Importantly, CSE exposure significantly reduced the number of ciliated cells, while it increased the number of Clara and goblet cells. CSE-dependent cell number changes were reflected by a reduction of acetylated tubulin levels, an increased expression of the basal cell marker KRT14, and increased secretion of CC10, but not by changes in transcript levels of CC10, MUC5AC, or FOXJ1. Our data demonstrate that cigarette smoke specifically alters the cellular composition of the airway epithelium by affecting basal cell differentiation in a post-transcriptional manner. AU - Schamberger, A.C. AU - Staab-Weijnitz, C.A. AU - Mise-Racek, N. AU - Eickelberg, O. C1 - 43219 C2 - 36355 CY - London TI - Cigarette smoke alters primary human bronchial epithelial cell differentiation at the air-liquid interface. JO - Sci. Rep. VL - 5 PB - Nature Publishing Group PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Fms-like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase constitutively expressed by acute myeloid leukaemia (AML) blasts. In addition, 25% of AML patients harbour a FLT3-ITD mutation, associated with inferior outcome due to increased relapse rate. Relapse might be propagated by interactions between AML blasts and the bone marrow microenvironment. Besides cellular elements of the microenvironment (e.g. mesenchymal stromal cells), bone marrow hypoxia has emerged as an additional crucial component. Hence, effects of hypoxia on FLT3 expression and biology could provide novel insight into AML biology. Here we show that 25% of AML patients down-regulate FLT3 expression on blasts in response to in vitro hypoxia (1% O2), which was independent of its mutational state. While virtually no AML cell lines regulate FLT3 in response to hypoxia, the down-regulation could be observed in Ba/F3 cells stably transfected with different FLT3 mutants. Hypoxia-mediated down-regulation was specific for FLT3, reversible and proteasome-dependent; with FLT3 half-life being significantly shorter at hypoxia. Also, PI-3K inhibition could partially abrogate down-regulation of FLT3. Hypoxia-mediated down-regulation of FLT3 conferred resistance against cytarabine in vitro. In conclusion, FLT3 expression in AML is dependent on the oxygen partial pressure, but response to hypoxia differs. AU - Sironi, S.* AU - Wagner, M.* AU - Kuett, A.* AU - Drolle, H.* AU - Polzer, H. AU - Spiekermann, K. AU - Rieger, C.* AU - Fiegl, M.* C1 - 47471 C2 - 39344 TI - Microenvironmental hypoxia regulates FLT3 expression and biology in AML. JO - Sci. Rep. VL - 5 PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Biology requires observations at multiple geometrical scales, a feature that is not typically offered by a single imaging modality. We developed a hybrid optical system that not only provides different contrast modes but also offers imaging at different geometrical scales, achieving uniquely broad resolution and a 1000-fold volume sampling increase compared to volumes scanned by optical microscopy. The system combines optoacoustic mesoscopy, optoacoustic microscopy and two-photon microscopy, the latter integrating second and third harmonic generation modes. Label-free imaging of a mouse ear and zebrafish larva ex-vivo demonstrates the contrast and scale complementarity provided by the hybrid system. We showcase the superior anatomical orientation offered by the label-free capacity and hybrid operation, over fluorescence microscopy, and the dynamic selection between field of view and resolution achieved, leading to new possibilities in biological visualization. AU - Soliman, D. AU - Tserevelakis, G.J. AU - Omar, M. AU - Ntziachristos, V. C1 - 46647 C2 - 37647 CY - London TI - Combining microscopy with mesoscopy using optical and optoacoustic label-free modes. JO - Sci. Rep. VL - 5 PB - Nature Publishing Group PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Severe vitamin D deficiency is known to cause rickets, however epidemiological studies and RCTs did not reveal conclusive associations for other parameters of bone health. In our study, we aimed to investigate the association between serum levels of 25(OH) vitamin D and bone turnover markers in a population-based sample of children. 