TY - JOUR AB - Background: Chronic non-communicable diseases (NCDs) are a major global health challenge, with unhealthy diets contributing significantly to their burden. Metabolomics data offer new possibilities for identifying nutritional biomarkers, as demonstrated in short-term intervention studies. This study investigated associations between habitual dietary intake and urinary metabolites, a not well-studied area. Methods: Data were available from 496 participants of the population-based MEIA study. Linear and median regression models examined associations between habitual dietary intake and metabolites, adjusted for possible confounders. K-means clustering identified urinary metabolite clusters, and multinomial regression models were applied to analyze associations between food intake and metabolite clusters. Results: Using linear regression models, previously reported associations could be replicated, including citrus intake with proline betaine, protein intake with urea, and fiber intake with hippurate. Novel findings include positive associations of poultry intake with taurine, indoxyl sulfate, 1-methylnicotinamide, and trimethylamine-N-oxide. Milk substitutes were positively associated with urinary uracil, pseudouridine, 4-hydroxyhippurate, and 3-hydroxyhippurate, and inversely associated with quinic acid. Dietary fiber intake showed a positive association with 3-(3-hydroxyphenyl)-3-hydroxypropionic acid and a negative association with indoxyl sulfate. We identified sucrose and taurine as key metabolites differentiating metabolite clusters. Multinomial regression analysis confirmed significantly different dietary associations across clusters, particularly for fruits, processed meat, poultry, and alcoholic beverages. Conclusions: This study highlights established and novel food–metabolite associations, demonstrating the potential of urinary metabolomics for use as nutritional biomarkers in individuals from the general population. AU - Blümlhuber, A.* AU - Freuer, D.* AU - Wawro, N. AU - Rohm, F.* AU - Meisinger, C.* AU - Linseisen, J.* C1 - 75068 C2 - 57753 CY - Mdpi Ag, Grosspeteranlage 5, Ch-4052 Basel, Switzerland SP - 441 - 441 TI - Association between habitual dietary intake and urinary metabolites in adults—results of a population-based study. JO - Metabolites VL - 15 IS - 7 PB - Mdpi PY - 2025 SN - 2218-1989 ER - TY - JOUR AB - Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of bovine paratuberculosis, a chronic granulomatous enteritis leading to economic losses and posing a risk to human health due to its zoonotic potential. The pathogen cannot reliably be detected by standard methods, and immunological procedures during the infection are not well understood. Therefore, the aim of our study was to explore host-pathogen interactions in MAP-infected dairy cows and to improve diagnostic tests. Serum proteomics analysis using quantitative label-free LC-MS/MS revealed 60 differentially abundant proteins in MAP-infected dairy cows compared to healthy controls from the same infected herd and 90 differentially abundant proteins in comparison to another control group from an uninfected herd. Pathway enrichment analysis provided new insights into the immune response to MAP and susceptibility to the infection. Furthermore, we found a higher abundance of Cathepsin S (CTSS) in the serum of MAP-infected dairy cows, which is involved in multiple enriched pathways associated with the immune system. Confirmed with Western blotting, we identified CTSS as a potential biomarker for bovine paratuberculosis. This study enabled a better understanding of procedures in the host-pathogen response to MAP and improved detection of paratuberculosis-diseased cattle. AU - Duda, H.C.* AU - von Toerne, C. AU - Korbonits, L.* AU - Didier, A.* AU - Scholz, A.M.* AU - Märtlbauer, E.* AU - Hauck, S.M. AU - Deeg, C.A.* C1 - 70554 C2 - 55683 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Cathepsin S is more abundant in serum of Mycobacterium avium subsp. paratuberculosis-Infected dairy cows. JO - Metabolites VL - 14 IS - 4 PB - Mdpi PY - 2024 SN - 2218-1989 ER - TY - JOUR AB - This Special Issue was initiated to celebrate and congratulate Prof [...]. AU - Liu, X.* AU - Weigert, C. C1 - 69857 C2 - 54999 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - State-of-the-art metabolomics and lipidomics in life sciences: Methods and applications. JO - Metabolites VL - 14 IS - 1 PB - Mdpi PY - 2024 SN - 2218-1989 ER - TY - JOUR AB - The underlying molecular mechanisms for the development of non-alcoholic fatty liver (NAFL) and its progression to advanced liver diseases remain elusive. Glyoxalase 1 (Glo1) loss, leading to elevated methylglyoxal (MG) and dicarbonyl stress, has been implicated in various diseases, including obesity-related conditions. This study aimed to investigate changes in the glyoxalase system in individuals with non-pathological liver fat. Liver biopsies were obtained from 30 individuals with a narrow range of BMI (24.6-29.8 kg/m2). Whole-body insulin sensitivity was assessed using HOMA-IR. Liver biopsies were analyzed for total triglyceride content, Glo1 and Glo2 mRNA, protein expression, and activity. Liquid chromatography-tandem mass spectrometry determined liver dicarbonyl content and oxidation and glycation biomarkers. Liver Glo1 activity showed an inverse correlation with HOMA-IR and liver triglyceride content, but not BMI. Despite reduced Glo1 activity, no associations were found with elevated liver dicarbonyls or glycation markers. A sex dimorphism was observed in Glo1, with females exhibiting significantly lower liver Glo1 protein expression and activity, and higher liver MG-H1 content compared to males. This study demonstrates that increasing liver fat, even within a non-pathological range, is associated with reduced Glo1 activity. AU - Peter, A. AU - Schleicher, E. AU - Kliemank, E. AU - Szendroedi, J. AU - Königsrainer, A.* AU - Häring, H.-U. AU - Nawroth, P.P. AU - Fleming, T. C1 - 70555 C2 - 55779 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Accumulation of non-pathological liver fat is associated with the loss of glyoxalase I activity in humans. JO - Metabolites VL - 14 IS - 4 PB - Mdpi PY - 2024 SN - 2218-1989 ER - TY - JOUR AB - Accurate risk prediction for myocardial infarction (MI) is crucial for preventive strategies, given its significant impact on global mortality and morbidity. Here, we propose a novel deep-learning approach to enhance the prediction of incident MI cases by incorporating metabolomics alongside clinical risk factors. We utilized data from the KORA cohort, including the baseline S4 and follow-up F4 studies, consisting of 1454 participants without prior history of MI. The dataset comprised 19 clinical variables and 363 metabolites. Due to the imbalanced nature of the dataset (78 observed MI cases and 1376 non-MI individuals), we employed a generative adversarial network (GAN) model to generate new incident cases, augmenting the dataset and improving feature representation. To predict MI, we further utilized multi-layer perceptron (MLP) models in conjunction with the synthetic minority oversampling technique (SMOTE) and edited nearest neighbor (ENN) methods to address overfitting and underfitting issues, particularly when dealing with imbalanced datasets. To enhance prediction accuracy, we propose a novel GAN for feature-enhanced (GFE) loss function. The GFE loss function resulted in an approximate 2% improvement in prediction accuracy, yielding a final accuracy of 70%. Furthermore, we evaluated the contribution of each clinical variable and metabolite to the predictive model and identified the 10 most significant variables, including glucose tolerance, sex, and physical activity. This is the first study to construct a deep-learning approach for producing 7-year MI predictions using the newly proposed loss function. Our findings demonstrate the promising potential of our technique in identifying novel biomarkers for MI prediction. AU - Yu, S. AU - Han, S. AU - Shi, M. AU - Harada, M. AU - Ge, J. AU - Li, X.* AU - Cai, X.* AU - Heier, M. AU - Kastenmüller, G. AU - Suhre, K.* AU - Gieger, C. AU - Koenig, W.* AU - Rathmann, W.* AU - Peters, A. AU - Wang-Sattler, R. C1 - 70753 C2 - 55826 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Prediction of myocardial infarction using a combined generative adversarial network model and feature-enhanced loss function. JO - Metabolites VL - 14 IS - 5 PB - Mdpi PY - 2024 SN - 2218-1989 ER - TY - JOUR AB - Volumetric absorptive microsampling (VAMS) has arisen as a relevant tool in biological analysis, offering simplified sampling procedures and enhanced stability. Most of the attention VAMS has received in the past decade has been from pharmaceutical research, with most of the published work employing VAMS targeting drugs or other exogenous compounds, such as toxins and pollutants. However, biomarker analysis by employing blood microsampling has high promise. Herein, a comprehensive review on the applicability of VAMS devices for the analysis of endogenous metabolites/biomarkers was performed. The study presents a full overview of the analysis process, incorporating all the steps in sample treatment and validation parameters. Overall, VAMS devices have proven to be reliable tools for the analysis of endogenous analytes with biological importance, often offering improved analyte stability in comparison with blood under ambient conditions as well as a convenient and straightforward sample acquisition model. AU - de Sá E Silva, D.M.* AU - Thaitumu, M.* AU - Theodoridis, G.* AU - Witting, M. AU - Gika, H.* C1 - 68694 C2 - 54903 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Volumetric absorptive microsampling in the analysis of endogenous metabolites. JO - Metabolites VL - 13 IS - 10 PB - Mdpi PY - 2023 SN - 2218-1989 ER - TY - JOUR AB - Obesity plays an important role in the development of insulin resistance and diabetes, but the molecular mechanism that links obesity and diabetes is still not completely understood. Here, we used 146 targeted metabolomic profiles from the German KORA FF4 cohort consisting of 1715 participants and associated them with obesity and type 2 diabetes. In the basic model, 83 and 51 metabolites were significantly associated with body mass index (BMI) and T2D, respectively. Those metabolites are branched-chain amino acids, acylcarnitines, lysophospholipids, or phosphatidylcholines. In the full model, 42 and 3 metabolites were significantly associated with BMI and T2D, respectively, and replicate findings in the previous studies. Sobel mediation testing suggests that the effect of BMI on T2D might be mediated via lipids such as sphingomyelin (SM) C16:1, SM C18:1 and diacylphosphatidylcholine (PC aa) C38:3. Moreover, mendelian randomization suggests a causal relationship that BMI causes the change of SM C16:1 and PC aa C38:3, and the change of SM C16:1, SM C18:1, and PC aa C38:3 contribute to T2D incident. Biological pathway analysis in combination with genetics and mice experiments indicate that downregulation of sphingolipid or upregulation of phosphatidylcholine metabolism is a causal factor in early-stage T2D pathophysiology. Our findings indicate that metabolites like SM C16:1, SM C18:1, and PC aa C38:3 mediate the effect of BMI on T2D and elucidate their role in obesity related T2D pathologies. AU - Dong, Q. AU - Sidra, S.* AU - Gieger, C. AU - Wang-Sattler, R. AU - Rathmann, W.* AU - Prehn, C. AU - Adamski, J. AU - Koenig, W.* AU - Peters, A. AU - Grallert, H. AU - Sharma, S. C1 - 67525 C2 - 54088 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Metabolic signatures elucidate the effect of body mass index on type 2 diabetes. JO - Metabolites VL - 13 IS - 2 PB - Mdpi PY - 2023 SN - 2218-1989 ER - TY - JOUR AB - The single point insulin sensitivity estimator (SPISE) is a recently developed fasting index for insulin sensitivity based on triglycerides, high density lipoprotein cholesterol, and body mass index. SPISE has been validated in juveniles and adults; still, its role during childhood remains unclear. To evaluate the age- and sex-specific distribution of SPISE, its correlation with established fasting indexes and its application as a prognostic marker for future dysglycemia during childhood and adolescence were assessed. We performed linear modeling and correlation analyses on a cross-sectional cohort of 2107 children and adolescents (age 5 to 18.4 years) with overweight or obesity. Furthermore, survival analyses were conducted upon a longitudinal cohort of 591 children with overweight/obesity (1712 observations) with a maximum follow-up time of nearly 20 years, targeting prediabetes/dysglycemia as the end point. The SPISE index decreased significantly with age (-0.34 units per year, p < 0.001) among children and adolescents with overweight and obesity. Sex did not have an influence on SPISE. There was a modest correlation between SPISE and established fasting markers of insulin resistance (R = -0.49 for HOMA-IR, R = -0.55 for QUICKI-IR). SPISE is a better prognostic marker for future dysglycemia (hazard ratio (HR) 3.47, 95% confidence interval (CI) 1.60-7.51, p < 0.01) than HOMA-IR and QUICKI-IR (HR 2.44, 95% CI 1.24-4.81, p < 0.05). The SPISE index is a surrogate marker for insulin resistance predicting emerging dysglycemia in children with overweight or obesity, and could, therefore, be applied to pediatric cohorts that lack direct insulin assessment. AU - Stein, R. AU - Koutny, F.* AU - Riedel, J.* AU - Doerr, N.* AU - Meyer, K. AU - Colombo, M.* AU - Vogel, M.* AU - Anderwald, C.H.* AU - Blüher, M. AU - Kiess, W.* AU - Körner, A. AU - Weghuber, D.