TY - JOUR AB - MicroRNAs (miRNAs) are short sequences of single-stranded non-coding RNAs that target messenger RNAs, leading to their repression or decay. Interestingly, miRNAs play a role in the cellular response to low oxygen levels, known as hypoxia, which is associated with reactive oxygen species and oxidative stress. However, the physiological implications of hypoxia-induced miRNAs ("hypoxamiRs") remain largely unclear. Here, we investigate the role of miR-210 in brown adipocyte differentiation and thermogenesis. We treated the cells under sympathetic stimulation with hypoxia, CoCl2, or IOX2. To manipulate miR-210, we performed reverse transfection with antagomiRs. Adipocyte markers expression, lipid accumulation, lipolysis, and oxygen consumption were measured. Hypoxia hindered BAT differentiation and suppressed sympathetic stimulation. Hypoxia-induced HIF-1α stabilization increased miR-210 in brown adipocytes. Interestingly, miR-210-5p enhanced differentiation under normoxic conditions but was insufficient to rescue the inhibition of brown adipocyte differentiation under hypoxic conditions. Although adrenergic stimulation activated HIF-1α signaling and upregulated miR-210 expression, inhibition of miR-210-5p did not significantly influence UCP1 expression or oxygen consumption. In summary, hypoxia and adrenergic stimulation upregulated miR-210, which impacted brown adipocyte differentiation and thermogenesis. These findings offer new insights for the physiological role of hypoxamiRs in brown adipose tissue, which could aid in understanding oxidative stress and treatment of metabolic disorders. AU - Caca, J.* AU - Bartelt, A. AU - Egea, V.* C1 - 73006 C2 - 56804 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Hypoxia regulates brown adipocyte differentiation and stimulates miR-210 by HIF-1α. JO - Int. J. Mol. Sci. VL - 26 IS - 1 PB - Mdpi PY - 2025 SN - 1661-6596 ER - TY - JOUR AB - Cholesterol is an essential plasma membrane component, and altered cholesterol metabolism has been linked to cholesterol accumulation in the airways of COPD and cystic fibrosis patients. However, its role in airway epithelial differentiation is not well understood. Tandem mass spectrometry-based proteomic analysis of differentiating primary human bronchial epithelial cells (phBECs) revealed an overall inhibition of the cholesterol biosynthesis pathway. We hypothesized that excess cholesterol impairs the differentiation of phBECs into a fully functional bronchial epithelium. PhBECs were differentiated in the presence of 80 µM cholesterol for 21 days, the main airway cell type populations monitored using qRT-PCR and immunofluorescent stainings, and epithelial barrier integrity was analyzed via transepithelial electrical resistance measurements. Chronic cholesterol exposure led to a significant increase in CC10+ secretory cells at the expense of ciliated cells. Pathway enrichment analysis suggested the tumor protein p53 as a master regulator of genes during normal differentiation of phBECs. Chronic cholesterol exposure drastically impaired the nuclear translocation of p53. Our findings suggest that this inhibition underlies the cholesterol-induced expansion of CC10+ secretory cell populations at the expense of ciliated cells. In conclusion, we identify cholesterol as an important regulator of normal bronchial epithelial cell differentiation through inhibition of p53 nuclear translocation. AU - Chakraborty, A. AU - Giraldo-Arias, J. AU - Merl-Pham, J. AU - Dick, E. AU - Mastalerz, M. AU - Zöller, M. AU - Marchi, H. AU - Le Gleut, R. AU - Hatz, R.* AU - Behr, J.* AU - Hilgendorff, A. AU - Hauck, S.M. AU - Staab-Weijnitz, C.A. C1 - 75429 C2 - 57986 CY - Mdpi Ag, Grosspeteranlage 5, Ch-4052 Basel, Switzerland SP - 8324 - 8324 TI - Cholesterol regulates airway epithelial cell differentiation by inhibiting p53 nuclear translocation. JO - Int. J. Mol. Sci. VL - 26 IS - 17 PB - Mdpi PY - 2025 SN - 1661-6596 ER - TY - JOUR AB - Long-COVID (LC) is characterized by diverse and persistent symptoms, potentially mirroring different molecular pathways. Recent data might offer that one of them is mediated by functional autoantibodies (fAAb) targeting G protein-coupled receptors (GPCR). Thus, the aim of this study was to investigate the clinical phenotype of patients with LC in relation to their GPCR-fAAb seropositivity. The present study recruited 194 patients with LC and profiled them based on self-reported symptoms. GPCR-fAAb seropositivity was identified by using a cardiomyocyte bioassay, testing the presence and functionality of the AAbs. Logistic regression, clustering, and decision tree analyses were applied to examine associations between GPCR-fAAb profiles and self-reported symptoms considering age and gender. The most prevalent GPCR-fAAbs in patients with LC were fAAB targeting the β2 adrenergic receptor (β2-fAAb, 92.8%), the muscarinergic M2 receptor (M2-fAAb, 87.1%), the Angiotensin II type 1 receptor (AT1-fAAb, 85.6%), and angiotensin (1–7) Mas receptor (MAS-fAAb, 85.6%). β2-fAAb showed a significant relation with dizziness, lack of concentration, and POTS, while Endothelin Type A receptor functional autoantibody (ET-A-fAAb) was significantly related to deterioration of pre-existing neurological disorders. Statistical analysis indicated a strong positive correlation between M2- and β2-fAAb; as in addition, an association of β2-fAAb and gender was observed to one of the major clinical symptoms (fatigue/PEM), a critical impact of GPCR-fAAb on LC-pathogenesis can be assumed. Summing up, the present data show that specific GPCR-fAAb are associated with distinct clinical phenotypes. Especially, the combination of M2- and β2-fAAb seemed to be essential for the LC-phenotype with a combination of fatigue/PEM and lack of concentration as major clinical symptoms. AU - Hofmann, S.* AU - Lucio, M. AU - Wallukat, G.* AU - Hoffmanns, J.* AU - Schröder, T.* AU - Raith, F.* AU - Szewczykowski, C.* AU - Skornia, A.* AU - Rech, J.* AU - Schottenhamml, J.* AU - Harrer, T.* AU - Ganslmayer, M.* AU - Mardin, C.Y.* AU - Flecks, M.* AU - Lakatos, P.* AU - Hohberger, B.* C1 - 75170 C2 - 57808 CY - Mdpi Ag, Grosspeteranlage 5, Ch-4052 Basel, Switzerland SP - 6746 - 6746 TI - Functional autoantibodies targeting G-protein-coupled receptors and their clinical phenotype in patients with long-COVID. JO - Int. J. Mol. Sci. VL - 26 IS - 14 PB - Mdpi PY - 2025 SN - 1661-6596 ER - TY - JOUR AB - Hutchinson–Gilford progeria syndrome (HGPS) is a rare, fatal, and premature aging disorder caused by progerin, a truncated form of lamin A that disrupts nuclear architecture, induces systemic inflammation, and accelerates senescence. While the farnesyltransferase inhibitor lonafarnib extends the lifespan by limiting progerin farnesylation, it does not address the chronic inflammation or the senescence-associated secretory phenotype (SASP), which worsens disease progression. In this study, we investigated the combined effects of baricitinib (BAR), a JAK1/2 inhibitor, and lonafarnib (FTI) in a LmnaG609G/G609G mouse model of HGPS. BAR + FTI therapy synergistically extended the lifespan by 25%, surpassing the effects of either monotherapy. Treated mice showed improved health, as evidenced by reduced kyphosis, better fur quality, decreased incidence of cataracts, and less severe dysgnathia. Histological analyses indicated reduced fibrosis in the dermal, hepatic, and muscular tissues, restored cellularity and thickness in the aortic media, and improved muscle fiber integrity. Mechanistically, BAR decreased the SASP and inflammatory markers (e.g., IL-6 and PAI-1), complementing the progerin-targeting effects of FTI. This preclinical study demonstrates the synergistic potential of BAR + FTI therapy in addressing HGPS systemic and tissue-specific pathologies, offering a promising strategy for enhancing both lifespan and health. AU - Krüger, P.* AU - Schroll, M.* AU - Fenzl, F.* AU - Hartinger, R.* AU - Lederer, E.* AU - Görlach, A.* AU - Gordon, L.B.* AU - Cavalcante, P.* AU - Iacomino, N.* AU - Rathkolb, B. AU - Aguilar-Pimentel, J.A. AU - Östereicher, M.A. AU - Spielmann, N. AU - Wolf, C.M.* AU - Hrabě de Angelis, M. AU - Djabali, K.* C1 - 74680 C2 - 57537 CY - Mdpi Ag, Grosspeteranlage 5, Ch-4052 Basel, Switzerland SP - 4849 - 4849 TI - Baricitinib and lonafarnib synergistically target Progerin and inflammation, improving lifespan and health in progeria mice. JO - Int. J. Mol. Sci. VL - 26 IS - 10 PB - Mdpi PY - 2025 SN - 1661-6596 ER - TY - JOUR AB - Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency (CAH) requires lifelong glucocorticoid replacement to manage cortisol deficiency and excessive androgen production. Conventional circadian treatment (CT) tries to mimic natural cortisol rhythms, whereas reverse-circadian treatment (RC) prioritizes the suppression of adrenal androgen excess overnight through evening dosing. Limited data exist on the immunological impact of these regimens. A bi-centric study was conducted, including 41 pediatric and adolescent CAH patients. Peripheral blood samples were collected from patients on conventional treatment (n = 38) or RC (n = 16), with 11 RC patients switching to conventional treatment. Immune cell phenotypes, cytokine profiles, and natural killer (NK) cell cytotoxicity were assessed. Patients receiving RC showed lower percentages of CD4+CD25+ T cells (p = 0.0139). After the switch, patients with RC presented with a higher percentage of non-classical monocytes (p = 0.0255) and a lower percentage of Th17 cells (p = 0.0195). A lower expression of CD107 was observed with RC (p < 0.0001), as well as a higher percentage of NKp30 (p = 0.0189). Comparing patients after the switch from RC to HC, patients with RC presented with a lower NKG2D expression (p = 0.0420). Both conventional treatment and RC exhibited distinct immunological impacts, with CT showing modest advantages in normalizing immune phenotypes. These findings suggest that CT may offer immunological benefits for managing young patients with congenital adrenal hyperplasia. AU - Nowotny, H.F.* AU - Choi, H.* AU - Ziegler, S.* AU - Doll, N.* AU - Bäuerle, A.* AU - Welp, A.C.* AU - Dubinski, I.* AU - Schiergens, K.* AU - Neumann, U.* AU - Tschaidse, L.* AU - Auer, M.K.* AU - Rothenfußer, S. AU - Schmidt, H.* AU - Reisch, N.* C1 - 73514 C2 - 57080 CY - Mdpi Ag, Grosspeteranlage 5, Ch-4052 Basel, Switzerland TI - Immunophenotypic implications of reverse-circadian glucocorticoid treatment in congenital adrenal hyperplasia. JO - Int. J. Mol. Sci. VL - 26 IS - 4 PB - Mdpi PY - 2025 SN - 1661-6596 ER - TY - JOUR AB - Antibiotics are indispensable in medical patient care, yet they may elicit off-target effects, particularly by affecting mitochondrial function. This study investigates three commonly used antibiotics, gentamicin, ciprofloxacin, and amoxicillin, for their direct effects on mitochondrial respiration and membrane potential. Using high-resolution respirometry, we show that gentamicin and ciprofloxacin markedly increase mitochondrial leak respiration in permeabilized human embryonic kidney cells, suggesting alterations in the mitochondrial inner membrane. This is supported by a gentamicin-induced decrease in mitochondrial membrane potential. Especially gentamicin, but also ciprofloxacin, dose- and time-dependently inhibit oxidative phosphorylation and the mitochondrial electron transfer capacity, pronouncedly in the NADH-linked but also in the succinate-linked pathway. Furthermore, gentamicin decreases Complex IV (CIV) activity in a time-dependent fashion. In contrast, amoxicillin has no significant effect on mitochondrial respiration. These findings emphasize the importance of evaluating the potential direct toxicity of antibiotics on mitochondria, as they are most critical off-target sites. High-resolution respirometry provides a powerful approach to characterize such effects early in the drug development process. AU - Sailer, J.* AU - Schmitt, S.* AU - Zischka, H. AU - Gnaiger, E.* C1 - 74897 C2 - 57663 CY - Mdpi Ag, Grosspeteranlage 5, Ch-4052 Basel, Switzerland SP - 5379 - 5379 TI - Direct effects of clinically relevant antibiotics on mitochondrial respiration. JO - Int. J. Mol. Sci. VL - 26 IS - 11 PB - Mdpi PY - 2025 SN - 1661-6596 ER - TY - JOUR AB - The effects of low-fat dairy products on insulin resistance (IR), hepatic steatosis, and gut microbiota composition in high-fat diet (HFD)-fed obese mice were examined. C57BL/6 male mice (n = 16/group) were fed a high-fat diet (HFD, 45% fat) or HFD supplemented with either fat-free milk (MILK), fat-free yogurt (YOG), or reduced-fat (19% milk fat) cheddar cheese (CHE) at 10% of the total energy intake for 8 weeks. Body weight, fat mass, liver lipids, and metabolic enzymes were evaluated. Compared with HFD, MILK reduced homeostatic assessment of insulin resistance along with increased hepatic insulin signaling and decreased hepatic gluconeogenic enzymes. YOG and MILK decreased hepatic triacylglycerol content and lipid droplet size, while CHE had no effect. In the liver, MILK and YOG downregulated de novo lipogenesis enzymes. In MILK, fat oxidation capacity was elevated. Compared with HFD, liver lipidomic analysis in MILK and YOG revealed unique profiles of decreased proinflammatory lipid species, including ceramides. Dairy feeding elicited an increase in beneficial bacteria, such as Streptococcus in YOG and Anaero-tignum in MILK, as shown by 16S rRNA sequencing of gut microbiota. In conclusion, the ability of milk and yogurt to reduce hepatic steatosis in HFD mice may be explained, at least in part, by the regulation of the gut microbiome and liver lipidome. AU - Yuzbashian, E.* AU - Fernando, D.N.* AU - Jacobs, R.L.* AU - Lesker, T.* AU - Strowig, T.* AU - Ussar, S. AU - Chan, C.B.* C1 - 74833 C2 - 57621 CY - Mdpi Ag, Grosspeteranlage 5, Ch-4052 Basel, Switzerland SP - 5026 - 5026 TI - A comparison of the effects of milk, yogurt, and cheese on insulin sensitivity, hepatic steatosis, and gut microbiota in diet-induced obese male mice. JO - Int. J. Mol. Sci. VL - 26 IS - 11 PB - Mdpi PY - 2025 SN - 1661-6596 ER - TY - JOUR AB - Galectins have the potential to interact with transmembrane glycoproteins to modulate their functions. Since galectin-1 interacts with PDGF-Rβ, we analyzed the effect of galectin-1 on PDGF-BB-mediated AKT signaling in primary human retinal pigment epithelial (RPE) cells and galectin-1-deficient immortalized human RPE cells (LGALS1-/-/ARPE-19) following incubation with PDGF-BB and galectin-1. Expression and localization of galectin-1, PDGF-Rβ and pAKT were investigated using western blot analysis and immunohistochemical staining. Cell proliferation of RPE cells was analyzed using BrdU ELISA. Following treatment of human RPE cells with human recombinant (hr)-galectin-1 and PDGF-BB, an intense clustering of PDGF-Rβ and colocalization with galectin-1 were detected. By Western blot analysis and immunocytochemistry of human RPE cells, an enhanced PDGF-BB-mediated expression of pAKT was observed, which was substantially reduced by additional incubation with hr-galectin-1. Vice versa, in LGALS1-/-/ARPE-19 cells, the PDGF-BB-induced pAKT signal was enhanced compared to wild-type cells. Furthermore, a decreased expression of PDGF-Rβ in human RPE cells was observed after treatment with PDGF-BB and hr-galectin-1, while in untreated LGALS1-/-/ARPE-19 cells, its constitutive expression was increased. In addition, after treatment of RPE cells with hr-galectin-1, the PDGF-BB-induced proliferation was markedly reduced. In summary, galectin-1 has the distinct potential to reduce PDGF-mediated pAKT signaling and proliferation in human RPE cells-an effect that is most likely facilitated via a decreased expression of PDGF-Rβ. AU - Bizzotto, M.* AU - Ostermaier, A.* AU - Liesenhoff, C.* AU - Ma, W.* AU - Geerlof, A. AU - Priglinger, S.G.* AU - Priglinger, C.S.* AU - Ohlmann, A.* C1 - 71719 C2 - 56383 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Galectin-1 attenuates PDGF-mediated AKT signaling in retinal pigment epithelial cells. JO - Int. J. Mol. Sci. VL - 25 IS - 17 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Among all nephropathies, diabetic kidney disease (DKD) is the most common cause of kidney impairment advancement to end-stage renal disease (ESRD). Although DKD has no cure, the disease is commonly managed by strict control of blood glucose and blood pressure, and in most of these cases, kidney function often deteriorates, resulting in dialysis, kidney replacement therapy, and high mortality. The difficulties in finding a cure for DKD are mainly due to a poor understanding of the underpinning complex cellular mechanisms that could be identified as druggable targets for the treatment of this disease. The review is thus aimed at giving insight into the interconnection between chronic hyperglycaemia and cellular mechanistic perturbations of nephropathy in diabetes. A comprehensive literature review of observational studies on DKD published within the past ten years, with 57 percent published within the past three years was carried out. The article search focused on original research studies and reviews published in English. The articles were explored using Google Scholar, Medline, Web of Science, and PubMed databases based on keywords, titles, and abstracts related to the topic. This article provides a detailed relationship between hyperglycaemia, oxidative stress, and various cellular mechanisms that underlie the onset and progression of the disease. Moreover, it also shows how these mechanisms affect organelle dysfunction, resulting in fibrosis and podocyte impairment. The advances in understanding the complexity of DKD mechanisms discussed in this review will expedite opportunities to develop new interventions for treating the disease. AU - Efiong, E.E. AU - Bazireh, H. AU - Fuchs, M. AU - Amadi, P.U.* AU - Effa, E.* AU - Sharma, S. AU - Schmaderer, C.* C1 - 72162 C2 - 56419 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Crosstalk of hyperglycaemia and cellular mechanisms in the pathogenesis of diabetic kidney disease. JO - Int. J. Mol. Sci. VL - 25 IS - 20 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Essential transition metals have key roles in oxygen transport, neurotransmitter synthesis, nucleic acid repair, cellular structure maintenance and stability, oxidative phosphorylation, and metabolism. The balance between metal deficiency and excess is typically ensured by several extracellular and intracellular mechanisms involved in uptake, distribution, and excretion. However, provoked by either intrinsic or extrinsic factors, excess iron, zinc, copper, or manganese can lead to cellular damage upon chronic or acute exposure, frequently attributed to oxidative stress. Intracellularly, mitochondria are the organelles that require the tightest control concerning reactive oxygen species production, which inevitably leaves them to be one of the most vulnerable targets of metal toxicity. Current therapies to counteract metal overload are focused on chelators, which often cause secondary effects decreasing patients' quality of life. New therapeutic options based on synthetic or natural antioxidants have proven positive effects against metal intoxication. In this review, we briefly address the cellular metabolism of transition metals, consequences of their overload, and current therapies, followed by their potential role in inducing oxidative stress and remedies thereof. AU - Fontes, A. AU - Jauch, A.T.* AU - Sailer, J.* AU - Engler, J.* AU - Azul, A.M.* AU - Zischka, H. C1 - 71307 C2 - 56046 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Metabolic derangement of essential transition metals and potential antioxidant therapies. JO - Int. J. Mol. Sci. VL - 25 IS - 14 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - lncRNAs are noncoding transcripts with tissue and cancer specificity. Particularly, in breast cancer, lncRNAs exhibit subtype-specific expression; they are particularly upregulated in luminal tumors. However, no gene signature-based laboratory tests have been developed for luminal breast cancer identification or the differential diagnosis of luminal tumors, since no luminal A- or B-specific genes have been identified. Particularly, luminal B patients are of clinical interest, since they have the most variable response to neoadjuvant treatment; thus, it is necessary to develop diagnostic and predictive biomarkers for these patients to optimize treatment decision-making and improve treatment quality. In this study, we analyzed the lncRNA expression profiles of breast cancer cell lines and patient tumor samples from RNA-Seq data to identify an lncRNA signature specific for luminal phenotypes. We identified an lncRNA signature consisting of LINC01016, GATA3-AS1, MAPT-IT1, and DSCAM-AS1 that exhibits luminal subtype-specific expression; among these lncRNAs, GATA3-AS1 is associated with the presence of residual disease (Wilcoxon test, p < 0.05), which is related to neoadjuvant chemotherapy resistance in luminal B breast cancer patients. Furthermore, analysis of GATA3-AS1 expression using RNA in situ hybridization (RNA ISH) demonstrated that this lncRNA is detectable in histological slides. Similar to estrogen receptors and Ki67, both commonly detected biomarkers, GATA3-AS1 proves to be a suitable predictive biomarker for clinical application in breast cancer laboratory tests. AU - González-Woge, M.* AU - Contreras-Espinosa, L.* AU - García-Gordillo, J.A.* AU - Aguilar-Villanueva, S.* AU - Bargallo-Rocha, E.* AU - Cabrera-Galeana, P.* AU - Vasquez-Mata, T.* AU - Cervantes-López, X.* AU - Vargas-Lías, D.S.* AU - Montiel-Manríquez, R.* AU - Bautista-Hinojosa, L.* AU - Rebollar-Vega, R.* AU - Castro-Hernández, C.* AU - Álvarez-Gómez, R.M.* AU - De La Rosa Velázquez, I.A. AU - Díaz-Chávez, J.* AU - Jiménez-Trejo, F.* AU - Arriaga-Canon, C.* AU - Herrera, L.A.* C1 - 71451 C2 - 56190 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - The expression profiles of lncRNAs are associated with neoadjuvant chemotherapy resistance in locally advanced, luminal B-type breast cancer. JO - Int. J. Mol. Sci. VL - 25 IS - 15 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications are adjusted to maintain functionality in response to temperature fluctuations, we investigated whether tRNA modifications represent an adaptation of bacteria to different growth temperatures (minimal, optimal, and maximal), focusing on closely related psychrophilic (P. halocryophilus and E. sibiricum), mesophilic (B. subtilis), and thermophilic (G. stearothermophilus) Bacillales. Utilizing an RNA sequencing approach combined with chemical pre-treatment of tRNA samples, we systematically profiled dihydrouridine (D), 4-thiouridine (s4U), 7-methyl-guanosine (m7G), and pseudouridine (Ψ) modifications at single-nucleotide resolution. Despite their close relationship, each bacterium exhibited a unique tRNA modification profile. Our findings revealed increased tRNA modifications in the thermophilic bacterium at its optimal growth temperature, particularly showing elevated levels of s4U8 and Ψ55 modifications compared to non-thermophilic bacteria, indicating a temperature-dependent regulation that may contribute to thermotolerance. Furthermore, we observed higher levels of D modifications in psychrophilic and mesophilic bacteria, indicating an adaptive strategy for cold environments by enhancing local flexibility in tRNAs. Our method demonstrated high effectiveness in identifying tRNA modifications compared to an established tool, highlighting its potential for precise tRNA profiling studies. AU - Hoffmann, A. AU - Lorenz, C.A.* AU - Fallmann, J.* AU - Wolff, P.* AU - Lechner, A.* AU - Betat, H.* AU - Mörl, M.* AU - Stadler, P.F.* C1 - 71562 C2 - 56303 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Temperature-dependent tRNA modifications in bacillales. JO - Int. J. Mol. Sci. VL - 25 IS - 16 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - The transient receptor potential vanilloid 4 (TRPV4) specifically functions as a mechanosensitive ion channel and is responsible for conveying changes in physical stimuli such as mechanical stress, osmotic pressure, and temperature. TRPV4 enables the entry of cation ions, particularly calcium ions, into the cell. Activation of TRPV4 channels initiates calcium oscillations, which trigger intracellular signaling pathways involved in a plethora of cellular processes, including tissue repair. Widely expressed throughout the body, TRPV4 can be activated by a wide array of physicochemical stimuli, thus contributing to sensory and physiological functions in multiple organs. This review focuses on how TRPV4 senses environmental cues and thereby initiates and maintains calcium oscillations, critical for responses to organ injury, tissue repair, and fibrosis. We provide a summary of TRPV4-induced calcium oscillations in distinct organ systems, along with the upstream and downstream signaling pathways involved. In addition, we delineate current animal and disease models supporting TRPV4 research and shed light on potential therapeutic targets for modulating TRPV4-induced calcium oscillation to promote tissue repair while reducing tissue fibrosis. AU - Jiang, D. AU - Guo, R. AU - Dai, R. AU - Knoedler, S. AU - Tao, J.* AU - Machens, H.G.* AU - Rinkevich, Y. C1 - 69875 C2 - 55299 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - The multifaceted functions of TRPV4 and calcium oscillations in tissue repair. JO - Int. J. Mol. Sci. VL - 25 IS - 2 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Endothelial dysfunction is a strong prognostic factor in predicting the development of cardiovascular diseases. Dysfunctional endothelium loses its homeostatic ability to regulate vascular tone and prevent overactivation of inflammation, leading to vascular dysfunction. These functions are critical for vascular homeostasis and arterial pressure control, the disruption of which may lead to hypertension. Hypertension itself can also cause endothelial dysfunction, as endothelial cells are susceptible to haemodynamic changes. Although it is unclear which of those factors appear first, they create a vicious circle further damaging multiple organs, including the heart and vessels. There are also sex-specific differences in homeostatic functions of the endothelium regarding vessel tone regulation, which may contribute to differences in arterial blood pressure between men and women. Even more importantly, there are sex-differences in the development of endothelial dysfunction and vessel remodelling. Hence, an understanding of the mechanisms of endothelial dysfunction and its contribution to pathological vascular remodelling during hypertension is of critical importance. This review addresses immunological and metabolic aspects in mechanisms of endothelial dysfunction and the resulting mechanisms in vascular remodelling with respect to arterial hypertension, including the potential role of sex-specific differences. AU - Kopaliani, I.* AU - Elsaid, B.* AU - Speier, S. AU - Deussen, A.* C1 - 72925 C2 - 56784 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Immune and metabolic mechanisms of endothelial dysfunction. JO - Int. J. Mol. Sci. VL - 25 IS - 24 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Since the emergence of coronavirus disease-19 (COVID-19) in 2019, it has been crucial to investigate the causes of severe cases, particularly the higher rates of hospitalization and mortality in individuals with obesity. Previous findings suggest that adipocytes may play a role in adverse COVID-19 outcomes in people with obesity. The impact of COVID-19 vaccination and infection on adipose tissue (AT) is currently unclear. We therefore analyzed 27 paired biopsies of visceral and subcutaneous AT from donors of the Leipzig Obesity BioBank that have been categorized into three groups (1: no infection/no vaccination; 2: no infection but vaccinated; 3: infected and vaccinated) based on COVID-19 antibodies to spike (indicating vaccination) and/or nucleocapsid proteins. We provide additional insights into the impact of COVID-19 on AT biology through a comprehensive histological transcriptome and serum proteome analysis. This study demonstrates that COVID-19 infection is associated with smaller average adipocyte size. The impact of infection on gene expression was significantly more pronounced in subcutaneous than in visceral AT and mainly due to immune system-related processes. Serum proteome analysis revealed the effects of the infection on circulating adiponectin, interleukin 6 (IL-6), and carbonic anhydrase 5A (CA5A), which are all related to obesity and blood glucose abnormalities. AU - Krupka, S. AU - Hoffmann, A. AU - Jasaszwili, M.* AU - Dietrich, A.* AU - Guiu-Jurado, E.* AU - Klöting, N. AU - Blüher, M. C1 - 70259 C2 - 55472 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Consequences of COVID-19 on adipose tissue signatures. JO - Int. J. Mol. Sci. VL - 25 IS - 5 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - The expression of FKBP5, and its resulting protein FKBP51, is strongly induced by glucocorticoids. Numerous studies have explored their involvement in a plethora of cellular processes and diseases. There is, however, a lack of knowledge on the role of the different RNA splicing variants and the two protein isoforms, one missing functional C-terminal motifs. In this study, we use in vitro models (HeLa and Jurkat cells) as well as peripheral blood cells of a human cohort (N = 26 male healthy controls) to show that the two expressed variants are both dynamically upregulated following dexamethasone, with significantly earlier increases (starting 1-2 h after stimulation) in the short isoform both in vitro and in vivo. Protein degradation assays in vitro showed a reduced half-life (4 h vs. 8 h) of the shorter isoform. Only the shorter isoform showed a subnuclear cellular localization. The two isoforms also differed in their effects on known downstream cellular pathways, including glucocorticoid receptor function, macroautophagy, immune activation, and DNA methylation regulation. The results shed light on the difference between the two variants and highlight the importance of differential analyses in future studies with implications for targeted drug design. AU - Martinelli, S.* AU - Hafner, K.* AU - Koedel, M.* AU - Knauer-Arloth, J. AU - Gassen, N.C.* AU - Binder, E.B.