Yvonne Böttcher

• McLeod, Anke; Rullmann, Michael; Hinderberger, Philipp; Böttcher, Yvonne; Müller, Ines & Hankir, Mohammed K. [Show all 12 contributors for this article] (2026). BDNF Val66Met polymorphism is linked to elevated levels of serotonin-transporter in the medial prefrontal cortex but not to altered eating behavior. Neuroscience. ISSN 0306-4522. 601, p. 148–154. doi: 10.1016/j.neuroscience.2026.03.008. Full text in Research Archive
• Zimmermann, Silke; Roomp, Kirsten; Meyer, Hans Jonas; Mathew, Akash; Struck, Manuel Florian & Blüher, Matthias [Show all 19 contributors for this article] (2025). Association of Lifestyle-Induced Weight Loss With Gene Expression in Subcutaneous Adipose Tissue in Metabolic Syndrome. Journal of Diabetes. ISSN 1753-0393. 17(4). doi: 10.1111/1753-0407.70083. Full text in Research Archive Show summary

  Aims Lifestyle-induced weight loss (LIWL) is considered an effective therapy for the treatment of metabolic syndrome (MetS). The role of differentially expressed genes (DEGs) in adipose tissue function and in the success of LIWL in MetS is still unclear. We investigated the effect of 6 months of LIWL on transcriptional regulation in subcutaneous adipose tissue (SAT). Aiming to identify a LIWL-associated “gene signature” in SAT, DEGs were fitted into a linear regression model. Materials and Methods The study is embedded in a prospective, two-arm, controlled, monocentric, randomized, 6-month interventional trial in individuals with MetS following LIWL. The trial included 43 nonsmoking, nondiabetic men aged 45–55 years with MetS. Results In total, we identified 642 DEGs in SAT after 6 months of LIWL. The identified DEGs were validated in two cross-sectional cohorts analyzing SAT from individuals with and without obesity. Gene enrichment analysis of the DEGs revealed the strongest association with cholesterol metabolic processes. Accordingly, DEGs were correlated with the lipid parameters HDL cholesterol, LDL cholesterol, and triglycerides in corresponding serum samples. We identified 3 genes with an AUC of 0.963 (95% CI: 0.906–1.0) associated with a loss of more than 10% of initial body weight that was maintained for at least 12 months after LIWL, namely SUMO3 (Small ubiquitin-related modifier 3), PRKG2 (Protein Kinase CGMP-Dependent 2), and ADAP2 (ArfGAP with Dual PH Domains 2). Conclusion In summary, we have identified DEGs in SAT after LIWL, which may play an important role in metabolic functions. In particular, altered gene expression in SAT may predict sustained weight loss.

• Svensson, Stina Ingrid Alice; Hoffmann, Anne; Hagemann, Tobias; Cayir, Akin; Saeed, Sadia & Ghosh, Adhideb [Show all 9 contributors for this article] (2025). Regulators of RNA m5C methylation are adipose tissue depot-specific expressed and correlate with clinical variables of obesity in humans. Frontiers in Endocrinology. 16. doi: 10.3389/fendo.2025.1647477. Full text in Research Archive Show summary

  Background: Obesity is a global health burden and recent evidence indicates that epitranscriptomic regulation is potentially involved in its etiology. The epitranscriptomic mark 5-methylcytosine (m5C) is implicated in cancer and recent data linked the gene expression of m5C writers, erasers and readers to diabetes, a well-known co-morbidity of obesity. Here, we tested whether gene expression of m5C regulators in paired samples of human visceral and subcutaneous adipose tissue is (i) adipose tissue depot-specific and (ii) correlates with important clinical variables of obesity. Methods: Intra-individually paired adipose tissue samples from human subcutaneous adipose tissue (SAT) and omental visceral adipose tissue (OVAT) were utilized from three different cohorts from the Leipzig Obesity Biobank including a large cross-sectional cohort, a two-step bariatric surgery cohort and a cohort of metabolically healthy vs unhealthy individuals (LOBB, total N=962). Data analysis on intra-individual samples was performed by using the paired Wilcoxon signed-rank test, while in comparisons on independent groups the unpaired Wilcoxon rank-sum test was employed. Bonferroni correction method was used to adjust multiple testing of p-values and Spearman’s rank correlation was used to assess associations. Results: We observed that multiple m5C regulators were differentially expressed between human subcutaneous and visceral adipose tissue depots. Interestingly, we found that for several regulators the effects were less pronounced after weight loss, whilst stronger in individuals with insulin resistance compared to their healthy counterparts. A strong correlation of m5C regulator expression with macrophages was observed in OVAT compared to its SAT counterpart. Correlations between m5C regulators with important clinical variables related to obesity were observed in all three cohorts. Conclusion: Our findings provide evidence for adipose tissue depot-specific gene expression of m5C regulators that correlate with clinical variables of obesity.