* C1 - 69680 C2 - 53869 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Single point insulin sensitivity estimator (SPISE) as a prognostic marker for emerging dysglycemia in children with overweight or obesity. JO - Metabolites VL - 13 IS - 1 PB - Mdpi PY - 2023 SN - 2218-1989 ER - TY - JOUR AB - Reduced expression of the plasma membrane citrate transporter SLC13A5, also known as INDY, has been linked to increased longevity and mitigated age-related cardiovascular and metabolic diseases. Citrate, a vital component of the tricarboxylic acid cycle, constitutes 1-5% of bone weight, binding to mineral apatite surfaces. Our previous research highlighted osteoblasts' specialized metabolic pathway facilitated by SLC13A5 regulating citrate uptake, production, and deposition within bones. Disrupting this pathway impairs bone mineralization in young mice. New Mendelian randomization analysis using UK Biobank data indicated that SNPs linked to reduced SLC13A5 function lowered osteoporosis risk. Comparative studies of young (10 weeks) and middle-aged (52 weeks) osteocalcin-cre-driven osteoblast-specific Slc13a5 knockout mice (Slc13a5cKO) showed a sexual dimorphism: while middle-aged females exhibited improved elasticity, middle-aged males demonstrated enhanced bone strength due to reduced SLC13A5 function. These findings suggest reduced SLC13A5 function could attenuate age-related bone fragility, advocating for SLC13A5 inhibition as a potential osteoporosis treatment. AU - Zahn, G.* AU - Baukmann, H.A.* AU - Wu, J.* AU - Jordan, J.* AU - Birkenfeld, A.L. AU - Dirckx, N.* AU - Schmidt, M.F.* C1 - 69044 C2 - 53826 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Targeting longevity gene SLC13A5: A novel approach to prevent age-related bone fragility and osteoporosis. JO - Metabolites VL - 13 IS - 12 PB - Mdpi PY - 2023 SN - 2218-1989 ER - TY - JOUR AB - The gut microbiome is of tremendous relevance to human health and disease, so it is a hot topic of omics-driven biomedical research. However, a valid identification of gut microbiota-associated molecules in human blood or urine is difficult to achieve. We hypothesize that bowel evacuation is an easy-to-use approach to reveal such metabolites. A non-targeted and modifying group-assisted metabolomics approach (covering 40 types of modifications) was applied to investigate urine samples collected in two independent experiments at various time points before and after laxative use. Fasting over the same time period served as the control condition. As a result, depletion of the fecal microbiome significantly affected the levels of 331 metabolite ions in urine, including 100 modified metabolites. Dominating modifications were glucuronidations, carboxylations, sulfations, adenine conjugations, butyrylations, malonylations, and acetylations. A total of 32 compounds, including common, but also unexpected fecal microbiota-associated metabolites, were annotated. The applied strategy has potential to generate a microbiome-associated metabolite map (M3) of urine from healthy humans, and presumably also other body fluids. Comparative analyses of M3 vs. disease-related metabolite profiles, or therapy-dependent changes may open promising perspectives for human gut microbiome research and diagnostics beyond analyzing feces. AU - Zheng, S.* AU - Zhou, L.* AU - Hoene, M.* AU - Peter, A. AU - Birkenfeld, A.L. AU - Weigert, C. AU - Liu, X.* AU - Zhao, X.* AU - Xu, G.* AU - Lehmann, R. C1 - 68693 C2 - 54902 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - A new biomarker profiling strategy for gut microbiome research: Valid association of metabolites to metabolism of microbiota detected by non-targeted metabolomics in human urine. JO - Metabolites VL - 13 IS - 10 PB - Mdpi PY - 2023 SN - 2218-1989 ER - TY - JOUR AB - Coronary artery disease (CAD) is a complex, multifactorial disease caused, in particular, by inflammation and cholesterol metabolism. At the molecular level, the role of tissue-specific signaling pathways leading to CAD is still largely unexplored. This study relied on two main resources: (1) genes with impact on atherosclerosis/CAD, and (2) liver-specific transcriptome analyses from human and mouse studies. The transcription factor activating transcription factor 3 (ATF3) was identified as a key regulator of a liver network relevant to atherosclerosis and linked to inflammation and cholesterol metabolism. ATF3 was predicted to be a direct and indirect (via MAF BZIP Transcription Factor F (MAFF)) regulator of low-density lipoprotein receptor (LDLR). Chromatin immunoprecipitation DNA sequencing (ChIP-seq) data from human liver cells revealed an ATF3 binding motif in the promoter regions of MAFF and LDLR. siRNA knockdown of ATF3 in human Hep3B liver cells significantly upregulated LDLR expression (p < 0.01). Inflammation induced by lipopolysaccharide (LPS) stimulation resulted in significant upregulation of ATF3 (p < 0.01) and subsequent downregulation of LDLR (p < 0.001). Liver-specific expression data from human CAD patients undergoing coronary artery bypass grafting (CABG) surgery (STARNET) and mouse models (HMDP) confirmed the regulatory role of ATF3 in the homeostasis of cholesterol metabolism. This study suggests that ATF3 might be a promising treatment candidate for lowering LDL cholesterol and reducing cardiovascular risk. AU - Bauer, S.* AU - Eigenmann, J.* AU - Zhao, Y.* AU - Fleig, J.* AU - Hawe, J.S.* AU - Pan, C.* AU - Bongiovanni, D.* AU - Wengert, S. AU - Ma, A.E.* AU - Lusis, A.J.* AU - Kovacic, J.C.* AU - Bjoerkegren, J.L.M.* AU - Maegdefessel, L.* AU - Schunkert, H.* AU - von Scheidt, M.* C1 - 66274 C2 - 52959 TI - Identification of the transcription factor ATF3 as a direct and indirect regulator of the LDLR. JO - Metabolites VL - 12 IS - 9 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Despite considerable morbidity and mortality, numerous cases of endocrine hypertension (EHT) forms, including primary aldosteronism (PA), pheochromocytoma and functional paraganglioma (PPGL), and Cushing's syndrome (CS), remain undetected. We aimed to establish signatures for the different forms of EHT, investigate potentially confounding effects and establish unbiased disease biomarkers. Plasma samples were obtained from 13 biobanks across seven countries and analyzed using untargeted NMR metabolomics. We compared unstratified samples of 106 PHT patients to 231 EHT patients, including 104 PA, 94 PPGL and 33 CS patients. Spectra were subjected to a multivariate statistical comparison of PHT to EHT forms and the associated signatures were obtained. Three approaches were applied to investigate and correct confounding effects. Though we found signatures that could separate PHT from EHT forms, there were also key similarities with the signatures of sample center of origin and sample age. The study design restricted the applicability of the corrections employed. With the samples that were available, no biomarkers for PHT vs. EHT could be identified. The complexity of the confounding effects, evidenced by their robustness to correction approaches, highlighted the need for a consensus on how to deal with variabilities probably attributed to preanalytical factors in retrospective, multicenter metabolomics studies. AU - Bliziotis, N.G.* AU - Kluijtmans, L.A.J.* AU - Tinnevelt, G.H.* AU - Reel, P.* AU - Reel, S.* AU - Langton, K.* AU - Robledo, M.* AU - Pamporaki, C.* AU - Pecori, A.* AU - Van Kralingen, J.* AU - Tetti, M.* AU - Engelke, U.F.H.* AU - Erlic, Z.* AU - Engel, J.* AU - Deutschbein, T.* AU - Nölting, S.* AU - Prejbisz, A.* AU - Richter, S.* AU - Adamski, J. AU - Januszewicz, A.* AU - Ceccato, F.* AU - Scaroni, C.* AU - Dennedy, M.C.* AU - Williams, T.A.* AU - Lenzini, L.* AU - Gimenez-Roqueplo, A.P.* AU - Davies, E.* AU - Fassnacht, M.* AU - Remde, H.* AU - Eisenhofer, G.* AU - Beuschlein, F.* AU - Kroiss, M.* AU - Jefferson, E.* AU - Zennaro, M.C.* AU - Wevers, R.A.* AU - Jansen, J.J.* AU - Deinum, J.* AU - Timmers, H.J.L.M.* C1 - 66037 C2 - 52538 TI - Preanalytical pitfalls in untargeted plasma nuclear magnetic resonance metabolomics of endocrine hypertension. JO - Metabolites VL - 12 IS - 8 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Bile acids, neutral sterols, and the gut microbiome are intricately intertwined and each affects human health and metabolism. However, much is still unknown about this relationship. This analysis included 1280 participants of the KORA FF4 study. Fecal metabolites (primary and secondary bile acids, plant and animal sterols) were analyzed using a metabolomics approach. Dirichlet regression models were used to evaluate associations between the metabolites and twenty microbial subgroups that were previously identified using latent Dirichlet allocation. Significant associations were identified between 12 of 17 primary and secondary bile acids and several of the microbial subgroups. Three subgroups showed largely positive significant associations with bile acids, and six subgroups showed mostly inverse associations with fecal bile acids. We identified a trend where microbial subgroups that were previously associated with “healthy” factors were here inversely associated with fecal bile acid levels. Conversely, subgroups that were previously associated with “unhealthy” factors were positively associated with fecal bile acid levels. These results indicate that further research is necessary regarding bile acids and microbiota composition, particularly in relation to metabolic health. AU - Breuninger, T.A.* AU - Wawro, N. AU - Freuer, D.* AU - Reitmeier, S.* AU - Artati, A. AU - Grallert, H. AU - Adamski, J. AU - Meisinger, C.* AU - Peters, A. AU - Haller, D.* AU - Linseisen, J.* C1 - 66295 C2 - 52786 TI - Fecal bile acids and neutral sterols are associated with latent microbial subgroups in the human gut. JO - Metabolites VL - 12 IS - 9 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Chronic respiratory diseases such as asthma are highly prevalent in industrialized countries. As cases are expected to rise, there is a growing demand for alternative therapies. Our recent research on the potential benefits of probiotics suggests that they could prevent and reduce the symptoms of many diseases by modulating the host immune system with secreted metabolites. This article presents the first steps of the research that led us to identify the immunoregulatory bioactivity of the amino acid D-Trp reported in our previous study. Here we analyzed the cell culture metabolic footprinting of 25 commercially available probiotic strains to associate metabolic pathway activity information with their respective immune modulatory activity observed in vitro. Crude probiotic supernatant samples were processed in three different ways prior to untargeted analysis in positive and negative ionization mode by direct infusion ESI-FT-ICR-MS: protein precipitation and solid phase extraction (SPE) using HLB and CN-E sorbent cartridges. The data obtained were submitted to multivariate statistical analyses to distinguish supernatant samples into the bioactive and non-bioactive group. Pathway analysis using discriminant molecular features showed an overrepresentation of the tryptophan metabolic pathway for the bioactive supernatant class, suggesting that molecules taking part in that pathway may be involved in the immunomodulatory activity observed in vitro. This work showcases the potential of metabolomics to drive product development and novel bioactive compound discovery out of complex biological samples in a top-down manner. AU - Fonseca, J.R. AU - Lucio, M. AU - Harir, M. AU - Schmitt-Kopplin, P. C1 - 64096 C2 - 52078 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Mining for active molecules in probiotic supernatant by combining non-targeted metabolomics and immunoregulation testing. JO - Metabolites VL - 12 IS - 1 PB - Mdpi PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Resistance training promotes metabolic health and stimulates muscle hypertrophy, but the precise routes by which resistance exercise (RE) conveys these health benefits are largely unknown. Aim: To investigate how acute RE affects human skeletal muscle metabolism. Methods: We collected vastus lateralis biopsies from six healthy male untrained volunteers at rest, before the first of 13 RE training sessions, and 45 min after the first and last bouts of RE. Biopsies were analysed using untargeted mass spectrometry-based metabolomics. Results: We measured 617 metabolites covering a broad range of metabolic pathways. In the untrained state RE altered 33 metabolites, including increased 3-methylhistidine and N-lactoylvaline, suggesting increased protein breakdown, as well as metabolites linked to ATP (xanthosine) and NAD (N1-methyl-2-pyridone-5-carboxamide) metabolism; the bile acid chenodeoxycholate also increased in response to RE in muscle opposing previous findings in blood. Resistance training led to muscle hypertrophy, with slow type I and fast/intermediate type II muscle fibre diameter increasing by 10.7% and 10.4%, respectively. Comparison of post-exercise metabolite levels between trained and untrained state revealed alterations of 46 metabolites, including decreased N-acetylated ketogenic amino acids and increased beta-citrylglutamate which might support growth. Only five of the metabolites that changed after acute exercise in the untrained state were altered after chronic training, indicating that training induces multiple metabolic changes not directly related to the acute exercise response. Conclusion: The human skeletal muscle metabolome is sensitive towards acute RE in the trained and untrained states and reflects a broad range of adaptive processes in response to repeated stimulation. AU - Gehlert, S.* AU - Weinisch, P. AU - Römisch-Margl, W. AU - Jaspers, R.T.* AU - Artati, A. AU - Adamski, J. AU - Dyar, K.A. AU - Aussieker, T.* AU - Jacko, D.