* C1 - 72545 C2 - 56621 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Differential dynamics and roles of FKBP51 isoforms and their implications for targeted therapies. JO - Int. J. Mol. Sci. VL - 25 IS - 22 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Lifestyle interventions can prevent type 2 diabetes (T2DM). However, some individuals do not experience anticipated improvements despite weight loss. Biomarkers to identify such individuals at early stages are lacking. Insulin-like growth factor 1 (IGF- 1) and Insulin-like growth factor binding protein 1(IGFBP-1) were shown to predict T2DM onset in prediabetes. We assessed whether these markers also predict the success of lifestyle interventions, thereby possibly guiding personalized strategies. We analyzed the fasting serum levels of IGF-1, IGFBP-1, and Insulin-like growth factor binding protein 2 (IGFBP-2) in relation to changes in metabolic and anthropometric parameters, including intrahepatic lipids (IHLs) and visceral adipose tissue (VAT) volume, measured by magnetic resonance imaging (MRI), in 345 participants with a high risk for prediabetes (54% female; aged 36-80 years). Participants were enrolled in three randomized dietary intervention trials and assessed both at baseline and one year post-intervention. Statistical analyses were performed using IBM SPSS Statistics (version 28), and significance was set at p < 0.05. Within the 1-year intervention, overall significant improvements were observed. Stratifying individuals by baseline IGF-1 and IGFBP-1 percentiles revealed significant differences: higher IGF-1 levels were associated with more favorable changes compared to lower levels, especially in VAT and IHL. Lower baseline IGFBP-1 levels were associated with greater improvements, especially in IHL and 2 h glucose. Higher bioactive IGF-1 levels might predict better metabolic outcomes following lifestyle interventions in prediabetes, potentially serving as biomarkers for personalized interventions. AU - Meyer, N.M.T.* AU - Kabisch, S.* AU - Dambeck, U.* AU - Honsek, C.* AU - Kemper, M.* AU - Gerbracht, C.* AU - Arafat, A.M.* AU - Birkenfeld, A.L. AU - Schwarz, P.E. AU - Machann, J. AU - Osterhoff, M.A.* AU - Weickert, M.O.* AU - Pfeiffer, A.F.H.* C1 - 70933 C2 - 55978 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - IGF-1 and IGFBP-1 as possible predictors of response to lifestyle intervention-results from randomized controlled trials. JO - Int. J. Mol. Sci. VL - 25 IS - 12 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Our understanding of rare disease genetics has been shaped by a monogenic disease model. While the traditional monogenic disease model has been successful in identifying numerous disease-associated genes and significantly enlarged our knowledge in the field of human genetics, it has limitations in explaining phenomena like phenotypic variability and reduced penetrance. Widening the perspective beyond Mendelian inheritance has the potential to enable a better understanding of disease complexity in rare disorders. Digenic inheritance is the simplest instance of a non-Mendelian disorder, characterized by the functional interplay of variants in two disease-contributing genes. Known digenic disease causes show a range of pathomechanisms underlying digenic interplay, including direct and indirect gene product interactions as well as epigenetic modifications. This review aims to systematically explore the background of digenic inheritance in rare disorders, the approaches and challenges when investigating digenic inheritance, and the current evidence for digenic inheritance in mitochondrial disorders. AU - Neuhofer, C. AU - Prokisch, H. C1 - 70648 C2 - 55796 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Digenic inheritance in rare disorders and mitochondrial disease-crossing the frontier to a more comprehensive understanding of etiology. JO - Int. J. Mol. Sci. VL - 25 IS - 9 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Understanding the systemic biochemistry of early pregnancy in the mare is essential for developing new diagnostics and identifying causes for pregnancy loss. This study aimed to elucidate the dynamic lipidomic changes occurring during the initial stages of equine pregnancy, with a specific focus on days 7 and 14 post-ovulation. By analysing and comparing the plasma lipid profiles of pregnant and non-pregnant mares, the objective of this study was to identify potential biomarkers for pregnancy and gain insights into the biochemical adaptations essential for supporting maternal recognition of pregnancy and early embryonic development. Employing discovery lipidomics, we analysed plasma samples from pregnant and non-pregnant mares on days 7 and 14 post-conception using the SCIEX ZenoTOF 7600 system. This high-resolution mass spectrometry approach enabled us to comprehensively profile and compare the lipidomes across these critical early gestational timepoints. Our analysis revealed significant lipidomic alterations between pregnant and non-pregnant mares and between days 7 and 14 of pregnancy. Key findings include the upregulation of bile acids, sphingomyelins, phosphatidylinositols, and triglycerides in pregnant mares. These changes suggest enhanced lipid synthesis and mobilization, likely associated with the embryo's nutritional requirements and the establishment of embryo-maternal interactions. There were significant differences in lipid metabolism between pregnant and non-pregnant mares, with a notable increase in the sterol lipid BA 24:1;O5 in pregnant mares as early as day 7 of gestation, suggesting it as a sensitive biomarker for early pregnancy detection. Notably, the transition from day 7 to day 14 in pregnant mares is characterized by a shift towards lipids indicative of membrane biosynthesis, signalling activity, and preparation for implantation. The study demonstrates the profound lipidomic shifts that occur in early equine pregnancy, highlighting the critical role of lipid metabolism in supporting embryonic development. These findings provide valuable insights into the metabolic adaptations during these period and potential biomarkers for early pregnancy detection in mares. AU - Perera, T.R.W.* AU - Bromfield, E.G.* AU - Gibb, Z.* AU - Nixon, B.* AU - Sheridan, A.R.* AU - Rupasinghe, T.* AU - Skerrett-Byrne, D.A. AU - Swegen, A.* C1 - 72161 C2 - 56416 TI - Plasma lipidomics reveals lipid signatures of early pregnancy in mares. JO - Int. J. Mol. Sci. VL - 25 IS - 20 PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Duchenne and Becker muscular dystrophies, caused by pathogenic variants in DMD, are the most common inherited neuromuscular conditions in childhood. These diseases follow an X-linked recessive inheritance pattern, and mainly males are affected. The most prevalent pathogenic variants in the DMD gene are copy number variants (CNVs), and most patients achieve their genetic diagnosis through Multiplex Ligation-dependent Probe Amplification (MLPA) or exome sequencing. Here, we investigated a female patient presenting with muscular dystrophy who remained genetically undiagnosed after MLPA and exome sequencing. RNA sequencing (RNAseq) from the patient's muscle biopsy identified an 85% reduction in DMD expression compared to 116 muscle samples included in the cohort. A de novo balanced translocation between chromosome 17 and the X chromosome (t(X;17)(p21.1;q23.2)) disrupting the DMD and BCAS3 genes was identified through trio whole genome sequencing (WGS). The combined analysis of RNAseq and WGS played a crucial role in the detection and characterisation of the disease-causing variant in this patient, who had been undiagnosed for over two decades. This case illustrates the diagnostic odyssey of female DMD patients with complex structural variants that are not detected by current panel or exome sequencing analysis. AU - Segarra-Casas, A.* AU - Yépez, V.A.* AU - Demidov, G.* AU - Laurie, S.* AU - Esteve-Codina, A.* AU - Gagneur, J. AU - Parkhurst, Y.* AU - Muni-Lofra, R.* AU - Harris, E.* AU - Marini-Bettolo, C.* AU - Straub, V.* AU - Töpf, A.* C1 - 71308 C2 - 56065 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - An integrated transcriptomics and genomics approach detects an X/Autosome translocation in a female with duchenne muscular dystrophy. JO - Int. J. Mol. Sci. VL - 25 IS - 14 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Atopic dermatitis (AD) is one of the most common chronic inflammatory skin diseases, with an increasing number of targeted therapies available. While biologics to treat AD exclusively target the key cytokines of type 2 immunity, Janus kinase inhibitors target a broad variety of cytokines, including IFN-γ. To better stratify patients for optimal treatment outcomes, the identification and characterization of subgroups, especially with regard to their IFNG expression, is of great relevance, as the role of IFNG in AD has not yet been fully clarified. This study aims to define AD subgroups based on their lesional IFNG expression and to characterize them based on their gene expression, T cell secretome and clinical attributes. RNA from the lesional and non-lesional biopsies of 48 AD patients was analyzed by RNA sequencing. Based on IFNG gene expression and the release of IFN-γ by lesional T cells, this cohort was categorized into three IFNG groups (high, medium, and low) using unsupervised clustering. The low IFNG group showed features of extrinsic AD with a higher prevalence of atopic comorbidities and impaired epidermal lipid synthesis. In contrast, patients in the high IFNG group had a higher average age and an activation of additional pro-inflammatory pathways. On the cellular level, higher amounts of M1 macrophages and natural killer cell signaling were detected in the high IFNG group compared to the low IFNG group by a deconvolution algorithm. However, both groups shared a common dupilumab response gene signature, indicating that type 2 immunity is the dominant immune shift in both subgroups. In summary, high and low IFNG subgroups correspond to intrinsic and extrinsic AD classifications and might be considered in the future for evaluating therapeutic efficacy or non-responders. AU - Wasserer, S.* AU - Jargosch, M. AU - Mayer, K.E.* AU - Eigemann, J. AU - Raunegger, T.* AU - Aydin, G.* AU - Eyerich, S. AU - Biedermann, T.* AU - Eyerich, K.* C1 - 70867 C2 - 55778 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Characterization of high and low IFNG-expressing subgroups in atopic dermatitis. JO - Int. J. Mol. Sci. VL - 25 IS - 11 PB - Mdpi PY - 2024 SN - 1661-6596 ER - TY - JOUR AB - Obesity is already accompanied by adipose tissue (AT) dysfunction and metabolic disease in children and increases the risk of premature death. Due to its energy-dissipating function, brown AT (BAT) has been discussed as being protective against obesity and related metabolic dysfunction. To analyze the molecular processes associated with BAT development, we investigated genome-wide expression profiles in brown and white subcutaneous and perirenal AT samples of children. We identified 39 upregulated and 26 downregulated genes in uncoupling protein 1 (UCP1)-positive compared to UCP1-negative AT samples. We prioritized for genes that had not been characterized regarding a role in BAT biology before and selected cordon-bleu WH2 repeat protein (COBL), mohawk homeobox (MKX) and myocilin (MYOC) for further functional characterization. The siRNA-mediated knockdown of Cobl and Mkx during brown adipocyte differentiation in vitro resulted in decreased Ucp1 expression, while the inhibition of Myoc led to increased Ucp1 expression. Furthermore, COBL, MKX and MYOC expression in the subcutaneous AT of children is related to obesity and parameters of AT dysfunction and metabolic disease, such as adipocyte size, leptin levels and HOMA-IR. In conclusion, we identify COBL, MKX and MYOC as potential regulators of BAT development and show an association of these genes with early metabolic dysfunction in children. AU - Abdul Majeed, S.* AU - Dunzendorfer, H.* AU - Weiner, J.* AU - Heiker, J.T. AU - Kiess, W.* AU - Körner, A. AU - Landgraf, K.* C1 - 67529 C2 - 54092 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - COBL, MKX and MYOC are potential regulators of brown adipose tissue development associated with obesity-related metabolic dysfunction in children. JO - Int. J. Mol. Sci. VL - 24 IS - 4 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Leber's hereditary optic neuropathy (LHON) is a disease that affects the optical nerve, causing visual loss. The diagnosis of LHON is mostly defined by the identification of three pathogenic variants in the mitochondrial DNA. Idebenone is widely used to treat LHON patients, but only some of them are responders to treatment. In our study, we assessed the maximal respiration rate (MRR) and other respiratory parameters in eight fibroblast lines from subjects carrying LHON pathogenic variants. We measured also the effects of idebenone treatment on cell growth and mtDNA amounts. Results showed that LHON fibroblasts had significantly reduced respiratory parameters in untreated conditions, but no significant gain in MRR after idebenone supplementation. No major toxicity toward mitochondrial function and no relevant compensatory effect in terms of mtDNA quantity were found for the treatment at the tested conditions. Our findings confirmed that fibroblasts from subjects harboring LHON pathogenic variants displayed impaired respiration, regardless of the disease penetrance and severity. Testing responsiveness to idebenone treatment in cultured cells did not fully recapitulate in vivo data. The in-depth evaluation of cellular respiration in fibroblasts is a good approach to evaluating novel mtDNA variants associated with LHON but needs further evaluation as a potential biomarker for disease prognosis and treatment responsiveness. AU - Baglivo, M.* AU - Nasca, A.* AU - Lamantea, E.* AU - Vinci, S.* AU - Spagnolo, M.* AU - Marchet, S.* AU - Prokisch, H. AU - Catania, A.* AU - Lamperti, C.* AU - Ghezzi, D.* C1 - 67945 C2 - 54423 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Evaluation of mitochondrial dysfunction and idebenone responsiveness in fibroblasts from Leber's hereditary optic neuropathy (LHON) subjects. JO - Int. J. Mol. Sci. VL - 24 IS - 16 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Clonal hematopoiesis (CH)-associated mutations increase the risk of atherosclerotic cardiovascular diseases. However, it is unclear whether the mutations detected in circulating blood cells can also be detected in tissues associated with atherosclerosis, where they could affect physiology locally. To address this, the presence of CH mutations in peripheral blood, atherosclerotic lesions and associated tissues was assessed in a pilot study of 31 consecutive patients with peripheral vascular disease (PAD) who underwent open surgical procedures. Next-generation sequencing was used to screen the most commonly mutated loci (DNMT3A, TET2, ASXL1 and JAK2). Twenty CH mutations were detected in peripheral blood of 14 (45%) patients, 5 of whom had more than one mutation. TET2 (11 mutations, 55%) and DNMT3A (8 mutations, 40%) were the most frequently affected genes. Altogether, 88% of the mutations detectable in peripheral blood were also present in the atherosclerotic lesions. Twelve patients also had mutations in perivascular fat or subcutaneous tissue. The presence of CH mutations in PAD-associated tissues as well as in blood suggests that CH mutations may make a previously unknown contribution to PAD disease biology. AU - Büttner, P.* AU - Böttner, J.* AU - Krohn, K.* AU - Baber, R.* AU - Platzbecker, U.* AU - Cross, M.* AU - Desch, S.* AU - Thiele, H.* AU - Steiner, S. AU - Scheinert, D.* AU - Metzeler, K.H.* AU - Branzan, D. C1 - 67528 C2 - 54091 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Clonal hematopoiesis mutations are present in atherosclerotic lesions in peripheral artery disease. JO - Int. J. Mol. Sci. VL - 24 IS - 4 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Extracellular vesicles (EVs), through their cargo, are important mediators of bystander responses in the irradiated bone marrow (BM). MiRNAs carried by EVs can potentially alter cellular pathways in EV-recipient cells by regulating their protein content. Using the CBA/Ca mouse model, we characterised the miRNA content of BM-derived EVs from mice irradiated with 0.1 Gy or 3 Gy using an nCounter analysis system. We also analysed proteomic changes in BM cells either directly irradiated or treated with EVs derived from the BM of irradiated mice. Our aim was to identify key cellular processes in the EV-acceptor cells regulated by miRNAs. The irradiation of BM cells with 0.1 Gy led to protein alterations involved in oxidative stress and immune and inflammatory processes. Oxidative stress-related pathways were also present in BM cells treated with EVs isolated from 0.1 Gy-irradiated mice, indicating the propagation of oxidative stress in a bystander manner. The irradiation of BM cells with 3 Gy led to protein pathway alterations involved in the DNA damage response, metabolism, cell death and immune and inflammatory processes. The majority of these pathways were also altered in BM cells treated with EVs from mice irradiated with 3 Gy. Certain pathways (cell cycle, acute and chronic myeloid leukaemia) regulated by miRNAs differentially expressed in EVs isolated from mice irradiated with 3 Gy overlapped with protein pathway alterations in BM cells treated with 3 Gy EVs. Six miRNAs were involved in these common pathways interacting with 11 proteins, suggesting the involvement of miRNAs in the EV-mediated bystander processes. In conclusion, we characterised proteomic changes in directly irradiated and EV-treated BM cells, identified processes transmitted in a bystander manner and suggested miRNA and protein candidates potentially involved in the regulation of these bystander processes. AU - Csordás, I.B.* AU - Rutten, E.A.* AU - Szatmári, T.* AU - Subedi, P. AU - Cruz-Garcia, L.* AU - Kis, D.* AU - Jezsó, B.* AU - von Toerne, C. AU - Forgács, M.* AU - Sáfrány, G.* AU - Tapio, S. AU - Badie, C.* AU - Lumniczky, K.* C1 - 67878 C2 - 54356 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - The miRNA content of bone marrow-derived extracellular vesicles contributes to protein pathway alterations involved in ionising radiation-induced bystander responses. JO - Int. J. Mol. Sci. VL - 24 IS - 10 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Beyond the influence of lifestyle-related risk factors for myocardial infarction (MI), the mechanisms of genetic predispositions for MI remain unclear. We sought to identify and characterize differentially expressed genes in early-onset MI in a translational approach. In an observational case-control study, transcriptomes from 112 early-onset MI individuals showed upregulated G protein-coupled receptor 15 (GPR15) expression in peripheral blood mononuclear cells compared to controls (fold change = 1.4, p = 1.87 × 10-7). GPR15 expression correlated with intima-media thickness (β = 0.8498, p = 0.111), C-reactive protein (β = 0.2238, p = 0.0052), ejection fraction (β = -0.9991, p = 0.0281) and smoking (β = 0.7259, p = 2.79 × 10-10). The relation between smoking and MI was diminished after the inclusion of GPR15 expression as mediator in mediation analysis (from 1.27 (p = 1.9 × 10-5) to 0.46 (p = 0.21)). The DNA methylation of two GPR15 sites was 1%/5% lower in early-onset MI individuals versus controls (p = 2.37 × 10-6/p = 0.0123), with site CpG3.98251219 significantly predicting risk for incident MI (hazard ratio = 0.992, p = 0.0177). The nucleotide polymorphism rs2230344 (C/T) within GPR15 was associated with early-onset MI (odds ratio = 3.61, p = 0.044). Experimental validation showed 6.3-fold increased Gpr15 expression in an ischemic mouse model (p < 0.05) and 4-fold increased Gpr15 expression in cardiomyocytes under ischemic stress (p < 0.001). After the induction of MI, Gpr15gfp/gfp mice showed lower survival (p = 0.042) and deregulated gene expression for response to hypoxia and signaling pathways. Using a translational approach, our data provide evidence that GPR15 is linked to cardiovascular diseases, mediating the adverse effects of smoking. AU - Haase, T.* AU - Müller, C.* AU - Stoffers, B.* AU - Kirn, P.* AU - Waldenberger, M. AU - Kaiser, F.J.* AU - Karakas, M.* AU - Kim, S.V.* AU - Voss, S.* AU - Wild, P.S.* AU - Lackner, K.J.* AU - Andersson, J.* AU - Söderberg, S.* AU - Lindner, D.* AU - Zeller, T.* C1 - 67175 C2 - 53497 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - G Protein-coupled receptor 15 expression is associated with myocardial infarction. JO - Int. J. Mol. Sci. VL - 24 IS - 1 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Mutations in the HFE/Hfe gene cause Hereditary Hemochromatosis (HH), a highly prevalent genetic disorder characterized by elevated iron deposition in multiple tissues. HFE acts in hepatocytes to control hepcidin expression, whereas HFE actions in myeloid cells are required for cell-autonomous and systemic iron regulation in aged mice. To address the role of HFE specifically in liver-resident macrophages, we generated mice with a selective Hfe deficiency in Kupffer cells (HfeClec4fCre). The analysis of the major iron parameters in this novel HfeClec4fCre mouse model led us to the conclusion that HFE actions in Kupffer cells are largely dispensable for cellular, hepatic and systemic iron homeostasis. AU - Knoop, P.* AU - Yilmaz, D.* AU - Paganoni, R.* AU - Steele-Perkins, P.* AU - Gruber, A.* AU - Akdogan, B. AU - Zischka, H. AU - Leopold, K.* AU - Vujić Spasić, M.* C1 - 67877 C2 - 54355 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Hfe actions in Kupffer cells are dispensable for hepatic and systemic iron metabolism. JO - Int. J. Mol. Sci. VL - 24 IS - 10 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - MicroRNAs (miRNAs) recently emerged as means of communication between insulin-sensitive tissues to mediate diabetes development and progression, and as such they present a valuable proxy for epigenetic alterations associated with type 2 diabetes. In order to identify miRNA markers for the precursor of diabetes called prediabetes, we applied a translational approach encompassing analysis of human plasma samples, mouse tissues and an in vitro validation system. MiR-652-3p, miR-877-5p, miR-93-5p, miR-130a-3p, miR-152-3p and let-7i-5p were increased in plasma of women with impaired fasting glucose levels (IFG) compared to those with normal fasting glucose and normal glucose tolerance (NGT). Among these, let-7i-5p and miR-93-5p correlated with fasting blood glucose levels. Human data were then compared to miRNome data obtained from islets of Langerhans and adipose tissue of 10-week-old female New Zealand Obese mice, which differ in their degree of hyperglycemia and liver fat content. Similar to human plasma, let-7i-5p was increased in adipose tissue and islets of Langerhans of diabetes-prone mice. As predicted by the in silico analysis, overexpression of let-7i-5p in the rat β-cell line INS-1 832/12 resulted in downregulation of insulin signaling pathway components (Insr, Rictor, Prkcb, Clock, Sos1 and Kcnma1). Taken together, our integrated approach highlighted let-7i-5p as a potential regulator of whole-body insulin sensitivity and a novel marker of prediabetes in women. AU - Kovác, L.* AU - Speckmann, T.* AU - Jähnert, M.* AU - Gottmann, P.* AU - Fritsche, L. AU - Häring, H.-U. AU - Birkenfeld, A.L. AU - Fritsche, A. AU - Schürmann, A.* AU - Ouni, M.* C1 - 68746 C2 - 54956 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Identification of MicroRNAs associated with prediabetic status in obese women. JO - Int. J. Mol. Sci. VL - 24 IS - 21 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - In the eye, an increase in galectin-1 is associated with various chorioretinal diseases, in which retinal pigment epithelium (RPE) cells play a crucial role in disease development and progression. Since little is known about the function of endogenous galectin-1 in these cells, we developed a galectin-1-deficient immortalized RPE cell line (ARPE-19-LGALS1-/-) using a sgRNA/Cas9 all-in-one expression vector and investigated its cell biological properties. Galectin-1 deficiency was confirmed by Western blot analysis and immunocytochemistry. Cell viability and proliferation were significantly decreased in ARPE-19-LGALS1-/- cells when compared to wild-type controls. Further on, an increased attachment of galectin-1-deficient RPE cells was observed by cell adhesion assay when compared to control cells. The diminished viability and proliferation, as well as the enhanced adhesion of galectin-1-deficient ARPE-19 cells, could be blocked, at least in part, by the additional treatment with human recombinant galectin-1. In addition, a significantly reduced migration was detected in ARPE-19-LGALS1-/- cells. In comparison to control cells, galectin-1-deficient RPE cells had enhanced expression of sm-α-actin and N-cadherin, whereas expression of E-cadherin showed no significant alteration. Finally, a compensatory expression of galectin-8 mRNA was observed in ARPE-19-LGALS1-/- cells. In conclusion, in RPE cells, endogenous galectin-1 has crucial functions for various cell biological processes, including viability, proliferation, migration, adherence, and retaining the epithelial phenotype. AU - Liesenhoff, C.* AU - Paulus, S.M.* AU - Havertz, C.* AU - Geerlof, A. AU - Priglinger, S.* AU - Priglinger, C.S.* AU - Ohlmann, A.* C1 - 67944 C2 - 54422 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Endogenous galectin-1 modulates cell biological properties of immortalized retinal pigment epithelial cells in vitro. JO - Int. J. Mol. Sci. VL - 24 IS - 16 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - We aimed to analyse whether patients with ischaemic stroke (IS) occurring within eight days after the onset of COVID-19 (IS-COV) are associated with a specific aetiology of IS. We used SUPERGNOVA to identify genome regions that correlate between the IS-COV cohort (73 IS-COV cases vs. 701 population controls) and different aetiological subtypes. Polygenic risk scores (PRSs) for each subtype were generated and tested in the IS-COV cohort using PRSice-2 and PLINK to find genetic associations. Both analyses used the IS-COV cohort and GWAS from MEGASTROKE (67,162 stroke patients vs. 454,450 population controls), GIGASTROKE (110,182 vs. 1,503,898), and the NINDS Stroke Genetics Network (16,851 vs. 32,473). Three genomic regions were associated (p-value < 0.05) with large artery atherosclerosis (LAA) and cardioembolic stroke (CES). We found four loci targeting the genes PITX2 (rs10033464, IS-COV beta = 0.04, p-value = 2.3 × 10−2, se = 0.02), previously associated with CES, HS6ST1 (rs4662630, IS-COV beta = −0.04, p-value = 1.3 × 10−3, se = 0.01), TMEM132E (rs12941838 IS-COV beta = 0.05, p-value = 3.6 × 10−4, se = 0.01), and RFFL (rs797989 IS-COV beta = 0.03, p-value = 1.0 × 10−2, se = 0.01). A statistically significant PRS was observed for LAA. Our results suggest that IS-COV cases are genetically similar to LAA and CES subtypes. Larger cohorts are needed to assess if the genetic factors in IS-COV cases are shared with the general population or specific to viral infection. AU - Llucià-Carol, L.* AU - Muiño, E.* AU - Cullell, N.* AU - Cárcel-Márquez, J.* AU - Lledós, M.* AU - Gallego-Fabrega, C.* AU - Martin-Campos, J.* AU - Martí-Fàbregas, J.* AU - Aguilera-Simón, A.* AU - Planas, A.M.* AU - DeDiego, M.L.* AU - de Felipe Mimbrera, A.* AU - Masjuan, J.* AU - Garcia-Madrona, S.* AU - Segura, T.* AU - González-Villar, E.* AU - Serrano-Heras, G.* AU - Domínguez Mayoral, A.* AU - Menéndez-Valladares, P.* AU - Montaner, J.* AU - Migeotte, I.* AU - Rahmouni, S.* AU - Darcis, G.* AU - Bernardo, D.* AU - Rojo, S.* AU - Schulte, E.C. AU - Protzer, U. AU - Fricke, L.* AU - Winter, C.* AU - Niemi, M.E.K.* AU - Cordioli, M.* AU - Delgado, P.* AU - Fernandez-Cadenas, I.* C1 - 68304 C2 - 54719 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Genetic architecture of ischaemic strokes after COVID-19 shows similarities with large vessel strokes. JO - Int. J. Mol. Sci. VL - 24 IS - 17 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Proteoglycans are central components of the extracellular matrix (ECM) and binding partners for inflammatory chemokines. Morphological differences in the ECM and increased inflammation are prominent features of the white adipose tissues in patients with obesity. The impact of obesity and weight loss on the expression of specific proteoglycans in adipose tissue is not well known. This study aimed to investigate the relationship between adiposity and proteoglycan expression. We analyzed transcriptomic data from two human bariatric surgery cohorts. In addition, RT-qPCR was performed on adipose tissues from female and male mice fed a high-fat diet. Both visceral and subcutaneous adipose tissue depots were analyzed. Adipose mRNA expression of specific proteoglycans, proteoglycan biosynthetic enzymes, proteoglycan partner molecules, and other ECM-related proteins were altered in both human cohorts. We consistently observed more profound alterations in gene expression of ECM targets in the visceral adipose tissues after surgery (among others VCAN (p = 0.000309), OGN (p = 0.000976), GPC4 (p = 0.00525), COL1A1 (p = 0.00221)). Further, gene analyses in mice revealed sex differences in these two tissue compartments in obese mice. We suggest that adipose tissue repair is still in progress long after surgery, which may reflect challenges in remodeling increased adipose tissues. This study can provide the basis for more mechanistic studies on the role of proteoglycans in adipose tissues in obesity. AU - Meen, A.J.* AU - Doncheva, A.I.* AU - Böttcher, Y.* AU - Dankel, S.N.* AU - Hoffmann, A. AU - Blüher, M. AU - Fernø, J.* AU - Mellgren, G.* AU - Ghosh, A.* AU - Sun, W.* AU - Dong, H.* AU - Noé, F.* AU - Wolfrum, C.* AU - Pejler, G.* AU - Dalen, K.T.* AU - Kolset, S.O.* C1 - 67788 C2 - 54266 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Obesity is associated with distorted proteoglycan expression in adipose tissue. JO - Int. J. Mol. Sci. VL - 24 IS - 8 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - It is with great pleasure that we introduce this Special Issue on "Homeostasis: Metals and Cellular Redox and Immunity Status" [...]. AU - Michalke, B. AU - Venkataramani, V.