25(OH)D, calcium (Ca), osteocalcin (OC), and β-Crosslaps (β-CTx) were measured in 2798 ten-year-old children from the German birth cohorts GINIplus and LISAplus. Linear regression was used to determine the association between bone turnover markers and 25(OH)D levels. 25(OH)D, OC, and β-CTx showed a clear seasonal variation. A 10 nmol/l increase in 25(OH)D was significantly associated with a 10.5 ng/l decrease (p < 0.001) in β-CTx after adjustment for design, sex, fasting status, time of blood drawn, BMI, growth rate, and detectable testosterone/estradiol. For OC alone no significant association with 25(OH)D was observed, whereas the β-CTx-to-OC ratio was inversely associated with 25(OH)D (-1.7% change, p < 0.001). When stratifying the analyses by serum calcium levels, associations were stronger in children with Ca levels below the median. This study in school-aged children showed a seasonal variation of 25(OH)D and the bone turnover markers OC and β-CTx. Furthermore a negative association between 25(OH)D and the bone resorption marker β-CTx was observed. AU - Thiering, E. AU - Brüske, I. AU - Kratzsch, J.* AU - Hofbauer, L.C.* AU - Berdel, D.* AU - von Berg, A.* AU - Lehmann, I.* AU - Hoffmann, B.* AU - Bauer, C.P.* AU - Koletzko, S.* AU - Heinrich, J. C1 - 47553 C2 - 40662 TI - Associations between serum 25-hydroxyvitamin D and bone turnover markers in a population based sample of German children. JO - Sci. Rep. VL - 5 PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease with a median life expectancy of 4-5 years after initial diagnosis. Early diagnosis and accurate monitoring of IPF are limited by a lack of sensitive imaging techniques that are able to visualize early fibrotic changes at the epithelial-mesenchymal interface. Here, we report a new x-ray imaging approach that directly visualizes the air-tissue interfaces in mice in vivo. This imaging method is based on the detection of small-angle x-ray scattering that occurs at the air-tissue interfaces in the lung. Small-angle scattering is detected with a Talbot-Lau interferometer, which provides the so-called x-ray dark-field signal. Using this imaging modality, we demonstrate-for the first time-the quantification of early pathogenic changes and their correlation with histological changes, as assessed by stereological morphometry. The presented radiography method is significantly more sensitive in detecting morphological changes compared with conventional x-ray imaging, and exhibits a significantly lower radiation dose than conventional x-ray CT. As a result of the improved imaging sensitivity, this new imaging modality could be used in future to reduce the number of animals required for pulmonary research studies. AU - Yaroshenko, A.* AU - Hellbach, K.* AU - Yildirim, A.Ö. AU - Conlon, T.M. AU - Fernandez, I.E. AU - Bech, M.* AU - Velroyen, A.* AU - Meinel, F.G.* AU - Auweter, S.* AU - Reiser, M.* AU - Eickelberg, O. AU - Pfeiffer, F.* C1 - 47462 C2 - 40568 TI - Improved In vivo assessment of pulmonary fibrosis in mice using X-ray dark-feld radiography. JO - Sci. Rep. VL - 5 PY - 2015 SN - 2045-2322 ER - TY - JOUR AB - The breakthrough capacity of optoacoustics for three-dimensional visualization of dynamic events in real time has been recently showcased. Yet, efficient spectral unmixing for functional imaging of entire volumetric regions is significantly challenged by motion artifacts in concurrent acquisitions at multiple wavelengths. Here, we introduce a method for simultaneous acquisition of multispectral volumetric datasets by introducing a microsecond-level delay between excitation laser pulses at different wavelengths. Robust performance is demonstrated by real-time volumetric visualization of functional blood parametrers in human vasculature with a handheld matrix array optoacoustic probe. This approach can avert image artifacts imposed by velocities greater than 2 m/s, thus, does not only facilitate imaging influenced by respiratory, cardiac or other intrinsic fast movements in living tissues, but can achieve artifact-free imaging in the presence of more significant motion, e.g. abrupt displacements during handheld-mode operation in a clinical environment. AU - Dean-Ben, X.L. AU - Bay, E. AU - Razansky, D. C1 - 31854 C2 - 34809 CY - London TI - Functional optoacoustic imaging