* AU - Bloch, W.* AU - Wackerhage, H.* AU - Kastenmüller, G. C1 - 65367 C2 - 52154 TI - Effects of acute and chronic resistance exercise on the skeletal muscle metabolome. JO - Metabolites VL - 12 IS - 5 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Metabolite identification in non-targeted NMR-based metabolomics remains a challenge. While many peaks of frequently occurring metabolites are assigned, there is a high number of unknowns in high-resolution NMR spectra, hampering biological conclusions for biomarker analysis. Here, we use a cluster analysis approach to guide peak assignment via statistical correlations, which gives important information on possible structural and/or biological correlations from the NMR spectrum. Unknown peaks that cluster in close proximity to known peaks form hypotheses for their metabolite identities, thus, facilitating metabolite annotation. Subsequently, metabolite identification based on a database search, 2D NMR analysis and standard spiking is performed, whereas without a hypothesis, a full structural elucidation approach would be required. The approach allows a higher identification yield in NMR spectra, especially once pathway-related subclusters are identified. AU - Heinzmann, S.S. AU - Waldenberger, M. AU - Peters, A. AU - Schmitt-Kopplin, P. C1 - 66549 C2 - 52935 TI - Cluster analysis statistical spectroscopy for the identification of metabolites in 1H NMR metabolomics. JO - Metabolites VL - 12 IS - 10 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Physical exercise is a powerful measure to prevent cardiometabolic diseases. However, the individual response to lifestyle interventions is variable and cannot, to date, be predicted. N-Lactoylphenylalanine (Lac-Phe) produced during exercise has recently been shown to mediate weight loss in obese mice. Lac-Phe could also contribute to, and potentially explain differences in, the effectiveness of exercise interventions in humans. Sedentary overweight and obese subjects completed an 8-week supervised endurance exercise intervention (n = 22). Before and after the intervention, plasma levels of Lac-Phe were determined by UHPLC-MS in the resting state and immediately after an acute bout of endurance exercise. Adipose tissue volume was quantified using MRI. Acute exercise caused a pronounced increase in Lac-Phe, both before and after the intervention. Higher levels of Lac-Phe after acute exercise were associated with a greater reduction in abdominal subcutaneous and, to a lower degree, visceral adipose tissue during the intervention. Lac-Phe produced during physical activity could contribute to weight loss by acting as a signaling molecule that regulates food intake, as previously shown in mice. Quantification of Lac-Phe during an exercise test could be employed as a tool to predict and potentially improve the individual response to exercise-based lifestyle interventions in overweight humans and those with obesity. AU - Hoene, M.* AU - Zhao, X.* AU - Machann, J. AU - Birkenfeld, A.L. AU - Heni, M. AU - Peter, A. AU - Niess, A.* AU - Moller, A. AU - Lehmann, R. AU - Xu, G.* AU - Weigert, C. C1 - 67263 C2 - 53540 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Exercise-induced N-lactoylphenylalanine predicts adipose tissue loss during endurance training in overweight and obese humans. JO - Metabolites VL - 13 IS - 1 PB - Mdpi PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - In recent years, a lack of stability of dairy products with extended shelf life (e.g., yoghurt products, UHT desserts) has occurred, with the corresponding products liquefying significantly after days or weeks. This project aimed to identify the enzymes responsible for the liquefaction of the affected products based on differential proteomic analyses. No evidence was found for the presence of starch-degrading bacteria in the affected products. With zymography and proteome analysis, we detected the cause of liquefaction in a pudding by contamination of its aroma component with an engineered amylolytic enzyme, cyclomaltodextrin glucanotransferase (CGTase) from Thermoanaerobacterium thermosulfurigenes. In addition, we detected contamination with Pseudomonas-derived proteolytic ATP-dependent Clp protease in one pudding batch and proteases in technically used amylases, which degraded β-caseins in another batch. Identification of these agents with liquefying properties in dairy products are useful for adjustment of production protocols and/or composition of additives, and thus shelf life extension. AU - Kleinwort, K.J.H.* AU - Weigand, M.* AU - Hoffmann, L.* AU - Degroote, R.L.* AU - Dietrich, R.* AU - Maertlbauer, E.P.* AU - Hauck, S.M. AU - Deeg, C.A.* C1 - 64710 C2 - 52065 TI - Pudding proteomics: Cyclomaltodextrin glucanotransferase and microbial proteases can liquefy extended shelf life dairy products. JO - Metabolites VL - 12 IS - 3 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Angiotensin-converting enzyme 2 (ACE2) has been identified as the cellular entry receptor for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). High ACE2 tissue expression and low glycine levels were suggested to increase susceptibility for SARS-CoV-2 infection and increasing circulating ACE2 has been proposed as one possible strategy to combat COVID-19. In humans, aerobic physical exercise induces an increase in plasma ACE2 in some individuals. However, it is not clear whether glycine and ACE2 levels depend on intrinsic exercise capacity or on exercise training. We used rats selectively bred for high intrinsic exercise capacity (HCR) or low exercise capacity (LCR) and tested the influence of this genetic predetermination and/or aerobic exercise on metabolites, ACE2 tissue expression and circulating ACE 2. ACE2 expression was measured in different tissues in the sedentary animals and again after 4 weeks of high-intensity aerobic exercise in both LCRs and HCRs. Sedentary HCRs exhibited significantly higher circulating ACE2 concentrations compared to LCRs, but a lower expression of ACE2 in all investigated tissues except for adipose tissue. Body weight was negatively correlated with serum ACE2 and positively correlated with ACE2 expression in the heart. Aerobic exercise caused a significant decrease in ACE2 expression in the lung, heart, muscle, and kidney both in LCRs and HCRs. Our results suggest that ACE2 expression, circulating ACE2 and glycine serum concentration are related to aerobic intrinsic exercise capacity and can be influenced with exercise. These results may support the hypothesis that physically fit individuals have a lower susceptibility for COVID-19 infection. AU - Klöting, N. AU - Schwarzer, M.* AU - Heyne, E.* AU - Ceglarek, U.* AU - Hoffmann, A. AU - Krohn, K.* AU - Doenst, T.* AU - Blüher, M. C1 - 65538 C2 - 52724 TI - Intrinsic exercise capacity affects glycine and angiotensin-converting enzyme 2 (ACE2) levels in sedentary and exercise trained rats. JO - Metabolites VL - 12 IS - 6 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Bovine paratuberculosis is a serious chronic disease of the gastrointestinal tract that causes economic losses and dramatically affects animal health in livestock. The underlying infectious agent, Mycobacterium avium subspecies paratuberculosis (MAP), cannot reliably be detected by standard diagnostic tests due to the long asymptomatic disease stage. The aim of this study was to detect proteomic changes in peripheral blood mononuclear cells (PBMC) from cows of the same herd with different MAP infection status after co-incubation with viable MAP in vitro using label-free LC-MS/MS. In our proteomic discovery experiment, we detected 2631 differentially regulated proteins between cows with negative MAP infection status (so-called MAP-resistant cows) and cows with positive MAP infection status (so-called persistently MAP-infected cows). In MAP-resistant cows, we detected enriched immune-related signaling pathways for TLR2 and MHC class II component proteins, among others, indicating a successful defensive immune response of the cows to MAP. In contrast, persistently MAP-infected cows were not directly enriched in immune-related signaling pathways associated with ITGA2B and KCNMA1, among others. The introduction of these distinct immune responses contributes to a better understanding of the bovine immune response and mechanisms of susceptibility to MAP. AU - Korbonits, L.* AU - Kleinwort, K.J.H.* AU - Amann, B.* AU - Didier, A.* AU - Märtlbauer, E.* AU - Hauck, S.M. AU - Deeg, C.A.* C1 - 66561 C2 - 52958 TI - Mycobacterium avium subsp. paratuberculosis infected cows reveal divergent immune response in bovine peripheral blood derived lymphocyte proteome. JO - Metabolites VL - 12 IS - 10 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - The angiotensin-converting enzyme 2 (ACE2) receptor has been identified as the entry receptor for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is abundantly expressed in many organs. With respect to the role of circulating ACE2 and its receptor expression in the pathogenesis of the SARS-CoV-2 infection, it is still debated whether diseases such as hypertension or pharmacotherapies, including ACE inhibitors and angiotensin receptor blockers that affect ACE2 receptor expression, may modulate the severity and outcome of the coronavirus disease 2019 (COVID-19). We therefore tested the hypothesis that treatment with the ACE inhibitor Ramipril affects organ-specific ACE2 receptor mRNA and protein expression as well as the serum metabolome in BioBreeding (BB) rats. Twelve male BioBreeding rats were randomly divided into a Ramipril (10 mg/kg body weight) treatment group or a control group (N = 12; n = 6 per group) over a period of seven days. Ramipril treatment resulted in the reduction of acylcarnitines (C3–C6) out of 64 metabolites. Among the different organs studied, only in the lungs did Ramipril treatment significantly increase both Ace2 mRNA and ACE2 receptor membrane protein levels. Increased ACE2 receptor lung expression after Ramipril treatment was not associated with differences in ACE2 serum concentrations between experimental groups. Our data provide experimental in vivo evidence that the ACE inhibitor Ramipril selectively increases pulmonary ACE2 receptor mRNA and protein levels and reduces acylcarnitines. AU - Kosacka, J.* AU - Berger, C.* AU - Ceglarek, U.* AU - Hoffmann, A. AU - Blüher, M. AU - Klöting, N. C1 - 64830 C2 - 52478 TI - Ramipril reduces acylcarnitines and distinctly increases angiotensinconverting enzyme 2 expression in lungs of rats. JO - Metabolites VL - 12 IS - 4 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Naturally occurring substances are valuable resources for drug development. In this respect, chalcones are known to be antiproliferative agents against prostate cancer cell lines through various mechanisms or targets. Based on the literature and preliminary results, we aimed to study and optimise the efficiency of a series of chalcones to inhibit androgen-converting AKR1C3, known to promote prostate cancer. A total of 12 chalcones with different substitution patterns were synthesised. Structure–activity relationships associated with these modifications on AKR1C3 inhibition were analysed by performing enzymatic assays and docking simulations. In addition, the selectivity and cytotoxicity of the compounds were assessed. In enzymatic assays, C-6′ hydroxylated derivatives were more active than C-6′ methoxylated derivatives. In contrast, C-4 methylation increased activity over C-4 hydroxylation. Docking results supported these findings with the most active compounds fitting nicely in the binding site and exhibiting strong interactions with key amino acid residues. The most effective inhibitors were not cytotoxic for HEK293T cells and selective for 17β-hydroxysteroid dehydrogenases not primarily involved in steroid hormone metabolism. Nevertheless, they inhibited several enzymes of the steroid metabolism pathways. Favourable substitutions that enhanced AKR1C3 inhibition of chalcones were identified. This study paves the way to further develop compounds from this series or related flavonoids with improved inhibitory activity against AKR1C3. AU - Möller, G. AU - Temml, V.* AU - Cala Peralta, A.* AU - Gruet, O.* AU - Richomme, P.* AU - Séraphin, D.* AU - Viault, G.* AU - Kraus, L.* AU - Huber-Cantonati, P.* AU - Schopfhauser, E.* AU - Pachmayr, J.* AU - Tokarz, J. AU - Schuster, D.* AU - Helesbeux, J.J.* AU - Dyar, K.A. C1 - 64304 C2 - 52174 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Analogues of natural chalcones as efficient inhibitors of AKR1C3. JO - Metabolites VL - 12 IS - 2 PB - Mdpi PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - White wine's oxidative stability after several years of bottle aging is synonymous to its organoleptic quality. In order to gain control over the cascade of chemical reactions that are implicated in that phenomenon, fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS)-based metabolomics and sensory evaluation were combined for the analysis of a vertical series of white wines from different vineyard plots. Data mining using supervised cluster analysis allowed the extraction of known and unknown sulfur- and nitrogen-containing molecular features, with oxidative stability molecular markers presenting an increased number of S and O atoms in their formulas. In their majority, S-containing molecular features possessed between 4 to ~12 O atoms, indicating the relatively higher importance of sulfonation reactions as opposed to dimerization reactions. Molecular networking, based on sulfonation reaction transformations, evidences the importance of hitherto unknown and/or minor sulfur dioxide binders (peptides, aldehydes, and polyphenols) on wine's oxidative stability. AU - Nikolantonaki, M.