* C1 - 67738 C2 - 54046 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Editorial to the special issue "Homeostasis: Metals and cellular redox and immunity status". JO - Int. J. Mol. Sci. VL - 24 IS - 5 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - The nuclear factor NF-kB is the master transcription factor in the inflammatory process by modulating the expression of pro-inflammatory genes. However, an additional level of complexity is the ability to promote the transcriptional activation of post-transcriptional modulators of gene expression as non-coding RNA (i.e., miRNAs). While NF-kB's role in inflammation-associated gene expression has been extensively investigated, the interplay between NF-kB and genes coding for miRNAs still deserves investigation. To identify miRNAs with potential NF-kB binding sites in their transcription start site, we predicted miRNA promoters by an in silico analysis using the PROmiRNA software, which allowed us to score the genomic region's propensity to be miRNA cis-regulatory elements. A list of 722 human miRNAs was generated, of which 399 were expressed in at least one tissue involved in the inflammatory processes. The selection of "high-confidence" hairpins in miRbase identified 68 mature miRNAs, most of them previously identified as inflammamiRs. The identification of targeted pathways/diseases highlighted their involvement in the most common age-related diseases. Overall, our results reinforce the hypothesis that persistent activation of NF-kB could unbalance the transcription of specific inflammamiRNAs. The identification of such miRNAs could be of diagnostic/prognostic/therapeutic relevance for the most common inflammatory-related and age-related diseases. AU - Micolucci, L.* AU - Matacchione, G.* AU - Albertini, M.C.* AU - Marra, M.* AU - Ramini, D.* AU - Giuliani, A.* AU - Sabbatinelli, J.* AU - Procopio, A.D.* AU - Olivieri, F.* AU - Marsico, A. AU - Monsurrò, V.* C1 - 67651 C2 - 53958 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - A data-mining approach to identify NF-kB-responsive microRNAs in tissues involved in inflammatory processes: Potential relevance in age-related diseases. JO - Int. J. Mol. Sci. VL - 24 IS - 6 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are anchored at the outer leaflet of eukaryotic plasma membranes (PMs) only by carboxy-terminal covalently coupled GPI. GPI-APs are known to be released from the surface of donor cells in response to insulin and antidiabetic sulfonylureas (SUs) by lipolytic cleavage of the GPI or upon metabolic derangement as full-length GPI-APs with the complete GPI attached. Full-length GPI-APs become removed from extracellular compartments by binding to serum proteins, such as GPI-specific phospholipase D (GPLD1), or insertion into the PMs of acceptor cells. Here, the interplay between the lipolytic release and intercellular transfer of GPI-APs and its potential functional impact was studied using transwell co-culture with human adipocytes as insulin-/SU-responsive donor cells and GPI-deficient erythroleukemia as acceptor cells (ELCs). Measurement of the transfer as the expression of full-length GPI-APs at the ELC PMs by their microfluidic chip-based sensing with GPI-binding α-toxin and GPI-APs antibodies and of the ELC anabolic state as glycogen synthesis upon incubation with insulin, SUs and serum yielded the following results: (i) Loss of GPI-APs from the PM upon termination of their transfer and decline of glycogen synthesis in ELCs, as well as prolongation of the PM expression of transferred GPI-APs upon inhibition of their endocytosis and upregulated glycogen synthesis follow similar time courses. (ii) Insulin and SUs inhibit both GPI-AP transfer and glycogen synthesis upregulation in a concentration-dependent fashion, with the efficacies of the SUs increasing with their blood glucose-lowering activity. (iii) Serum from rats eliminates insulin- and SU-inhibition of both GPI-APs' transfer and glycogen synthesis in a volume-dependent fashion, with the potency increasing with their metabolic derangement. (iv) In rat serum, full-length GPI-APs bind to proteins, among them (inhibited) GPLD1, with the efficacy increasing with the metabolic derangement. (v) GPI-APs are displaced from serum proteins by synthetic phosphoinositolglycans and then transferred to ELCs with accompanying stimulation of glycogen synthesis, each with efficacies increasing with their structural similarity to the GPI glycan core. Thus, both insulin and SUs either block or foster transfer when serum proteins are depleted of or loaded with full-length GPI-APs, respectively, i.e., in the normal or metabolically deranged state. The transfer of the anabolic state from somatic to blood cells over long distance and its "indirect" complex control by insulin, SUs and serum proteins support the (patho)physiological relevance of the intercellular transfer of GPI-APs. AU - Müller, G. AU - Müller, T.D. C1 - 67739 C2 - 54047 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Transfer of proteins from cultured human adipose to blood cells and induction of anabolic phenotype are controlled by serum, insulin and sulfonylurea drugs. JO - Int. J. Mol. Sci. VL - 24 IS - 5 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - The World Health Organization recommends exclusive breastfeeding on demand until at least the sixth month of life. Breast milk or infant formula is the infant's primary food source until the age of one year, followed by the gradual introduction of other foods. During weaning, the intestinal microbiota evolves to a profile close to that of the adult, and its disruption can result in an increased incidence of acute infectious diseases. We aimed to determine whether a novel starting formula (INN) provides gut microbiota compositions more similar to those of breastfed (BF) infants from 6 to 12 months of age compared to a standard formula (STD). This study included 210 infants (70 per group) who completed the intervention until they reached the age of 12 months. In the intervention period, infants were divided into three groups. Group 1 received an INN formula with a lower protein content, a casein to whey protein ratio of approximately 70/30, twice as much docosahexaenoic acid as the STD formula, a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis, BPL1TM HT), and twice as much arachidonic acid as the STD formula contained. The second group received the STD formula, while the third group was exclusively BF for exploratory purposes. In the course of the study, visits were conducted at 6 months and 12 months of age. Compared to the BF and STD groups, the Bacillota phylum levels in the INN group were significantly reduced after 6 months. At the end of 6 months, the alpha diversity indices of the BF and INN groups differed significantly from those of the STD group. At 12 months, the Verrucomicrobiota phylum levels in the STD group were significantly lower than those in the BF and INN groups. Based on the comparison between 6 and 12 months, the Bacteroidota phylum levels in the BF group were significantly higher than those in the INN and STD groups. When comparing the INN group with the BF and STD groups, Clostridium sensu stricto 1 was significantly higher in the INN group. The STD group had higher levels of calprotectin than the INN and BF groups at 6 months. The immunoglobulin A levels in the STD group were significantly lower than those in the INN and BF groups after 6 months. Both formulas had significantly higher levels of propionic acid than the BF group at 6 months. At 6 months, the STD group showed a higher quantification of all metabolic pathways than the BF group. The INN formula group exhibited similar behavior to the BF group, except for the superpathway of phospholipid biosynthesis (E. coli). We hypothesize that the novel INN formula may promote an intestinal microbiota that is more similar to the microbiota of an infant who consumes only human milk before the weaning period. AU - Plaza-Díaz, J.* AU - Ruiz Ojeda, F.J. AU - Morales, J.* AU - Martín-Masot, R.* AU - Climent, E.* AU - Silva, * AU - Martinez-Blanch, J.F.* AU - Enrique, M.* AU - Tortajada, M.* AU - Ramon, D.* AU - Alvarez, B.* AU - Chenoll, E.* AU - Gil, Á. C1 - 67787 C2 - 54265 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Innova 2020: A follow-up study of the fecal microbiota of infants using a novel infant formula between 6 months and 12 months of age. JO - Int. J. Mol. Sci. VL - 24 IS - 8 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Exclusive breastfeeding is highly recommended for infants for at least the first six months of life. However, for some mothers, it may be difficult or even impossible to do so. This can lead to disturbances in the gut microbiota, which in turn may be related to a higher incidence of acute infectious diseases. Here, we aimed to evaluate whether a novel starting formula versus a standard formula provides a gut microbiota composition more similar to that of breastfed infants in the first 6 months of life. Two hundred and ten infants (70/group) were enrolled in the study and completed the intervention until 12 months of age. For the intervention period, infants were divided into three groups: Group 1 received formula 1 (INN) with a lower amount of protein, a proportion of casein to whey protein ratio of about 70/30 by increasing the content of α-lactalbumin, and with double the amount of docosahexaenoic acid/arachidonic acid than the standard formula; INN also contained a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis). Group 2 received the standard formula (STD) and the third group was exclusively breastfed (BF) for exploratory analysis. During the study, visits were made at 21 days, 2, 4, and 6 months of age, with ±3 days for the visit at 21 days of age, ±1 week for the visit at 2 months, and ±2 weeks for the others. Here, we reveal how consuming the INN formula promotes a similar gut microbiota composition to those infants that were breastfed in terms of richness and diversity, genera, such as Bacteroides, Bifidobacterium, Clostridium, and Lactobacillus, and calprotectin and short-chain fatty acid levels at 21 days, 2 and 6 months. Furthermore, we observed that the major bacteria metabolic pathways were more alike between the INN formula and BF groups compared to the STD formula group. Therefore, we assume that consumption of the novel INN formula might improve gut microbiota composition, promoting a healthier intestinal microbiota more similar to that of an infant who receives exclusively human milk. AU - Ruiz Ojeda, F.J. AU - Plaza-Díaz, J.* AU - Morales, J.* AU - Álvarez-Calatayud, G.* AU - Climent, E.* AU - Silva, A.* AU - Martinez-Blanch, J.F.* AU - Enrique, M.* AU - Tortajada, M.* AU - Ramon, D.* AU - Alvarez, B.* AU - Chenoll, E.* AU - Gil, A.* C1 - 67439 C2 - 54137 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Effects of a novel infant formula on the fecal microbiota in the first six months of life: The INNOVA 2020 Study. JO - Int. J. Mol. Sci. VL - 24 IS - 3 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Kidney fibrosis is a major culprit in the development and progression of chronic kidney disease (CKD), ultimately leading to the irreversible loss of organ function. Thymocyte differentiation antigen-1 (Thy-1) controls many core functions of fibroblasts relevant to fibrogenesis but is also found in a soluble form (sThy-1) in serum and urine. We investigated the association of sThy-1 with clinical parameters in patients with CKD receiving hemodialysis treatment compared to individuals with a preserved renal function. Furthermore, Thy-1 tissue expression was detected in a mouse model of diabetic CKD (eNOS-/-; db/db) and non-diabetic control mice (eNOS-/-). Serum and urinary sThy-1 concentrations significantly increased with deteriorating renal function, independent of the presence of diabetes. Serum creatinine is the major, independent, and inverse predictor of serum sThy-1 levels. Moreover, sThy-1 is not only predicted by markers of renal function but is also itself an independent and strong predictor of markers of renal function, i.e., serum creatinine. Mice with severe diabetic CKD show increased Thy-1 mRNA and protein expression in the kidney compared to control animals, as well as elevated urinary sThy-1 levels. Pro-fibrotic mediators, such as interleukin (IL)-4, IL-13, IL-6 and transforming growth factor β, increase Thy-1 gene expression and release of sThy-1 from fibroblasts. Our data underline the role of Thy-1 in the control of kidney fibrosis in CKD and raise the opportunity that Thy-1 may function as a renal antifibrotic factor. AU - Saalbach, A.* AU - Anderegg, U.* AU - Wendt, R.* AU - Beige, J.* AU - Bachmann, A.* AU - Klöting, N. AU - Blüher, M. AU - Zhang, M.Z.* AU - Harris, R.C.* AU - Stumvoll, M.* AU - Tönjes, A.* AU - Ebert, T.* C1 - 67442 C2 - 54139 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Antifibrotic soluble thy-1 correlates with renal dysfunction in chronic kidney disease. JO - Int. J. Mol. Sci. VL - 24 IS - 3 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Previously, we found that human pancreatic preadipocytes (PPAs) and islets influence each other and that the crosstalk with the fatty liver via the hepatokine fetuin-A/palmitate induces inflammatory responses. Here, we examined whether the mRNA-expression of pancreatic extracellular matrix (ECM)-forming and -degrading components differ in PPAs from individuals with normal glucose regulation (PPAs-NGR), prediabetes (PPAs-PD), and type 2 diabetes (PPAs-T2D), and whether fetuin-A/palmitate impacts ECM-formation/degradation and associated monocyte invasion. Human pancreatic resections were analyzed (immuno)histologically. PPAs were studied for mRNA expression by real-time PCR and protein secretion by Luminex analysis. Furthermore, co-cultures with human islets and monocyte migration assays in Transwell plates were conducted. We found that in comparison with NGR-PPAs, TIMP-2 mRNA levels were lower in PPAs-PD, and TGF-β1 mRNA levels were higher in PPAs-T2D. Fetuin-A/palmitate reduced fibronectin, decorin, TIMP-1/-2 and TGF-ß1 mRNA levels. Only fibronectin was strongly downregulated by fetuin-A/palmitate independently of the glycemic status. Co-culturing of PPAs with islets increased TIMP-1 mRNA expression in islets. Fetuin-A/palmitate increased MMP-1, usherin and dermatopontin mRNA-levels in co-cultured islets. A transmigration assay showed increased monocyte migration towards PPAs, which was enhanced by fetuin-A/palmitate. This was more pronounced in PPAs-T2D. The expression of distinct ECM components differs in PPAs-PD and PPAs-T2D compared to PPAs-NGR, suggesting that ECM alterations can occur even in mild hyperglycemia. Fetuin-A/palmitate impacts on ECM formation/degradation in PPAs and co-cultured islets. Fetuin-A/palmitate also enhances monocyte migration, a process which might impact on matrix turnover. AU - Siegel-Axel, D. AU - Barroso Oquendo, M. AU - Gerst, F. AU - Fend, F.* AU - Wagner, R. AU - Heni, M. AU - Königsrainer, A.* AU - Häring, H.-U. AU - Fritsche, A. AU - Schleicher, E. AU - Birkenfeld, A.L. AU - Stefan, N. C1 - 68104 C2 - 54582 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Extracellular matrix expression in human pancreatic fat cells of patients with normal glucose regulation, prediabetes and type 2 diabetes. JO - Int. J. Mol. Sci. VL - 24 IS - 13 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - In previous genome-wide association studies (GWAS), genetic loci associated with obesity and impaired fat distribution (FD) have been identified. In the present study, we elucidated the role of the PEMT gene, including the waist-hip-ratio-associated single nucleotide polymorphism rs4646404, and its influence on obesity-related metabolic traits. DNA from 2926 metabolically well-characterized subjects was used for genotyping. PEMT expression was analyzed in paired visceral (vis) and subcutaneous (sc) adipose tissue (AT) from a subset of 574 individuals. Additionally, PEMT expression was examined in vis, sc AT and liver tissue in a separate cohort of 64 patients with morbid obesity and liver disease. An in vitro Pemt knockdown was conducted in murine epididymal and inguinal adipocytes. Our findings highlight tissue-specific variations in PEMT mRNA expression across the three studied tissues. Specifically, vis PEMT mRNA levels correlated significantly with T2D and were implicated in the progression of non-alcoholic steatohepatitis (NASH), in contrast to liver tissue, where no significant associations were found. Moreover, sc PEMT expression showed significant correlations with several anthropometric- and metabolic-related parameters. The rs4646404 was associated with vis AT PEMT expression and also with diabetes-related traits. Our in vitro experiments supported the influence of PEMT on adipogenesis, emphasizing its role in AT biology. In summary, our data suggest that PEMT plays a role in regulating FD and has implications in metabolic diseases. AU - Sun, C.* AU - Holstein, D.J.F.* AU - Garcia-Cubero, N.* AU - Moulla, Y.* AU - Stroh, C.* AU - Dietrich, A.* AU - Schön, M.R.* AU - Gärtner, D.* AU - Lohmann, T.* AU - Dressler, M.* AU - Stumvoll, M. AU - Blüher, M. AU - Kovacs, P.* AU - Guiu-Jurado, E.* C1 - 68929 C2 - 53772 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - The role of phosphatidylethanolamine N-methyltransferase (PEMT) and its waist-hip-ratio-associated locus rs4646404 in obesity-related metabolic Traits and liver disease. JO - Int. J. Mol. Sci. VL - 24 IS - 23 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Aberrant miRNA expression has been associated with a large number of human diseases. Therefore, targeting miRNAs to regulate their expression levels has become an important therapy against diseases that stem from the dysfunction of pathways regulated by miRNAs. In recent years, small molecules have demonstrated enormous potential as drugs to regulate miRNA expression (i.e., SM-miR). A clear understanding of the mechanism of action of small molecules on the upregulation and downregulation of miRNA expression allows precise diagnosis and treatment of oncogenic pathways. However, outside of a slow and costly process of experimental determination, computational strategies to assist this on an ad hoc basis have yet to be formulated. In this work, we developed, to the best of our knowledge, the first cross-platform prediction tool, DeepsmirUD, to infer small-molecule-mediated regulatory effects on miRNA expression (i.e., upregulation or downregulation). This method is powered by 12 cutting-edge deep-learning frameworks and achieved AUC values of 0.843/0.984 and AUCPR values of 0.866/0.992 on two independent test datasets. With a complementarily constructed network inference approach based on similarity, we report a significantly improved accuracy of 0.813 in determining the regulatory effects of nearly 650 associated SM-miR relations, each formed with either novel small molecule or novel miRNA. By further integrating miRNA-cancer relationships, we established a database of potential pharmaceutical drugs from 1343 small molecules for 107 cancer diseases to understand the drug mechanisms of action and offer novel insight into drug repositioning. Furthermore, we have employed DeepsmirUD to predict the regulatory effects of a large number of high-confidence associated SM-miR relations. Taken together, our method shows promise to accelerate the development of potential miRNA targets and small molecule drugs. AU - Sun, J.* AU - Ru, J. AU - Ramos-Mucci, L.* AU - Qi, F.* AU - Chen, Z.* AU - Chen, S.* AU - Cribbs, A.P.* AU - Deng, L. AU - Wang, X.* C1 - 67441 C2 - 54140 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - DeepsmirUD: Prediction of regulatory effects on microRNA expression mediated by small molecules using deep learning. JO - Int. J. Mol. Sci. VL - 24 IS - 3 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease, including end-stage kidney disease, and increases the risk of cardiovascular mortality. Although the treatment options for DKD, including angiotensin-converting enzyme inhibitors, angiotensin II receptor blockers, sodium-glucose cotransporter 2 inhibitors, and mineralocorticoid receptor antagonists, have advanced, their efficacy is still limited. Thus, a deeper understanding of the molecular mechanisms of DKD onset and progression is necessary for the development of new and innovative treatments for DKD. The complex pathogenesis of DKD includes various different pathways, and the mechanisms of DKD can be broadly classified into inflammatory, fibrotic, metabolic, and hemodynamic factors. Here, we summarize the recent findings in basic research, focusing on each factor and recent advances in the treatment of DKD. Collective evidence from basic and clinical research studies is helpful for understanding the definitive mechanisms of DKD and their regulatory systems. Further comprehensive exploration is warranted to advance our knowledge of the pathogenesis of DKD and establish novel treatments and preventive strategies. AU - Watanabe, K.* AU - Sato, E.* AU - Mishima, E. AU - Miyazaki, M.* AU - Tanaka, T.* C1 - 67174 C2 - 53425 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - What's new in the molecular mechanisms of diabetic kidney disease: Recent advances. JO - Int. J. Mol. Sci. VL - 24 IS - 1 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) are a new class of medications for managing renal anemia in patients with chronic kidney disease (CKD). In addition to their erythropoietic activity, HIF-PHIs exhibit multifaceted effects on iron and glucose metabolism, mitochondrial metabolism, and angiogenesis through the regulation of a wide range of HIF-responsive gene expressions. However, the systemic biological effects of HIF-PHIs in CKD patients have not been fully explored. In this prospective, single-center study, we comprehensively investigated changes in plasma metabolomic profiles following the switch from an erythropoiesis-stimulating agent (ESA) to an HIF-PHI, daprodustat, in 10 maintenance hemodialysis patients. Plasma metabolites were measured before and three months after the switch from an ESA to an HIF-PHI. Among 106 individual markers detected in plasma, significant changes were found in four compounds (erythrulose, n-butyrylglycine, threonine, and leucine), and notable but non-significant changes were found in another five compounds (inositol, phosphoric acid, lyxose, arabinose, and hydroxylamine). Pathway analysis indicated decreased levels of plasma metabolites, particularly those involved in phosphatidylinositol signaling, ascorbate and aldarate metabolism, and inositol phosphate metabolism. Our results provide detailed insights into the systemic biological effects of HIF-PHIs in hemodialysis patients and are expected to contribute to an evaluation of the potential side effects that may result from long-term use of this class of drugs. AU - Watanabe, K.* AU - Sato, E.* AU - Mishima, E. AU - Moriya, S.* AU - Sakabe, T.* AU - Sato, A.* AU - Fujiwara, M.* AU - Fujimaru, T.* AU - Ito, Y.* AU - Taki, F.* AU - Nagahama, M.* AU - Tanaka, K.* AU - Kazama, J.J.* AU - Nakayama, M.* C1 - 67943 C2 - 54421 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Changes in metabolomic profiles induced by switching from an erythropoiesis-stimulating agent to a hypoxia-inducible factor prolyl hydroxylase inhibitor in hemodialysis patients: A pilot study. JO - Int. J. Mol. Sci. VL - 24 IS - 16 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - CRISPR/Cas systems are some of the most promising tools for therapeutic genome editing. The use of these systems is contingent on the optimal designs of guides and homology-directed repair (HDR) templates. While this design can be achieved in silico, validation and further optimization are usually performed with the help of reporter systems. Here, we describe a novel reporter system, termed BETLE, that allows for the fast, sensitive, and cell-specific detection of genome editing and template-specific HDR by encoding multiple reporter proteins in different open-reading frames. Out-of-frame non-homologous end joining (NHEJ) leads to the expression of either secretable NanoLuc luciferase, enabling a highly sensitive and low-cost analysis of editing, or fluorescent mTagBFP2, allowing for the enumeration and tissue-specific localization of genome-edited cells. BETLE includes a site to validate CRISPR/Cas systems for a sequence-of-interest, making it broadly adaptable. We evaluated BETLE using a defective moxGFP with a 39-base-pair deletion and showed spCas9, saCas9, and asCas12a editing as well as sequence-specific HDR and the repair of moxGFP in cell lines with single and multiple reporter integrants. Taken together, these data show that BETLE allows for the rapid detection and optimization of CRISPR/Cas genome editing and HDR in vitro and represents a state-of the art tool for future applications in vivo. AU - Wettengel, J.M. AU - Hansen-Palmus, L. AU - Yusova, S.* AU - Rust, L.* AU - Biswas, S.* AU - Carson, J.* AU - Ryu, J.* AU - Bimber, B.N.* AU - Hennebold, J.D.* AU - Burwitz, B.J.* C1 - 67805 C2 - 54283 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - A multifunctional and highly adaptable reporter system for CRISPR/Cas editing. JO - Int. J. Mol. Sci. VL - 24 IS - 9 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Biallelic variants in ABCA3, the gene encoding the lipid transporter ATP-binding cassette subfamily A member 3 (ABCA3) that is predominantly expressed in alveolar type II cells, may cause interstitial lung diseases in children (chILD) and adults. Currently, there is no proven therapy, but, frequently, hydroxychloroquine (HCQ) is used empirically. We hypothesized that the in vitro responsiveness to HCQ might correlate to patients' clinical outcomes from receiving HCQ therapy. The clinical data of the subjects with chILD due to ABCA3 deficiency and treated with HCQ were retrieved from the literature and the Kids Lung Register data base. The in vitro experiments were conducted on wild type (WT) and 16 mutant ABCA3-HA-transfected A549 cells. The responses of the functional read out were assessed as the extent of deviation from the untreated WT. With HCQ treatment, 19 patients had improved or unchanged respiratory conditions, and 20 had respiratory deteriorations, 5 of whom transiently improved then deteriorated. The in vitro ABCA3 functional assays identified two variants with complete response, five with partial response, and nine with no response to HCQ. The variant-specific HCQ effects in vivo closely correlated to the in vitro data. An ABCA3+ vesicle volume above 60% of the WT volume was linked to responsiveness to HCQ; the HCQ treatment response was concentration dependent and differed for variants in vitro. We generated evidence for an ABCA3 variant-dependent impact of the HCQ in vitro. This may also apply for HCQ treatment in vivo, as supported by the retrospective and uncontrolled data from the treatment of chILD due to ABCA3 deficiency. AU - Yang, X.* AU - Forstner, M.* AU - Rapp, C.K.* AU - Rothenaigner, I. AU - Li, Y.* AU - Hadian, K. AU - Griese, M.* C1 - 67806 C2 - 54284 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - ABCA3 deficiency-variant-specific response to hydroxychloroquine. JO - Int. J. Mol. Sci. VL - 24 IS - 9 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - As the first barrier of the human body, the skin has been of great concern for its wound healing and regeneration. The healing of large, refractory wounds is difficult to be repaired by cell proliferation at the wound edges and usually requires manual intervention for treatment. Therefore, therapeutic tools such as stem cells, biomaterials, and cytokines have been applied to the treatment of skin wounds. Skin microenvironment modulation is a key technology to promote wound repair and skin regeneration. In recent years, a series of novel bioactive materials that modulate the microenvironment and cell behavior have been developed, showing the ability to efficiently facilitate wound repair and skin attachment regeneration. Meanwhile, our lab found that the fascial layer has an indispensable role in wound healing and repair, and this review summarizes the research progress of related bioactive materials and their role in wound healing. AU - Ye, H. AU - Rinkevich, Y. C1 - 67440 C2 - 54138 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Fascia layer-a novel target for the application of biomaterials in skin wound healing. JO - Int. J. Mol. Sci. VL - 24 IS - 3 PB - Mdpi PY - 2023 SN - 1661-6596 ER - TY - JOUR AB - Atopic eczema (AE) is an inflammatory skin disorder affecting approximately 20% of children worldwide and early onset can lead to asthma and allergies. Currently, the mechanisms of the disease are not fully understood. Metabolomics, the analysis of small molecules in the skin produced by the host and microbes, opens a window to observe the mechanisms of the disease which then may lead to new drug targets for AE treatment. Here, we review the latest advances in AE metabolomics, highlighting both the lipid and non-lipid molecules, along with reviewing the metabolites currently known to reside in the skin. AU - Afghani, J. AU - Traidl-Hoffmann, C. AU - Schmitt-Kopplin, P. AU - Reiger, M. AU - Müller, C. C1 - 65928 C2 - 52636 TI - An overview of the latest metabolomics studies on atopic eczema with new directions for study. JO - Int. J. Mol. Sci. VL - 23 IS - 15 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Triple-negative breast cancer is the most common and most deadly cancer among women. Radiation is a mainstay of treatment, administered after surgery, and used in the hope that any remaining cancer cells will be destroyed. While the cancer cell response is normally the focus of radiation therapy, little is known about the tumor microenvironment response after irradiation. It is widely reported that increased collagen expression and deposition are associated with cancer progression and poor prognosis in breast cancer patients. Aside from the classical fibrotic response, ratios of collagen isoforms have not been studied in a radiated tumor microenvironment. Here, we created one healthy co-culture of stromal fibroblasts and adipose-derived stem cells, and one triple-negative breast cancer co-culture, made of stromal fibroblasts, adipose derived stem cells, and triple-negative breast cancer cells. After irradiation, growth and decellularization of co-cultures, we reseeded the breast cancer cells for 24 h and analyzed the samples using mass spectrometry. Proteomic analysis revealed that collagen VI, a highly oncogenic collagen isoform linked to breast cancer, was decreased in the irradiated cancer co-culture. This indicates that the anti-cancer impact of radiation may be not only cell ablative, but also influential in creating a less oncogenic microenvironment. AU - Brett, E.* AU - Rosemann, M. AU - Azimzadeh, O. AU - Pagani, A.* AU - Prahm, C.* AU - Daigeler, A.* AU - Duscher, D.* AU - Kolbenschlag, J.* C1 - 65855 C2 - 52943 TI - Irradiated triple-negative breast cancer co-culture produces a less oncogenic extracellular matrix. JO - Int. J. Mol. Sci. VL - 23 IS - 15 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Diabetes is among the most prevalent diseases of the modern world and is strongly linked to an increased risk of numerous neurodegenerative disorders, although the exact pathophysiological mechanisms are not clear yet. Insulin resistance is a serious pathological condition, connecting type 2 diabetes, metabolic syndrome, and obesity. Recently, insulin resistance has been proven to be connected also to cognitive decline and dementias, including the most prevalent form, Alzheimer's disease. The relationship between diabetes and Alzheimer's disease regarding pathophysiology is so significant that it has been proposed that some presentations of the condition could be termed type 3 diabetes. AU - Cater, M.