of moving objects using microsecond-delay acquisition of multispectral three-dimensional tomographic data. JO - Sci. Rep. VL - 4 PB - Nature Publishing Group PY - 2014 SN - 2045-2322 ER - TY - JOUR AB - Upstream transcription factor 1 (USF1) allelic variants significantly influence future risk of cardiovascular disease and overall mortality in females. We investigated sex-specific effects of USF1 gene allelic variants on serum indices of lipoprotein metabolism, early markers of asymptomatic atherosclerosis and their changes during six years of follow-up. In addition, we investigated the cis-regulatory role of these USF1 variants in artery wall tissues in Caucasians. In the Cardiovascular Risk in Young Finns Study, 1,608 participants (56% women, aged 31.9 ± 4.9) with lipids and cIMT data were included. For functional study, whole genome mRNA expression profiling was performed in 91 histologically classified atherosclerotic samples. In females, serum total, LDL cholesterol and apoB levels increased gradually according to USF1 rs2516839 genotypes TT < CT < CC and rs1556259 AA < AG < GG as well as according to USF1 H3 (GCCCGG) copy number 0 < 1 < 2. Furthermore, the carriers of minor alleles of rs2516839 (C) and rs1556259 (G) of USF1 gene had decreased USF1 expression in atherosclerotic plaques (P = 0.028 and 0.08, respectively) as compared to non-carriers. The genetic variation in USF1 influence USF1 transcript expression in advanced atherosclerosis and regulates levels and metabolism of circulating apoB and apoB-containing lipoprotein particles in sex-dependent manner, but is not a major determinant of early markers of atherosclerosis. AU - Fan, Y.M.* AU - Hernesniemi, J.* AU - Oksala, N.* AU - Levula, M.* AU - Raitoharju, E.* AU - Collings, A.* AU - Hutri-Kähönen, N.* AU - Juonala, M.* AU - Marniemi, J.* AU - Lyytikäinen, L.-P.* AU - Seppälä, I.* AU - Mennander, A.* AU - Tarkka, M.* AU - Kangas, A.J.* AU - Soininen, P.* AU - Salenius, J.P.* AU - Klopp, N. AU - Illig, T. AU - Laitinen, T.* AU - Ala-Korpela, M.* AU - Laaksonen, R.* AU - Viikari, J.* AU - Kähönen, M.* AU - Raitakari, O.T.* AU - Lehtimäki, T.* C1 - 31052 C2 - 34148 CY - London TI - Upstream Transcription Factor 1 (USF1) allelic variants regulate lipoprotein metabolism in women and USF1 expression in atherosclerotic plaque. JO - Sci. Rep. VL - 4 PB - Nature Publishing Group PY - 2014 SN - 2045-2322 ER - TY - JOUR AB - Photoacoustic imaging is a novel hybrid imaging modality combining the high spatial resolution of optical imaging with the high penetration depth of ultrasound imaging. Here, for the first time, we evaluate the efficacy of various photosensitizers that are widely used as photodynamic therapeutic (PDT) agents as photoacoustic contrast agents. Photoacoustic imaging of photosensitizers exhibits advantages over fluorescence imaging, which is prone to photobleaching and autofluorescence interference. In this work, we examined the photoacoustic activity of 5 photosensitizers: zinc phthalocyanine, protoporphyrin IX, 2,4-bis [4-(N,N-dibenzylamino)-2,6-dihydroxyphenyl] squaraine, chlorin e6 and methylene blue in phantoms, among which zinc phthalocyanine showed the highest photoacoustic activity. Subsequently, we evaluated its tumor localization efficiency and biodistribution at multiple time points in a murine model using photoacoustic imaging. We observed that the probe localized at the tumor within 10 minutes post injection, reaching peak accumulation around 1 hour and was cleared within 24 hours, thus, demonstrating the potential of photosensitizers as photoacoustic imaging contrast agents in vivo. This means that the known advantages of photosensitizers such as preferential tumor uptake and PDT efficacy can be combined with photoacoustic imaging capabilities to achieve longitudinal monitoring of cancer progression and therapy in vivo. AU - Ho, C.J.* AU - Balasundaram, G.* AU - Driessen, W.H.P. AU - McLaren, R.* AU - Wong, C.L.* AU - Dinish, U.S.* AU - Attia, A.B.E.* AU - Ntziachristos, V. AU - Olivo, M.