* AU - Romanet, R.* AU - Lucio, M. AU - Schmitt-Kopplin, P. AU - Gougeon, R.* C1 - 64886 C2 - 52581 TI - Sulfonation reactions behind the Fate of white wine's shelf-life. JO - Metabolites VL - 12 IS - 4 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resulting in non-standardized datasets demanding customized annotation workflows. We present an ecosystem of R packages, centered around the MetaboCoreUtils, MetaboAnnotation and CompoundDb packages that together provide a modular infrastructure for the annotation of untargeted metabolomics data. Initial annotation can be performed based on MS1 properties such as m/z and retention times, followed by an MS2-based annotation in which experimental fragment spectra are compared against a reference library. Such reference databases can be created and managed with the CompoundDb package. The ecosystem supports data from a variety of formats, including, but not limited to, MSP, MGF, mzML, mzXML, netCDF as well as MassBank text files and SQL databases. Through its highly customizable functionality, the presented infrastructure allows to build reproducible annotation workflows tailored for and adapted to most untargeted LC-MS-based datasets. All core functionality, which supports base R data types, is exported, also facilitating its re-use in other R packages. Finally, all packages are thoroughly unit-tested and documented and are available on GitHub and through Bioconductor. AU - Rainer, J.* AU - Vicini, A.* AU - Salzer, L. AU - Stanstrup, J.* AU - Badia, J.M.* AU - Neumann, S.* AU - Stravs, M.A.* AU - Hernandes, V.V.* AU - Gatto, L.* AU - Gibb, S.* AU - Witting, M. C1 - 64384 C2 - 52214 TI - A modular and expandable ecosystem for metabolomics data annotation in R. JO - Metabolites VL - 12 IS - 2 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Hypertension is a major global health problem with high prevalence and complex associated health risks. Primary hypertension (PHT) is most common and the reasons behind primary hypertension are largely unknown. Endocrine hypertension (EHT) is another complex form of hypertension with an estimated prevalence varying from 3 to 20% depending on the population studied. It occurs due to underlying conditions associated with hormonal excess mainly related to adrenal tumours and sub-categorised: primary aldosteronism (PA), Cushing's syndrome (CS), pheochromocytoma or functional paraganglioma (PPGL). Endocrine hypertension is often misdiagnosed as primary hypertension, causing delays in treatment for the underlying condition, reduced quality of life, and costly antihypertensive treatment that is often ineffective. This study systematically used targeted metabolomics and high-throughput machine learning methods to predict the key biomarkers in classifying and distinguishing the various subtypes of endocrine and primary hypertension. The trained models successfully classified CS from PHT and EHT from PHT with 92% specificity on the test set. The most prominent targeted metabolites and metabolite ratios for hypertension identification for different disease comparisons were C18:1, C18:2, and Orn/Arg. Sex was identified as an important feature in CS vs. PHT classification. AU - Reel, S.* AU - Reel, P.S.* AU - Erlic, Z.* AU - Amar, L.* AU - Pecori, A.* AU - Larsen, C.K.* AU - Tetti, M.* AU - Pamporaki, C.* AU - Prehn, C. AU - Adamski, J. AU - Prejbisz, A.* AU - Ceccato, F.* AU - Scaroni, C.* AU - Kroiss, M.* AU - Dennedy, M.C.* AU - Deinum, J.* AU - Eisenhofer, G.* AU - Langton, K.* AU - Mulatero, P.* AU - Reincke, M.* AU - Rossi, G.P.* AU - Lenzini, L.* AU - Davies, E.* AU - Gimenez-Roqueplo, A.P.* AU - Assié, G.* AU - Blanchard, A.* AU - Zennaro, M.C.* AU - Beuschlein, F.* AU - Jefferson, E.R.* C1 - 65984 C2 - 52546 TI - Predicting hypertension subtypes with machine learning using targeted metabolites and their ratios. JO - Metabolites VL - 12 IS - 8 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Plants are continuously interacting with other organisms to optimize their performance in a changing environment. Mycorrhization is known to affect the plant growth and nutrient status, but it also can lead to adjusted plant defense and alter interactions with other trophic levels. Here, we studied the effect of Laccaria bicolor-mycorrhization on the poplar (Populus x canescens) metabolome and volatilome on trees with and without a poplar leaf beetle (Chrysomela populi) infestation. We analyzed the leaf and root metabolomes employing liquid chromatography–mass spectrometry, and the leaf volatilome employing headspace sorptive extraction combined with gas-chromatography– mass spectrometry. Mycorrhization caused distinct metabolic adjustments in roots, young/infested leaves and old/not directly infested leaves. Mycorrhization adjusted the lipid composition, the abundance of peptides and, especially upon herbivory, the level of various phenolic compounds. The greatest change in leaf volatile organic compound (VOC) emissions occurred four to eight days following the beetle infestation. Together, these results prove that mycorrhization affects the whole plant metabolome and may influence poplar aboveground interactions. The herbivores and the mycorrhizal fungi interact with each other indirectly through a common host plant, a result that emphasizes the importance of community approach in chemical ecology. AU - Sivaprakasam Padmanaban, P.B. AU - Rosenkranz, M. AU - Zhu, P. AU - Kaling, M. AU - Schmidt, A.* AU - Schmitt-Kopplin, P. AU - Polle, A.* AU - Schnitzler, J.-P. C1 - 64303 C2 - 52173 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Mycorrhiza-Tree-Herbivore Interactions: Alterations in poplar metabolome and volatilome. JO - Metabolites VL - 12 IS - 2 PB - Mdpi PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Genome-wide association studies (GWAS) with non-targeted metabolomics have identified many genetic loci of biomedical interest. However, metabolites with a high degree of missingness, such as drug metabolites and xenobiotics, are often excluded from such studies due to a lack of statistical power and higher uncertainty in their quantification. Here we propose ratios between related drug metabolites as GWAS phenotypes that can drastically increase power to detect genetic associations between pairs of biochemically related molecules. As a proof-of-concept we conducted a GWAS with 520 individuals from the Qatar Biobank for who at least five of the nine available acetaminophen metabolites have been detected. We identified compelling evidence for genetic variance in acetaminophen glucuronidation and methylation by UGT2A15 and COMT, respectively. Based on the metabolite ratio association profiles of these two loci we hypothesized the chemical structure of one of their products or substrates as being 3-methoxyacetaminophen, which we then confirmed experimentally. Taken together, our study suggests a novel approach to analyze metabolites with a high degree of missingness in a GWAS setting with ratios, and it also demonstrates how pharmacological pathways can be mapped out using non-targeted metabolomics measurements in large population-based studies. AU - Thareja, G.* AU - Evans, A.M.* AU - Wood, S.D.* AU - Stephan, N.* AU - Zaghlool, S.* AU - Halama, A.* AU - Kastenmüller, G. AU - Belkadi, A.* AU - Albagha, O.M.E.* AU - Suhre, K.* C1 - 65539 C2 - 52725 TI - Ratios of acetaminophen metabolites identify new loci of pharmacogenetic relevance in a genome-wide association study. JO - Metabolites VL - 12 IS - 6 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Kombucha is a traditional fermented beverage obtained from the transformation of sugared black tea by a community of yeasts and bacteria. Kombucha production recently became industrialized, but its quality standards remain poorly defined. Metabolomic analyses were applied using FT-ICR-MS to characterize the impacts of production phases and the type of tea on the non-volatile chemical composition of kombucha. Independently from tea type, the first phase of acidification in open vessel was characterized by the release of gluconate and gallate from acetic acid bacteria metabolism and probably from polymeric polyphenols, respectively. The second phase of carbonation in closed vessel induced a consumption or transformation of oleic acid that could be consecutive of oxygen limitation. The first phase had the most impact on molecular diversity, but tea type mainly influenced the global composition in polyphenol profile. Black tea polyphenols were more impacted by microbial activity compared to green tea polyphenols. AU - Tran, T.* AU - Romanet, R.* AU - Roullier-Gall, C.* AU - Verdier, F.* AU - Martin, A.* AU - Schmitt-Kopplin, P. AU - Alexandre, H.* AU - Grandvalet, C.* AU - Tourdot-Maréchal, R.* C1 - 64385 C2 - 52215 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Non-targeted metabolomic analysis of the kombucha production process. JO - Metabolites VL - 12 IS - 2 PB - Mdpi PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Kombucha is a fermented beverage obtained through the activity of a complex microbial community of yeasts and bacteria. Exo‐metabolomes of kombucha microorganisms were analyzed using FT‐ICR‐MS to investigate their interactions. A simplified set of microorganisms including two yeasts (Brettanomyces bruxellensis and Hanseniaspora valbyensis) and one acetic acid bacterium (Acetobacter indonesiensis) was used to investigate yeast–yeast and yeast–acetic acid bacterium interactions. A yeast–yeast interaction was characterized by the release and consumption of fatty acids and peptides, possibly in relationship to commensalism. A yeast–acetic acid bacterium interaction was different depending on yeast species. With B. bruxellensis, fatty acids and peptides were mainly produced along with consumption of sucrose, fatty acids and polysaccharides. In opposition, the presence of H. valbyensis induced mainly the decrease of polyphenols, peptides, fatty acids, phenolic acids and putative isopropyl malate and phenylpyruvate and few formulae have been produced. With all three microorganisms, the formulae involved with the yeast–yeast interactions were consumed or not produced in the presence of A. indonesiensis. The impact of the yeasts’ presence on A. indonesiensis was consistent regardless of the yeast species with a commensal consumption of compounds associated to the acetic acid bacterium by yeasts. In detail, hydroxystearate from yeasts and dehydroquinate from A. indonesiensis were potentially consumed in all cases of yeast(s)–acetic acid bacterium pairing, highlighting mutualistic behavior. AU - Tran, T.* AU - Roullier‐gall, C.* AU - Verdier, F.* AU - Martin, A.* AU - Schmitt-Kopplin, P. AU - Alexandre, H.* AU - Grandvalet, C.* AU - Tourdot‐maréchal, R.* C1 - 64673 C2 - 52400 TI - Microbial interactions in Kombucha through the lens of metabolomics. JO - Metabolites VL - 12 IS - 3 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Glycation products produced by the non-enzymatic reaction between reducing carbohydrates and amino compounds have received increasing attention in both food- and health-related research. Although liquid chromatography mass spectrometry (LC-MS) methods for analyzing glycation products already exist, only a few common advanced glycation end products (AGEs) are usually covered by quantitative methods. Untargeted methods for comprehensively analyzing glycation products are still lacking. The aim of this study was to establish a method for simultaneously characterizing a wide range of free glycation products using the untargeted metabolomics approach. In this study, Maillard model systems consisting of a multitude of heterogeneous free glycation products were chosen for systematic method optimization, rather than using a limited number of standard compounds. Three types of hydrophilic interaction liquid chromatography (HILIC) columns (zwitterionic, bare silica, and amide) were tested due to their good retention for polar compounds. The zwitterionic columns showed better performance than the other two types of columns in terms of the detected feature numbers and detected free glycation products. Two zwitterionic columns were selected for further mobile phase optimization. For both columns, the neutral mobile phase provided better peak separation, whereas the acidic condition provided a higher quality of chromatographic peak shapes. The ZIC-cHILIC column operating under acidic conditions offered the best potential to discover glycation products in terms of providing good peak shapes and maintaining comparable compound coverage. Finally, the optimized HILIC-MS method can detect 70% of free glycation product features despite interference from the complex endogenous metabolites from biological matrices, which showed great application potential for glycation research and can help discover new biologically important glycation products. AU - Yan, Y. AU - Hemmler, D. AU - Schmitt-Kopplin, P. C1 - 67097 C2 - 53468 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - HILIC-MS for untargeted profiling of the free glycation product diversity. JO - Metabolites VL - 12 IS - 12 PB - Mdpi PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Mammalian INDY (mINDY, NaCT, gene symbol SLC13A5) is a potential target for the treatment of metabolically associated fatty liver disease (MAFLD). This study evaluated the effects of a selective, cross-species active, non-competitive, non-substrate-like inhibitor of NaCT. First, the small molecule inhibitor ETG-5773 was evaluated for citrate and succinate uptake and fatty acid synthesis in cell lines expressing both human NaCT and mouse Nact. Once its suitability was established, the inhibitor was evaluated in a diet-induced obesity (DIO) mouse model. DIO mice treated with 15 mg/kg compound ETG-5773 twice daily for 28 days had reduced body weight, fasting blood glucose, and insulin, and improved glucose tolerance. Liver triglycerides were significantly reduced, and body composition was improved by reducing fat mass, supported by a significant reduction in the expression of genes for lipogenesis such as SREBF1 and SCD1. Most of these effects were also evident after a seven-day treatment with the same dose. Further mechanistic investigation in the seven-day study showed increased plasma β-hydroxybutyrate and activated hepatic adenosine monophosphate-activated protein kinase (AMPK), reflecting findings from Indy (-/-) knockout mice. These results suggest that the inhibitor ETG-5773 blocked citrate uptake mediated by mouse and human NaCT to reduce liver steatosis and body fat and improve glucose regulation, proving the concept of NaCT inhibition as a future liver treatment for MAFLD. AU - Zahn, G.