* AU - Hölter, S.M. C1 - 66448 C2 - 52949 TI - A pathophysiological intersection of diabetes and alzheimer's disease. JO - Int. J. Mol. Sci. VL - 23 IS - 19 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - In the pathophysiology of autoimmune-mediated uveitis, granulocytes have emerged as possible disease mediators and were shown to be pre-activated in equine recurrent uveitis (ERU), a spontaneous disease model. We therefore used granulocytes from ERU horses to identify early molecular mechanisms involved in this dysregulated innate immune response. Primary granulocytes from healthy and ERU horses were stimulated with IL8, and cellular response was analyzed with differential proteomics, which revealed significant differences in protein abundance of 170 proteins in ERU. Subsequent ingenuity pathway analysis identified three activated canonical pathways "PKA signaling", "PTEN signaling" and "leukocyte extravasation". Clustered to the leukocyte extravasation pathway, we found the membrane-type GPI-anchored protease MMP25, which was increased in IL8 stimulated ERU granulocytes. These findings point to MMP25 as a possible regulator of granulocyte extravasation in uveitis and a role of this molecule in the impaired integrity of the blood-retina-barrier. In conclusion, our analyses show a clearly divergent reaction profile of pre-activated granulocytes upon IL8 stimulation and provide basic information for further in-depth studies on early granulocyte activation in non-infectious ocular diseases. This may be of interest for the development of new approaches in uveitis diagnostics and therapy. Raw data are available via ProteomeXchange with identifier PXD013648. AU - Hoffmann, A.L.C.* AU - Hauck, S.M. AU - Deeg, C.A.* AU - Degroote, R.L.* C1 - 66161 C2 - 53099 TI - Pre-activated granulocytes from an autoimmune uveitis model show divergent pathway activation profiles upon IL8 stimulation in vitro. JO - Int. J. Mol. Sci. VL - 23 IS - 17 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Microbeam radiotherapy (MRT), an experimental high-dose rate concept with spatial fractionation at the micrometre range, has shown a high therapeutic potential as well as good preservation of normal tissue function in pre-clinical studies. We investigated the suitability of MRT as a simultaneously integrated boost (SIB) in conventional whole-brain irradiation (WBRT). A 174 Gy MRT SIB was administered with an array of quasi-parallel, 50 µm wide microbeams spaced at a centre-to-centre distance of 400 µm either on the first or last day of a 5 × 4 Gy radiotherapy schedule in healthy adult C57 BL/6J mice and in F98 glioma cell cultures. The animals were observed for signs of intracranial pressure and focal neurologic signs. Colony counts were conducted in F98 glioma cell cultures. No signs of acute adverse effects were observed in any of the irradiated animals within 3 days after the last irradiation fraction. The tumoricidal effect on F98 cell in vitro was higher when the MRT boost was delivered on the first day of the irradiation course, as opposed to the last day. Therefore, the MRT SIB should be integrated into a clinical radiotherapy schedule as early as possible. AU - Jaekel, F.* AU - Bräuer-Krisch, E.* AU - Bartzsch, S. AU - Laissue, J.* AU - Blattmann, H.* AU - Scholz, M.* AU - Soloviova, J.* AU - Hildebrandt, G.* AU - Schueltke, E.* C1 - 65931 C2 - 52639 TI - Microbeam irradiation as a simultaneously integrated boost in a conventional whole-brain radiotherapy protocol. JO - Int. J. Mol. Sci. VL - 23 IS - 15 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Lung epithelial organoids for the hazard assessment of inhaled nanomaterials offer a promising improvement to in vitro culture systems used so far. Organoids grow in three-dimensional (3D) spheres and can be derived from either induced pluripotent stem cells (iPSC) or primary lung tissue stem cells from either human or mouse. In this perspective we will highlight advantages and disadvantages of traditional culture systems frequently used for testing nanomaterials and compare them to lung epithelial organoids. We also discuss the differences between tissue and iPSC-derived organoids and give an outlook in which direction the whole field could possibly go with these versatile tools. AU - Kastlmeier, M.T. AU - Günther, E. AU - Stöger, T. AU - Voss, C. C1 - 67092 C2 - 53461 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Lung organoids for hazard assessment of nanomaterials. JO - Int. J. Mol. Sci. VL - 23 IS - 24 PB - Mdpi PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Although the common pathology of Alzheimer's disease (AD) and white matter hyperintensities (WMH) is disputed, the gene TREML2 has been implicated in both conditions: its whole-blood gene expression was associated with WMH volume and its missense variant rs3747742 with AD risk. We re-examined those associations within one comprehensive dataset of the general population, additionally searched for cross-relations and illuminated the role of the apolipoprotein E (APOE) ε4 status in the associations. For our linear regression and linear mixed effect models, we used 1949 participants from the Study of Health in Pomerania (Germany). AD was assessed using a continuous pre-symptomatic MRI-based score evaluating a participant's AD-related brain atrophy. In our study, increased whole-blood TREML2 gene expression was significantly associated with reduced WMH volume but not with the AD score. Conversely, rs3747742-C was significantly associated with a reduced AD score but not with WMH volume. The APOE status did not influence the associations. In sum, TREML2 robustly associated with WMH volume and AD-related brain atrophy on different molecular levels. Our results thus underpin TREML2's role in neurodegeneration, might point to its involvement in AD and WMH via different biological mechanisms, and highlight TREML2 as a worthwhile target for disentangling the two pathologies. AU - Kühn, A.L.* AU - Frenzel, S.* AU - Teumer, A.* AU - Wittfeld, K.* AU - Garvert, L.* AU - Weihs, A.* AU - Homuth, G.* AU - Prokisch, H. AU - Bülow, R.* AU - Nauck, M.* AU - Völker, U.* AU - Völzke, H.* AU - Grabe, H.J.* AU - Van der Auwera, S.* C1 - 66858 C2 - 53329 TI - TREML2 gene expression and its missense variant rs3747742 associate with white matter hyperintensity volume and Alzheimer's disease-related brain atrophy in the general population. JO - Int. J. Mol. Sci. VL - 23 IS - 22 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Diverse isotopes such as 2H, 3He, 10Be, 11C and 14C occur in nuclear reactions in ion beam radiotherapy, in cosmic ray shielding, or are intentionally accelerated in dating techniques. However, only a few studies have specifically addressed the biological effects of diverse isotopes and were limited to energies of several MeV/u. A database of simulations with the PARTRAC biophysical tool is presented for H, He, Li, Be, B and C isotopes at energies from 0.5 GeV/u down to stopping. The doses deposited to a cell nucleus and also the yields per unit dose of single- and double-strand breaks and their clusters induced in cellular DNA are predicted to vary among diverse isotopes of the same element at energies < 1 MeV/u, especially for isotopes of H and He. The results may affect the risk estimates for astronauts in deep space missions or the models of biological effectiveness of ion beams and indicate that radiation protection in 14C or 10Be dating techniques may be based on knowledge gathered with 12C or 9Be. AU - Kundrát, P.* AU - Friedland, W. AU - Baiocco, G.* C1 - 66859 C2 - 53330 TI - Track structure-based simulations on DNA damage induced by diverse isotopes. JO - Int. J. Mol. Sci. VL - 23 IS - 22 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Element analysis in clinical or biological samples is important due to the essential role in clinical diagnostics, drug development, and drug-effect monitoring. Particularly, the specific forms of element binding, actual redox state, or their spatial distribution in tissue or in single cells are of interest in medical research. This review summarized exciting combinations of sophisticated sample delivery systems hyphenated to inductively coupled plasma-mass spectrometry (ICP-MS), enabling a broadening of information beyond the well-established outstanding detection capability. Deeper insights into pathological disease processes or intracellular distribution of active substances were provided, enabling a better understanding of biological processes and their dynamics. Examples were presented from spatial elemental mapping in tissue, cells, or spheroids, also considering elemental tagging. The use of natural or artificial tags for drug monitoring was shown. In the context of oxidative stress and ferroptosis iron, redox speciation gained importance. Quantification methods for Fe2+, Fe3+, and ferritin-bound iron were introduced. In Wilson's disease, free and exchangeable copper play decisive roles; the respective paragraph provided information about hyphenated Cu speciation techniques, which provide their fast and reliable quantification. Finally, single cell ICP-MS provides highly valuable information on cell-to-cell variance, insights into uptake of metal-containing drugs, and their accumulation and release on the single-cell level. AU - Michalke, B. C1 - 65446 C2 - 52685 TI - Review about powerful combinations of advanced and hy-phenated sample introduction techniques with inductively coupled plasma- mass spectrometry (ICP-MS) for elucidating trace element species in pathologic conditions on a molecular level. JO - Int. J. Mol. Sci. VL - 23 IS - 11 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - (1) Adipsin is an adipokine that may link increased fat mass and adipose tissue dysfunction to obesity-related cardiometabolic diseases. Here, we investigated whether adipsin serum concentrations and adipose tissue (AT) adipsin mRNA expression are related to parameters of AT function, obesity and type 2 diabetes (T2D). (2) Methods: A cohort of 637 individuals with a wide range of age and body weight (Age: 18–85 years; BMI: 19–70 kg/m2 ) with (n = 237) or without (n = 400) T2D was analyzed for serum adipsin concentrations by ELISA and visceral (VAT) and subcutaneous (SAT) adipsin mRNA expression by RT-PCR. (3) Results: Adipsin serum concentrations were significantly higher in patients with T2D compared to normoglycemic individuals. We found significant positive univariate relationships of adipsin serum concentrations with age (r = 0.282, p < 0.001), body weight (r = 0.264, p<0.001), fasting plasma glucose (r = 0.136, p = 0.006) and leptin serum concentrations (r = 0.362, p < 0.001). Neither VAT nor SAT adipsin mRNA expression correlated with adipsin serum concentrations after adjusting for age, sex and BMI. Independent of T2D status, we found significantly higher adipsin expression in SAT compared to VAT (4) Conclusions: Our data suggest that adipsin serum concentrations are strongly related to obesity and age. However, neither circulating adipsin nor adipsin AT expression reflects parameters of impaired glucose or lipid metabolism in patients with obesity with or without T2D. AU - Milek, M.* AU - Moulla, Y.* AU - Kern, M. AU - Stroh, C.* AU - Dietrich, A.* AU - Schön, M.R.* AU - Gärtner, D.* AU - Lohmann, T.* AU - Dressler, M.* AU - Kovacs, P.* AU - Stumvoll, M. AU - Blüher, M. AU - Guiu-Jurado, E. C1 - 64340 C2 - 52185 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Adipsin serum concentrations and adipose tissue expression in people with obesity and type 2 diabetes. JO - Int. J. Mol. Sci. VL - 23 IS - 4 PB - Mdpi PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Glycosylphosphatidylinositol-anchored proteins (GPI-APs), which are anchored at the outer leaflet of plasma membranes (PM) only by a carboxy-terminal GPI glycolipid, are known to fulfill multiple enzymic and receptor functions at the cell surface. Previous studies revealed that full-length GPI-APs with the complete GPI anchor attached can be released from and inserted into PMs in vitro. Moreover, full-length GPI-APs were recovered from serum, dependent on the age and metabolic state of rats and humans. Here, the possibility of intercellular control of metabolism by the intercellular transfer of GPI-APs was studied. Mutant K562 erythroleukemia (EL) cells, mannosamine-treated human adipocytes and methyl-ß-cyclodextrin-treated rat adipocytes as acceptor cells for GPI-APs, based on their impaired PM expression of GPI-APs, were incubated with full-length GPI-APs, prepared from rat adipocytes and embedded in micelle-like complexes, or with EL cells and human adipocytes with normal expression of GPI-APs as donor cells in transwell co-cultures. Increases in the amounts of full-length GPI-APs at the PM of acceptor cells as a measure of their transfer was assayed by chip-based sensing. Both experimental setups supported both the transfer and upregulation of glycogen (EL cells) and lipid (adipocytes) synthesis. These were all diminished by serum, serum GPIspecific phospholipase D, albumin, active bacterial PI-specific phospholipase C or depletion of total GPI-APs from the culture medium. Serum inhibition of both transfer and glycogen/lipid synthesis was counteracted by synthetic phosphoinositolglycans (PIGs), which closely resemble the structure of the GPI glycan core and caused dissociation of GPI-APs from serum proteins. Finally, large, heavily lipid-loaded donor and small, slightly lipid-loaded acceptor adipocytes were most effective in stimulating transfer and lipid synthesis. In conclusion, full-length GPI-APs can be transferred between adipocytes or between blood cells as well as between these cell types. Transfer and the resulting stimulation of lipid and glycogen synthesis, respectively, are downregulated by serum proteins and upregulated by PIGs. These findings argue for the (patho)physiological relevance of the intercellular transfer of GPI-APs in general and its role in the paracrine vs. endocrine (dys)regulation of metabolism, in particular. Moreover, they raise the possibility of the use of full-length GPI-APs as therapeutics for metabolic diseases. AU - Müller, G. AU - Müller, T.D. C1 - 65585 C2 - 52387 TI - Biological role of the intercellular transfer of glycosylphosphatidylinositol-anchored proteins: Stimulation of lipid and glycogen synthesis. JO - Int. J. Mol. Sci. VL - 23 IS - 13 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Peroxisomal biogenesis disorders (PBDs) are a heterogeneous group of genetic diseases. Multiple peroxisomal pathways are impaired, and very long chain fatty acids (VLCFA) are the first line biomarkers for the diagnosis. The clinical presentation of PBDs may range from severe, lethal multisystemic disorders to milder, late-onset disease. The vast majority of PBDs belong to Zellweger Spectrum Disordes (ZSDs) and represents a continuum of overlapping clinical symptoms, with Zellweger syndrome being the most severe and Heimler syndrome the less severe disease. Mild clinical conditions frequently present normal or slight biochemical alterations, making the diagnosis of these patients challenging. In the present study we used a combined WES and RNA-seq strategy to diagnose a patient presenting with retinal dystrophy as the main clinical symptom. Results showed the patient was compound heterozygous for mutations in PEX1. VLCFA were normal, but retrospective analysis of lysosphosphatidylcholines (LPC) containing C22:0-C26:0 species was altered. This simple test could avoid the diagnostic odyssey of patients with mild phenotype, such as the individual described here, who was diagnosed very late in adult life. We provide functional data in cell line models that may explain the mild phenotype of the patient by demonstrating the hypomorphic nature of a deep intronic variant altering PEX1 mRNA processing. AU - Muñoz-Pujol, G.* AU - Alforja-Castiella, S.* AU - Casaroli-Marano, R.* AU - Morales-Romero, B.* AU - García-Villoria, J.* AU - Yépez, V.A.* AU - Gagneur, J.* AU - Gusic, M. AU - Prokisch, H. AU - Tort, F.* AU - Ribes, A.* C1 - 66544 C2 - 53210 TI - Diagnostic odyssey in an adult patient with ophthalmologic abnormalities and hearing loss: Contribution of RNA-seq to the diagnosis of a PEX1 deficiency. JO - Int. J. Mol. Sci. VL - 23 IS - 20 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Cell communication via exosomes is capable of influencing cell fate in stress situations such as exposure to ionizing radiation. In vitro and in vivo studies have shown that exosomes might play a role in out-of-target radiation effects by carrying molecular signaling mediators of radiation damage, as well as opposite protective functions resulting in resistance to radiotherapy. However, a global understanding of exosomes and their radiation-induced regulation, especially within the context of an intact mammalian organism, has been lacking. In this in vivo study, we demonstrate that, compared to sham-irradiated (SI) mice, a distinct pattern of proteins and miRNAs is found packaged into circulating plasma exosomes after whole-body and partial-body irradiation (WBI and PBI) with 2 Gy X-rays. A high number of deregulated proteins (59% of WBI and 67% of PBI) was found in the exosomes of irradiated mice. In total, 57 and 13 miRNAs were deregulated in WBI and PBI groups, respectively, suggesting that the miRNA cargo is influenced by the tissue volume exposed to radiation. In addition, five miRNAs (miR-99b-3p, miR-200a-3p, miR-200a, miR-182-5p, miR-182) were commonly overexpressed in the exosomes from the WBI and PBI groups. In this study, particular emphasis was also given to the determination of the in vivo effect of exosome transfer by intracranial injection in the highly radiosensitive neonatal cerebellum at postnatal day 3. In accordance with a major overall anti-apoptotic function of the commonly deregulated miRNAs, here, we report that exosomes from the plasma of irradiated mice, especially in the case of WBI, prevent radiation-induced apoptosis, thus holding promise for exosome-based future therapeutic applications against radiation injury. AU - Pazzaglia, S.* AU - Tanno, B.* AU - De Stefano, I.* AU - Giardullo, P.* AU - Leonardi, S.* AU - Merla, C.* AU - Babini, G.* AU - Tuncay Cagatay, S.* AU - Mayah, A.* AU - Kadhim, M.* AU - Lyng, F.M.* AU - von Toerne, C. AU - Zhan, Z.N. AU - Subedi, P. AU - Tapio, S. AU - Saran, A.* AU - Mancuso, M.* C1 - 64339 C2 - 52327 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Micro-RNA and proteomic profiles of plasma-derived exosomes from irradiated mice reveal molecular changes preventing apoptosis in neonatal cerebellum. JO - Int. J. Mol. Sci. VL - 23 IS - 4 PB - Mdpi PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - The formation of pathological bone deposits within soft tissues, termed heterotopic ossification (HO), is common after trauma. However, the severity of HO formation varies substantially between individuals, from relatively isolated small bone islands through to extensive soft tissue replacement by bone giving rise to debilitating symptoms. The aim of this study was to identify novel candidate therapeutic molecular targets for severe HO. We conducted a genome-wide scan in men and women with HO of varying severity following hip replacement for osteoarthritis. HO severity was dichotomized as mild or severe, and association analysis was performed with adjustment for age and sex. We next confirmed expression of the gene encoded by the lead signal in human bone and in primary human mesenchymal stem cells. We then examined the effect of gene knockout in a murine model of osseous trans-differentiation, and finally we explored transcription factor phosphorylation in key pathways perturbed by the gene. Ten independent signals were suggestively associated with HO severity, with KIF26B as the lead. We subsequently confirmed KIF26B expression in human bone and upregulation upon BMP2-induced osteogenic differentiation in primary human mesenchymal stem cells, and also in a rat tendo-Achilles model of post-traumatic HO. CRISPR-Cas9 mediated knockout of Kif26b inhibited BMP2-induced Runx2, Sp7/Osterix, Col1A1, Alp, and Bglap/Osteocalcin expression and mineralized nodule formation in a murine myocyte model of osteogenic trans-differentiation. Finally, KIF26B deficiency inhibited ERK MAP kinase activation during osteogenesis, whilst augmenting p38 and SMAD 1/5/8 phosphorylation. Taken together, these data suggest a role for KIF26B in modulating the severity of post-traumatic HO and provide a potential novel avenue for therapeutic translation. AU - Pickering, G.A.E.* AU - Felix-Ilemhenbhio, F.* AU - Clark, M.J.* AU - Kocsy, K.* AU - Simpson, J.* AU - Bellantuono, I.* AU - Gartland, A.* AU - Wilkinson, J.M.* AU - Hatzikotoulas, K. AU - Kiss-Toth, E.* C1 - 65978 C2 - 53023 TI - The kinesin gene KIF26B modulates the severity of post-traumatic heterotopic ossification. JO - Int. J. Mol. Sci. VL - 23 IS - 16 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Antibiotic-resistant bacteria pose one of the major threats to human health worldwide. The issue is fundamental in the case of chronic wound treatment. One of the latest trends to over-come the problem is the search for new antibacterial agents based on silver. Thus, the aim of this research was to synthesize the silver-lactoferrin complex as a new generation of substances for the treatment of infected wounds. Moreover, one of the tasks was to investigate the formation mechanisms of the respective complexes and the influence of different synthesis conditions on the features of final product. The batch-sorption study was performed by applying the Langmuir and Freun-dlich isotherm models for the process description. Characterization of the complexes was carried out by spectroscopy, spectrometry, and separation techniques, as well as with electron microscopy. Additionally, the biological properties of the complex were evaluated, i.e., the antibacterial activity against selected bacteria and the impact on L929 cell-line viability. The results indicate the formation of a heterogeneous silver–lactoferrin complex that comprises silver nanoparticles. The complex has higher antibacterial strength than both native bovine lactoferrin and Ag+, while being comparable to silver toxicity. AU - Pryshchepa, O.* AU - Pomastowski, P.* AU - Rafińska, K.* AU - Gołębiowski, A.* AU - Rogowska, A.* AU - Monedeiro-Milanowski, M.* AU - Sagandykova, G.* AU - Michalke, B. AU - Schmitt-Kopplin, P. AU - Gloc, M.* AU - Dobrucka, R.* AU - Kurzydłowski, K.* AU - Buszewski, B.* C1 - 65590 C2 - 52396 TI - Synthesis, physicochemical characterization, and antibacterial performance of silver-lactoferrin complexes. JO - Int. J. Mol. Sci. VL - 23 IS - 13 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - The development of new functional materials based on porphyrins requires fast and accurate prediction of their spectral properties. The available models in the literature for absorption wavelength and extinction coefficient of the Soret band have low accuracy for this class of compounds. We collected spectral data for porphyrins to extend the literature set and compared the performance of global and local models for their modelling using different machine learning methods. Interestingly, extension of the public database contributed models with lower accuracies compared to the models, which we built using porphyrins only. The later model calculated acceptable RMSE = 2.26 for prediction of the absorption band of 335 porphyrins synthesized in our laboratory, but had a low accuracy (RMSE = 0.52) for extinction coefficient. A development of models using only compounds from our laboratory significantly decreased errors for these compounds (RMSE = 0.5 and 0.042 for absorption band and extinction coefficient, respectively), but limited their applicability only to these homologous series. When developing models, one should clearly keep in mind their potential use and select a strategy that could contribute the most accurate predictions for the target application. The models and data are publicly available. AU - Rusanov, A.I.* AU - Dmitrieva, O.A.* AU - Mamardashvili, N.Z.* AU - Tetko, I.V. C1 - 64144 C2 - 52091 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - More is not always better: Local models provide accurate predictions of spectral properties of porphyrins. JO - Int. J. Mol. Sci. VL - 23 IS - 3 PB - Mdpi PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades. AU - Scaltsoyiannes, V.* AU - Corre, N.* AU - Waltz, F. AU - Giegé, P.* C1 - 64689 C2 - 52409 TI - Types and functions of mitoribosome-specific ribosomal proteins across eukaryotes. JO - Int. J. Mol. Sci. VL - 23 IS - 7 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Post-COVID-19 syndrome (PCS) is characterized by persisting sequelae after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). PCS can affect patients with all COVID-19 disease severities. As previous studies have revealed impaired blood flow as a provoking factor triggering PCS, it was the aim of the present study to investigate the potential association between self-reported chronic fatigue and retinal microcirculation in patients with PCS, potentially indicating an objective biomarker. A prospective study was performed, including 201 subjects: 173 patients with PCS and 28 controls. Retinal microcirculation was visualized by OCT angiography (OCT-A) and quantified using the Erlangen-Angio-Tool as macula and peripapillary vessel density (VD). Chronic fatigue (CF) was assessed according to the variables of Bell’s score, age and gender. VDs in the superficial vascular plexus (SVP), intermediate capillary plexus (ICP) and deep capillary plexus (DCP) were analyzed, considering the repetitions (12 times). Seropositivity for autoantibodies targeting G protein-coupled receptors (GPCR-AAbs) was determined by an established cardiomyocyte bioassay. Taking account of the repetitions, a mixed model was performed to detect possible differences in the least square means between the different groups included in the analysis. An age effect in relation to VD was observed between patients and controls (p < 0.0001). Gender analysis showed that women with PCS showed lower VD levels in the SVP compared to male patients (p = 0.0015). The PCS patients showed significantly lower VDs in the ICP as compared to the controls (p = 0.0001 (CI: 0.32; 1)). Moreover, considering PCS patients, the mixed model revealed a significant difference between those with chronic fatigue (CF) and those without CF with respect to VDs in the SVP (p = 0.0033 (CI: −4.5; −0.92)). The model included variables of age, gender and Bell’s score, representing a subjective marker for CF. Consequently, retinal microcirculation might serve as an objective biomarker in subjectively reported chronic fatigue in patients with PCS. AU - Schlick, S.* AU - Lucio, M. AU - Wallukat, G.* AU - Bartsch, A.* AU - Skornia, A.* AU - Hoffmanns, J.* AU - Szewczykowski, C.* AU - Schröder, T.* AU - Raith, F.* AU - Rogge, L.* AU - Heltmann, F.* AU - Moritz, M.* AU - Beitlich, L.* AU - Schottenhamml, J.* AU - Herrmann, M.* AU - Harrer, T.* AU - Ganslmayer, M.* AU - Kruse, F.E.* AU - Lämmer, R.* AU - Mardin, C.* AU - Hohberger, B.* C1 - 66882 C2 - 53345 TI - Post-COVID-19 syndrome: Retinal microcirculation as a potential marker for chronic fatigue. JO - Int. J. Mol. Sci. VL - 23 IS - 22 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Glutathione peroxidase 4 (Gpx4) and arachidonic acid 15 lipoxygenase (Alox15) are counterplayers in oxidative lipid metabolism and both enzymes have been implicated in spermatogenesis. However, the roles of the two proteins in acrosomal exocytosis have not been explored in detail. Here we characterized Gpx4 distribution in mouse sperm and detected the enzyme not only in the midpiece of the resting sperm but also at the anterior region of the head, where the acrosome is localized. During sperm capacitation, Gpx4 translocated to the post-acrosomal compartment. Sperm from Gpx4+/Sec46Ala mice heterozygously expressing a catalytically silent enzyme displayed an increased expression of phosphotyrosyl proteins, impaired acrosomal exocytosis after in vitro capacitation and were not suitable for in vitro fertilization. Alox15-deficient sperm showed normal acrosome reactions but when crossed into a Gpx4-deficient background spontaneous acrosomal exocytosis was observed during capacitation and these cells were even less suitable for in vitro fertilization. Taken together, our data indicate that heterozygous expression of a catalytically silent Gpx4 variant impairs acrosomal exocytosis and in vitro fertilization. Alox15 deficiency hardly impacted the acrosome reaction but when crossed into the Gpx4-deficient background spontaneous acrosomal exocytosis was induced. The detailed molecular mechanisms for the observed effects may be related to the compromised redox homeostasis. AU - Soria-Tiedemann, M.* AU - Michel, G.* AU - Urban, I.* AU - Aldrovandi, M. AU - O'Donnell, V.B.* AU - Stehling, S.* AU - Kühn, H.* AU - Borchert, A.* C1 - 66160 C2 - 53098 TI - Unbalanced expression of glutathione peroxidase 4 and arachidonate 15-lipoxygenase affects acrosome reaction and in vitro fertilization. JO - Int. J. Mol. Sci. VL - 23 IS - 17 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - The prevalence of nonalcoholic fatty liver disease (NAFLD), recently also re-defined as metabolic dysfunction associated fatty liver disease (MAFLD), is rapidly increasing, affecting ~25% of the world population. MALFD/NAFLD represents a spectrum of liver pathologies including the more benign hepatic steatosis and the more advanced non-alcoholic steatohepatitis (NASH). NASH is associated with enhanced risk for liver fibrosis and progression to cirrhosis and hepatocellular carcinoma. Hepatic stellate cells (HSC) activation underlies NASH-related fibrosis. Here, we discuss the profibrogenic pathways, which lead to HSC activation and fibrogenesis, with a particular focus on the intercellular hepatocyte-HSC and macrophage-HSC crosstalk. AU - Subramanian, P.* AU - Hampe, J.* AU - Tacke, F.