• Svensson, Stina Ingrid Alice; Saeed, Sadia; Hoffmann, Anne; Ghosh, Adhideb; Wolfrum, Christian & Dahl, Mai Britt [Show all 15 contributors for this article] (2025). HOOK1 Gene Expression and DNA Methylation in Obesity and Related Cardiometabolic Traits. Obesity Facts. ISSN 1662-4025. doi: 10.1159/000547603. Full text in Research Archive Show summary

  Introduction: Accumulation of fat in omental visceral adipose tissue (OVAT) is strongly linked to metabolic diseases. Our recent findings show a distinct and more accessible chromatin landscape of the visceral depot compared to its subcutaneous counterpart. Based on integrated analysis of chromatin accessibility and transcriptomics, we identified previously unrecognised genes linked with obesity. Here, we performed in-depth analyses of one of the candidates, HOOK1, and tested for depot-specific gene expression, correlation with clinical traits and regulatory mechanisms including DNA methylation. Methods: We utilised intra-individually paired adipose tissue samples of human OVAT and subcutaneous adipose tissue (SAT) from our in-house cohort (N = 78). Gene expression was measured using real-time quantitative PCR and pyrosequencing was used to determine DNA methylation levels. Data were analysed for differential gene expression and DNA methylation differences between SAT and OVAT, along with correlation analyses with clinical variables related to obesity. Results were validated in adipose tissue samples from 1,618 donors of the Leipzig Obesity Biobank. Results: We observed consistently higher HOOK1 gene expression in OVAT compared to SAT and successfully confirmed this effect direction in several validation cohorts. We further identified that HOOK1 gene expression correlated with body mass index and hip circumference. We discovered a relationship between DNA methylation of the HOOK1 promoter with clinical variables important for liver function. Conclusion: Our data show that HOOK1 gene expression is adipose tissue depot-specific. We observed that gene expression and DNA methylation are correlated to clinical variables of obesity, suggesting that HOOK1 may play a role in obesity and its sequelae.

• Saeed, Sadia; Hoffmann, Anne; Svensson, Stina Ingrid Alice; Visnovska, Martina; Hagemann, Tobias & Ghosh, Adhideb [Show all 13 contributors for this article] (2025). Integrative analysis of gene expression and histone modifications for DES, DSP, GJA1 and SMOC2 in adipose tissue reveals potential relationship to cardiometabolic health. Molecular medicine (Cambridge, Mass. Print). ISSN 1076-1551. 31. doi: 10.1186/s10020-025-01391-3. Full text in Research Archive Show summary

  Abstract Background Adipose tissue influences cardiometabolic health through its endocrine activity and its role in regulating inflammation, lipid metabolism, and cardiovascular function. The expression of cardiac-associated genes within adipose tissue may reflect or contribute to cardiometabolic risk, yet this relationship remains poorly understood. This study investigates the expression profiles of the cardiac function associated genes GJA1 , DES , DSP and SMOC2 in human adipose tissue, and analyses their associations with cardiometabolic traits. Additionally, we explore epigenomic mechanisms that may underlie their differential gene expression. Methods Expression profiling and functional enrichment analyses were conducted to identify depot-specific cardiac gene expression patterns. Quantitative PCR validated gene expression in paired subcutaneous (SAT) and omental visceral adipose tissue (OVAT) samples from 78 individuals with obesity. Gene expression was further validated in three independent cohorts ( N  = 1,548 total). Associations with clinical traits were assessed using Spearman correlations and multivariate linear regression, adjusted for age, sex, and BMI. Integration with transcriptomic and proteomic datasets publicly available from the Adipose Tissue Knowledge Portal was performed to strengthen clinical relevance. Epigenomic profiling using genome-wide ChIP-seq for histone marks (H3K4me3, H3K4me1, H3K27ac, H3K27me3) was conducted in paired SAT and OVAT samples from five individuals. Results DES , DSP , GJA1 , and SMOC2 were significantly upregulated in OVAT compared to SAT. DES , DSP , and SMOC2 showed consistent expression patterns across all cohorts, while GJA1 exhibited context-dependent regulation. Gene expression in SAT was negatively correlated with cardiometabolic traits, including blood pressure, insulin resistance, and liver function markers. These associations were confirmed by regression analysis and supported by publicly available multi-omics data. Epigenetic analyses revealed OVAT-specific enrichment of active histone marks and reduced repressive marks, supporting higher differential transcriptional activity in OVAT. Conclusions Depot-specific gene expression of DES , DSP , and SMOC2 in adipose tissue is robustly linked to cardiometabolic traits and supported by distinct epigenetic landscapes in OVAT vs SAT, highlighting their potential as novel biomarkers for cardiometabolic health.