* AU - Willmes, D.M.* AU - El-Agroudy, N.N. AU - Yarnold, C.* AU - Jarjes-Pike, R.* AU - Schaertl, S.* AU - Schreiter, K.* AU - Gehrmann, W.* AU - Wong, A.K.C.* AU - Zordan, T.* AU - König, J.* AU - Jordan, J.* AU - Birkenfeld, A.L. C1 - 65985 C2 - 53027 TI - A novel and cross-species active mammalian INDY (NaCT) inhibitor ameliorates hepatic steatosis in mice with diet-induced obesity. JO - Metabolites VL - 12 IS - 8 PY - 2022 SN - 2218-1989 ER - TY - JOUR AB - Our skin influences our physical and mental health, and its chemical composition can reflect environmental and disease conditions. Therefore, through sampling the skin metabolome, we can provide a promising window into the mechanisms of the body. However, the broad application of skin metabolomics has recently been hampered by a lack of easy and widely applicable sampling methods. Here, we present a novel rapid, simple, and, most importantly, painless and non-invasive sampling technique suitable for clinical studies of fragile or weakened skin. The method is called WET PREP and is simply a lavage of the skin which focuses on capturing the metabolome. We systematically evaluate WET PREPs in comparison with the non-invasive method of choice in skin metabolomics, swab collection, using ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS2) on two complementary chromatographic columns (C18 reversed phase and hydrophilic interaction chromatography). We also integrate targeted analyses of key metabolites of skin relevance. Overall, WET PREP provides a strikingly more stable shared metabolome across sampled individuals, while also being able to capture unique individual metabolites with a high consistency in intra-individual reproducibility. With the exception of (phospho-)lipidomic studies, we recommend WET PREPs as the preferred skin metabolome sampling technique due to the quick preparation time, low cost, and gentleness for the patient. AU - Afghani, J.* AU - Huelpuesch, C.* AU - Schmitt-Kopplin, P. AU - Traidl-Hoffmann, C.* AU - Reiger, M. AU - Müller, C. C1 - 62440 C2 - 50872 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Enhanced access to the health-related skin metabolome by fast, reproducible and non-invasive WET PREP sampling. JO - Metabolites VL - 11 IS - 7 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Normal brain function highly relies on the appropriate functioning of astrocytes. These glial cells are strategically situated between blood vessels and neurons, provide significant substrate support to neuronal demand, and are sensitive to neuronal activity and energy-related molecules. Astrocytes respond to many metabolic conditions and regulate a wide array of physiological processes, including cerebral vascular remodeling, glucose sensing, feeding, and circadian rhythms for the control of systemic metabolism and behavior-related responses. This regulation ultimately elicits counterregulatory mechanisms in order to couple whole-body energy availability with brain function. Therefore, understanding the role of astrocyte crosstalk with neighboring cells via the release of molecules, e.g., gliotransmitters, into the parenchyma in response to metabolic and neuronal cues is of fundamental relevance to elucidate the distinct roles of these glial cells in the neuroendocrine control of metabolism. Here, we review the mechanisms underlying astrocyte-released gliotransmitters that have been reported to be crucial for maintaining homeostatic regulation of systemic metabolism. AU - De Bernardis Murat, C. AU - García-Cáceres, C. C1 - 63346 C2 - 51270 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Astrocyte gliotransmission in the regulation of systemic metabolism. JO - Metabolites VL - 11 IS - 11 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Acute anorexia nervosa (AN) constitutes an extreme physiological state. We aimed to detect state related metabolic alterations during inpatient admission and upon short-and long-term weight regain. In addition, we tested the hypothesis that metabolite concentrations adapt to those of healthy controls (HC) after long-term weight regain. Thirty-five female adolescents with AN and 25 female HC were recruited. Based on a targeted approach 187 metabolite concentrations were detected at inpatient admission (T0 ), after short-term weight recovery (T1; half of target-weight) and close to target weight (T2 ). Pattern hunter and time course analysis were performed. The highest number of significant differences in metabolite concentrations (N = 32) were observed between HC and T1 . According to the detected main pattern, metabolite concentrations at T2 became more similar to those of HC. The course of single metabolite concentrations (e.g., glutamic acid) revealed different metabolic subtypes within the study sample. Patients with AN after short-term weight regain are in a greater “metabolic imbalance” than at starvation. After long-term weight regain, patients reach a metabolite profile similar to HC. Our results might be confounded by different metabolic subtypes of patients with AN. AU - Föcker, M.* AU - Cecil, A. AU - Prehn, C. AU - Adamski, J. AU - Albrecht, M.* AU - Adams, F.* AU - Hinney, A.* AU - Libuda, L.* AU - Bühlmeier, J.* AU - Hebebrand, J.* AU - Peters, T.* AU - Antel, J.* C1 - 60906 C2 - 49740 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Evaluation of metabolic profiles of patients with anorexia nervosa at inpatient admission, short-and long-term weight regain—descriptive and pattern analysis. JO - Metabolites VL - 11 IS - 1 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Nuclear magnetic resonance (NMR) spectroscopy is well-established to address questions in large-scale untargeted metabolomics. Although several approaches in data processing and analysis are available, significant issues remain. NMR spectroscopy of urine generates information-rich but complex spectra in which signals often overlap. Furthermore, slight changes in pH and salt concentrations cause peak shifting, which introduces, in combination with baseline irregularities, un-informative noise in statistical analysis. Within this work, a straight-forward data processing tool addresses these problems by applying a non-linear curve fitting model based on Voigt function line shape and integration of the underlying peak areas. This method allows a rapid untargeted analysis of urine metabolomics datasets without relying on time-consuming 2D-spectra based deconvolution or information from spectral libraries. The approach is validated with spiking experiments and tested on a human urine 1H dataset compared to conventionally used methods and aims to facilitate metabolomics data analysis. AU - Haslauer, K.E. AU - Schmitt-Kopplin, P. AU - Heinzmann, S.S. C1 - 61946 C2 - 50408 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Data processing optimization in untargeted metabolomics of urine using Voigt lineshape model non-linear regression analysis. JO - Metabolites VL - 11 IS - 5 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Biological exploration of early biomarkers for chronic kidney disease (CKD) in (pre)diabetic individuals is crucial for personalized management of diabetes. Here, we evaluated two candidate biomarkers of incident CKD (sphingomyelin (SM) C18:1 and phosphatidylcholine diacyl (PC aa) C38:0) concerning kidney function in hyperglycemic participants of the Cooperative Health Research in the Region of Augsburg (KORA) cohort, and in two biofluids and six organs of leptin receptor-deficient (db/db) mice and wild type controls. Higher serum concentrations of SM C18:1 and PC aa C38:0 in hyperglycemic individuals were found to be associated with lower estimated glomerular filtration rate (eGFR) and higher odds of CKD. In db/db mice, both metabolites had a significantly lower concentration in urine and adipose tissue, but higher in the lungs. Additionally, db/db mice had significantly higher SM C18:1 levels in plasma and liver, and PC aa C38:0 in adrenal glands. This cross-sectional human study confirms that SM C18:1 and PC aa C38:0 associate with kidney dysfunction in pre(diabetic) individuals, and the animal study suggests a potential implication of liver, lungs, adrenal glands, and visceral fat in their systemic regulation. Our results support further validation of the two phospholipids as early biomarkers of renal disease in patients with (pre)diabetes. AU - Huang, J. AU - Covic, M. AU - Huth, C. AU - Rommel, M. AU - Adam, J. AU - Zukunft, S. AU - Prehn, C. AU - Wang, L. AU - Nano, J. AU - Scheerer, M.F. AU - Neschen, S. AU - Kastenmüller, G. AU - Gieger, C. AU - Laxy, M. AU - Schliess, F.* AU - Adamski, J. AU - Suhre, K.* AU - Hrabě de Angelis, M. AU - Peters, A. AU - Wang-Sattler, R. C1 - 61344 C2 - 49825 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Validation of candidate phospholipid biomarkers of chronic kidney disease in hyperglycemic individuals and their organ-specific exploration in leptin receptor-deficient db/db mouse. JO - Metabolites VL - 11 IS - 2 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - The development of obesity and type 2 diabetes (T2D) has been associated with impaired mitochondrial function. In pancreatic beta (β) cells, mitochondrial energy metabolism plays a central role in triggering and controlling glucose-stimulated insulin secretion (GSIS). Here, we have explored whether mitochondrial bioenergetic parameters assessed with Seahorse extracellular flux technology can quantitatively predict insulin secretion. We metabolically stressed male C57BL/6 mice by high-fat feeding (HFD) and measured the glucose sensitivity of islet respiration and insulin secretion. The diet-induced obese (DIO) mice developed hyperinsulinemia, but no pathological secretory differences were apparent between isolated DIO and chow islets. Real-time extracellular flux analysis, however, revealed a lower respiratory sensitivity to glucose in DIO islets. Correlation of insulin secretion with respiratory parameters uncovers compromised insulin secretion in DIO islets by oxidative power. Normalization to increased insulin contents during DIO improves the quantitative relation between GSIS and respiration, allowing to classify dysfunctional properties of pancreatic insulin secretion, and thereby serving as valuable biomarker for pancreatic islet glucose responsiveness and health. AU - Kabra, U.* AU - Affourtit, C.* AU - Jastroch, M. C1 - 62438 C2 - 50871 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Respiratory parameters for the classification of dysfunctional insulin secretion by pancreatic islets. JO - Metabolites VL - 11 IS - 6 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Mycobacterium avium subspecies paratuberculosis (MAP) are detectable viable in milk and other dairy products. The molecular mechanisms allowing the adaptation of MAP in these products are still poorly understood. To obtain information about respective adaptation of MAP in milk, we differentially analyzed the proteomes of MAP cultivated for 48 h in either milk at 37 °C or 4 °C or Middlebrook 7H9 broth as a control. From a total of 2197 MAP proteins identified, 242 proteins were at least fivefold higher in abundance in milk. MAP responded to the nutritional shortage in milk with upregulation of 32% of proteins with function in metabolism and 17% in fatty acid metabolism/synthesis. Additionally, MAP upregulated clusters of 19% proteins with roles in stress responses and immune evasion, 19% in transcription/translation, and 13% in bacterial cell wall synthesis. Dut, MmpL4_1, and RecA were only detected in MAP incubated in milk, pointing to very important roles of these proteins for MAP coping with a stressful environment. Dut is essential and plays an exclusive role for growth, MmpL4_1 for virulence through secretion of specific lipids, and RecA for SOS response of mycobacteria. Further, 35 candidates with stable expression in all conditions were detected, which could serve as targets for detection. Data are available via ProteomeXchange with identifier PXD027444. AU - Kleinwort, K.J.H.* AU - Hobmaier, B.F.* AU - Mayer, R.* AU - Hölzel, C.* AU - Degroote, R.L.* AU - Märtlbauer, E.* AU - Hauck, S.M. AU - Deeg, C.A.