* AU - Chavakis, T. C1 - 65648 C2 - 52849 TI - Fibrogenic pathways in metabolic dysfunction associated fatty liver disease (MAFLD). JO - Int. J. Mol. Sci. VL - 23 IS - 13 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - GRB14/COBLL1 locus has been shown to be associated with body fat distribution (FD), but neither the causal gene nor its role in metabolic diseases has been elucidated. We hypothesize that GRB14/COBLL1 may act as the causal genes for FD-related SNPs (rs10195252 and rs6738627), and that they may be regulated by SNP to effect obesity-related metabolic traits. We genotyped rs10195252 and rs6738627 in 2860 subjects with metabolic phenotypes. In a subgroup of 560 subjects, we analyzed GRB14/COBLL1 gene expression in paired visceral and subcutaneous adipose tissue (AT) samples. Mediation analyses were used to determine the causal relationship between SNPs, AT GRB14/COBLL1 mRNA expression, and obesity-related traits. In vitro gene knockdown of Grb14/Cobll1 was used to test their role in adipogenesis. Both gene expressions in AT are correlated with waist circumference. Visceral GRB14 mRNA expression is associated with FPG and HbA1c. Both SNPs are associated with triglycerides, FPG, and leptin levels. Rs10195252 is associated with HbA1c and seems to be mediated by visceral AT GRB14 mRNA expression. Our data support the role of the GRB14/COBLL1 gene expression in body FD and its locus in metabolic sequelae: in particular, lipid metabolism and glucose homeostasis, which is likely mediated by AT GRB14 transcript levels. AU - Sun, C.* AU - Förster, F.* AU - Gutsmann, B.* AU - Moulla, Y.* AU - Stroh, C.* AU - Dietrich, A.* AU - Schoen, M.R.* AU - Gaertner, D.* AU - Lohmann, T.* AU - Dressler, M.* AU - Stumvoll, M. AU - Blüher, M. AU - Kovacs, P.* AU - Breitfeld, J.* AU - Guiu-Jurado, E. C1 - 65929 C2 - 52637 TI - Metabolic effects of the waist-to-hip ratio associated locus GRB14/COBLL1 are related to GRB14 expression in adipose tissue. JO - Int. J. Mol. Sci. VL - 23 IS - 15 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - The gastrointestinal tract is the largest mucosal surface in our body and accommodates the majority of the total lymphocyte population. Being continuously exposed to both harmless antigens and potentially threatening pathogens, the intestinal mucosa requires the integration of multiple signals for balancing immune responses. This integration is certainly supported by tissue-resident intestinal mesenchymal cells (IMCs), yet the molecular mechanisms whereby IMCs contribute to these events remain largely undefined. Recent studies using single-cell profiling technologies indicated a previously unappreciated heterogeneity of IMCs and provided further knowledge which will help to understand dynamic interactions between IMCs and hematopoietic cells of the intestinal mucosa. In this review, we focus on recent findings on the immunological functions of IMCs: On one hand, we discuss the steady-state interactions of IMCs with epithelial cells and hematopoietic cells. On the other hand, we summarize our current knowledge about the contribution of IMCs to the development of intestinal inflammatory conditions, such as infections, inflammatory bowel disease, and fibrosis. By providing a comprehensive list of cytokines and chemokines produced by IMCs under homeostatic and inflammatory conditions, we highlight the significant immunomodulatory and tissue niche forming capacities of IMCs. AU - Szente-Pasztoi, M. AU - Ohnmacht, C. C1 - 64966 C2 - 52590 TI - Tissue niches formed by intestinal mesenchymal stromal cells in mucosal homeostasis and immunity. JO - Int. J. Mol. Sci. VL - 23 IS - 9 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - Long COVID (LC) describes the clinical phenotype of symptoms after infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnostic and therapeutic options are limited, as the pathomechanism of LC is elusive. As the number of acute SARS-CoV-2 infections was and is large, LC will be a challenge for the healthcare system. Previous studies revealed an impaired blood flow, the formation of microclots, and autoimmune mechanisms as potential factors in this complex interplay. Since functionally active autoantibodies against G-protein-coupled receptors (GPCR-AAbs) were observed in patients after SARS-CoV-2 infection, this study aimed to correlate the appearance of GPCR-AAbs with capillary microcirculation. The seropositivity of GPCR-AAbs was measured by an established cardiomyocyte bioassay in 42 patients with LC and 6 controls. Retinal microcirculation was measured by OCT–angiography and quantified as macula and peripapillary vessel density (VD) by the Erlangen-Angio Tool. A statistical analysis yielded impaired VD in patients with LC compared to the controls, which was accentuated in female persons. A significant decrease in macula and peripapillary VD for AAbs targeting adrenergic β2-receptor, MAS-receptor angiotensin-II-type-1 receptor, and adrenergic α1-receptor were observed. The present study might suggest that a seropositivity of GPCR-AAbs can be linked to an impaired retinal capillary microcirculation, potentially mirroring the systemic microcirculation with consecutive clinical symptoms. AU - Szewczykowski, C.* AU - Mardin, C.* AU - Lucio, M. AU - Wallukat, G.* AU - Hoffmanns, J.* AU - Schröder, T.* AU - Raith, F.* AU - Rogge, L.* AU - Heltmann, F.* AU - Moritz, M.* AU - Beitlich, L.* AU - Schottenhamml, J.* AU - Herrmann, M.* AU - Harrer, T.* AU - Ganslmayer, M.* AU - Kruse, F.E.* AU - Kräter, M.* AU - Guck, J.* AU - Lämmer, R.* AU - Zenkel, M.* AU - Gießl, A.* AU - Hohberger, B.* C1 - 65588 C2 - 52395 TI - Long COVID: Association of functional autoantibodies against G-protein-coupled receptors with an impaired retinal microcirculation. JO - Int. J. Mol. Sci. VL - 23 IS - 13 PY - 2022 SN - 1661-6596 ER - TY - JOUR AB - DNA methylation changes may predispose becoming IgE-sensitized to allergens. We analyzed whether DNA methylation in peripheral blood mononuclear cells (PBMC) is associated with IgE sensitization at 5 years of age (5Y). DNA methylation was measured in 288 PBMC samples from 74 mother/child pairs from the birth cohort ALADDIN (Assessment of Lifestyle and Allergic Disease During INfancy) using the HumanMethylation450BeadChip (Illumina). PBMCs were obtained from the mothers during pregnancy and from their children in cord blood, at 2 years and 5Y. DNA methylation levels at each time point were compared between children with and without IgE sensitization to allergens at 5Y. For replication, CpG sites associated with IgE sensitization in ALADDIN were evaluated in whole blood DNA of 256 children, 4 years old, from the BAMSE (Swedish abbreviation for Children, Allergy, Milieu, Stockholm, Epidemiology) cohort. We found 34 differentially methylated regions (DMRs) associated with IgE sensitization to airborne allergens and 38 DMRs associated with sensitization to food allergens in children at 5Y (Sidak p ≤ 0.05). Genes associated with airborne sensitization were enriched in the pathway of endocytosis, while genes associated with food sensitization were enriched in focal adhesion, the bacterial invasion of epithelial cells, and leukocyte migration. Furthermore, 25 DMRs in maternal PBMCs were associated with IgE sensitization to airborne allergens in their children at 5Y, which were functionally annotated to the mTOR (mammalian Target of Rapamycin) signaling pathway. This study supports that DNA methylation is associated with IgE sensitization early in life and revealed new candidate genes for atopy. Moreover, our study provides evidence that maternal DNA methylation levels are associated with IgE sensitization in the child supporting early in utero effects on atopy predisposition. AU - Acevedo, N.* AU - Scala, G.* AU - Merid, S.K.* AU - Frumento, P.* AU - Bruhn, S.* AU - Andersson, A.* AU - Ogris, C. AU - Bottai, M.* AU - Pershagen, G.* AU - Koppelman, G.H.* AU - Melén, E.* AU - Sonnhammer, E.* AU - Alm, J.* AU - Söderhäll, C.* AU - Kere, J.* AU - Greco, D.* AU - Scheynius, A.* C1 - 61020 C2 - 50016 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - DNA methylation levels in mononuclear leukocytes from the mother and her child are associated with ige sensitization to allergens in early life. JO - Int. J. Mol. Sci. VL - 22 IS - 2 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Extracellular matrix (ECM) remodeling plays important roles in both white adipose tissue (WAT) and the skeletal muscle (SM) metabolism. Excessive adipocyte hypertrophy causes fibro-sis, inflammation, and metabolic dysfunction in adipose tissue, as well as impaired adipogenesis. Similarly, disturbed ECM remodeling in SM has metabolic consequences such as decreased insulin sensitivity. Most of described ECM molecular alterations have been associated with DNA sequence variation, alterations in gene expression patterns, and epigenetic modifications. Among others, the most important epigenetic mechanism by which cells are able to modulate their gene expression is DNA methylation. Epigenome-Wide Association Studies (EWAS) have become a powerful approach to identify DNA methylation variation associated with biological traits in humans. Likewise, Genome-Wide Association Studies (GWAS) and gene expression microarrays have allowed the study of whole-genome genetics and transcriptomics patterns in obesity and metabolic diseases. The aim of this review is to explore the molecular basis of ECM in WAT and SM remodeling in obesity and the consequences of metabolic complications. For that purpose, we reviewed scientific literature including all omics approaches reporting genetic, epigenetic, and transcriptomic (GWAS, EWAS, and RNA-seq or cDNA arrays) ECM-related alterations in WAT and SM as associated with metabolic dysfunction and obesity. AU - Anguita-Ruiz, A.* AU - Bustos-Aibar, M.* AU - Plaza-Díaz, J.* AU - Méndez-Gutiérrez, A.* AU - Alcalá-Fdez, J.* AU - Aguilera, C.M.* AU - Ruiz Ojeda, F.J. C1 - 61536 C2 - 50330 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Omics approaches in adipose tissue and skeletal muscle addressing the role of extracellular matrix in obesity and metabolic dysfunction. JO - Int. J. Mol. Sci. VL - 22 IS - 5 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Several transmembrane mucins have demonstrated that they contribute intracellularly to induce fibrotic processes. The extracellular domain of MUC16 is considered as a biomarker for disease progression and death in IPF patients. However, there is no evidence regarding the signalling capabilities of MUC16 that contribute to IPF development. Here, we demonstrate that MUC16 was overexpressed in the lung tissue of IPF patients (n = 20) compared with healthy subjects (n = 17) and localised in fibroblasts and hyperplastic alveolar type II cells. Repression of MUC16 expression by siRNA-MUC16 transfection inhibited the TGF-β1-induced fibrotic processes such as mesenchymal/ myofibroblast transformations of alveolar type II A549 cells and lung fibroblasts, as well as fibroblast proliferation. SiRNA-MUC16 transfection also decreased the TGF-β1-induced SMAD3 phosphorylation, thus inhibiting the Smad Binding Element activation. Immunoprecipitation assays and confocal immunofluorescence showed the formation of a protein complex between MUC16/p-SMAD3 in the cell membrane after TGF-β1 stimulation. This study shows that MUC16 is overexpressed in IPF and collaborates with the TGF-β1 canonical pathway to induce fibrotic processes. Therefore, direct or indirect targeting of MUC16 could be a potential drug target for human IPF. AU - Ballester, B. AU - Milara, J.* AU - Montero, P.* AU - Cortijo, J.* C1 - 62352 C2 - 50802 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Muc16 is overexpressed in idiopathic pulmonary fibrosis and induces fibrotic responses mediated by transforming growth factor-β1 canonical pathway. JO - Int. J. Mol. Sci. VL - 22 IS - 12 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Treatment-induced neuropathy in diabetes (TIND) is defined by the occurrence of an acute neuropathy within 8 weeks of an abrupt decrease in glycated hemoglobin-A1c (HbA1c). The underlying pathogenic mechanisms are still incompletely understood with only one mouse model being explored to date. The aim of this study was to further explore the hypothesis that an abrupt insulin-induced fall in HbA1c may be the prime causal factor of developing TIND. BB/OKL (bio breeding/OKL, Ottawa Karlsburg Leipzig) diabetic rats were randomized in three groups, receiving insulin treatment by implanted subcutaneous osmotic insulin pumps for 3 months, as follows: Group one received 2 units per day; group two 1 unit per day: and group three 1 unit per day in the first month, followed by 2 units per day in the last two months. We serially examined blood glucose and HbA1c levels, motor-and sensory/mixed afferent conduction velocities (mNCV and csNCV) and peripheral nerve morphology, including intraepidermal nerve fiber density and numbers of Iba-1 (ionized calcium binding adaptor molecule 1) positive macrophages in the sciatic nerve. Only in BB/OKL rats of group three, with a rapid decrease in HbA1c of more than 2%, did we find a significant decrease in mNCV in sciatic nerves (81% of initial values) after three months of treatment as compared to those group three rats with a less marked decrease in HbA1c <2% (mNCV 106% of initial values, p ≤ 0.01). A similar trend was observed for sensory/mixed afferent nerve conduction velocities: csNCV were reduced in BB/OKL rats with a rapid decrease in HbA1c >2% (csNCV 90% of initial values), compared to those rats with a mild decrease <2% (csNCV 112% of initial values, p ≤ 0.01). Moreover, BB/OKL rats of group three with a decrease in HbA1c >2% showed significantly greater infiltration of macrophages by about 50% (p ≤ 0.01) and a decreased amount of calcitonin gene related peptide (CGRP) positive nerve fibers as compared to the animals with a milder decrease in HbA1c. We conclude that a mild acute neuropathy with inflammatory components was induced in BB/OKL rats as a consequence of an abrupt decrease in HbA1c caused by high-dose insulin treatment. This experimentally induced neuropathy shares some features with TIND in humans and may be further explored in studies into the pathogenesis and treatment of TIND. AU - Baum, P.* AU - Koj, S.* AU - Klöting, N. AU - Blüher, M. AU - Classen, J.* AU - Paeschke, S.* AU - Gericke, M.* AU - Toyka, K.V.* AU - Nowicki, M.* AU - Kosacka, J.* C1 - 61228 C2 - 50104 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Treatment-induced neuropathy in diabetes (Tind)—developing a disease model in type 1 diabetic rats. JO - Int. J. Mol. Sci. VL - 22 IS - 4 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Leptin and its receptor are essential for regulating food intake, energy expenditure, glucose homeostasis and fertility. Mutations within leptin or the leptin receptor cause early-onset obesity and hyperphagia, as described in human and animal models. The effect of both heterozygous and homozygous variants is much more investigated than compound heterozygous ones. Recently, we discovered a spontaneous compound heterozygous mutation within the leptin receptor, resulting in a considerably more obese phenotype than described for the homozygous leptin receptor deficient mice. Accordingly, we focus on compound heterozygous mutations of the leptin receptor and their effects on health, as well as possible therapy options in human and animal models in this review. AU - Berger, C.* AU - Klöting, N. C1 - 61906 C2 - 50300 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Leptin receptor compound heterozygosity in humans and animal models. JO - Int. J. Mol. Sci. VL - 22 IS - 9 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Palmitoleic acid (C16:1n7) has been identified as a regulator of physiological cardiac hypertrophy. In the present study, we aimed to investigate the molecular pathways involved in C16:1n7 responses in primary murine cardiomyocytes (PCM) and a mouse model of isoproterenol (ISO)-induced cardiac damage. PCMs were stimulated with C16:1n7 or a vehicle. Afterwards, RNA sequencing was performed using an Illumina HiSeq sequencer. Confirmatory analysis was performed in PCMs and HL-1 cardiomyocytes. For an in vivo study, 129 sv mice were orally treated with a vehicle or C16:1n7 for 22 days. After 5 days of pre-treatment, the mice were injected with ISO (25 mg/kg/d s. c.) for 4 consecutive days. Cardiac phenotyping was performed using echocardiography. In total, 129 genes were differentially expressed in PCMs stimulated with C16:1n7, including Angiopoietin-like factor 4 (Angptl4) and Pyruvate Dehydrogenase Kinase 4 (Pdk4). Both Angptl4 and Pdk4 are proxisome proliferator-activated receptor α/δ (PPARα/δ) target genes. Our in vivo results indicated cardioprotective and anti-fibrotic effects of C16:1n7 application in mice. This was associated with the C16:1n7-dependent regulation of the cardiac PPAR-specific signaling pathways. In conclusion, our experiments demonstrated that C16:1n7 might have protective effects on cardiac fibrosis and inflammation. Our study may help to develop future lipid-based therapies for catecholamine-induced cardiac damage. AU - Betz, I.R.* AU - Qaiyumi, S.J.* AU - Goeritzer, M.* AU - Thiele, A.* AU - Brix, S.* AU - Beyhoff, N.* AU - Grune, J.* AU - Klopfleisch, R.* AU - Greulich, F. AU - Uhlenhaut, N.H. AU - Kintscher, U.* AU - Foryst-Ludwig, A.* C1 - 63608 C2 - 51601 TI - Cardioprotective effects of palmitoleic acid (C16:1n7) in a mouse model of catecholamine-induced cardiac damage are mediated by PPAR activation. JO - Int. J. Mol. Sci. VL - 22 IS - 23 PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Mutations in the SPATA5 gene are associated with epilepsy, hearing loss and mental retardation syndrome (EHLMRS). While SPATA5 is ubiquitously expressed and is attributed a role within mitochondrial morphogenesis during spermatogenesis, there is only limited knowledge about the associated muscular and molecular pathology. This study reports on a comprehensive workup of muscular pathology, including proteomic profiling and microscopic studies, performed on an 8‐year‐old girl with typical clinical presentation of EHLMRS, where exome analysis revealed two clinically relevant, compound‐heterozygous variants in SPATA5. Proteomic profiling of a quadriceps biopsy showed the dysregulation of 82 proteins, out of which 15 were localized in the mitochondrion, while 19 were associated with diseases presenting with phenotypical overlap to EHLMRS. Histological staining of our patient’s muscle biopsy hints towards mitochondrial pathology, while the identification of dysregulated proteins attested to the vulnerability of the cell beyond the mitochondria. Through our study we provide insights into the molecular etiology of EHLMRS and provide further evidence for a muscle pathology associated with SPATA5 deficiency, including a pathological histochemical pattern accompanied by dysregulated protein expression. AU - Braun, F.* AU - Hentschel, A.* AU - Sickmann, A.* AU - Marteau, T.* AU - Hertel, S.* AU - Förster, F.* AU - Prokisch, H. AU - Wagner, M. AU - Wortmann, S.* AU - Della Marina, A.* AU - Kölbel, H.* AU - Roos, A.* AU - Schara‐Schmidt, U.* C1 - 62665 C2 - 50920 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Muscular and molecular pathology associated with SPATA5 deficiency in a child with EHLMRS. JO - Int. J. Mol. Sci. VL - 22 IS - 15 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Nkx6-1 is a member of the Nkx family of homeodomain transcription factors (TFs) that regulates motor neuron development, neuron specification and pancreatic endocrine and β-cell differentiation. To facilitate the isolation and tracking of Nkx6-1-expressing cells, we have generated a novel Nkx6-1 Venus fusion (Nkx6-1-VF) reporter allele. The Nkx6-1-VF knock-in reporter is regulated by endogenous cis-regulatory elements of Nkx6-1 and the fluorescent protein fusion does not interfere with the TF function, as homozygous mice are viable and fertile. The nuclear localization of Nkx6-1-VF protein reflects the endogenous Nkx6-1 protein distribution. During embryonic pancreas development, the reporter protein marks the pancreatic ductal progenitors and the endocrine lineage, but is absent in the exocrine compartment. As expected, the levels of Nkx6-1-VF reporter are upregulated upon β-cell differentiation during the major wave of endocrinogenesis. In the adult islets of Langerhans, the reporter protein is exclusively found in insulin-secreting β-cells. Importantly, the Venus reporter activities allow successful tracking of β-cells in live-cell imaging and their specific isolation by flow sorting. In summary, the generation of the Nkx6-1-VF reporter line reflects the expression pattern and dynamics of the endogenous protein and thus provides a unique tool to study the spatio-temporal expression pattern of this TF during organ development and enables isolation and tracking of Nkx6-1-expressing cells such as pancreatic β-cells, but also neurons and motor neurons in health and disease. AU - Burtscher, I. AU - Tarquis Medina, M. AU - Schirge, S. AU - Beckenbauer, J. AU - Bakhti, M. AU - Lickert, H. C1 - 61714 C2 - 50133 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Generation of a novel nkx6-1 venus fusion reporter mouse line. JO - Int. J. Mol. Sci. VL - 22 IS - 7 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Genome-wide association studies have identified adenylyl cyclase type 5 (ADCY5) as candidate gene for diabetes-related quantitative traits and an increased risk of type 2 diabetes. Mice with a whole-body deletion of Adcy5 (Adcy5 ) do not develop obesity, glucose intolerance and insulin resistance, have improved cardiac function and increased longevity. Here, we investigated Adcy5 knockout mice (Adcy5 ) to test the hypothesis that changes in adipose tissue (AT) may con-tribute to the reported healthier phenotype. In contrast to previous reports, we found that deletion of Adcy5 did not confer any physiological or biochemical benefits. However, this unexpected find-ing allowed us to investigate the effects of Adcy5 depletion on AT independently of lower body weight and a metabolically healthier phenotype. Adcy5 mice exhibited an increased number of smaller adipocytes, lower mean adipocyte size and a distinct AT gene expression pattern with mid-line 1 (Mid1) as the most significantly downregulated gene compared to control mice. Our Adcy5 model challenges previously described beneficial effects of Adcy5 deficiency and suggests that targeting Adcy5 does not improve insulin sensitivity and may therefore limit the relevance of ADCY5 as potential drug target. –/– –/– –/– –/– AU - Dommel, S.* AU - Hoffmann, A. AU - Berger, C.* AU - Kern, M. AU - Klöting, N. AU - Kannt, A.* AU - Blüher, M. C1 - 61892 C2 - 50296 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Effects of whole-body adenylyl cyclase 5 (Adcy5) deficiency on systemic insulin sensitivity and adipose tissue. JO - Int. J. Mol. Sci. VL - 22 IS - 9 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - The mechanisms of how obesity contributes to the development of cardio-metabolic diseases are not entirely understood. Obesity is frequently associated with adipose tissue dysfunction, characterized by, e.g., adipocyte hypertrophy, ectopic fat accumulation, immune cell infiltration, and the altered secretion of adipokines. Factors secreted from adipose tissue may induce and/or maintain a local and systemic low-grade activation of the innate immune system. Attraction of mac-rophages into adipose tissue and altered crosstalk between macrophages, adipocytes, and other cells of adipose tissue are symptoms of metabolic inflammation. Among several secreted factors attract-ing immune cells to adipose tissue, chemotactic C-C motif chemokine ligand 2 (CCL2) (also de-scribed as monocyte chemoattractant protein-1 (MCP-1)) has been shown to play a crucial role in adipose tissue macrophage infiltration. In this review, we aimed to summarize and discuss the current knowledge on CCL2 with a focus on its role in linking obesity to cardio-metabolic diseases. AU - Dommel, S.* AU - Blüher, M. C1 - 61229 C2 - 50107 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Does C-C motif chemokine ligand 2 (CCL2) link obesity to a pro-inflammatory state? JO - Int. J. Mol. Sci. VL - 22 IS - 3 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Mitochondrial DNA deletions affect energy metabolism at tissue-specific and cell-specific threshold levels, but the pathophysiological mechanisms determining cell fate remain poorly under-stood. Chronic progressive external ophthalmoplegia (CPEO) is caused by mtDNA deletions and characterized by a mosaic distribution of muscle fibers with defective cytochrome oxidase (COX) activity, interspersed among fibers with retained functional respiratory chain. We used diagnostic histochemistry to distinguish COX-negative from COX-positive fibers in nine muscle biopsies from CPEO patients and performed laser capture microdissection (LCM) coupled to genome-wide gene expression analysis. To gain molecular insight into the pathogenesis, we applied network and pathway analysis to highlight molecular differences of the COX-positive and COX-negative fiber transcriptome. We then integrated our results with proteomics data that we previously obtained comparing COX-positive and COX-negative fiber sections from three other patients. By virtue of the combination of LCM and a multi-omics approach, we here provide a comprehensive resource to tackle the pathogenic changes leading to progressive respiratory chain deficiency and disease in mitochondrial deletion syndromes. Our data show that COX-negative fibers upregulate transcripts involved in translational elongation and protein synthesis. Furthermore, based on functional annotation analysis, we find that mitochondrial transcripts are the most enriched among those with significantly different expression between COX-positive and COX-negative fibers, indicating that our unbiased large-scale approach resolves the core of the pathogenic changes. Further enrich-ments include transcripts encoding LIM domain proteins, ubiquitin ligases, proteins involved in RNA turnover, and, interestingly, cell cycle arrest and cell death. These pathways may thus have a functional association to the molecular pathogenesis of the disease. Overall, the transcriptome and proteome show a low degree of correlation in CPEO patients, suggesting a relevant contribution of post-transcriptional mechanisms in shaping this disease phenotype. AU - Elstner, M.* AU - Olszewski, K.* AU - Prokisch, H. AU - Klopstock, T.* AU - Murgia, M.* C1 - 63325 C2 - 51470 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Multi-omics approach to mitochondrial dna damage in human muscle fibers. JO - Int. J. Mol. Sci. VL - 22 IS - 20 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Over the past decade, cell therapy has found many applications in the treatment of different diseases. Some of the cells already used in clinical practice include stem cells and CAR‐T cells. Compared with traditional drugs, living cells are much more complicated systems that must be strictly controlled to avoid undesirable migration, differentiation, or proliferation. One of the approaches used to prevent such side effects involves monitoring cell distribution in the human body by any noninvasive technique, such as magnetic resonance imaging (MRI). Long‐term tracking of stem cells with artificial magnetic labels, such as magnetic nanoparticles, is quite problematic because such labels can affect the metabolic process and cell viability. Additionally, the concentration of exogenous labels will decrease during cell division, leading to a corresponding decrease in signal intensity. In the current work, we present a new type of genetically encoded label based on encapsulin from Myxococcus xanthus bacteria, stably expressed in human mesenchymal stem cells (MSCs) and coexpressed with ferroxidase as a cargo protein for nanoparticles’ synthesis inside encapsulin shells. mZip14 protein was expressed for the enhancement of iron transport into the cell. Together, these three proteins led to the synthesis of iron‐containing nanoparticles in mesenchymal stem cells—without affecting cell viability—and increased contrast properties of MSCs in MRI. AU - Gabashvili, A.N.* AU - Vodopyanov, S.S.* AU - Chmelyuk, N.S.* AU - Sarkisova, V.A.* AU - Fedotov, K.A.* AU - Efremova, M.V. AU - Abakumov, M.A.* C1 - 63517 C2 - 51574 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Encapsulin based self‐assembling iron‐containing protein nanoparticles for stem cells mri visualization. JO - Int. J. Mol. Sci. VL - 22 IS - 22 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Astrocytes are a type of glial cell anatomically and functionally integrated into the neuronal regulatory circuits for the neuroendocrine control of metabolism. Being functional integral compounds of synapses, astrocytes are actively involved in the physiological regulatory aspects of metabolic control, but also in the pathological processes that link neuronal dysfunction and obesity. Between brain areas, the hypothalamus harbors specialized functional circuits that seem selectively vulnerable to metabolic damage, undergoing early cellular rearrangements which are thought to be at the core of the pathogenesis of diet-induced obesity. Such changes in the hypothalamic brain region consist of a rise in proinflammatory cytokines, the presence of a reactive phenotype in astrocytes and microglia, alterations in the cytoarchitecture and synaptology of hypothalamic circuits, and angio-genesis, a phenomenon that cannot be found elsewhere in the brain. Increasing evidence points to the direct involvement of hypothalamic astrocytes in such early metabolic disturbances, thus moving the study of these glial cells to the forefront of obesity research. Here we provide a comprehensive review of the most relevant findings of molecular and pathophysiological mechanisms by which hypothalamic astrocytes might be involved in the pathogenesis of obesity. AU - Gonzales García, I. AU - García-Cáceres, C. C1 - 62247 C2 - 50553 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Hypothalamic astrocytes as a specialized and responsive cell population in obesity. JO - Int. J. Mol. Sci. VL - 22 IS - 12 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Radiation-induced damage to normal lung parenchyma remains a dose-limiting factor in thorax-associated radiotherapy (RT). Severe early and late complications with lungs can increase the risk of morbidity in cancer patients after RT. Herein, senescence of lung epithelial cells following RT-induced cellular stress, or more precisely the respective altered secretory profile, the senescence-associated secretory phenotype (SASP), was suggested as a central process for the initiation and progression of pneumonitis and pulmonary fibrosis. We previously reported that abrogation of certain aspects of the secretome of senescent lung cells, in particular, signaling inhibition of the SASP-factor Ccl2/Mcp1 mediated radioprotection especially by limiting endothelial dysfunction. Here, we investigated the therapeutic potential of a combined metformin treatment to protect normal lung tissue from RT-induced senescence and associated lung injury using a preclinical mouse model of radiation-induced pneumopathy. Metformin treatment efficiently limited RT-induced senescence and SASP expression levels, thereby limiting vascular dysfunctions, namely increased vascular permeability associated with increased extravasation of circulating immune and tumor cells early after irradiation (acute effects). Complementary in vitro studies using normal lung epithelial cell lines confirmed the senescence-limiting effect of metformin following RT finally resulting in radioprotection, while fostering RT-induced cellular stress of cultured malignant epithelial cells accounting for radiosensitization. The radioprotective action of metformin for normal lung tissue without simultaneous protection or preferable radiosensitization of tumor tissue might increase tumor control probabilities and survival because higher radiation doses could be used. AU - Hansel, C.