• Rønningen, Torunn; Zeng, Yong; Dahl, Mai Britt; Wang, Junbai; Visnovska, Martina & Tannæs, Tone Møller [Show all 18 contributors for this article] (2025). Global mapping of RNA N6-methyladenosine (m6A) in human subcutaneous and visceral adipose tissue reveals novel targets that correlate with clinical variables of obesity. Biomarker Research. 13(1). doi: 10.1186/s40364-025-00857-0. Full text in Research Archive Show summary

  Abstract Background Obesity is a major health challenge and fat accumulation in visceral depots is more strongly associated with metabolic comorbidities than deposition in subcutaneous depots. Epitranscriptomic regulation of gene expression by N 6 -methyladenosine (m 6 A) influences various aspects of RNA metabolism, however the m 6 A methylome in human adipose tissue and its relationship with fat distribution has not yet been investigated in detail. Methods In this study, we performed epitranscriptomic mapping of m 6 A in intra-individually paired samples of subcutaneous (SAT) and omental visceral adipose tissue (OVAT) from women with normal weight (BMI ≤25, n  = 3) and obesity (BMI ≥35, n  = 10) using meRIP-seq (discovery cohort). We further investigated differential m 6 A methylation for specific target genes in a larger cohort of individuals with obesity ( n  = 72, validation cohort) using meRIP-qPCR. meRIP-seq was performed for primary adipocytes from a subset of the patients ( n  = 4) to account for cell type specific differences. Results We here provide the first global map of m 6 A in human adipose tissue in paired samples of SAT and OVAT. We show an overall high overlap in m 6 A sites between individuals and depots, but also distinct depot-specific differences. We identify 339 target genes showing depot-specific m 6 A methylation. Depot-specific methylation was validated for selected sites in SEMA3A , SNAP47 and PPP1R9A in a larger validation cohort. We additionally identify differentially methylated targets between lean individuals and individuals with obesity, including TSC22D1 , FMNL2 and IL1R1 . By combining data from primary adipocytes with data from corresponding bulk adipose tissue, we identified a higher number of genes containing m 6 A in non-adipocyte cells in OVAT compared to SAT. Mechanistically, we show for selected targets that m 6 A affects RNA lifetime in pre-adipocyte cell culture models. Importantly, m 6 A methylation in selected targets correlates with clinically important variables related to obesity, fat distribution and glucose metabolism. Conclusions We identify a catalogue of novel targets showing adipose tissue depot specific m 6 A methylation, with potential as biomarkers in metabolic disease. Our findings underscore the regulatory role of m 6 A in obesity and provide valuable insights for future research. The datasets generated represent a significant resource for further insight in adipose tissue biology and its implications for metabolic health.