* C1 - 62875 C2 - 51133 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Mycobacterium avium subsp. paratuberculosis proteome changes profoundly in milk. JO - Metabolites VL - 11 IS - 8 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Hepatic iron overload can cause severe organ damage; therefore, an early diagnosis and the identification of potential risk factors is crucial. We aimed to investigate the sex-specific distribution of hepatic iron content (HIC) in a population-based cohort and identify relevant associated factors from a panel of markers. We analyzed N = 353 participants from a cross-sectional sample (KORA FF4) who underwent whole-body magnetic resonance imaging. HIC was assessed by single-voxel spectroscopy with a high-speed T2-corrected multi-echo technique. A large panel of markers, including anthropometric, genetic, and laboratory values, as well as behavioral risk factors were assessed. Relevant factors associated with HIC were identified by variable selection based on LASSO regression with bootstrap resampling. HIC in the study sample (mean age at examination: 56.0 years, 58.4% men) was significantly lower in women (mean ± SD: 39.2 ± 4.1 s-1) than in men (41.8 ± 4.7 s-1, p < 0.001). Relevant factors associated with HIC were HbA1c as well as prediabetes for men and visceral adipose tissue as well as age for women. Hepatic fat, alcohol consumption, and genetic risk score for iron levels were associated with HIC in both sexes. In conclusion, there are sex-specific associations of HIC with markers of body composition, glucose metabolism, and alcohol consumption. AU - Maier, L. AU - von Krüchten, R.* AU - Lorbeer, R.* AU - Filler, J. AU - Nattenmüller, J.* AU - Thorand, B. AU - Koenig, W.* AU - Rathmann, W.* AU - Bamberg, F.* AU - Schlett, C.L.* AU - Peters, A. AU - Rospleszcz, S. C1 - 63880 C2 - 51779 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Distribution and associated factors of hepatic iron-A population-based imaging study. JO - Metabolites VL - 11 IS - 12 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Regular physical activity is an effective strategy to prevent and ameliorate aging-associ-ated diseases. In particular, training increases muscle performance and improves whole-body me-tabolism. Since exercise affects the whole organism, it has countless health benefits. The systemic effects of exercise can, in part, be explained by communication between the contracting skeletal muscle and other organs and cell types. While small proteins and peptides known as myokines are the most prominent candidates to mediate this tissue cross-talk, recent investigations have paid in-creasing attention to metabolites. The purpose of this review is to highlight the potential role of tricarboxylic acid (TCA) metabolites as humoral mediators of exercise adaptation processes. We focus on TCA metabolites that are released from human skeletal muscle in response to exercise and provide an overview of their potential auto-, para-or endocrine health-promoting effects. AU - Maurer, J.* AU - Hoene, M.* AU - Weigert, C. C1 - 62784 C2 - 51062 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Signals from the circle: Tricarboxylic acid cycle intermediates as myometabokines. JO - Metabolites VL - 11 IS - 8 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Lysosomal storage diseases (LSDs) are a heterogeneous group of inherited metabolic diseases caused by mutations in genes encoding for proteins involved in the lysosomal degradation of macromolecules. They occur in approximately 1 in 5000 live births and pose a lifelong risk. Therefore, to achieve the maximum benefit from LSDs therapies, a fast and early diagnosis of the disease is required. In this framework, biomarker discovery is a significant factor in disease diagnosis and in predicting its outcomes. On the other hand, the dried blood spot (DBS)based metabolomics platform can open up new pathways for studying non-directional hypothesis approaches to biomarker discovery. This study aims to increase the efficiency of the developed methods for biomarker development in the context of rare diseases, with an improved impact on the reliability of the detected compounds. Thereby, we conducted two independent experiments and integrated them into the screening of the human blood metabolome: (1) comparison of EDTA blood and filter cards in terms of their suitability for metabolomics studies; (2) optimization of the extraction method: a side-by-side comparison of a series of buffers to the best utility to the disease of interest. The findings were compared to previous studies across parameters such as metabolite coverage, sample type suitability, and stability. The results indicate that measurements of metabolites are susceptible to differences in pre-analytical conditions and extraction solvents. This proposed approach can increase the positive rate of the future development of biomarkers. Altogether, the procedure can be easily adapted and applied to other studies, where the limited number of samples is a common barrier. AU - Rus, C.M.* AU - Di Bucchianico, S. AU - Cozma, C.* AU - Zimmermann, R. AU - Bauer, P.* C1 - 62381 C2 - 50849 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Dried Blood Spot (Dbs) methodology study for biomarker discovery in Dried Blood Spot (lsd).  JO - Metabolites VL - 11 IS - 6 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Metabolomics and lipidomics recently gained interest in the model organism Caenorhabditis elegans (C. elegans). The fast development, easy cultivation and existing forward and reverse genetic tools make the small nematode an ideal organism for metabolic investigations in development, aging, different disease models, infection, or toxicology research. The conducted type of analysis is strongly depending on the biological question and requires different analytical approaches. Metabolomic analyses in C. elegans have been performed using nuclear magnetic resonance (NMR) spectroscopy, direct infusion mass spectrometry (DI-MS), gas-chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) or combinations of them. In this review we provide general information on the employed techniques and their advantages and disadvantages in regard to C. elegans metabolomics. Additionally, we reviewed different fields of application, e.g., longevity, starvation, aging, development or metabolism of secondary metabolites such as ascarosides or maradolipids. We also summarised applied bioinformatic tools that recently have been used for the evaluation of metabolomics or lipidomics data from C. elegans. Lastly, we curated metabolites and lipids from the reviewed literature, enabling a prototypic collection which serves as basis for a future C. elegans specific metabolome database. AU - Salzer, L. AU - Witting, M. C1 - 61947 C2 - 50526 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Quo vadis Caenorhabditis elegans metabolomics - A review of current methods and applications to explore metabolism in the nematode. JO - Metabolites VL - 11 IS - 5 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Plants produce a huge number of functionally and chemically different natural products that play an important role in linking the plant with the adjacent environment. Plants can also absorb and transform external organic compounds (xenobiotics). Currently there are only a few studies concerning the effects of xenobiotics and their transformation products on plant metabolites using a mass spectrometric untargeted screening strategy. This study was designed to investigate the changes of the Phragmites australis metabolome following/after diclofenac or carbamazepine incubation, using a serial coupling of reversed-phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC) combined with accurate high-resolution time-of-flight mass spectrometer (TOF-MS). An untargeted screening strategy of metabolic fingerprints was developed to purposefully compare samples from differently treated P. australis plants, revealing that P. australis responded to each drug differently. When solvents with significantly different polarities were used, the metabolic profiles of P. australis were found to change significantly. For instance, the production of polyphenols (such as quercetin) in the plant increased after diclofenac incubation. Moreover, the pathway of unsaturated organic acids became more prominent, eventually as a reaction to protect the cells against reactive oxygen species (ROS). Hence, P. australis exhibited an adaptive mechanism to cope with each drug. Consequently, the untargeted screening approach is essential for understanding the complex response of plants to xenobiotics. AU - Wahman, R.* AU - Sauvetre, A. AU - Schröder, P. AU - Moser, S.* AU - Letzel, T.* C1 - 60904 C2 - 49738 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Untargeted metabolomics studies on drug-incubated phragmites Australis profiles. JO - Metabolites VL - 11 IS - 1 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Metabolomics approaches provide a vast array of analytical datasets, which require a comprehensive analytical, statistical, and biochemical workflow to reveal changes in metabolic profiles. The biological interpretation of mass spectrometric metabolomics results is still obstructed by the reliable identification of the metabolites as well as annotation and/or classification. In this work, the whole Lemna minor (common duckweed) was extracted using various solvents and analyzed utilizing polarity-extended liquid chromatography (reversed-phase liquid chromatography (RPLC)-hydrophilic interaction liquid chromatography (HILIC)) connected to two time-of-flight (TOF) mass spectrometer types, individually. This study (introduces and) discusses three relevant topics for the untargeted workflow: (1) A comparison study of metabolome samples was performed with an untargeted data handling workflow in two different labs with two different mass spectrometers using the same plant material type. (2) A statistical procedure was observed prioritizing significant detected features (dependent and independent of the mass spectrometer using the predictive methodology Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA). (3) Relevant features were transferred to a prioritization tool (the FOR-IDENT platform (FI)) and were compared with the implemented compound database PLANT-IDENT (PI). This compound database is filled with relevant compounds of the Lemnaceae, Poaceae, Brassicaceae, and Nymphaceae families according to analytical criteria such as retention time (polarity and LogD (pH 7)) and accurate mass (empirical formula). Thus, an untargeted analysis was performed using the new tool as a prioritization and identification source for a hidden-target screening strategy. Consequently, forty-two compounds (amino acids, vitamins, flavonoids) could be recognized and subsequently validated in Lemna metabolic profile using reference standards. The class of flavonoids includes free aglycons and their glycosides. Further, according to our knowledge, the validated flavonoids robinetin and norwogonin were for the first time identified in the Lemna minor extracts. AU - Wahman, R.* AU - Moser, S.* AU - Bieber, S.* AU - Cruzeiro, C. AU - Schröder, P. AU - Gilg, A.* AU - Lesske, F.* AU - Letzel, T.* C1 - 63881 C2 - 51780 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Untargeted analysis of Lemna minor Metabolites: Workflow and prioritization strategy comparing highly confident features between different mass spectrometers. JO - Metabolites VL - 11 IS - 12 PB - Mdpi PY - 2021 SN - 2218-1989 ER - TY - JOUR AB - Glycomics measurements, like all other high-throughput technologies, are subject to technical variation due to fluctuations in the experimental conditions. The removal of this non-biological signal from the data is referred to as normalization. Contrary to other omics data types, a systematic evaluation of normalization options for glycomics data has not been published so far. In this paper, we assess the quality of different normalization strategies for glycomics data with an innovative approach. It has been shown previously that Gaussian Graphical Models (GGMs) inferred from glycomics data are able to identify enzymatic steps in the glycan synthesis pathways in a data-driven fashion. Based on this finding, here, we quantify the quality of a given normalization method according to how well a GGM inferred from the respective normalized data reconstructs known synthesis reactions in the glycosylation pathway. The method therefore exploits a biological measure of goodness. We analyzed 23 different normalization combinations applied to six large-scale glycomics cohorts across three experimental platforms: Liquid Chromatography – ElectroSpray Ionization-Mass Spectrometry (LC-ESI-MS), Ultra High Performance Liquid Chromatography with Fluorescence Detection (UHPLC-FLD), and Matrix Assisted Laser Desorption Ionization – Furier Transform Ion Cyclotron Resonance – Mass Spectrometry (MALDI-FTICR-MS). Based on our results, we recommend normalizing glycan data using the ‘Probabilistic Quotient’ method followed by log-transformation, irrespective of the measurement platform. This recommendation is further supported by an additional analysis, where we ranked normalization methods based on their statistical associations with age, a factor known to associate with glycomics measurements. AU - Benedetti, E. AU - Gerstner, N. AU - Pučić-Baković, M.* AU - Keser, T.* AU - Reiding, K.R.* AU - Ruhaak, L.R.* AU - Štambuk, T.* AU - Selman, M.H.J.* AU - Rudan, I.* AU - Polašek, O.* AU - Hayward, C.* AU - Beekman, M.* AU - Slagboom, E.* AU - Wuhrer, M.* AU - Dunlop, M.G.* AU - Lauc, G.