* AU - Barr, S.* AU - Schemann, A.V.* AU - Lauber, K. AU - Hess J. AU - Unger, K. AU - Zitzelsberger, H. AU - Jendrossek, V.* AU - Klein, D.* C1 - 62395 C2 - 50793 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Metformin protects against radiation-induced acute effects by limiting senescence of bronchial-epithelial cells. JO - Int. J. Mol. Sci. VL - 22 IS - 13 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Background: Amino acids have a central role in cell metabolism, and intracellular changes contribute to the pathogenesis of various diseases, while the role and specific organ distribution of dipeptides is largely unknown. Method: We established a sensitive, rapid and reliable UPLC-MS/MS method for quantification of 36 dipeptides. Dipeptide patterns were analyzed in brown and white adipose tissues, brain, eye, heart, kidney, liver, lung, muscle, sciatic nerve, pancreas, spleen and thymus, serum and urine of C57BL/6N wildtype mice and related to the corresponding amino acid profiles. Results: A total of 30 out of the 36 investigated dipeptides were detected with organ-specific distribution patterns. Carnosine and anserine were most abundant in all organs, with the highest concentrations in muscles. In liver, Asp-Gln and Ala-Gln concentrations were high, in the spleen and thymus, Glu-Ser and Gly-Asp. In serum, dipeptide concentrations were several magnitudes lower than in organ tissues. In all organs, dipeptides with C-terminal proline (Gly-Pro and Leu-Pro) were present at higher concentrations than dipeptides with N-terminal proline (Pro-Gly and Pro-Leu). Organ-specific amino acid profiles were related to the dipeptide profile with several amino acid concentrations being related to the isomeric form of the dipeptides. Aspartate, histidine, proline and serine tissue concentrations correlated with dipeptide concentrations, when the amino acids were present at the C-but not at the N-terminus. Conclusion: Our multi-dipeptide quantification approach demonstrates organ-specific dipeptide distribution. This method allows us to understand more about the dipeptide metabolism in disease or in healthy state. AU - Heidenreich, E.* AU - Pfeffer, T.* AU - Kracke, T.* AU - Mechtel, N.* AU - Nawroth, P.P. AU - Hoffmann, G.F.* AU - Schmitt, C.P.* AU - Hell, R.* AU - Poschet, G.* AU - Peters, V.* C1 - 63019 C2 - 51215 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - A novel uplc-ms/ms method identifies organ-specific dipeptide profiles. JO - Int. J. Mol. Sci. VL - 22 IS - 18 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Mammals rapidly heal wounds through fibrous connective tissue build up and tissue contraction. Recent findings from mouse attribute wound healing to physical mobilization of a fibroelastic connective tissue layer that resides beneath the skin, termed subcutaneous fascia or superficial fascia, into sites of injury. Fascial mobilization assembles diverse cell types and matrix components needed for rapid wound repair. These observations suggest that the factors directly affecting fascial mobility are responsible for chronic skin wounds and excessive skin scarring. In this review, we discuss the link between the fascia's unique tissue anatomy, composition, biomechanical, and rheologic properties to its ability to mobilize its tissue assemblage. Fascia is thus at the forefront of tissue pathology and a better understanding of how it is mobilized may crystallize our view of wound healing alterations during aging, diabetes, and fibrous disease and create novel therapeutic strategies for wound repair. AU - Jiang, D. AU - Rinkevich, Y. C1 - 62868 C2 - 51120 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Furnishing wound repair by the subcutaneous fascia. JO - Int. J. Mol. Sci. VL - 22 IS - 16 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Background: Treatment resistance of glioblastoma multiforme to chemo-and radiotherapy remains a challenge yet to overcome. In particular, the O6-methylguanine-DNA-methyltransferase (MGMT) promoter unmethylated patients have only little benefit from chemotherapy treatment using temozolomide since MGMT counteracts its therapeutic efficacy. Therefore, new treatment options in radiotherapy need to be developed to inhibit MGMT and increase radiotherapy response. Methods: Lomeguatrib, a highly specific MGMT inhibitor, was used to inactivate MGMT protein in vitro. Radiosensitivity of established human glioblastoma multiforme cell lines in combination with lomeguatrib was investigated using the clonogenic survival assay. Inhibition of MGMT was analyzed using Western Blot. Cell cycle distribution and apoptosis were investigated to determine the effects of lomeguatrib alone as well as in combination with ionizing radiation. Results: Lomeguatrib significantly decreased MGMT protein and reduced radiation-induced G2/M arrest. A radiosensitizing effect of lomeguatrib was observed when administered at 1 µM and increased radioresistance at 20 µM. Conclusion: Low concentrations of lomeguatrib elicit radiosensitization, while high concentrations mediate a radioprotective effect. AU - Kirstein, A. AU - Schilling, D. AU - Combs, S.E. AU - Schmid, T.E. C1 - 62377 C2 - 50695 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Lomeguatrib increases the radiosensitivity of mgmt unmethylated human glioblastoma multiforme cell lines. JO - Int. J. Mol. Sci. VL - 22 IS - 13 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - We aimed to validate the effect of non-canonical splice site variants in the RPGR gene in five patients from four families diagnosed with retinitis pigmentosa. Four variants located in intron 2 (c.154 + 3_154 + 6del), intron 3 (c.247 + 5G>A), intron 7 (c.779-5T>G), and intron 13 (c.1573-12A>G), respectively, were analyzed by means of in vitro splice assays. Splicing analysis revealed different aberrant splicing events, including exon skipping and intronic nucleotide addition, which are predicted to lead either to an in-frame deletion affecting relevant protein domains or to a frameshift of the open reading frame. Our data expand the landscape of pathogenic variants in RPGR, thereby increasing the genetic diagnostic rate in retinitis pigmentosa and allowing patients harboring the analyzed variants to be enrolled in clinical trials. AU - Kortüm, F.* AU - Kieninger, S.* AU - Mazzola, P.* AU - Kohl, S.* AU - Wissinger, B.* AU - Prokisch, H. AU - Stingl, K.* AU - Weisschuh, N.* C1 - 61085 C2 - 50041 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - X-linked retinitis pigmentosa caused by non-canonical splice site variants in RPGR. JO - Int. J. Mol. Sci. VL - 22 IS - 2 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Background: Transition metals play a crucial role in brain metabolism: since they exist in different oxidation states they are involved in ROS generation, but they are also co-factors of enzymes in cellular energy metabolism or oxidative defense. Methods: Paired serum and cerebrospinal fluid (CSF) samples were analyzed for iron, zinc, copper and manganese as well as for speciation using SEC-ICP-DRC-MS. Brain extracts from Mn-exposed rats were additionally analyzed with SEC-ICP-DRC-MS. Results: The concentration patterns of transition metal size fractions were correlated between serum and CSF: Total element concentrations were significantly lower in CSF. Fe-ferritin was decreased in CSF whereas a LMW Fe fraction was relatively increased. The 400–600 kDa Zn fraction and the Cu-ceruloplasmin fraction were decreased in CSF, by contrast the 40–80 kDa fraction, containing Cu-and Zn-albumin, relatively increased. For manganese, the α-2-macroglobulin fraction showed significantly lower concentration in CSF, whereas the citrate Mn fraction was enriched. Results from the rat brain extracts supported the findings from human paired serum and CSF samples. Conclusions: Transition metals are strictly controlled at neural barriers (NB) of neurologic healthy patients. High molecular weight species are down-concentrated along NB, however, the Mn-citrate fraction seems to be less controlled, which may be problematic under environmental load. AU - Michalke, B. AU - Berthele, A.* AU - Venkataramani, V.* C1 - 62828 C2 - 51084 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Simultaneous quantification and speciation of trace metals in paired serum and CSF samples by size exclusion chromatography–inductively coupled plasma–dynamic reaction cell–mass spectrometry (SEC-DRC-ICP-MS). JO - Int. J. Mol. Sci. VL - 22 IS - 16 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Disparities between risk, treatment outcomes and survival rates in cancer patients across the world may be attributed to socioeconomic factors. In addition, the role of ancestry is frequently discussed. In preclinical studies, high‐throughput drug screens in cancer cell lines have empowered the identification of clinically relevant molecular biomarkers of drug sensitivity; however, the genetic ancestry from tissue donors has been largely neglected in this setting. In order to address this, here, we show that the inferred ancestry of cancer cell lines is conserved and may impact drug response in patients as a predictive covariate in high‐throughput drug screens. We found that there are differential drug responses between European and East Asian ancestries, especially when treated with PI3K/mTOR inhibitors. Our finding emphasizes a new angle in precision medicine, as cancer intervention strategies should consider the germline landscape, thereby reducing the failure rate of clinical trials. AU - Nguyen, B.H.P. AU - Ohnmacht, A. AU - Sharifli, S. AU - Garnett, M.J.* AU - Menden, M.P. C1 - 63091 C2 - 51132 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Inferred ancestral origin of cancer cell lines associates with differential drug response. JO - Int. J. Mol. Sci. VL - 22 IS - 18 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - The brain undergoes ionizing radiation exposure in many clinical situations, particularly during radiotherapy for brain tumors. The critical role of the hippocampus in the pathogenesis of radiation-induced neurocognitive dysfunction is well recognized. The goal of this study is to test the potential contribution of non-targeted effects in the detrimental response of the hippocampus to irradiation and to elucidate the mechanisms involved. C57Bl/6 mice were whole body (WBI) or partial body (PBI) irradiated with 0.1 or 2.0 Gy of X-rays or sham irradiated. PBI consisted of the exposure of the lower third of the mouse body, whilst the upper two thirds were shielded. Hippocampi were collected 15 days or 6 months post-irradiation and a multi-omics approach was adopted to assess the molecular changes in non-coding RNAs, proteins and metabolic levels, as well as histological changes in the rate of hippocampal neurogenesis. Notably, at 2.0 Gy the pattern of early molecular and histopathological changes induced in the hippocampus at 15 days following PBI were similar in quality and quantity to the effects induced by WBI, thus providing a proof of principle of the existence of out-of-target radiation response in the hippocampus of conventional mice. We detected major alterations in DAG/IP3 and TGF-β signaling pathways as well as in the expression of proteins involved in the regulation of long-term neuronal synaptic plasticity and synapse organization, coupled with defects in neural stem cells self-renewal in the hippocampal dentate gyrus. However, compared to the persistence of the WBI effects, most of the PBI effects were only transient and tended to decrease at 6 months post-irradiation, indicating important mechanistic difference. On the contrary, at low dose we identified a progressive accumulation of molecular defects that tended to manifest at later post-irradiation times. These data, indicating that both targeted and non-targeted radiation effects might contribute to the pathogenesis of hippocampal radiation-damage, have general implications for human health. AU - Pazzaglia, S.* AU - Tanno, B.* AU - Antonelli, F.* AU - Giardullo, P.* AU - Babini, G.* AU - Subedi, P. AU - Azimzadeh, O. AU - Zhan, Z.N. AU - Oleksenko, K. AU - Metzger, F. AU - von Toerne, C. AU - Traynor, D.* AU - Medipally, D.* AU - Meade, A.D.* AU - Kadhim, M.* AU - Lyng, F.M.* AU - Tapio, S. AU - Saran, A.* AU - Mancuso, M.* C1 - 61895 C2 - 50297 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Out-of-field hippocampus from partial-body irradiated mice displays changes in multi-omics profile and defects in neurogenesis. JO - Int. J. Mol. Sci. VL - 22 IS - 8 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum was investi-gated that oxidizes anthraquinone dyes, lignin model compounds, and general peroxidase substrates such as ABTS efficiently. Unlike related enzymes, an aspartate residue replaces the first glycine of the conserved GXXDG motif in Dictyostelium DyPA. In solution, Dictyostelium DyPA exists as a stable dimer with the side chain of Asp146 contributing to the stabilization of the dimer interface by extending the hydrogen bond network connecting two monomers. To gain mechanistic insights, we solved the Dicty-ostelium DyPA structures in the absence of substrate as well as in the presence of potassium cyanide and veratryl alcohol to 1.7, 1.85, and 1.6 Å resolution, respectively. The active site of Dictyostelium DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an acti-vated oxygen or CN− molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from H2O2 during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in Dictyostelium DyPA. Further, we identified two substrate-binding pockets per monomer in Dictyostelium DyPA at the dimer interface. Long-range electron transfer pathways associated with a hydrogen-bonding network that connects the substrate-binding sites with the heme moiety are described. AU - Rai, A.* AU - Klare, J.P.* AU - Reinke, P.Y.A.* AU - Englmaier, F. AU - Fohrer, J.* AU - Fedorov, R.* AU - Taft, M.H.* AU - Chizhov, I.* AU - Curth, U.* AU - Plettenburg, O. AU - Manstein, D.J.* C1 - 62256 C2 - 50749 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Structural and biochemical characterization of a dye-decolorizing peroxidase from Dictyostelium discoideum. JO - Int. J. Mol. Sci. VL - 22 IS - 12 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - The mechanisms underlying the transport of leptin into the brain are still largely unclear. While the leptin receptor has been implicated in the transport process, recent evidence has suggested an additional role of LRP2 (megalin). To evaluate the function of LRP2 for leptin transport across the blood-brain barrier (BBB), we developed a novel leptin-luciferase fusion protein (pLG), which stimulated leptin signaling and was transported in an in vitro BBB model based on porcine endothelial cells. The LRP inhibitor RAP did not affect leptin transport, arguing against a role of LRP2. In line with this, the selective deletion of LRP2 in brain endothelial cells and epithelial cells of the choroid plexus did not influence bodyweight, body composition, food intake, or energy expenditure of mice. These findings suggest that LRP2 at the BBB is not involved in the transport of leptin into the brain, nor in the development of obesity as has previously been described. AU - Sandin, E.S.* AU - Folberth, J.* AU - Müller-Fielitz, H.* AU - Pietrzik, C.U.* AU - Herold, E.* AU - Willnow, T.E.* AU - Pfluger, P.T. AU - Nogueiras, R.* AU - Prévot, V.* AU - Schwaninger, M.* C1 - 62015 C2 - 50591 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Is LRP2 involved in leptin transport over the blood-brain barrier and development of obesity? JO - Int. J. Mol. Sci. VL - 22 IS - 9 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Online Chemical Modeling Environment (OCHEM) was used for QSAR analysis of a set of ionic liquids (ILs) tested against multi-drug resistant (MDR) clinical isolate Acinetobacter baumannii and Staphylococcus aureus strains. The predictive accuracy of regression models has coefficient of determination q2 = 0.66 − 0.79 with cross-validation and independent test sets. The models were used to screen a virtual chemical library of ILs, which was designed with targeted activity against MDR Acinetobacter baumannii and Staphylococcus aureus strains. Seven most promising ILs were selected, synthesized, and tested. Three ILs showed high activity against both these MDR clinical isolates. AU - Semenyuta, I.V.* AU - Trush, M.M.* AU - Kovalishyn, V.V.* AU - Rogalsky, S.P.* AU - Hodyna, D.M.* AU - Karpov, P. AU - Xia, Z. AU - Tetko, I.V. AU - Metelytsia, L.O.* C1 - 61007 C2 - 50006 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Structure-activity relationship modeling and experimental validation of the imidazolium and pyridinium based ionic liquids as potential antibacterials of mdr Acinetobacter baumannii and Staphylococcus aureus. JO - Int. J. Mol. Sci. VL - 22 IS - 2 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Synaptotagmin-13 (Syt13) is an atypical member of the vesicle trafficking synaptotagmin protein family. The expression pattern and the biological function of this Ca2+-independent protein are not well resolved. Here, we have generated a novel Syt13-Venus fusion (Syt13-VF) fluorescence reporter allele to track and isolate tissues and cells expressing Syt13 protein. The reporter allele is regulated by endogenous cis-regulatory elements of Syt13 and the fusion protein follows an identical expression pattern of the endogenous Syt13 protein. The homozygous reporter mice are viable and fertile. We identify the expression of the Syt13-VF reporter in different regions of the brain with high expression in tyrosine hydroxylase (TH)-expressing and oxytocin-producing neuroendocrine cells. Moreover, Syt13-VF is highly restricted to all enteroendocrine cells in the adult intestine that can be traced in live imaging. Finally, Syt13-VF protein is expressed in the pancreatic endocrine lineage, allowing their specific isolation by flow sorting. These findings demonstrate high expression levels of Syt13 in the endocrine lineages in three major organs harboring these secretory cells. Collectively, the Syt13-VF reporter mouse line provides a unique and reliable tool to dissect the spatio-temporal expression pattern of Syt13 and enables isolation of Syt13-expressing cells that will aid in deciphering the molecular functions of this protein in the neuroendocrine system. AU - Tarquis Medina, M. AU - Scheibner, K. AU - Gonzales García, I. AU - Bastidas-Ponce, A. AU - Sterr, M. AU - Jaki, J. AU - Schirge, S. AU - García-Cáceres, C. AU - Lickert, H. AU - Bakhti, M. C1 - 63564 C2 - 51589 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Synaptotagmin-13 is a neuroendocrine marker in brain, intestine and pancreas. JO - Int. J. Mol. Sci. VL - 22 IS - 22 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Biological aging research is expected to reveal modifiable molecular mechanisms that can be harnessed to slow or possibly reverse unhealthy trajectories. However, there is first an urgent need to define consensus molecular markers of healthy and unhealthy aging. Established aging hallmarks are all linked to metabolism, and a ‘rewired’ metabolic circuitry has been shown to accelerate or delay biological aging. To identify metabolic signatures distinguishing healthy from unhealthy aging trajectories, we performed nontargeted metabolomics on skeletal muscles from 2-month-old and 21-month-old mice, and after dietary and lifestyle interventions known to impact biological aging. We hypothesized that common metabolic signatures would highlight specific pathways and processes promoting healthy aging, while revealing the molecular underpinnings of unhealthy aging. Here, we report 50 metabolites that commonly distinguished aging trajectories in all cohorts, including 18 commonly reduced under unhealthy aging and 32 increased. We stratified these metabolites according to known relationships with various aging hallmarks and found the greatest associations with oxidative stress and nutrient sensing. Collectively, our data suggest interventions aimed at maintaining skeletal muscle arginine and lysine may be useful therapeutic strategies to minimize biological aging and maintain skeletal muscle health, function, and regenerative capacity in old age. AU - Tokarz, J. AU - Möller, G. AU - Artati, A. AU - Huber, S. AU - Zeigerer, A. AU - Blaauw, B.* AU - Adamski, J. AU - Dyar, K.A. C1 - 62706 C2 - 50976 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Common muscle metabolic signatures highlight arginine and lysine metabolism as potential therapeutic targets to combat unhealthy aging. JO - Int. J. Mol. Sci. VL - 22 IS - 15 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - The deepest evolutionary branches of the trypsin/chymotrypsin family of serine proteases are represented by the digestive enzymes of the gastrointestinal tract and the multi-domain proteases of the blood coagulation and complement system. Similar to the very old digestive system, highly diverse cleavage specificities emerged in various cell lineages of the immune defense system during vertebrate evolution. The four neutrophil serine proteases (NSPs) expressed in the myelomonocyte lineage, neutrophil elastase, proteinase 3, cathepsin G, and neutrophil serine protease 4, collectively display a broad repertoire of (S1) specificities. The origin of NSPs can be traced back to a circulating liver-derived trypsin-like protease, the complement factor D ancestor, whose activity is tightly controlled by substrate-induced activation and TNFα-induced locally upregulated protein secretion. However, the present-day descendants are produced and converted to mature enzymes in precursor cells of the bone marrow and are safely sequestered in granules of circulating neutrophils. The potential site and duration of action of these cell-associated serine proteases are tightly controlled by the recruitment and activation of neutrophils, by stimulus-dependent regulated secretion of the granules, and by various soluble inhibitors in plasma, interstitial fluids, and in the inflammatory exudate. An extraordinary dynamic range and acceleration of immediate defense responses have been achieved by exploiting the high structural plasticity of the trypsin fold. AU - Weiss, S.A. AU - Rehm, S.R.T. AU - Perera, N.C.* AU - Biniossek, M.L.* AU - Schilling, O.* AU - Jenne, D. C1 - 61295 C2 - 50112 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Origin and expansion of the serine protease repertoire in the myelomonocyte lineage. JO - Int. J. Mol. Sci. VL - 22 IS - 4 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Cardiovascular diseases (CVD) annually take almost 18 million lives worldwide. Most lethal events occur months or years after the initial presentation. Indeed, many patients experience repeated complications or require multiple interventions (recurrent events). Apart from affecting the individual, this leads to high medical costs for society. Personalized treatment strategies aiming at prediction and prevention of recurrent events rely on early diagnosis and precise prognosis. Complementing the traditional environmental and clinical risk factors, multi-omics data provide a holistic view of the patient and disease progression, enabling studies to probe novel angles in risk stratification. Specifically, predictive molecular markers allow insights into regulatory networks, pathways, and mechanisms underlying disease. Moreover, artificial intelligence (AI) represents a powerful, yet adaptive, framework able to recognize complex patterns in large-scale clinical and molecular data with the potential to improve risk prediction. Here, we review the most recent advances in risk prediction of recurrent cardiovascular events, and discuss the value of molecular data and biomarkers for understanding patient risk in a systems biology context. Finally, we introduce explainable AI which may improve clinical decision systems by making predictions transparent to the medical practitioner. AU - Westerlund, A. AU - Hawe, J.S.* AU - Heinig, M. AU - Schunkert, H.* C1 - 63128 C2 - 51337 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Risk prediction of cardiovascular events by exploration of molecular data with explainable artificial intelligence. JO - Int. J. Mol. Sci. VL - 22 IS - 19 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - In the mammalian brain, cortical interneurons (INs) are a highly diverse group of cells. A key neurophysiological question concerns how each class of INs contributes to cortical circuit function and whether specific roles can be attributed to a selective cell type. To address this question, researchers are integrating knowledge derived from transcriptomic, histological, electrophysiological, developmental, and functional experiments to extensively characterise the different classes of INs. Our hope is that such knowledge permits the selective targeting of cell types for therapeutic endeavours. This review will focus on two of the main types of INs, namely the parvalbumin (PV+) or somatostatin (SOM+)-containing cells, and summarise the research to date on these classes. AU - Williams, R.H. AU - Riedemann, T.* C1 - 62913 C2 - 51001 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Development, diversity and death of mge-derived cortical interneurons. JO - Int. J. Mol. Sci. VL - 22 IS - 17 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Sphingosine-1-phosphate (S1P), is a signaling sphingolipid which acts as a bioactive lipid mediator. We assessed whether S1P had multiplex effects in regulating the large-conductance Ca2+-activated K+ channel (BKCa ) in catecholamine-secreting chromaffin cells. Using multiple patch-clamp modes, Ca2+ imaging, and computational modeling, we evaluated the effects of S1P on the Ca2+-activated K+ currents (IK(Ca) ) in bovine adrenal chromaffin cells and in a pheochromocytoma cell line (PC12). In outside-out patches, the open probability of BKCa channel was reduced with a mean-closed time increment, but without a conductance change in response to a low-concentration S1P (1 µM). The intracellular Ca2+ concentration (Cai ) was elevated in response to a high-dose (10 µM) but not low-dose of S1P. The single-channel activity of BKCa was also enhanced by S1P (10 µM) in the cell-attached recording of chromaffin cells. In the whole-cell voltage-clamp, a low-dose S1P (1 µM) suppressed IK(Ca), whereas a high-dose S1P (10 µM) produced a biphasic response in the amplitude of IK(Ca), i.e., an initial decrease followed by a sustained increase. The S1P-induced IK(Ca) enhancement was abolished by BAPTA. Current-clamp studies showed that S1P (1 µM) increased the action potential (AP) firing. Simulation data revealed that the decreased BKCa conductance leads to increased AP firings in a modeling chromaffin cell. Over a similar dosage range, S1P (1 µM) inhibited IK(Ca) and the permissive role of S1P on the BKCa activity was also effectively observed in the PC12 cell system. The S1P-mediated IK(Ca) stimulation may result from the elevated Cai, whereas the inhibition of BKCa activity by S1P appears to be direct. By the differentiated tailoring BKCa channel function, S1P can modulate stimulus-secretion coupling in chromaffin cells. AU - Wu, A.Z.* AU - Ohn, T.-L. AU - Shei, R.J.* AU - Wu, H.F.* AU - Chen, Y.C.* AU - Lee, H.C.* AU - Dai, D.F.* AU - Wu, S.N.* C1 - 61404 C2 - 50213 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Permissive modulation of sphingosine-1-phosphate-enhanced intracellular calcium on BKCa channel of chromaffin cells. JO - Int. J. Mol. Sci. VL - 22 IS - 4 PB - Mdpi PY - 2021 SN - 1661-6596 ER - TY - JOUR AB - Epidemiological studies on workers employed at the Mayak plutonium enrichment plant have demonstrated an association between external gamma ray exposure and an elevated risk of ischemic heart disease (IHD). In a previous study using fresh-frozen post mortem samples of the cardiac left ventricle of Mayak workers and non-irradiated controls, we observed radiation-induced alterations in the heart proteome, mainly downregulation of mitochondrial and structural proteins. As the control group available at that time was younger than the irradiated group, we could not exclude age as a confounding factor. To address this issue, we have now expanded our study to investigate additional samples using archival formalin-fixed paraffin-embedded (FFPE) tissue. Importantly, the control group studied here is older than the occupationally exposed (>500 mGy) group. Label-free quantitative proteomics analysis showed that proteins involved in the lipid metabolism, sirtuin signaling, mitochondrial function, cytoskeletal organization, and antioxidant defense were the most affected. A histopathological analysis elucidated large foci of fibrotic tissue, myocardial lipomatosis and lymphocytic infiltrations in the irradiated samples. These data highlight the suitability of FFPE material for proteomics analysis. The study confirms the previous results emphasizing the role of adverse metabolic changes in the radiation-associated IHD. Most importantly, it excludes age at the time of death as a confounding factor. AU - Azimzadeh, O. AU - Azizova, T.* AU - Merl-Pham, J. AU - Blutke, A. AU - Moseeva, M.* AU - Zubkova, O.