• Keller, Maria; Vogel, Mandy; Garten, Antje; Svensson, Stina Ingrid Alice; Rossi, Elena & Kovacs, Peter [Show all 8 contributors for this article] (2025). Epigenetics of Childhood Obesity. Hormone Research in Paediatrics. ISSN 1663-2818. doi: 10.1159/000543467. Full text in Research Archive Show summary

  Background: Childhood obesity has become a global pandemic and is one of the strongest risk factors for cardiovascular disease later in life. The correlation of epigenetic marks with obesity and related traits is being elucidated. This review summarizes the latest research and its challenges in the study of epigenetics of (childhood) obesity. Summary: Epigenome-wide association studies helped identify novel targets and methylation sites that are important in the pathophysiology of obesity. In the future, such sites will become essential for developing methylation risk scores (MRS) for metabolic and cardiovascular diseases. Although MRS are very promising for predicting the individual risk of obesity, the implementation of MRS is challenging and has not been introduced into clinical practice so far. Key Messages: Future research will undoubtedly discover numerous methylation sites that may be involved in the development of obesity and its comorbidities, especially at a young age. This will contribute to a better understanding of the complex etiology of human obesity. From a clinical perspective, the overarching aim was to generate MRS that is robust for reliable and accurate prediction of obesity and its comorbidities.

• Dragland, Jenny Sofie; Liu, Gege; Nilsen, Hilde; Böttcher, Yvonne & Wang, Junbai (2025). EpiMapper: A new tool for analyzing high-throughput sequencing from CUT&Tag. Computers in Biology and Medicine. ISSN 0010-4825. 186. doi: 10.1016/j.compbiomed.2025.109692. Full text in Research Archive Show summary

  Since the invention of next-generation sequencing, new methods have been developed to understand the regulation of gene expression through epigenetic markers. Among these, CUT&Tag (Cleavage Under Targets and Tagmentation) analysis has emerged as an efficient epigenomic profiling technique with low input requirements, high sensitivity, and low background signals. Although wet-lab techniques are available, data analysis remains challenging for scientists without expert-level computational skills. Therefore, we developed EpiMapper, a new Python package that simplifies the data analysis of CUT&Tag sequencing and similar techniques, such as ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) or ChIP-seq (chromatin immunoprecipitation [ChIP] assays with sequencing), and allows biomedical scientists to easily interpret the results. This new package includes every necessary step, from quality control to annotation and differential peak analysis. In particular, EpiMapper has improved functionality (e.g., reproducibility assessment) compared to previous analysis protocols and visualization plots and provides new features, such as genome annotation and differential peak analysis. Using three case studies, two on CUT&Tag and one on ATAC-seq data, the EpiMapper Python package successfully reproduced previous results.

• Saeed, Sadia; Poulsen, Lars La Cour; Visnovska, Martina; Hoffmann, Anne; Ghosh, Adhideb & Wolfrum, Christian [Show all 18 contributors for this article] (2025). Chromatin landscape in paired human visceral and subcutaneous adipose tissue and its impact on clinical variables in obesity. EBioMedicine. 114. doi: 10.1016/j.ebiom.2025.105653. Full text in Research Archive Show summary

  Background Obesity is a global health challenge and adipose tissue exhibits distinct depot-specific characteristics impacting differentially on the risk of metabolic comorbidities. Methods Here, we integrate chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from intra-individually paired human subcutaneous (SAT) and omental visceral adipose tissue (OVAT) samples to unveil depot-specific regulatory mechanisms. Findings We identified twice as many depot-specific differentially accessible regions (DARs) in OVAT compared to SAT. SAT-specific regions showed enrichment for adipose tissue enhancers involving genes controlling extracellular matrix organization and metabolic processes. In contrast, OVAT-specific regions showed enrichment in promoters linked to genes associated with cardiomyopathies. Moreover, OVAT-specific regions were enriched for bivalent transcription start site and repressive chromatin states, suggesting a “lingering” regulatory state. Motif analysis identified CTCF and BACH1 as most significantly enriched motifs in SAT and OVAT-specific DARs, respectively. Distinct gene sets correlated with important clinical variables of obesity, fat distribution measures, as well as insulin, glucose, and lipid metabolism. Interpretation We provide an integrated analysis of chromatin accessibility and transcriptional profiles in paired human SAT and OVAT samples, offering new insights into the regulatory landscape of adipose tissue and highlighting depot-specific mechanisms in obesity pathogenesis.