* AU - Krumsiek, J. C1 - 59615 C2 - 48877 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Systematic evaluation of normalization methods for glycomics data based on performance of network inference. JO - Metabolites VL - 10 IS - 7 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - Metabolomics studies have seen a steady growth due to the development and implementation of affordable and high-quality metabolomics platforms. In large metabolite panels, measurement values are frequently missing and, if neglected or sub-optimally imputed, can cause biased study results. We provided a publicly available, user-friendly R script to streamline the imputation of missing endogenous, unannotated, and xenobiotic metabolites. We evaluated the multivariate imputation by chained equations (MICE) and k-nearest neighbors (kNN) analyses implemented in our script by simulations using measured metabolites data from the Netherlands Epidemiology of Obesity (NEO) study (n = 599). We simulated missing values in four unique metabolites from different pathways with different correlation structures in three sample sizes (599, 150, 50) with three missing percentages (15%, 30%, 60%), and using two missing mechanisms (completely at random and not at random). Based on the simulations, we found that for MICE, larger sample size was the primary factor decreasing bias and error. For kNN, the primary factor reducing bias and error was the metabolite correlation with its predictor metabolites. MICE provided consistently higher performance measures particularly for larger datasets (n > 50). In conclusion, we presented an imputation workflow in a publicly available R script to impute untargeted metabolomics data. Our simulations provided insight into the effects of sample size, percentage missing, and correlation structure on the accuracy of the two imputation methods. AU - Faquih, T.* AU - van Smeden, M.* AU - Luo, J.* AU - le Cessie, S.* AU - Kastenmüller, G. AU - Krumsiek, J.* AU - Noordam, R.* AU - van Heemst, D.* AU - Rosendaal, F.R.* AU - van Hylckama Vlieg, A.* AU - Willems van Dijk, K.* AU - Mook-Kanamori, D.O.* C1 - 60629 C2 - 49501 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland SP - 1-23 TI - A workflow for missing values imputation of untargeted metabolomics data. JO - Metabolites VL - 10 IS - 12 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - Folates are a group of B(9)vitamins playing an important role in many metabolic processes such as methylation reactions, nucleotide synthesis or oxidation and reduction processes. However, humans are not able to synthesize folates de novo and thus rely on external sources thereof. Baker's yeast (Saccharomyces cerevisiae) has been shown to produce high amounts of this vitamin but extensive identification of its folate metabolism is still lacking. Therefore, we optimized and compared different sample preparation and purification procedures applying solid phase extraction (SPE). Strong anion exchange (SAX), C18 and hydrophilic-lipophilic-balanced (HLB) materials were tested for their applicability in future metabolomics studies. SAX turned out to be the preferred material for the quantitative purification of folates. Qualification of several folate vitamers was achieved by ultra-high pressure liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-Q-ToF-MS) measurements and quantification was performed by liquid chromatography tandem mass spectrometry (LC-MS/MS) applying stable isotope dilution assays (SIDAs). The oxidation products-pyrazino-triazine (MeFox) was included into the SIDA method for total folate determination and validation. Applying the best protocol (SAX) in regard to folate recovery, we analyzed 32 different vitamers in different polyglutamate states up to nonaglutamates, of which we could further identify 26 vitamers based on tandem-MS (MS2) spectra. Total folate quantification revealed differences in formyl folate contents depending on the cartridge chemistry used for purification. These are supposedly a result of interconversion reactions occurring during sample preparation due to variation in pH adjustments for the different purification protocols. The occurrence of interconversion and oxidation reactions should be taken into consideration in sample preparation procedures for metabolomics analyses with a focus on folates. AU - Gmelch, L.* AU - Wirtz, D.* AU - Witting, M. AU - Weber, N.* AU - Striegel, L.* AU - Schmitt-Kopplin, P. AU - Rychlik, M. C1 - 59788 C2 - 49042 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Comprehensive vitamer profiling of folate mono- and polyglutamates in baker's yeast (Saccharomyces cerevisiae) as a function of different sample preparation procedures. JO - Metabolites VL - 10 IS - 8 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - Metabolomics can be a tool to identify dietary biomarkers. However, reported food-metabolite associations have been inconsistent, and there is a need to explore further associations. Our aims were to confirm previously reported food-metabolite associations and to identify novel food-metabolite associations. We conducted a cross-sectional analysis of data from 849 participants (57% men) of the PopGen cohort. Dietary intake was obtained using FFQ and serum metabolites were profiled by an untargeted metabolomics approach. We conducted a systematic literature search to identify previously reported food-metabolite associations and analyzed these associations using linear regression. To identify potential novel food-metabolite associations, datasets were split into training and test datasets and linear regression models were fitted to the training datasets. Significant food-metabolite associations were evaluated in the test datasets. Models were adjusted for covariates. In the literature, we identified 82 food-metabolite associations. Of these, 44 associations were testable in our data and confirmed associations of coffee with 12 metabolites, of fish with five, of chocolate with two, of alcohol with four, and of butter, poultry and wine with one metabolite each. We did not identify novel food-metabolite associations; however, some associations were sex-specific. Potential use of some metabolites as biomarkers should consider sex differences in metabolism. AU - Langenau, J.* AU - Oluwagbemigun, K.* AU - Brachem, C.* AU - Lieb, W.* AU - di Giuseppe, R.* AU - Artati, A. AU - Kastenmüller, G. AU - Weinhold, L.* AU - Schmid, M.* AU - Nöthlings, U.* C1 - 60611 C2 - 49500 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Blood metabolomic profiling confirms and identifies biomarkers of food intake. JO - Metabolites VL - 10 IS - 11 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - Differentiation of preadipocytes into mature adipocytes is a highly complex cellular process. At lipidome level, the adipogenesis remains poorly characterized. To investigate the lipidomic changes during human adipogenesis, we used the Lipidyze (TM) assay, which quantified 743 lipid species from 11 classes. The undifferentiated human SGBS cell strain showed a heterogeneous lipid class composition with the most abundant classes, phosphatidylethanolamines (PE), phosphatidylcholines (PC), and sphingomyelins (SM). The differentiation process was accompanied by increased ceramide concentrations. After completion of differentiation around day 4, massive lipid remodeling occurred during maturation, characterized by substantial synthesis of diacylglycerols (DAG), lysophosphatidylethanolamines (LPE), PC, PE, SM, and triacylglycerols (TAG). Lipid species composition became more homogeneous during differentiation to highly concentrated saturated and monounsaturated long-chain fatty acids (LCFA), with the four most abundant being C16:0, C16:1, C18:0, and C18:1. Simultaneously, the amount of polyunsaturated and very long-chain fatty acids (VLCFA) markedly decreased. High negative correlation coefficients between PE and PC species containing VLCFA and TAG species as well as between ceramides and SM imply that PE, PC, and ceramides might have served as additional sources for TAG and SM synthesis, respectively. These results highlight the enormous remodeling at the lipid level over several lipid classes during adipogenesis. AU - Miehle, F. AU - Möller, G. AU - Cecil, A. AU - Lintelmann, J. AU - Wabitsch, M.* AU - Tokarz, J. AU - Adamski, J. AU - Haid, M. C1 - 59241 C2 - 48685 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Lipidomic phenotyping reveals extensive lipid remodeling during adipogenesis in human adipocytes. JO - Metabolites VL - 10 IS - 6 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - A large part of metabolomics research relies on experiments involving mouse models, which are usually 6 to 20 weeks of age. However, in this age range mice undergo dramatic developmental changes. Even small age differences may lead to different metabolomes, which in turn could increase inter-sample variability and impair the reproducibility and comparability of metabolomics results. In order to learn more about the variability of the murine plasma metabolome, we analyzed male and female C57BL/6J, C57BL/6NTac, 129S1/SvImJ, and C3HeB/FeJ mice at 6, 10, 14, and 20 weeks of age, using targeted metabolomics (BIOCRATES AbsoluteIDQ™ p150 Kit). Our analysis revealed high variability of the murine plasma metabolome during adolescence and early adulthood. A general age range with minimal variability, and thus a stable metabolome, could not be identified. Age-related metabolomic changes as well as the metabolite profiles at specific ages differed markedly between mouse strains. This observation illustrates the fact that the developmental timing in mice is strain specific. We therefore stress the importance of deliberate strain choice, as well as consistency and precise documentation of animal age, in metabolomics studies. AU - Pann, P. AU - Hrabě de Angelis, M. AU - Prehn, C. AU - Adamski, J. C1 - 60612 C2 - 49446 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Mouse age matters: How age affects the murine plasma metabolome. JO - Metabolites VL - 10 IS - 11 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - This study compared metabolite shifts induced by training for, participation in, and recovery from a marathon race competition among athletes divided into three groups based on fitness (relative maximum oxygen uptake (VO(2)max)) and performance levels (net running time). Plasma samples from 76 male runners participating in the Munich Marathon were analyzed for metabolite shifts using a targeted metabolomics panel. For the entire cohort of runners, pronounced increases were measured immediately after the race for plasma concentrations of acylcarnitines (AC), the ratio (palmitoylcarnitine + stearoylcarnitine)/free carnitine that is used as a proxy for the activity of the mitochondrial enzyme carnitine palmitoyltransferase, and arginine-related metabolites, with decreases in most amino acids (AA) and phospholipids. Plasma levels of AA and phospholipids were strongly increased 24 and 72 h post-race. Post-race plasma concentrations of AC and arginine-related metabolites were higher in the low compared to top performers, indicating an accumulation of fatty acids and a reliance on protein catabolism to provide energy after the marathon event. This study showed that marathon race competition is associated with an extensive and prolonged perturbation in plasma metabolite concentrations with a strong AC signature that is greater in the slower, less aerobically fit runners. Furthermore, changes in the arginine-related metabolites were observed. AU - Schader, J.F.* AU - Haid, M. AU - Cecil, A. AU - Schoenfeld, J.* AU - Halle, M.* AU - Pfeufer, A. AU - Prehn, C. AU - Adamski, J. AU - Nieman, D.C.* AU - Scherr, J.* C1 - 58508 C2 - 48217 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Metabolite shifts induced by marathon race competition differ between athletes based on level of fitness and performance: A substudy of the enzy-magIC study. JO - Metabolites VL - 10 IS - 3 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - Genome scale metabolic models (GSMs) are a representation of the current knowledge on the metabolism of a given organism or superorganism. They group metabolites, genes, enzymes and reactions together to form a mathematical model and representation that can be used to analyze metabolic networks in silico or used for analysis of omics data. Beside correct mass and charge balance, correct structural annotation of metabolites represents an important factor for analysis of these metabolic networks. However, several metabolites in different GSMs have no or only partial structural information associated with them. Here, a new systematic nomenclature for acyl-based metabolites such as fatty acids, acyl-carnitines, acyl-coenzymes A or acyl-carrier proteins is presented. This nomenclature enables one to encode structural details in the metabolite identifiers and improves human readability of reactions. As proof of principle, it was applied to the fatty acid biosynthesis and degradation in the Caenorhabditis elegans consensus model WormJam. AU - Witting, M. C1 - 58757 C2 - 48397 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Suggestions for standardized identifiers for fatty acyl compounds in genome scale metabolic models and their application to the wormjam caenorhabditis elegans model. JO - Metabolites VL - 10 IS - 4 PB - Mdpi PY - 2020 SN - 2218-1989 ER - TY - JOUR AB - Ageing, one of the largest risk factors for many complex diseases, is highly interconnected to metabolic processes. Investigating the changes in metabolite concentration during ageing among healthy individuals offers us unique insights to healthy ageing. We aim to identify ageing-associated metabolites that are independent from chronological age to deepen our understanding of the long-term changes in metabolites upon ageing. Sex-stratified longitudinal analyses were performed using fasting serum samples of 590 healthy KORA individuals (317 women and 273 men) who participated in both baseline (KORA S4) and seven-year follow-up (KORA F4) studies. Replication was conducted using serum samples of 386 healthy CARLA participants (195 women and 191 men) in both baseline (CARLA-0) and four-year follow-up (CARLA-1) studies. Generalized estimation equation models were performed on each metabolite to identify ageing-associated metabolites after adjusting for baseline chronological age, body mass index, physical activity, smoking status, alcohol intake and systolic blood pressure. Literature researches were conducted to understand their biochemical relevance. Out of 122 metabolites analysed, we identified and replicated five (C18, arginine, ornithine, serine and tyrosine) and four (arginine, ornithine, PC aa C36:3 and PC ae C40:5) significant metabolites in women and men respectively. Arginine decreased, while ornithine increased in both sexes. These metabolites are involved in several ageing processes: apoptosis, mitochondrial dysfunction, inflammation, lipid metabolism, autophagy and oxidative stress resistance. The study reveals several significant ageing-associated metabolite changes with two-time-point measurements on healthy individuals. Larger studies are required to confirm our findings. AU - Chak, C.M. AU - Lacruz, M.E.