* AU - Anastasov, N. AU - Feuchtinger, A. AU - Hauck, S.M. AU - Atkinson, M.J. AU - Tapio, S. C1 - 60141 C2 - 49210 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Chronic occupational exposure to ionizing radiation induces alterations in the structure and metabolism of the heart: A proteomic analysis of human formalin-fixed paraffin-embedded (FFPE) cardiac tissue. JO - Int. J. Mol. Sci. VL - 21 IS - 18 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - The vascular system is critical infrastructure that transports oxygen and nutrients around the body, and dynamically adapts its function to an array of environmental changes. To fulfil the demands of diverse organs, each with unique functions and requirements, the vascular system displays vast regional heterogeneity as well as specialized cell types. Our understanding of the heterogeneity of vascular cells and the molecular mechanisms that regulate their function is beginning to benefit greatly from the rapid development of single cell technologies. Recent studies have started to analyze and map vascular beds in a range of organs in healthy and diseased states at single cell resolution. The current review focuses on recent biological insights on the vascular system garnered from single cell analyses. We cover the themes of vascular heterogeneity, phenotypic plasticity of vascular cells in pathologies such as atherosclerosis and cardiovascular disease, as well as the contribution of defective microvasculature to the development of neurodegenerative disorders such as Alzheimer's disease. Further adaptation of single cell technologies to study the vascular system will be pivotal in uncovering the mechanisms that drive the array of diseases underpinned by vascular dysfunction. AU - Bondareva, O. AU - Sheikh, B. C1 - 59620 C2 - 48936 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Vascular homeostasis and inflammation in health and disease-lessons from single cell technologies. JO - Int. J. Mol. Sci. VL - 21 IS - 13 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Molecular communication between irradiated and unirradiated neighbouring cells initiates radiation-induced bystander effects (RIBE) and out-of-field (abscopal) effects which are both an example of the non-targeted effects (NTE) of ionising radiation (IR). Exosomes are small membrane vesicles of endosomal origin and newly identified mediators of NTE. Although exosome-mediated changes are well documented in radiation therapy and oncology, there is a lack of knowledge regarding the role of exosomes derived from inside and outside the radiation field in the early and delayed induction of NTE following IR. Therefore, here we investigated the changes in exosome profile and the role of exosomes as possible molecular signalling mediators of radiation damage. Exosomes derived from organs of whole body irradiated (WBI) or partial body irradiated (PBI) mice after 24 h and 15 days post-irradiation were transferred to recipient mouse embryonic fibroblast (MEF) cells and changes in cellular viability, DNA damage and calcium, reactive oxygen species and nitric oxide signalling were evaluated compared to that of MEF cells treated with exosomes derived from unirradiated mice. Taken together, our results show that whole and partial-body irradiation increases the number of exosomes, instigating changes in exosome-treated MEF cells, depending on the source organ and time after exposure. AU - Cagatay, S.T.* AU - Mayah, A.* AU - Mancuso, M.* AU - Giardullo, P.* AU - Pazzaglia, S.* AU - Saran, A.* AU - Daniel, A.* AU - Traynor, D.* AU - Meade, A.D.* AU - Lyng, F.* AU - Tapio, S. AU - Kadhim, M.* C1 - 60532 C2 - 49331 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Phenotypic and functional characteristics of exosomes derived from irradiated mouse organs and their role in the mechanisms driving non-targeted effects. JO - Int. J. Mol. Sci. VL - 21 IS - 21 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Long-term exposure of liquid preserved boar spermatozoa to seminal plasma (SP) can cause dramatic sperm injury. This study examined whether boar specificity exists in the sensitivity of spermatozoa to SP and whether correspondent biomarkers can be identified. Consecutive ejaculates (n= 4-5) collected from 19 boars were centrifuged, diluted with a pH-stablising extender with 10% (v/v) autologous SP and evaluated by computer-assisted semen analysis and flow cytometry. Up until 144 h storage, four boars showed consistently high sperm motility, viability and mitochondria activity, and one boar showed consistently low values. Intra-boar variability was high in the other boars. Screening of SP (n= 12 samples) for protein markers using mass spectrometry identified three protein candidates of which the granulin precursor, legumain and AWN were 0.5 to 0.9 log2-fold less abundant (p< 0.05) in SP-resistant compared to SP-sensitive samples. Lipidome analysis by mass spectrometry revealed 568 lipids showing no difference between the SP-groups. The most abundant lipids were cholesterol (42,442 pmol), followed by phosphatidylserine (20,956 pmol) and ether-linked phosphatidylethanolamine (13,039 pmol). In conclusion, three candidate proteins were identified which might be indicative of SP-tolerance of sperm during long-term storage. Noteworthy, a first lipidomic profile of boar SP is presented. AU - Hoefner, L.* AU - Luther, A.* AU - Palladini, A. AU - Froehlich, T.* AU - Waberski, D.* C1 - 60466 C2 - 49467 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Tolerance of stored boar spermatozoa to autologous seminal plasma: A proteomic and lipidomic approach. JO - Int. J. Mol. Sci. VL - 21 IS - 18 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Non-alcoholic fatty liver disease (NAFLD) is rising in prevalence, and a better pathophysiologic understanding of the transition to its inflammatory phenotype (NASH) is key to the development of effective therapies. To evaluate the contribution of the NLRP3 inflammasome and its downstream effectors IL-1 and IL-18 in this process, we applied the true-to-life “American lifestyle-induced obesity syndrome” (ALiOS) diet mouse model. Development of obesity, fatty liver and liver damage was investigated in mice fed for 24 weeks according to the ALiOS protocol. Lipidomic changes in mouse livers were compared to human NAFLD samples. Receptor knockout mice for IL-1 and IL-18 were used to dissect the impact of downstream signals of inflammasome activity on the development of NAFLD. The ALiOS diet induced obesity and liver steatosis. The lipidomic changes closely mimicked changes in human NAFLD. A pro-inflammatory gene expression pattern in liver tissue and increased serum liver transaminases indicated early liver damage in the absence of histological evidence of NASH. Mechanistically, Il-18r−/−-but not Il-1r−/− mice were protected from early liver damage, possibly due to silencing of the pro-inflammatory gene expression pattern. Our study identified NLRP3 activation and IL-18R-dependent signaling as potential modulators of early liver damage in NAFLD, preceding development of histologic NASH. AU - Hohenester, S.* AU - Kanitz, V.* AU - Schiergens, T.* AU - Einer, C. AU - Nagel, J.* AU - Wimmer, R.* AU - Reiter, F.P.* AU - Gerbes, A.L.* AU - de Toni, E.N.* AU - Bauer, C.* AU - Holdt, L.* AU - Mayr, D.* AU - Rust, C.* AU - Schnurr, M.* AU - Zischka, H. AU - Geier, A.* AU - Denk, G.* C1 - 60574 C2 - 49414 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - IL-18 but not IL-1 signaling is pivotal for the initiation of liver injury in murine non-alcoholic fatty liver disease. JO - Int. J. Mol. Sci. VL - 21 IS - 22 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Scarring and regeneration are two physiologically opposite endpoints to skin injuries, with mammals, including humans, typically healing wounds with fibrotic scars. We aim to provide an updated review on fibroblast heterogeneity as determinants of the scarring-regeneration continuum. We discuss fibroblast-centric mechanisms that dictate scarring-regeneration continua with a focus on intercellular and cell-matrix adhesion. Improved understanding of fibroblast lineage-specific mechanisms and how they determine scar severity will ultimately allow for the development of antiscarring therapies and the promotion of tissue regeneration. AU - Jiang, D. AU - Rinkevich, Y. C1 - 57978 C2 - 48266 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Scars or regeneration?-Dermal fibroblasts as drivers of diverse skin in wound responses. JO - Int. J. Mol. Sci. VL - 21 IS - 2 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Chagas disease, caused byTrypanosoma cruzi(T. cruzi), affects nearly eight million people worldwide. There are currently only limited treatment options, which cause several side effects and have drug resistance. Thus, there is a great need for a novel, improved Chagas treatment. Bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) has emerged as a promising pharmacological target. Moreover, some human dihydrofolate reductase (HsDHFR) inhibitors such as trimetrexate also inhibitT. cruziDHFR-TS (TcDHFR-TS). These compounds serve as a starting point and a reference in a screening campaign to search for newTcDHFR-TS inhibitors. In this paper, a novel virtual screening approach was developed that combines classical docking with protein-ligand interaction profiling to identify drug repositioning opportunities againstT. cruziinfection. In this approach, some food and drug administration (FDA)-approved drugs that were predicted to bind with high affinity toTcDHFR-TS and whose predicted molecular interactions are conserved among known inhibitors were selected. Overall, ten putativeTcDHFR-TS inhibitors were identified. These exhibited a similar interaction profile and a higher computed binding affinity, compared to trimetrexate. Nilotinib, glipizide, glyburide and gliquidone were tested onT. cruziepimastigotes and showed growth inhibitory activity in the micromolar range. Therefore, these compounds could lead to the development of new treatment options for Chagas disease. AU - Juárez-Saldivar, A.* AU - Schroeder, M.* AU - Salentin, S.* AU - Haupt, V.J.* AU - Saavedra, E.* AU - Vázquez, C.* AU - Reyes-Espinosa, F.* AU - Herrera-Mayorga, V.* AU - Villalobos-Rocha, J.C.* AU - Garcia Perez, C. AU - Campillo, N.E.* AU - Rivera, G.* C1 - 59506 C2 - 48885 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Computational drug repositioning for chagas disease using protein-ligand interaction profiling. JO - Int. J. Mol. Sci. VL - 21 IS - 12 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Congenital cataracts are the prime cause for irreversible blindness in children. The global incidence of congenital cataract is 2.2–13.6 per 10,000 births, with the highest prevalence in Asia. Nearly half of the congenital cataracts are of familial nature, with a predominant autosomal dominant pattern of inheritance. Over 38 of the 45 mapped loci for isolated congenital or infantile cataracts have been associated with a mutation in a specific gene. The clinical and genetic heterogeneity of congenital cataracts makes the molecular diagnosis a bit of a complicated task. Hence, whole exome sequencing (WES) was utilized to concurrently screen all known cataract genes and to examine novel candidate factors for a disease-causing mutation in probands from 11 pedigrees affected with familial congenital cataracts. Analysis of the WES data for known cataract genes identified causative mutations in six pedigrees (55%) in PAX6, FYCO1 (two variants), EPHA2, P3H2, TDRD7 and an additional likely causative mutation in a novel gene NCOA6, which represents the first dominant mutation in this gene. This study identifies a novel cataract gene not yet linked to human disease. NCOA6 is a transcriptional coactivator that interacts with nuclear hormone receptors to enhance their transcriptional activator function. AU - Kandaswamy, D.K. AU - Prakash, M.V.S.* AU - Graw, J. AU - Koller, S.* AU - Magyar, I.* AU - Tiwari, A.* AU - Berger, W.* AU - Santhiya, S.T.* C1 - 60887 C2 - 49721 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Application of WES towards molecular investigation of congenital cataracts: Identification of novel alleles and genes in a hospital-based cohort of South India. JO - Int. J. Mol. Sci. VL - 21 IS - 24 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Natural products comprise a rich reservoir for innovative drug leads and are a constant source of bioactive compounds. To find pharmacological targets for new or already known natural products using modern computer-aided methods is a current endeavor in drug discovery. Nature's treasures, however, could be used more effectively. Yet, reliable pipelines for the large-scale target prediction of natural products are still rare. We developed an in silico workflow consisting of four independent, stand-alone target prediction tools and evaluated its performance on dihydrochalcones (DHCs)-a well-known class of natural products. Thereby, we revealed four previously unreported protein targets for DHCs, namely 5-lipoxygenase, cyclooxygenase-1, 17 beta-hydroxysteroid dehydrogenase 3, and aldo-keto reductase 1C3. Moreover, we provide a thorough strategy on how to perform computational target predictions and guidance on using the respective tools. AU - Mayr, F.* AU - Möller, G. AU - Garscha, U.* AU - Fischer, J.* AU - Castaño, P.R.* AU - Inderbinen, S.G.* AU - Temml, V.* AU - Waltenberger, B.* AU - Schwaiger, S.* AU - Hartmann, R.W.* AU - Gege, C.* AU - Martens, S.* AU - Odermatt, A.* AU - Pandey, A.V.* AU - Werz, O.* AU - Adamski, J. AU - Stuppner, H.* AU - Schuster, D.* C1 - 60186 C2 - 49300 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Finding new molecular targets of familiar natural products using in silico target prediction. JO - Int. J. Mol. Sci. VL - 21 IS - 19 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Normal tissue toxicity is a dose-limiting factor in radiation therapy. Therefore, a detailed understanding of the normal tissue response to radiation is necessary to predict the risk of normal tissue toxicity and to development strategies for tissue protection. One component of normal tissue that is continuously exposed during therapeutic irradiation is the circulating population of peripheral blood mononuclear cells (PBMC). PBMCs are highly sensitive to ionizing radiation (IR); however, little is known about how IR affects the PBMC response on a systemic level. It was the aim of this study to investigate whether IR was capable to induce changes in the composition and function of extracellular vesicles (EVs) secreted from PBMCs after radiation exposure to different doses. Therefore, whole blood samples from healthy donors were exposed to X-ray radiation in the clinically relevant doses of 0, 0.1, 2 or 6 Gy and PBMC-secreted EVs were isolated 72 h later. Proteome and miRNome analysis of EVs as well as functional studies were performed. Secreted EVs showed a dose-dependent increase in the number of significantly deregulated proteins and microRNAs. For both, proteome and microRNA data, principal component analysis showed a dose-dependent separation of control and exposed groups. Integrated pathway analysis of the radiation-regulated EV proteins and microRNAs consistently predicted an association of deregulated molecules with apoptosis, cell death and survival. Functional studies identified endothelial cells as an efficient EV recipient system, in which irradiation of recipient cells further increased the uptake. Furthermore an apoptosis suppressive effect of EVs from irradiated PBMCs in endothelial recipient cells was detected. In summary, this study demonstrates that IR modifies the communication between PBMCs and endothelial cells. EVs from irradiated PBMC donors were identified as transmitters of protective signals to irradiated endothelial cells. Thus, these data may lead to the discovery of biomarker candidates for radiation dosimetry and even more importantly, they suggest EVs as a novel systemic communication pathway between irradiated normal, non-cancer tissues. AU - Mörtl, S. AU - Buschmann, D.* AU - Azimzadeh, O. AU - Schneider, M. AU - Kell, R. AU - Winkler, K. AU - Tapio, S. AU - Hornhardt, S.* AU - Merl-Pham, J. AU - Pfaffl, M.W.* AU - Atkinson, M.J. C1 - 58758 C2 - 48350 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Radiation exposure of peripheral mononuclear blood cells alters the composition and function of extracellular vesicles JO - Int. J. Mol. Sci. VL - 21 IS - 7 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - In 1921, a Canadian research team led by Frederick Banting and John Macleod succeeded in the isolation of insulin from pancreatic homogenate [...]. AU - Müller, T.D. AU - Habegger, K.* C1 - 57838 C2 - 48118 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Revisiting the pharmacological value of glucagon: An editorial for the special Issue "The biology and pharmacology of glucagon". JO - Int. J. Mol. Sci. VL - 21 IS - 2 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Shared metabolomic patterns at delivery have been suggested to underlie the mother-to-child transmission of adverse metabolic health. This study aimed to investigate whether mothers with gestational diabetes mellitus (GDM) and their offspring show similar metabolomic patterns several years postpartum. Targeted metabolomics (including 137 metabolites) was performed in plasma samples obtained during an oral glucose tolerance test from 48 mothers with GDM and their offspring at a cross-sectional study visit 8 years after delivery. Partial Pearson’s correlations between the area under the curve (AUC) of maternal and offspring metabolites were calculated, yielding so-called Gaussian graphical models. Spearman’s correlations were applied to investigate correlations of body mass index (BMI), Matsuda insulin sensitivity index (ISI-M), dietary intake, and physical activity between generations, and correlations of metabolite AUCs with lifestyle variables. This study revealed that BMI, ISI-M, and the AUC of six metabolites (carnitine, taurine, proline, SM(-OH) C14:1, creatinine, and PC ae C34:3) were significantly correlated between mothers and offspring several years postpartum. Intergenerational metabolite correlations were independent of shared BMI, ISI-M, age, sex, and all other metabolites. Furthermore, creatinine was correlated with physical activity in mothers. This study suggests that there is long-term metabolic programming in the offspring of mothers with GDM and informs us about targets that could be addressed by future intervention studies. AU - Ott, R. AU - Pawlow, X. AU - Weiss, A. AU - Hofelich, A. AU - Herbst, M. AU - Hummel, N. AU - Prehn, C. AU - Adamski, J. AU - Römisch-Margl, W. AU - Kastenmüller, G. AU - Ziegler, A.-G. AU - Hummel, S. C1 - 60843 C2 - 49661 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Intergenerational metabolomic analysis of mothers with a history of gestational diabetes mellitus and their offspring. JO - Int. J. Mol. Sci. VL - 21 IS - 24 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Jumonji-domain-containing protein 6 (JMJD6) is a Fe(II) and 2-oxogluterate (2OG) dependent oxygenase involved in gene regulation through post-translationally modifying nuclear proteins. It is highly expressed in many cancer types and linked to tumor progression and metastasis. Four alternatively-splicedjmjd6transcripts were annotated. Here, we focus on the two most abundantly expressed ones, which we calljmjd6-2andjmjd6-Ex5.TCGA SpliceSeqdata revealed a significant decrease ofjmjd6-Ex5transcripts in patients and postmortem tissue of several tumors. The two protein isoforms are distinguished by their C-terminal sequences, which include a serine-rich region (polyS-domain) in JMJD6-2 that is not present in JMJD6-Ex5. Immunoprecipitation followed by LC-MS/MS for JMJD6-Ex5 shows that different sets of proteins interact with JMJD6-2 and JMJD6-Ex5 with only a few overlaps. In particular, we found TFIIF-associating CTD phosphatase (FCP1), proteins of the survival of motor neurons (SMN) complex, heterogeneous nuclear ribonucleoproteins (hnRNPs) and upstream binding factor (UBF) to interact with JMJD6-Ex5. Like JMJD6-2, both UBF and FCP1 comprise a polyS-domain. The polyS domain of JMJD6-2 might block the interaction with polyS-domains of other proteins. In contrast, JMJD6-2 interacts with many SR-like proteins with arginine/serine-rich (RS)-domains, including several splicing factors. In an HIV-based splicing reporter assay, co-expression of JMJD6-2 inhibited exon inclusion, whereas JMJD6-Ex5 did not have any effect. Furthermore, the silencing ofjmjd6by siRNAs favoredjmjd6-Ex5transcripts, suggesting that JMJD6 controls splicing of its own pre-mRNA. The distinct molecular properties of JMJD6-2 and JMJD6-Ex5 open a lead into the functional implications of the variations of their relative abundance in tumors. AU - Raguz, N. AU - Heim, A.* AU - Engal, E.* AU - Wesche, J. AU - Merl-Pham, J. AU - Hauck, S.M. AU - Erkelenz, S.* AU - Schaal, H.* AU - Bensaude, O.* AU - Wolf, A. AU - Salton, M.* AU - Böttger, A.* C1 - 60073 C2 - 49222 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - JMJD6 regulates splicing of its own gene resulting in alternatively spliced isoforms with different nuclear targets. JO - Int. J. Mol. Sci. VL - 21 IS - 18 PB - Mdpi PY - 2020 SN - 1661-6596 ER - TY - JOUR AB - Chronic exposure to low-dose ionizing radiation is associated with an increased risk of cardiovascular disease. Alteration in energy metabolism has been suggested to contribute to radiation-induced heart pathology, mitochondrial dysfunction being a hallmark of this disease. The goal of this study was to investigate the regulatory role of acetylation in heart mitochondria in the long-term response to chronic radiation. ApoE-deficient C57Bl/6J mice were exposed to low-dose-rate (20 mGy/day) gamma radiation for 300 days, resulting in a cumulative total body dose of 6.0 Gy. Heart mitochondria were isolated and analyzed using quantitative proteomics. Radiation-induced proteome and acetylome alterations were further validated using immunoblotting, enzyme activity assays, and ELISA. In total, 71 proteins showed peptides with a changed acetylation status following irradiation. The great majority (94%) of the hyperacetylated proteins were involved in the TCA cycle, fatty acid oxidation, oxidative stress response and sirtuin pathway. The elevated acetylation patterns coincided with reduced activity of mitochondrial sirtuins, increased the level of Acetyl-CoA, and were accompanied by inactivation of major cardiac metabolic regulators PGC-1 alpha and PPAR alpha. These observations suggest that the changes in mitochondrial acetylation after irradiation is associated with impairment of heart metabolism. We propose a novel mechanism involved in the development of late cardiac damage following chronic irradiation. AU - Barjaktarovic, Z. AU - Merl-Pham, J. AU - Braga-Tanaka, I.* AU - Tanaka, S.* AU - Hauck, S.M. AU - Saran, A.* AU - Mancuso, M.* AU - Atkinson, M.J. AU - Tapio, S. AU - Azimzadeh, O. C1 - 57207 C2 - 47610 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Hyperacetylation of cardiac mitochondrial proteins is associated with metabolic impairment and sirtuin downregulation after chronic total body irradiation of ApoE -/- mice. JO - Int. J. Mol. Sci. VL - 20 IS - 20 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - Mitochondria play a central role in non-alcoholic fatty liver disease (NAFLD) progression and in the control of cell death signalling during the progression to hepatocellular carcinoma (HCC). Associated with the metabolic syndrome, NAFLD is mostly driven by insulin-resistant white adipose tissue lipolysis that results in an increased hepatic fatty acid influx and the ectopic accumulation of fat in the liver. Upregulation of beta-oxidation as one compensatory mechanism leads to an increase in mitochondrial tricarboxylic acid cycle flux and ATP generation. The progression of NAFLD is associated with alterations in the mitochondrial molecular composition and respiratory capacity, which increases their vulnerability to different stressors, including calcium and pro-inflammatory molecules, which result in an increased generation of reactive oxygen species (ROS) that, altogether, may ultimately lead to mitochondrial dysfunction. This may activate further pro-inflammatory pathways involved in the progression from steatosis to steatohepatitis (NASH). Mushroom-enriched diets, or the administration of their isolated bioactive compounds, have been shown to display beneficial effects on insulin resistance, hepatic steatosis, oxidative stress, and inflammation by regulating nutrient uptake and lipid metabolism as well as modulating the antioxidant activity of the cell. In addition, the gut microbiota has also been described to be modulated by mushroom bioactive molecules, with implications in reducing liver inflammation during NAFLD progression. Dietary mushroom extracts have been reported to have anti-tumorigenic properties and to induce cell-death via the mitochondrial apoptosis pathway. This calls for particular attention to the potential therapeutic properties of these natural compounds which may push the development of novel pharmacological options to treat NASH and HCC. We here review the diverse effects of mushroom-enriched diets in liver disease, emphasizing those effects that are dependent on mitochondria. AU - Fontes, A. AU - Alemany-Pagès, M.* AU - Oliveira, P.J.* AU - Ramalho-Santos, J.* AU - Zischka, H. AU - Azul, A.M.* C1 - 56773 C2 - 47326 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Antioxidant versus pro-apoptotic effects of mushroom-enriched diets on mitochondria in liver disease. JO - Int. J. Mol. Sci. VL - 20 IS - 16 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - Brown adipose tissue (BAT) thermogenesis is a conserved mechanism to maintain body temperature in mammals. However, since BAT contribution to energy expenditure can represent a relevant modulator of metabolic homeostasis, many studies have focused on the nervous system and endocrine factors that control the activity of this tissue. There is long-established evidence that the counter-regulatory hormone glucagon negatively influences energy balance, enhances satiety, and increases energy expenditure. Despite compelling evidence showing that glucagon has direct action on BAT thermogenesis, recent findings are questioning this conventional attribute of glucagon action. Glucagon like peptide-1 (GLP-1) is an incretin secreted by the intestinal tract which strongly decreases feeding, and, furthermore, improves metabolic parameters associated with obesity and diabetes. Therefore, GLP-1 receptors (GLP-1-R) have emerged as a promising target in the treatment of metabolic disorders. In this short review, we will summarize the latest evidence in this regard, as well as the current therapeutic glucagon- and GLP-1-based approaches to treating obesity. AU - Gonzales García, I. AU - Milbank, E.* AU - Diéguez, C.* AU - López, M.* AU - Contreras, C.* C1 - 56623 C2 - 47241 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Glucagon, GLP-1 and thermogenesis. JO - Int. J. Mol. Sci. VL - 20 IS - 14 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - In children, ketamine sedation is often used during radiological procedures. Combined exposure of ketamine and radiation at doses that alone did not affect learning and memory induced permanent cognitive impairment in mice. The aim of this study was to elucidate the mechanism behind this adverse outcome. Neonatal male NMRI mice were administered ketamine (7.5 mg kg(-1)) and irradiated (whole-body, 100 mGy or 200 mGy, Cs-137) one hour after ketamine exposure on postnatal day 10. The control mice were injected with saline and sham-irradiated. The hippocampi were analyzed using label-free proteomics, immunoblotting, and Golgi staining of CA1 neurons six months after treatment. Mice co-exposed to ketamine and low-dose radiation showed alterations in hippocampal proteins related to neuronal shaping and synaptic plasticity. The expression of brain-derived neurotrophic factor, activity-regulated cytoskeleton-associated protein, and postsynaptic density protein 95 were significantly altered only after the combined treatment (100 mGy or 200 mGy combined with ketamine, respectively). Increased numbers of basal dendrites and branching were observed only after the co-exposure, thereby constituting a possible reason for the displayed alterations in behavior. These data suggest that the risk of radiation-induced neurotoxic effects in the pediatric population may be underestimated if based only on the radiation dose. AU - Hladik, D. AU - Buratovic, S.* AU - von Toerne, C. AU - Azimzadeh, O. AU - Subedi, P. AU - Philipp, J. AU - Winkler, S. AU - Feuchtinger, A. AU - Samson, E. AU - Hauck, S.M. AU - Stenerlöw, B.* AU - Eriksson, P.* AU - Atkinson, M.J. AU - Tapio, S. C1 - 57492 C2 - 47813 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Combined treatment with low-dose ionizing radiation and ketamine induces adverse changes in CA1 neuronal structure in murine hippocampi. JO - Int. J. Mol. Sci. VL - 20 IS - 23 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - Glucagon's ability to increase energy expenditure has been known for more than 60 years, yet the mechanisms underlining glucagon's thermogenic effect still remain largely elusive. Over the last years, significant efforts were directed to unravel the physiological and cellular underpinnings of how glucagon regulates energy expenditure. In this review, we summarize the current knowledge on how glucagon regulates systems metabolism with a special emphasis on its acute and chronic thermogenic effects. AU - Kleinert, M. AU - Sachs, S. AU - Habegger, K.M.* AU - Hofmann, S.M. AU - Müller, T.D. C1 - 57247 C2 - 47667 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Glucagon regulation of energy expenditure. JO - Int. J. Mol. Sci. VL - 20 IS - 21 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - KcsA is a tetrameric potassium channel formed out of four identical monomeric subunits used as a standard model for selective potassium transport and pH-dependent gating. Large conformational changes are reported for tetramer and monomer upon gating, and the response of the monomer being controversial with the two major studies partially contradicting each other. KcsA was analyzed as functional tetramers embedded in liposomes and as monomer subunits with confocal Raman microscopy under physiological conditions for the active and the closed channel state, using 532 nm excitation to avoid introducing conformational changes during the measurement. Channel function was confirmed using liposome flux assay. While the classic fingerprint region below 1800 rel. cm(-1) in the Raman spectrum of the tetramer was unaffected, the CH-stretching region between 2800 and 3200 rel. cm(-1) was found to be strongly affected by the conformation. No pH-dependency was observed in the Raman spectra of the monomer subunits, which closely resembled the Raman spectrum of the tetramer in its active conformation, indicating that the open conformation of the monomer and not the closed conformation as postulated may equal the relaxed state of the molecule. AU - Kniggendorf, A.K.* AU - Schmidt, D. AU - Roth, B.* AU - Plettenburg, O. AU - Zeilinger, C.