• Cayir, Akin; Tannæs, Tone Møller; Saeed, Sadia; Blüher, Matthias & Böttcher, Yvonne (2024). Protocol for chromatin immunoprecipitation of histone modifications in frozen adipose tissue. STAR Protocols. 5(3). doi: 10.1016/j.xpro.2024.103163. Full text in Research Archive Show summary

  Chromatin immunoprecipitation (ChIP) combined with sequencing has revolutionized our understanding of gene regulation; however, its application to frozen adipose tissue presents unique challenges due to the high levels of lipid content. Here, we present a protocol for ChIP of histone modifications in human frozen adipose tissue. We describe steps for tissue preparation, chromatin isolation, sonication, pre-clearing of chromatin, and immunoprecipitation. We then detail procedures for elution, crosslink reversal, chromatin purification, quality control, and library synthesis.

• Meen, Astri Jeanette; Doncheva, Atanaska Ivanova; Böttcher, Yvonne; Dankel, Simon N; Hoffmann, Anne & Blüher, Matthias [Show all 16 contributors for this article] (2023). Obesity Is Associated with Distorted Proteoglycan Expression in Adipose Tissue. International Journal of Molecular Sciences. ISSN 1661-6596. 24(8). doi: 10.3390/ijms24086884. Full text in Research Archive Show summary

  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.

• Keller, Maria; Svensson, Stina Ingrid Alice; Rohde-Zimmermann, Kerstin; Kovacs, Peter & Böttcher, Yvonne (2023). Genetics and Epigenetics in Obesity: What Do We Know so Far? Current Obesity Reports. 12, p. 482–501. doi: 10.1007/s13679-023-00526-z. Full text in Research Archive Show summary

  Abstract Purpose of Review Enormous progress has been made in understanding the genetic architecture of obesity and the correlation of epigenetic marks with obesity and related traits. This review highlights current research and its challenges in genetics and epigenetics of obesity. Recent Findings Recent progress in genetics of polygenic traits, particularly represented by genome-wide association studies, led to the discovery of hundreds of genetic variants associated with obesity, which allows constructing polygenic risk scores (PGS). In addition, epigenome-wide association studies helped identifying novel targets and methylation sites being important in the pathophysiology of obesity and which are essential for the generation of methylation risk scores (MRS). Despite their great potential for predicting the individual risk for obesity, the use of PGS and MRS remains challenging. Summary Future research will likely discover more loci being involved in obesity, which will contribute to better understanding of the complex etiology of human obesity. The ultimate goal from a clinical perspective will be generating highly robust and accurate prediction scores allowing clinicians to predict obesity as well as individual responses to body weight loss-specific life-style interventions.

• Boughanem, Hatim; Böttcher, Yvonne; Tomé-Carneiro, João; Hazas, María-Carmen López de las; Dávalos, Alberto & Cayir, Akin [Show all 7 contributors for this article] (2022). The emergent role of mitochondrial RNA modifications in metabolic alterations. Wiley Interdisciplinary Reviews (WIREs RNA). ISSN 1757-7004. doi: 10.1002/wrna.1753. Full text in Research Archive Show summary

  Mitochondrial epitranscriptomics refers to the modifications occurring in all the different RNA types of mitochondria. Although the number of mitochondrial RNA modifications is less than those in cytoplasm, substantial evidence indicates that they play a critical role in accurate protein synthesis. Recent evidence supported those modifications in mitochondrial RNAs also have crucial implications in mitochondrial-related diseases. In the light of current knowledge about the involvement, the association between mitochondrial RNA modifications and diseases arises from studies focusing on mutations in both mitochondrial and nuclear DNA genes encoding enzymes involved in such modifications. Here, we review the current evidence available for mitochondrial RNA modifications and their role in metabolic disorders, and we also explore the possibility of using them as promising targets for prevention and early detection. Finally, we discuss future directions of mitochondrial epitranscriptomics in these metabolic alterations, and how these RNA modifications may offer a new diagnostic and theragnostic avenue for preventive purposes.