* AU - Adam, J. AU - Brandmaier, S. AU - Covic, M. AU - Huang, J. AU - Meisinger, C. AU - Tiller, D.* AU - Prehn, C. AU - Adamski, J. AU - Berger, U.* AU - Gieger, C. AU - Peters, A. AU - Kluttig, A.* AU - Wang-Sattler, R. C1 - 55634 C2 - 46497 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Ageing investigation using two-time-point metabolomics data from KORA and CARLA studies. JO - Metabolites VL - 9 IS - 3 PB - Mdpi PY - 2019 SN - 2218-1989 ER - TY - JOUR AB - Kit-based assays, such as AbsoluteIDQ(TM) p150, are widely used in large cohort studies and provide a standardized method to quantify blood concentrations of phosphatidylcholines (PCs). Many disease-relevant associations of PCs were reported using this method. However, their interpretation is hampered by lack of functionally-relevant information on the detailed fatty acid side-chain compositions as only the total number of carbon atoms and double bonds is identified by the kit. To enable more substantiated interpretations, we characterized these PC sums using the side-chain resolving Lipidyzer(TM) platform, analyzing 223 samples in parallel to the AbsoluteIDQ(TM). Combining these datasets, we estimated the quantitative composition of PC sums and subsequently tested their replication in an independent cohort. We identified major constituents of 28 PC sums, revealing also various unexpected compositions. As an example, PC 16:0_22:5 accounted for more than 50% of the PC sum with in total 38 carbon atoms and 5 double bonds (PC aa 38:5). For 13 PC sums, we found relatively high abundances of odd-chain fatty acids. In conclusion, our study provides insights in PC compositions in human plasma, facilitating interpretation of existing epidemiological data sets and potentially enabling imputation of PC compositions for future meta-analyses of lipidomics data. AU - Quell, J. AU - Römisch-Margl, W. AU - Haid, M. AU - Krumsiek, J. AU - Skurk, T.* AU - Halama, A.* AU - Stephan, N.* AU - Adamski, J. AU - Hauner, H.* AU - Mook-Kanamori, D.O.* AU - Mohney, R.P.* AU - Daniel, H.* AU - Suhre, K.* AU - Kastenmüller, G. C1 - 56289 C2 - 46955 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Characterization of bulk phosphatidylcholine compositions in human plasma using side-chain resolving lipidomics. JO - Metabolites VL - 9 IS - 6 PB - Mdpi PY - 2019 SN - 2218-1989 ER - TY - JOUR AB - Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub. AU - Stanstrup, J.* AU - Broeckling, C.D.* AU - Helmus, R.* AU - Hoffmann, N.* AU - Mathé, E.* AU - Naake, T.* AU - Nicolotti, L.* AU - Peters, K.* AU - Rainer, J.* AU - Salek, R.M.* AU - Schulze, T.* AU - Schymanski, E.L.* AU - Stravs, M.A.* AU - Thévenot, E.A.* AU - Treutler, H.* AU - Weber, R.J.M.* AU - Willighagen, E.* AU - Witting, M. AU - Neumann, S.* C1 - 56962 C2 - 47368 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - The metaRbolomics Toolbox in Bioconductor and beyond. JO - Metabolites VL - 9 IS - 10 PB - Mdpi PY - 2019 SN - 2218-1989 ER - TY - JOUR AB - Determination of metabolomic signatures of pulmonary function and chronic obstructive pulmonary disease (COPD) in the general population could aid in identification and understanding of early disease processes. Metabolome measurements were performed on serum from 4742 individuals (2354 African-Americans and 1529 European-Americans from the Atherosclerosis Risk in Communities study and 859 Europeans from the Cooperative Health Research in the Region of Augsburg study). We examined 368 metabolites in relation to cross-sectional measures of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), their ratio (FEV1/FVC) and COPD using multivariable regression followed by meta-analysis. At a false discovery rate of 0.05, 95 metabolites were associated with FEV1 and 100 with FVC (73 overlapping), including inverse associations with branched-chain amino acids and positive associations with glutamine. Ten metabolites were associated with FEV1/FVC and seventeen with COPD (393 cases). Enriched pathways of amino acid metabolism were identified. Associations with FEV1 and FVC were not driven by individuals with COPD. We identified novel metabolic signatures of pulmonary function and COPD in African and European ancestry populations. These may allow development of biomarkers in the general population of early disease pathogenesis, before pulmonary function has decreased to levels diagnostic for COPD. AU - Yu, B.* AU - Flexeder, C. AU - McGarrah, R.W.* AU - Wyss, A.* AU - Morrison, A.C.* AU - North, K.E.* AU - Boerwinkle, E.* AU - Kastenmüller, G. AU - Gieger, C. AU - Suhre, K.* AU - Karrasch, S. AU - Peters, A. AU - Wagner, G.R.* AU - Michelotti, G.A.* AU - Mohney, R.P.* AU - Schulz, H. AU - London, S.J.* C1 - 55805 C2 - 46582 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Metabolomics identifies novel blood biomarkers of pulmonary function and COPD in the general population. JO - Metabolites VL - 9 IS - 4 PB - Mdpi PY - 2019 SN - 2218-1989 ER - TY - JOUR AB - Night shift work can have a serious impact on health. Here, we assess whether and how night shift work influences the metabolite profiles, specifically with respect to different chronotype classes. We have recruited 100 women including 68 nurses working both, day shift and night shifts for up to 5 consecutive days and collected 3640 spontaneous urine samples. About 424 waking-up urine samples were measured using a targeted metabolomics approach. To account for urine dilution, we applied three methods to normalize the metabolite values: creatinine-, osmolality- and regression-based normalization. Based on linear mixed effect models, we found 31 metabolites significantly (false discovery rate <0.05) affected in nurses working in night shifts. One metabolite, acylcarnitine C10:2, was consistently identified with all three normalization methods. We further observed 11 and 4 metabolites significantly associated with night shift in early and late chronotype classes, respectively. Increased levels of medium- and long chain acylcarnitines indicate a strong impairment of the fatty acid oxidation. Our results show that night shift work influences acylcarnitines and BCAAs, particularly in nurses in the early chronotype class. Women with intermediate and late chronotypes appear to be less affected by night shift work. AU - Rotter, M. AU - Brandmaier, S. AU - Covic, M. AU - Burek, K.* AU - Hertel, J.* AU - Troll, M. AU - Bader, E. AU - Adam, J. AU - Prehn, C. AU - Rathkolb, B. AU - Hrabě de Angelis, M. AU - Grabe, H.J.* AU - Daniel, H.* AU - Kantermann, T.* AU - Harth, V.* AU - Illig, T.* AU - Pallapies, D.* AU - Behrens, T.* AU - Brüning, T.* AU - Adamski, J. AU - Lickert, H. AU - Rabstein, S.* AU - Wang-Sattler, R. C1 - 54182 C2 - 45274 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Night shift work affects urine metabolite profiles of nurses with early chronotype. JO - Metabolites VL - 8 IS - 3 PB - Mdpi PY - 2018 SN - 2218-1989 ER - TY - JOUR AB - In this review, we summarize established and recent bioinformatic and statistical methods for the analysis of NMR-based metabolomics. Data analysis of NMR metabolic fingerprints exhibits several challenges, including unwanted biases, high dimensionality, and typically low sample numbers. Common analysis tasks comprise the identification of differential metabolites and the classification of specimens. However, analysis results strongly depend on the preprocessing of the data, and there is no consensus yet on how to remove unwanted biases and experimental variance prior to statistical analysis. Here, we first review established and new preprocessing protocols and illustrate their pros and cons, including different data normalizations and transformations. Second, we give a brief overview of state-of-the-art statistical analysis in NMR-based metabolomics. Finally, we discuss a recent development in statistical data analysis, where data normalization becomes obsolete. This method, called zero-sum regression, builds metabolite signatures whose estimation as well as predictions are independent of prior normalization. AU - Zacharias, H.U. AU - Altenbuchinger, M.* AU - Gronwald, W.* C1 - 54200 C2 - 45438 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Statistical analysis of NMR metabolic fingerprints: Established methods and recent advances. JO - Metabolites VL - 8 IS - 3 PB - Mdpi PY - 2018 SN - 2218-1989 ER - TY - JOUR AB - Modified quantitative structure retention relationships (QSRRs) are proposed and applied to describe two retention data sets: A set of 94 metabolites studied by a hydrophilic interaction chromatography system under organic content gradient conditions and a set of tryptophan and its major metabolites analyzed by a reversed-phase chromatographic system under isocratic as well as pH and/or simultaneous pH and organic content gradient conditions. According to the proposed modification, an additional descriptor is added to a conventional QSRR expression, which is the analyte retention time, tR(R), measured under the same elution conditions, but in a second chromatographic column considered as a reference one. The 94 metabolites were studied on an Amide column using a Bare Silica column as a reference. For the second dataset, a Kinetex EVO C18 and a Gemini-NX column were used, where each of them was served as a reference column of the other. We found in all cases a significant improvement of the performance of the QSRR models when the descriptor tR(R) was considered. AU - Zisi, C.* AU - Sampsonidis, I.* AU - Fasoula, S.* AU - Papachristos, K.* AU - Witting, M. AU - Gika, H.G.* AU - Nikitas, P.* AU - Pappa-Louisi, A.* C1 - 50548 C2 - 42627 TI - QSRR modeling for metabolite standards analyzed by two different chromatographic columns using multiple linear regression. JO - Metabolites VL - 7 IS - 1 PY - 2017 SN - 2218-1989 ER - TY - JOUR AB - The research presented stemmed from the observations that female plants of the annual dioecious Mercurialis annua outlive male plants. This led to the hypothesis that female plants of M. annua would be more tolerant to stress than male plants. This hypothesis was addressed in a comprehensive way, by comparing morphological, biochemical and metabolomics changes in female and male plants during their development and under salinity. There were practically no differences between the genders in vegetative development and physiological parameters. However, under salinity conditions, female plants produced significantly more new reproductive nodes. Gender-linked differences in peroxidase (POD) and glutathione transferases (GSTs) were involved in anti-oxidation, detoxification and developmental processes in M. annua. ¹H NMR metabolite profiling of female and male M. annua plants showed that under salinity the activity of the TCA cycle increased. There was also an increase in betaine in both genders, which may be explainable by its osmo-compatible function under salinity. The concentration of ten metabolites changed in both genders, while 'Female-only-response' to salinity was detected for five metabolites. In conclusion, dimorphic responses of M. annua plant genders to stress may be attributed to female plants' capacity to survive and complete the reproductive life cycle. AU - Orlofsky, E.M.* AU - Kozhoridze, G.* AU - Lyubenova, L. AU - Ostrozhenkova, E.* AU - Winkler, J.B. AU - Schröder, P. AU - Bacher, A.* AU - Eisenreich, W.* AU - Guy, M.* AU - Golan-Goldhirsh, A.* C1 - 48504 C2 - 41123 TI - Sexual dimorphism in the response of Mercurialis annua to stress. JO - Metabolites VL - 6 IS - 2 PY - 2016 SN - 2218-1989 ER - TY - JOUR AB - Metabolism has frequently been analyzed from a network perspective. A major question is how network properties correlate with biological features like growth rates, flux patterns and enzyme essentiality. Using methods from graph theory as well as established topological categories of metabolic systems, we analyze the essentiality of metabolic reactions depending on the growth medium and identify the topological footprint of these reactions. We find that the typical topological context of a medium-dependent essential reaction is systematically different from that of a globally essential reaction. In particular, we observe systematic differences in the distribution of medium-dependent essential reactions across three-node subgraphs (the network motif signature of medium-dependent essential reactions) compared to globally essential or globally redundant reactions. In this way, we provide evidence that the analysis of metabolic systems on the few-node subgraph scale is meaningful for explaining dynamic patterns. This topological characterization of medium-dependent essentiality provides a better understanding of the interplay between reaction deletions and environmental conditions. AU - Sonnenschein, N.* AU - Marr, C. AU - Hütt, M.-T.* C1 - 11318 C2 - 30609 SP - 632-647 TI - A topological characterization of medium-dependent essential metabolic reactions. JO - Metabolites VL - 2 IS - 3 PB - MDPI PY - 2012 SN - 2218-1989 ER -