* C1 - 31634 C2 - 34619 CY - London TI - Multifunctional photosensitizer-based contrast agents for photoacoustic imaging. JO - Sci. Rep. VL - 4 PB - Nature Publishing Group PY - 2014 SN - 2045-2322 ER - TY - JOUR AB - The need for higher yielding and better-adapted crop plants for feeding the world's rapidly growing population has raised the question of how to systematically utilize large genebank collections with their wide range of largely untouched genetic diversity. Phenotypic data that has been recorded for decades during various rounds of seed multiplication provides a rich source of information. Their usefulness has remained limited though, due to various biases induced by conservation management over time or changing environmental conditions. Here, we present a powerful procedure that permits an unbiased trait-based selection of plant samples based on such phenotypic data. Applying this technique to the wheat collection of one of the largest genebanks worldwide, we identified groups of plant samples displaying contrasting phenotypes for selected traits. As a proof of concept for our discovery pipeline, we resequenced the entire major but conserved flowering time locus Ppd-D1 in just a few such selected wheat samples - and nearly doubled the number of hitherto known alleles. AU - Keilwagen, J.* AU - Kilian, B.* AU - Özkan, H.* AU - Babben, S.* AU - Perovic, D.* AU - Mayer, K.F.X. AU - Walther, A.* AU - Poskar, C.H.* AU - Ordon, F.* AU - Eversole, K.* AU - Börner, A.* AU - Ganal, M.* AU - Knüpffer, H.* AU - Graner, A.* AU - Friedel, S.* C1 - 31595 C2 - 34636 CY - London TI - Separating the wheat from the chaff - a strategy to utilize plant genetic resources from ex situ genebanks. JO - Sci. Rep. VL - 4 PB - Nature Publishing Group PY - 2014 SN - 2045-2322 ER - TY - JOUR AB - The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function. AU - Purahong, W.* AU - Schloter, M. AU - Pecyna, M.J.* AU - Kapturska, D.* AU - Däumlich, V.* AU - Mital, S.* AU - Buscot, F.* AU - Hofrichter, M.* AU - Gutknecht, J.L.* AU - Krüger, D.* C1 - 42750 C2 - 35336 TI - Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe. JO - Sci. Rep. VL - 4 PY - 2014 SN - 2045-2322 ER - TY - JOUR AB - Nerve cells and spontaneous coordinated behavior first appeared near the base of animal evolution in the common ancestor of cnidarians and bilaterians. Experiments on the cnidarian Hydra have demonstrated that nerve cells are essential for this behavior, although nerve cells in Hydra are organized in a diffuse network and do not form ganglia. Here we show that the gap junction protein innexin-2 is expressed in a small group of nerve cells in the lower body column of Hydra and that an anti-innexin-2 antibody binds to gap junctions in the same region. Treatment of live animals with innexin-2 antibody eliminates gap junction staining and reduces spontaneous body column contractions. We conclude that a small subset of nerve cells, connected by gap junctions and capable of synchronous firing, act as a pacemaker to coordinate the contraction of the body column in the absence of ganglia. AU - Takaku, Y.* AU - Hwang, J.S.* AU - Wolf, A. AU - Böttger, A.* AU - Shimizu, H.* AU - David, C.N.* AU - Gojobori, T.* C1 - 30556 C2 - 33687 TI - Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps. JO - Sci. Rep. VL - 4 PY - 2014 SN - 2045-2322 ER - TY - JOUR AB - An important role of the type 2 diabetes risk variant rs7903146 in TCF7L2 in metabolic actions of various tissues, in particular of the liver, has recently been demonstrated by functional animal studies. Accordingly, the TT diabetes risk allele may lead to currently unknown alterations in human. Our study revealed no differences in the kinetics of glucose, insulin, C-peptide and non-esterified fatty acids during an OGTT in homozygous participants from a German diabetes risk cohort (n = 1832) carrying either the rs7903146 CC (n = 15) or the TT (n = 15) genotype. However, beta-cell function was impaired for TT carriers. Covering more than 4000 metabolite ions the plasma metabolome did not reveal any differences between genotypes. Our study argues against a relevant impact of TCF7L2 rs7903146 on the systemic level in humans, but confirms the role in the pathogenesis of type 2 diabetes in humans as a mechanism impairing insulin secretion. AU - Wagner, R. AU - Li, J.* AU - Kenar, E.* AU - Kohlbacher, O.* AU - Machicao, F. AU - Häring, H.-U. AU - Fritsche, A. AU - Xu, G.