• Huroz, Sergio Carracedo; Lirussi, Lisa; Alsøe, Lene; Segers, Filip; Wang, Changliang & Bartosova, Zdenka [Show all 21 contributors for this article] (2022). SMUG1 regulates fat homeostasis leading to a fatty liver phenotype in mice. DNA Repair. ISSN 1568-7864. 120. doi: 10.1016/j.dnarep.2022.103410. Full text in Research Archive
• Doncheva, Atanaska Ivanova; Norheim, Frode Amador; Hjorth, Marit; Grujic, Mirjana; Paivandy, Aida & Dankel, Simon N [Show all 14 contributors for this article] (2021). Serglycin Is Involved in Adipose Tissue Inflammation in Obesity. Journal of Immunology. ISSN 0022-1767. 208(1), p. 121–132. doi: 10.4049/jimmunol.2100231. Full text in Research Archive Show summary

  Chronic local inflammation of adipose tissue is an important feature of obesity. Serglycin is a proteoglycan highly expressed by various immune cell types known to infiltrate adipose tissue under obese conditions. To investigate if serglycin expression has an impact on diet-induced adipose tissue inflammation, we subjected Srgn+/+ and Srgn−/− mice (C57BL/6J genetic background) to an 8-wk high-fat and high-sucrose diet. The total body weight was the same in Srgn+/+ and Srgn−/− mice after diet treatment. Expression of white adipose tissue genes linked to inflammatory pathways were lower in Srgn−/− mice. We also noted reduced total macrophage abundance, a reduced proportion of proinflammatory M1 macrophages, and reduced formation of crown-like structures in adipose tissue of Srgn−/− compared with Srgn+/+ mice. Further, Srgn−/− mice had more medium-sized adipocytes and fewer large adipocytes. Differentiation of preadipocytes into adipocytes (3T3-L1) was accompanied by reduced Srgn mRNA expression. In line with this, analysis of single-cell RNA sequencing data from mouse and human adipose tissue supports that Srgn mRNA is predominantly expressed by various immune cells, with low expression in adipocytes. Srgn mRNA expression was higher in obese compared with lean humans and mice, accompanied by an increased expression of immune cell gene markers. SRGN and inflammatory marker mRNA expression was reduced upon substantial weight loss in patients after bariatric surgery. Taken together, this study introduces a role for serglycin in the regulation of obesity-induced adipose inflammation.

• Rønningen, Torunn; Dahl, Mai Britt; Valderhaug, Tone Gretland; Cayir, Akin; Keller, Maria & Tönjes, Anke [Show all 8 contributors for this article] (2021). m6A Regulators in Human Adipose Tissue - Depot-Specificity and Correlation With Obesity. Frontiers in Endocrinology. 12. doi: 10.3389/fendo.2021.778875. Full text in Research Archive Show summary

  Background: N6-methyladenosine (m6A) is one of the most abundant post-transcriptional modifications on mRNA influencing mRNA metabolism. There is emerging evidence for its implication in metabolic disease. No comprehensive analyses on gene expression of m6A regulators in human adipose tissue, especially in paired adipose tissue depots, and its correlation with clinical variables were reported so far. We hypothesized that inter-depot specific gene expression of m6A regulators may differentially correlate with clinical variables related to obesity and fat distribution. Methods: We extracted intra-individually paired gene expression data (omental visceral adipose tissue (OVAT) N=48; subcutaneous adipose tissue (SAT) N=56) of m6A regulators from an existing microarray dataset. We also measured gene expression in another sample set of paired OVAT and SAT (N=46) using RT-qPCR. Finally, we extracted existing gene expression data from peripheral mononuclear blood cells (PBMCs) and single nucleotide polymorphisms (SNPs) in METTL3 and YTHDF3 from genome wide data from the Sorbs population (N=1049). The data were analysed for differential gene expression between OVAT and SAT; and for association with obesity and clinical variables. We further tested for association of SNP markers with gene expression and clinical traits. Results: In adipose tissue we observed that several m6A regulators (WTAP, VIRMA, YTHDC1 and ALKBH5) correlate with obesity and clinical variables. Moreover, we found adipose tissue depot specific gene expression for METTL3, WTAP, VIRMA, FTO and YTHDC1. In PBMCs, we identified ALKBH5 and YTHDF3 correlated with obesity. Genetic markers in METTL3 associate with BMI whilst SNPs in YTHDF3 are associated with its gene expression. Conclusions: Our data show that expression of m6A regulators correlates with obesity, is adipose tissue depot-specific and related to clinical traits. Genetic variation in m6A regulators adds an additional layer of variability to the functional consequences.