* C1 - 56273 C2 - 46961 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - pH-dependent conformational changes of KcsA tetramer and monomer probed by raman spectroscopy. JO - Int. J. Mol. Sci. VL - 20 IS - 11 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - Cysteine cathepsin C (CatC) is a ubiquitously expressed, lysosomal aminopeptidase involved in the activation of zymogens of immune-cell-associated serine proteinases (elastase, cathepsin G, proteinase 3, neutrophil serine proteinase 4, lymphocyte granzymes, and mast cell chymases). CatC is first synthetized as an inactive zymogen containing an intramolecular chain propeptide, the dimeric form of which is processed into the mature tetrameric form by proteolytic cleavages. A molecular modeling analysis of proCatC indicated that its propeptide displayed a similar fold to those of other lysosomal cysteine cathepsins, and could be involved in dimer formation. Our in vitro experiments revealed that human proCatC was processed and activated by CatF, CatK, and CatV in two consecutive steps of maturation, as reported for CatL and CatS previously. The unique positioning of the propeptide domains in the proCatC dimer complex allows this order of cleavages to be understood. The missense mutation Leu172Pro within the propeptide region associated with the Papillon-Lefevre and Haim-Munk syndrome altered the proform stability as well as the maturation of the recombinant Leu172Pro proform. AU - Lamort, A.-S. AU - Hamon, Y.* AU - Czaplewski, C.* AU - Gieldon, A.* AU - Seren, S.* AU - Coquet, L.* AU - Lecaille, F.* AU - Lesner, A.* AU - Lalmanach, G.* AU - Gauthier, F.* AU - Jenne, D. AU - Korkmaz, B.* C1 - 56983 C2 - 47391 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Processing and maturation of cathepsin C zymogen: A biochemical and molecular modeling analysis. JO - Int. J. Mol. Sci. VL - 20 IS - 19 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - Pancreatic cancer has a poor prognosis. New treatment options are urgently required to improve patient outcomes. One promising new class of anticancer drugs are synthetic histone deacetylase inhibitors (HDACi) which modulate chromatin structure and gene expression by blocking histone deacetylation. In this study, we aimed at comparing the in vitro capacities of the HDACi SAHA and CUDC-101 to increase radiosensitivity of human pancreatic tumor cell lines. Therefore, three pancreatic cancer cell lines (Su.86.86, MIA Paca-2, T3M-4) were treated with SAHA (1.5-5 mu M) or CUDC-101 (0.25-3 mu M) and after 24 h irradiated. Cell proliferation, clonogenic survival and apoptosis was determined. Additionally, cell lysates were investigated for the expression of apoptosis-related proteins. CUDC-101 and SAHA increased the radiation sensitivity of pancreatic tumor cell lines in a dose-dependent manner. This was evidenced by cell proliferation and clonogenic survival. Furthermore, enhanced radiation sensitivity after CUDC-101 or SAHA treatment was confirmed for Su.86.86 and T3M-4 cells in a 3-D microtissue approach. Increased amounts of subG1 cells and diminished full length PARP-1 suggest increased radiation-induced apoptosis after SAHA or CUDC-101 treatment. The comparison of both inhibitors in these assays manifested CUDC-101 as more potent radiosensitizer than SAHA. In line, western blot quantification of the apoptosis-inhibitory proteins XIAP and survivin showed a stronger down-regulation in response to CUDC-101 treatment than after SAHA application. These proteins may contribute to the synergy between HDAC inhibition and radiation response. In conclusion, these preclinical results suggest that treatment with the HDAC inhibitors CUDC-101 or SAHA can enhance radiation-induced cytotoxicity in human pancreatic cells. However, comparison of both inhibitors identified the multi target inhibitor CUDC-101 as more potent radiosensitizer than the HDAC inhibitor SAHA. AU - Mörtl, S. AU - Payer, S. AU - Kell, R. AU - Winkler, K. AU - Anastasov, N. AU - Atkinson, M.J. C1 - 56555 C2 - 47135 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Comparison of Radiosensitization by HDAC Inhibitors CUDC-101 and SAHA in Pancreatic Cancer Cells. JO - Int. J. Mol. Sci. VL - 20 IS - 13 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - The present study gives an overview of the binding energetics of the homologous heterodimers of cruzipain-chagasin based on the binding energy (Delta G(b)) prediction obtained with FoldX. This analysis involves a total of 70 homologous models of the cruzipain-chagasin complex which were constructed by homology from the combinatory variation of nine papain-like cysteine peptidase structures and seven cysteine protease inhibitor structures (as chagasin-like and cystatin-like inhibitors). Only 32 systems have been evaluated experimentally, Delta G(b)(experimental) values previously reported. Therefore, the result of the multiple analysis in terms of the thermodynamic parameters, are shown as relative energy |Delta Delta G| = |Delta G(b)(from) (FoldX) - Delta G(b)(experimental)|. Nine models were identified that recorded |Delta Delta G| < 1.3, five models to 2.8 > |Delta Delta G| > 1.3 and the other 18 models, values of |Delta Delta G| > 2.8. The energetic analysis of the contribution of Delta H and Delta S to Delta G(b) to the 14-molecular model presents a Delta G(b) mostly Delta H-driven at neutral pH and at an ionic strength (I) of 0.15 M. The dependence of Delta G(b)(I,pH) at 298 K to the cruzipain-chagasin complex predicts a linear dependence of Delta G(b)(I). The computational protocol allowed the identification and prediction of thermodynamics binding energy parameters for cruzipain-chagasin-like heterodimers. AU - Reyes-Espinosa, F.* AU - Juárez-Saldivar, A.* AU - Palos, I.* AU - Herrera-Mayorga, V.* AU - Garcia Perez, C. AU - Rivera, G.* C1 - 55696 C2 - 46474 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - In silico analysis of homologous heterodimers of cruzipain-chagasin from structural models built by homology. JO - Int. J. Mol. Sci. VL - 20 IS - 6 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - The extracellular matrix (ECM) is a network of different proteins and proteoglycans that controls differentiation, migration, repair, survival, and development, and it seems that its remodeling is required for healthy adipose tissue expansion. Obesity drives an excessive lipid accumulation in adipocytes, which provokes immune cells infiltration, fibrosis (an excess of deposition of ECM components such as collagens, elastin, and fibronectin) and inflammation, considered a consequence of local hypoxia, and ultimately insulin resistance. To understand the mechanism of this process is a challenge to treat the metabolic diseases. This review is focused at identifying the putative role of ECM in adipose tissue, describing its structure and components, its main tissue receptors, and how it is affected in obesity, and subsequently the importance of an appropriate ECM remodeling in adipose tissue expansion to prevent metabolic diseases. AU - Ruiz Ojeda, F.J. AU - Méndez-Gutiérrez, A.* AU - Aguilera, C.M.* AU - Plaza-Díaz, J.* C1 - 57017 C2 - 47441 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Extracellular matrix remodeling of adipose Ttssue in obesity and metabolic diseases. JO - Int. J. Mol. Sci. VL - 20 IS - 19 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - The exponential increase of patients with diabetes mellitus urges for novel therapeutic strategies to reduce the socioeconomic burden of this disease. The loss or dysfunction of insulin-producing beta -cells, in patients with type 1 and type 2 diabetes respectively, put these cells at the center of the disease initiation and progression. Therefore, major efforts have been taken to restore the beta -cell mass by cell-replacement or regeneration approaches. Implementing novel therapies requires deciphering the developmental mechanisms that generate beta -cells and determine the acquisition of their physiological phenotype. In this review, we summarize the current understanding of the mechanisms that coordinate the postnatal maturation of beta -cells and define their functional identity. Furthermore, we discuss different routes by which beta -cells lose their features and functionality in type 1 and 2 diabetic conditions. We then focus on potential mechanisms to restore the functionality of those beta -cell populations that have lost their functional phenotype. Finally, we discuss the recent progress and remaining challenges facing the generation of functional mature beta -cells from stem cells for cell-replacement therapy for diabetes treatment. AU - Salinno, C. AU - Cota, P. AU - Bastidas-Ponce, A. AU - Tarquis Medina, M. AU - Lickert, H. AU - Bakhti, M. C1 - 57246 C2 - 47666 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - β-cell maturation and identity in health and disease. JO - Int. J. Mol. Sci. VL - 20 IS - 21 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - Glucose phosphorylating enzymes are crucial in the regulation of basic cellular processes, including metabolism and gene expression. Glucokinases and hexokinases provide a pool of phosphorylated glucose in an adenosine diphosphate (ADP)- and ATP-dependent manner to shape the cell metabolism. The glucose processing enzymes from Kluyveromyces lactis are poorly characterized despite the emerging contribution of this yeast strain to industrial and laboratory scale biotechnology. The first reports on K. lactis glucokinase (KlGlk1) positioned the enzyme as an essential component required for glucose signaling. Nevertheless, no biochemical and structural information was available until now. Here, we present the first crystal structure of KlGlk1 together with biochemical characterization, including substrate specificity and enzyme kinetics. Additionally, comparative analysis of the presented structure and the prior structures of lactis hexokinase (KlHxk1) demonstrates the potential transitions between open and closed enzyme conformations upon ligand binding. AU - Zak, K.M. AU - Kalińska, M.* AU - Wątor, E.* AU - Kuśka, K.* AU - Krutyhołowa, R.* AU - Dubin, G.* AU - Popowicz, G.M. AU - Grudnik, P.* C1 - 57002 C2 - 47427 CY - St Alban-anlage 66, Ch-4052 Basel, Switzerland TI - Crystal structure of kluyveromyces lactis glucokinase (KlGlk1). JO - Int. J. Mol. Sci. VL - 20 IS - 19 PB - Mdpi PY - 2019 SN - 1661-6596 ER - TY - JOUR AB - Advanced glycation end-products (AGEs) are non-enzymatic protein and amino acid adducts as well as DNA adducts which form from dicarbonyls and glucose. AGE formation is enhanced in diabetes and is associated with the development of diabetic complications. In the current review, we discuss mechanisms that lead to enhanced AGE levels in the context of diabetes and diabetic complications. The methylglyoxal-detoxifying glyoxalase system as well as alternative pathways of AGE detoxification are summarized. Therapeutic approaches to interfere with different pathways of AGE formation are presented. AU - Brings, S.* AU - Fleming, T. AU - Freichel, M.* AU - Muckenthaler, M.U.* AU - Herzig, S. AU - Nawroth, P.P. C1 - 51172 C2 - 42968 TI - Dicarbonyls and advanced glycation end-products in the development of diabetic complications and targets for intervention. JO - Int. J. Mol. Sci. VL - 18 IS - 5 PY - 2017 SN - 1661-6596 ER - TY - JOUR AB - Ghrelin was discovered in 1999 as the endogenous ligand of the growth-hormone secretagogue receptor 1a (GHSR1a). Since then, ghrelin has been found to exert a plethora of physiological effects that go far beyond its initial characterization as a growth hormone (GH) secretagogue. Among the numerous well-established effects of ghrelin are the stimulation of appetite and lipid accumulation, the modulation of immunity and inflammation, the stimulation of gastric motility, the improvement of cardiac performance, the modulation of stress, anxiety, taste sensation and reward-seeking behavior, as well as the regulation of glucose metabolism and thermogenesis. Due to a variety of beneficial effects on systems' metabolism, pharmacological targeting of the endogenous ghrelin system is widely considered a valuable approach to treat metabolic complications, such as chronic inflammation, gastroparesis or cancer-associated anorexia and cachexia. The aim of this review is to discuss and highlight the broad pharmacological potential of ghrelin pathway modulation for the treatment of anorexia, cachexia, sarcopenia, cardiopathy, neurodegenerative disorders, renal and pulmonary disease, gastrointestinal (GI) disorders, inflammatory disorders and metabolic syndrome. AU - Collden, G. AU - Tschöp, M.H. AU - Müller, T.D. C1 - 50918 C2 - 42982 CY - Basel TI - Therapeutic potential of targeting the ghrelin pathway. JO - Int. J. Mol. Sci. VL - 18 IS - 4 PB - Mdpi Ag PY - 2017 SN - 1661-6596 ER - TY - JOUR AB - Single cell organisms can surprisingly exceed the number of human protein-coding genes, which are thus not at the origin of the complexity of an organism. In contrast, the relative amount of non-protein-coding sequences increases consistently with organismal complexity. Moreover, the mammalian transcriptome predominantly comprises non-(protein)-coding RNAs (ncRNA), of which the long ncRNAs (lncRNAs) constitute the most abundant part. lncRNAs are highly species- and tissue-specific with very versatile modes of action in accordance with their binding to a large spectrum of molecules and their diverse localization. lncRNAs are transcriptional regulators adding an additional regulatory layer in biological processes and pathophysiological conditions. Here, we review lncRNAs affecting metabolic organs with a focus on the liver, pancreas, skeletal muscle, cardiac muscle, brain, and adipose organ. In addition, we will discuss the impact of lncRNAs on metabolic diseases such as obesity and diabetes. In contrast to the substantial number of lncRNA loci in the human genome, the functionally characterized lncRNAs are just the tip of the iceberg. So far, our knowledge concerning lncRNAs in energy homeostasis is still in its infancy, meaning that the rest of the iceberg is a treasure chest yet to be discovered. AU - Giroud, M. AU - Scheideler, M. C1 - 52542 C2 - 44062 CY - Basel TI - Long non-coding RNAs in metabolic organs and energy homeostasis. JO - Int. J. Mol. Sci. VL - 18 IS - 12 PB - Mdpi Ag PY - 2017 SN - 1661-6596 ER - TY - JOUR AB - Aquaporins (AQPs) are small integral membrane proteins with 13 members in mammals and are essential for water transport across membranes. They are found in many different tissues and cells. Currently, there are conflicting results regarding retinal aquaporin expression and subcellular localization between genome and protein analyses and among various species. AQP4, 7, 9 and 11 were described in the retina of men; whereas AQP6, 8 and 10 were earlier identified in rat retinas and AQP4, 5 and 11 in horses. Since there is a lack of knowledge regarding AQP expression on protein level in retinas of different animal models, we decided to analyze retinal cellular expression of AQP4, 5 and 11 in situ with immunohistochemistry. AQP4 was detected in all 15 explored species, AQP5 and AQP11 in 14 out of 15. Interestingly, AQP4 was unambiguously expressed in Muller glial cells, whereas AQP5 was differentially allocated among the species analyzed. AQP11 expression was Muller glial cell-specific in 50% of the animals, whereas in the others, AQP11 was detected in ganglion cell layer and at photoreceptor outer segments. Our data indicate a disparity in aquaporin distribution in retinas of various animals, especially for AQP5 and 11. AU - Amann, B.* AU - Kleinwort, K.J.* AU - Hirmer, S.* AU - Sekundo, W.* AU - Kremmer, E. AU - Hauck, S.M. AU - Deeg, C.A.* C1 - 49128 C2 - 41630 CY - Basel TI - Expression and distribution pattern of aquaporin 4, 5 and 11 in retinas of 15 different species. JO - Int. J. Mol. Sci. VL - 17 IS - 7 PB - Mdpi Ag PY - 2016 SN - 1661-6596 ER - TY - JOUR AB - Polymorphisms in genes involved in the oxidative stress response may partially explain the documented heterogeneous associations between traffic-related air pollution (TRAP) exposure and asthma and allergies in children. We investigated whether the GSTT1, GSTM1 and GSTP1 gene polymorphisms modified the associations between TRAP exposure during the first year of life and asthma, wheeze and hay fever in adolescence. We used a birth cohort of 620 high risk infants from the Melbourne Atopy Cohort Study. TRAP exposure during the first year of life was defined as the cumulative length of major roads within 150 m of each participant’s residence during the first year of life. Wheeze, asthma and hay fever were measured at ages 12 (n = 370) and 18 (n = 434) years. The associations and interactions with glutathione S-transferases (GST s) were investigated using regression models. Overall, there was no relationship between TRAP exposure during the first year of life and current asthma, wheeze and hay fever at ages 12 or 18 years. However, in GSTT1 null carriers, every 100 m increase in cumulative lengths of major road exposure during the first year of life was associated with a 2.31-fold increased risk of wheeze and a 2.15-fold increased risk of asthma at 12 years. TRAP is associated with some respiratory outcomes in carriers of genetic polymorphisms in oxidative stress metabolism genes. AU - Bowatte, G.* AU - Lodge, C.J.* AU - Lowe, A.J.* AU - Erbas, B.* AU - Dennekamp, M.* AU - Marks, G.B.* AU - Perret, J.* AU - Hui, J.* AU - Wjst, M. AU - Gurrin, L.C.* AU - Allen, K.J.* AU - Abramson, M.J.* AU - Matheson, M.C.* AU - Dharmage, S.C.* C1 - 48435 C2 - 41157 CY - Basel TI - Do variants in GSTs modify the association between traffic air pollution and asthma in adolescence? JO - Int. J. Mol. Sci. VL - 17 IS - 4 PB - Mdpi Ag PY - 2016 SN - 1661-6596 ER - TY - JOUR AB - MicroRNAs (miRNAs) are master regulators of drug resistance and have been previously proposed as potential biomarkers for the prediction of therapeutic response in colorectal cancer (CRC). Sorafenib, a multi-kinase inhibitor which has been approved for the treatment of liver, renal and thyroid cancer, is currently being studied as a monotherapy in selected molecular subtypes or in combination with other drugs in metastatic CRC. In this study, we explored sorafenib-induced cellular effects in Kirsten rat sarcoma viral oncogene homolog olog (KRAS) wild-type and KRAS-mutated CRC cell lines (Caco-2 and HRT-18), and finally profiled expression changes of specific miRNAs within the miRNome (>1000 human miRNAs) after exposure to sorafenib. Overall, sorafenib induced a time- and dose-dependent growth-inhibitory effect through S-phase cell cycle arrest in KRAS wild-type and KRAS-mutated CRC cells. In HRT-18 cells, two human miRNAs (hsa-miR-597 and hsa-miR-720) and two small RNAs (SNORD 13 and hsa-miR-3182) were identified as specifically sorafenib-induced. In Caco-2 cells, nine human miRNAs (hsa-miR-3142, hsa-miR-20a, hsa-miR-4301, hsa-miR-1290, hsa-miR-4286, hsa-miR-3182, hsa-miR-3142, hsa-miR-1246 and hsa-miR-720) were identified to be differentially regulated post sorafenib treatment. In conclusion, we confirmed sorafenib as a potential anti-neoplastic treatment strategy for CRC cells by demonstrating a growth-inhibitory and cell cycle-arresting effect of this drug. Changes in the miRNome indicate that some specific miRNAs might be relevant as indicators for sorafenib response, drug resistance and potential targets for combinatorial miRNA-based drug strategies. AU - Pehserl, A.-M.* AU - Ress, A.L.* AU - Stanzer, S.* AU - Resel, M.* AU - Karbiener, M.* AU - Stadelmeyer, E.* AU - Stiegelbauer, V.* AU - Gerger, A.* AU - Mayr, C.* AU - Scheideler, M. AU - Huetterer, G.C.* AU - Bauernhofer, T.* AU - Kiesslich, T.* AU - Pichler, M.* C1 - 50144 C2 - 42032 CY - Basel TI - Comprehensive analysis of miRNome alterations in response to sorafenib treatment in colorectal cancer cells. JO - Int. J. Mol. Sci. VL - 17 IS - 12 PB - Mdpi Ag PY - 2016 SN - 1661-6596 ER - TY - JOUR AB - MicroRNAs represent ~22 nt long endogenous small RNA molecules that have been experimentally shown to regulate gene expression post-transcriptionally. One main interest in miRNA research is the investigation of their functional roles, which can typically be accomplished by identification of mi-/mRNA interactions and functional annotation of target gene sets. We here present a novel method "miRlastic", which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network. For the network inference, we applied linear regression modeling with elastic net regularization on matched microRNA and messenger RNA expression profiling data to perform feature selection on prior knowledge from sequence-based target prediction resources. The novelty of miRlastic inference originates in predicting data-driven intra-transcriptome regulatory relationships through feature selection. With synthetic data, we showed that miRlastic outperformed commonly used methods and was suitable even for low sample sizes. To gain insight into the functional role of miRNAs and to determine joint functional properties of miRNA clusters, we introduced a local enrichment analysis procedure. The principle of this procedure lies in identifying regions of high functional similarity by evaluating the shortest paths between genes in the network. We can finally assign functional roles to the miRNAs by taking their regulatory relationships into account. We thoroughly evaluated miRlastic on a cohort of head and neck cancer (HNSCC) patients provided by The Cancer Genome Atlas. We inferred an mi-/mRNA regulatory network for human papilloma virus (HPV)-associated miRNAs in HNSCC. The resulting network best enriched for experimentally validated miRNA-target interaction, when compared to common methods. Finally, the local enrichment step identified two functional clusters of miRNAs that were predicted to mediate HPV-associated dysregulation in HNSCC. Our novel approach was able to characterize distinct pathway regulations from matched miRNA and mRNA data. An R package of miRlastic was made available through: http://icb.helmholtz-muenchen.de/mirlastic. AU - Sass, S. AU - Pitea, A. AU - Unger, K. AU - Hess J. AU - Müller, N.S. AU - Theis, F.J. C1 - 47579 C2 - 39368 SP - 30204-30222 TI - MicroRNA-target network inference and local network enrichment analysis identify two microRNA clusters with distinct functions in head and neck squamous cell carcinoma. JO - Int. J. Mol. Sci. VL - 16 IS - 12 PY - 2015 SN - 1661-6596 ER - TY - JOUR AB - Retinal pigment epithelium (RPE) builds the outer blood-retinal barrier of the eye. Since one typical feature of the autoimmune disease, equine recurrent uveitis (ERU), is the breakdown of this barrier, we recently performed comparative analysis of healthy and uveitic RPE. We identified for the first time peripherin 2, which is responsible for visual perception and retina development, to be localized in RPE. The purpose of this study was therefore to validate our findings by characterizing the expression patterns of peripherin 2 in RPE and retina. We also investigated whether peripherin 2 expression changes in ERU and if it is expressed by the RPE itself. Via immunohistochemistry, significant downregulation of peripherin 2 in uveitic RPE compared to the control was detectable, but there was no difference in healthy and uveitic retina. A further interesting finding was the clear distinction between peripherin 2 and the phagocytosis marker, rhodopsin, in healthy RPE. In conclusion, changes in the expression pattern of peripherin 2 selectively affect RPE, but not retina, in ERU. Moreover, peripherin 2 is clearly detectable in healthy RPE due to both phagocytosis and the expression by the RPE cells themselves. Our novel findings are very promising for better understanding the molecular mechanisms taking place on RPE in uveitis. AU - Uhl, P.B.* AU - Amann, B.* AU - Hauck, S.M. AU - Deeg, C.A.* C1 - 43188 C2 - 36307 CY - Basel SP - 2678-2692 TI - Novel localization of peripherin 2, the photoreceptor-specific retinal degeneration slow protein, in retinal pigment epithelium. JO - Int. J. Mol. Sci. VL - 16 IS - 2 PB - Mdpi Ag PY - 2015 SN - 1661-6596 ER - TY - JOUR AB - The thyroid hormone derivative 3-iodothyronamine (3-T1AM) exerts metabolic effects in vivo that contradict known effects of thyroid hormones. 3-T1AM acts as a trace amine-associated receptor 1 (TAAR1) agonist and activates Gs signaling in vitro. Interestingly, 3-T1AM-meditated in vivo effects persist in Taar1 knockout-mice indicating that further targets of 3-T1AM might exist. Here, we investigated another member of the TAAR family, the only scarcely studied mouse and human trace-amine-associated receptor 8 (Taar8b, TAAR8). By RT-qPCR and locked-nucleic-acid (LNA) in situ hybridization, Taar8b expression in different mouse tissues was analyzed. Functionally, we characterized TAAR8 and Taar8b with regard to cell surface expression and signaling via different G-protein-mediated pathways. Cell surface expression was verified by ELISA, and cAMP accumulation was quantified by AlphaScreen for detection of Gs and/or Gi/o signaling. Activation of G-proteins Gq/11 and G12/13 was analyzed by reporter gene assays. Expression analyses revealed at most marginal Taar8b expression and no gender differences for almost all analyzed tissues. In heart, LNA-in situ hybridization demonstrated the absence of Taar8b expression. We could not identify 3-T1AM as a ligand for TAAR8 and Taar8b, but both receptors were characterized by a basal Gi/o signaling activity, a so far unknown signaling pathway for TAARs. AU - Mühlhaus, J.* AU - Dinter, J.* AU - Nürnberg, D.* AU - Rehders, M.* AU - Depke, M.* AU - Golchert, J.* AU - Homuth, G.* AU - Yi, C.-X. AU - Morin, S. AU - Köhrle, J.* AU - Brix, K.* AU - Tschöp, M.H. AU - Kleinau, G.* AU - Biebermann, H.* C1 - 42747 C2 - 35333 SP - 20638-20655 TI - Analysis of human TAAR8 and murine Taar8b mediated signaling pathways and expression profile. JO - Int. J. Mol. Sci. VL - 15 IS - 11 PY - 2014 SN - 1661-6596 ER - TY - JOUR AB - An appropriate insulin secretion by pancreatic beta-cells is necessary to maintain glucose homeostasis. A rise in plasma glucose leads to increased metabolism and an elevated cytoplasmic ATP/ADP ratio that finally triggers insulin granule exocytosis. In addition to this triggering pathway, one or more amplifying pathways-activated by amino acids or fatty acid-enhance secretion by promoting insulin granule recruitment to, and priming at, the plasma membrane. The aim of this study was to clarify the impact of the mitochondrial respiratory activity on fatty acid-induced insulin secretion that was assessed by an extracellular flux analyzer. Treatment of isolated mouse islets with glucose (20 mM) increased insulin secretion 18-fold and correlated with ATP-synthesizing respiration. Furthermore, oxygen consumption rate (OCR) significantly increased by 62% in response to glucose, whereas the addition of palmitate resulted only in a minor increase of OCR at both 2.8 mM (11%) and 20 mM glucose (21%). The addition of palmitate showed a pronounced increase of coupling efficiency (CE) at 2.8 mM glucose but no further insulin secretion. However, treatment with palmitate at 20 mM glucose increased insulin secretion about 32-fold accompanied by a small increase in CE. Thus, fatty acid induced respiration has a minor impact on insulin secretion. Our data clearly demonstrate that fatty acids in contrast to glucose play a minor role for respiration-mediated insulin secretion. In the presence of high glucose, fatty acids contribute partially to amplifying pathways of insulin secretion by further increasing mitochondrial activity in the islets of Langerhans. AU - Schulz, N.* AU - Kluth, O.* AU - Jastroch, M. AU - Schürmann, A.* C1 - 27568 C2 - 32725 SP - 18989-18998 TI - Minor role of mitochondrial respiration for fatty-acid induced insulin secretion. JO - Int. J. Mol. Sci. VL - 14 IS - 9 PB - MDPI PY - 2013 SN - 1661-6596 ER - TY - JOUR AB - Nitric oxide (NO) has been demonstrated as an essential regulator of several physiological processes in plants. The understanding of the molecular mechanism underlying its critical role constitutes a major field of research. NO can exert its biological function through different ways, such as the modulation of gene expression, the mobilization of second messengers, or interplays with protein kinases. Besides this signaling events, NO can be responsible of the posttranslational modifications (PTM) of target proteins. Several modifications have been identified so far, whereas metal nitrosylation, the tyrosine nitration and the S-nitrosylation can be considered as the main ones. Recent data demonstrate that these PTM are involved in the control of a wide range of physiological processes in plants, such as the plant immune system. However, a great deal of effort is still necessary to pinpoint the role of each PTM in plant physiology. Taken together, these new advances in proteomic research provide a better comprehension of the role of NO in plant signaling. AU - Astier, J. AU - Lindermayr, C. C1 - 11547 C2 - 30717 SP - 15193-15208 TI - Nitric oxide-dependent posttranslational modification in plants: An update. JO - Int. J. Mol. Sci. VL - 13 IS - 11 PB - MDPI AG PY - 2012 SN - 1661-6596 ER - TY - JOUR AB - The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of equine recurrent uveitis, an autoimmune inflammatory disease in horses leading to breakdown of the outer blood-retinal barrier and influx of autoreactive T-cells into affected horses’ vitrei. Cell surface proteins of native and cultured RPE cells from eye-healthy horses were captured by biotinylation, analyzed by high resolution mass spectrometry coupled to liquid chromatography (LC MS/MS), and the most interesting candidates were validated by PCR, immunoblotting and immunocytochemistry. A total of 112 proteins were identified, of which 84% were cell surface membrane proteins. Twenty-three of these proteins were concurrently expressed by both cell states, 28 proteins exclusively by native RPE cells. Among the latter were two RPE markers with highly specialized RPE functions: cellular retinaldehyde-binding protein (CRALBP) and retinal pigment epithelium-specific protein 65kDa (RPE65). Furthermore, 61 proteins were only expressed by cultured RPE cells and absent in native cells. As we believe that initiating events, leading to the breakdown of the outer blood-retinal barrier, take place at the cell surface of RPE cells as a particularly exposed barrier structure, this differential characterization of cell surface proteomes of native and cultured equine RPE cells is a prerequisite for future studies. AU - Szober, C.M.* AU - Hauck, S.M. AU - Euler, K.N.* AU - Fröhlich, K.J.H.* AU - Alge-Priglinger, C.S.* AU - Ueffing, M. AU - Deeg, C.A.* C1 - 11051 C2 - 30480 SP - 14053-14072 TI - Profound re-organization of cell surface proteome in equine retinal pigment epithelial cells in response to in vitro culturing. JO - Int. J. Mol. Sci. VL - 13 IS - 11 PB - MDPI AG PY - 2012 SN - 1661-6596 ER -