* AU - Lehmann, R. C1 - 31607 C2 - 34633 CY - London TI - Clinical and non-targeted metabolomic profiling of homozygous carriers of transcription factor 7-like 2 variant rs7903146. JO - Sci. Rep. VL - 4 PB - Nature Publishing Group PY - 2014 SN - 2045-2322 ER - TY - JOUR AB - The protein-protein interaction (PPI) networks are dynamically organized as modules, and are typically described by hub dichotomy: 'party' hubs act as intramodule hubs and are coexpressed with their partners, yet 'date' hubs act as coordinators among modules and are incoherently expressed with their partners. However, there remains skepticism about the existence of hub dichotomy. Since different algorithms and data sets were used in previous studies to test the model of hub classification, the conclusions may be largely influenced by the potential inherent biases. In this study, we evaluated two data sets of yeast interactome, and systematically investigated the behavior of hubs from multiple perspectives including co-expression patterns, topological roles and functional classifications. Our results revealed consistency between the two data sets, confirming the presence of hub dichotomy. Furthermore, we analyzed a human interactome data set, and demonstrated that the modular architecture of the PPI networks was more complicated than hub dichotomy. AU - Chang, X.* AU - Xu, T. AU - Li, Y.* AU - Wang, K.* C1 - 24539 C2 - 31581 TI - Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs. JO - Sci. Rep. VL - 3 PB - Nature Publishing Group PY - 2013 SN - 2045-2322 ER - TY - JOUR AB - FKBP38 regulates apoptosis through unique interactions with multiple regulators including Bcl-2. Interestingly, the peptidylprolyl isomerase activity of FKBP38 is only detectable when it binds to calcium-saturated calmodulin (CaM/Ca2+). This, in turn, permits the formation of a complex with Bcl-2. FKBP38 thereby provides an important link between isomerase activity and apoptotic pathways. Here, we show that the N-terminal extension (residues 1-32) preceding the catalytic domain of FKBP38 has an autoinhibitory activity. The core isomerase activity of FKBP38 is inhibited by transient interactions involving the flexible N-terminal extension that precedes the catalytic domain. Notably, CaM/Ca2+ binds to this N-terminal extension and thereby releases the autoinhibitory contacts between the N-terminal extension and the catalytic domain, thus potentiating the isomerase activity of FKBP38. Our data demonstrate how CaM/Ca2+ modulates the catalytic activity of FKBP38. AU - Kang, C.B.* AU - Ye, H.* AU - Chia, J.* AU - Choi, B.H.* AU - Dhe-Paganon, S.* AU - Simon, B.* AU - Schütz, U. AU - Sattler, M. AU - Yoon, H.S.* C1 - 28134 C2 - 32965 TI - Functional role of the flexible N-terminal extension of FKBP38 in catalysis. JO - Sci. Rep. VL - 3 PB - Nature Publishing PY - 2013 SN - 2045-2322 ER - TY - JOUR AB - Linked to diverse biological processes, groundwater ecosystems deliver essential services to mankind, the most important of which is the provision of drinking water. In contrast to surface waters, ecological aspects of groundwater systems are ignored by the current European Union and national legislation. Groundwater management and protection measures refer exclusively to its good physicochemical and quantitative status. Current initiatives in developing ecologically sound integrative assessment schemes by taking groundwater fauna into account depend on the initial classification of subsurface bioregions. In a large scale survey, the regional and biogeographical distribution patterns of groundwater dwelling invertebrates were examined for many parts of Germany. Following an exploratory approach, our results underline that the distribution patterns of invertebrates in groundwater are not in accordance with any existing bioregional classification system established for surface habitats. In consequence, we propose to develope a new classification scheme for groundwater ecosystems based on stygoregions. AU - Stein, H.* AU - Griebler, C. AU - Berkhoff, S.* AU - Matzke, D.* AU - Fuchs, A.* AU - Hahn, H.J.* C1 - 10441 C2 - 30252 TI - Stygoregions - a promising approach to a bioregional classification of groundwater systems. JO - Sci. Rep. VL - 2 PB - Nature Publishing Group PY - 2012 SN - 2045-2322 ER -