• Tomé-Carneiro, João; Hazas, María-Carmen López de Las; Boughanem, Hatim; Böttcher, Yvonne; Cayir, Akin & González, Manuel Macias [Show all 7 contributors for this article] (2021). Up–to–date on the evidence linking miRNA-related epitranscriptomic modifications and disease settings. Can these modifications affect cross-kingdom regulation? RNA Biology. ISSN 1547-6286. 18(2), p. 586–599. doi: 10.1080/15476286.2021.2002003. Full text in Research Archive
• Sletner, Line; Moen, Aina Elisabeth Fossum; Yajnik, Chittaranjan S; Kiryushchenko, Nadezhda; Sommer, Christine & Birkeland, Kåre Inge [Show all 8 contributors for this article] (2021). Maternal Glucose and LDL-Cholesterol Levels Are Related to Placental Leptin Gene Methylation, and, Together With Nutritional Factors, Largely Explain a Higher Methylation Level Among Ethnic South Asians. Frontiers in Endocrinology. 12. doi: 10.3389/fendo.2021.809916. Full text in Research Archive Show summary

  Background Leptin, mainly secreted by fat cells, plays a core role in the regulation of appetite and body weight, and has been proposed as a mediator of metabolic programming. During pregnancy leptin is also secreted by the placenta, as well as being a key regulatory cytokine for the development, homeostatic regulation and nutrient transport within the placenta. South Asians have a high burden of type 2 diabetes, partly attributed to a “thin-fat-phenotype”. Objective Our aim was to investigate how maternal ethnicity, adiposity and glucose- and lipid/cholesterol levels in pregnancy are related to placental leptin gene ( LEP ) DNA methylation. Methods We performed DNA methylation analyses of 13 placental LEP CpG sites in 40 ethnic Europeans and 40 ethnic South Asians participating in the STORK-Groruddalen cohort. Results South Asian ethnicity and gestational diabetes (GDM) were associated with higher placental LEP methylation. The largest ethnic difference was found for CpG11 [5.8% (95% CI: 2.4, 9.2), p<0.001], and the strongest associations with GDM was seen for CpG5 [5.2% (1.4, 9.0), p=0.008]. Higher maternal LDL-cholesterol was associated with lower placental LEP methylation, in particular for CpG11 [-3.6% (-5.5, -1.4) per one mmol/L increase in LDL, p<0.001]. After adjustments, including for nutritional factors involved in the one-carbon-metabolism cycle (vitamin D, B12 and folate levels), ethnic differences in placental LEP methylation were strongly attenuated, while associations with glucose and LDL-cholesterol persisted. Conclusions Maternal glucose and lipid metabolism is related to placental LEP methylation, whilst metabolic and nutritional factors largely explain a higher methylation level among ethnic South Asians.

• Fragoso-Bargas, Nicolas; Opsahl, Julia Onsrud; Kiryushchenko, Nadezhda; Böttcher, Yvonne; Lee-Ødegård, Sindre & Qvigstad, Elisabeth [Show all 15 contributors for this article] (2021). Cohort profile: Epigenetics in Pregnancy (EPIPREG) – Population-based sample of European and South Asian pregnant women with epigenome-wide DNA methylation (850k) in peripheral blood leukocytes. PLOS ONE. 16(8), p. 1–15. doi: 10.1371/journal.pone.0256158. Full text in Research Archive Show summary

  Pregnancy is a valuable model to study the association between DNA methylation and several cardiometabolic traits, due to its direct potential to influence mother’s and child’s health. Epigenetics in Pregnancy (EPIPREG) is a population-based sample with the aim to study associations between DNA-methylation in pregnancy and cardiometabolic traits in South Asian and European pregnant women and their offspring. This cohort profile paper aims to present our sample with genetic and epigenetic data and invite researchers with similar cohorts to collaborative projects, such as replication of ours or their results and meta-analysis. In EPIPREG we have quantified epigenome-wide DNA methylation in maternal peripheral blood leukocytes in gestational week 28±1 in Europeans (n = 312) and South Asians (n = 168) that participated in the population-based cohort STORK Groruddalen, in Norway. DNA methylation was measured with Infinium MethylationEPIC BeadChip (850k sites), with technical validation of four CpG sites using bisulphite pyrosequencing in a subset (n = 30). The sample is well characterized with few missing data on e.g. genotype, universal screening for gestational diabetes, objectively measured physical activity, bioelectrical impedance, anthropometrics, biochemical measurements, and a biobank with maternal serum and plasma, urine, placenta tissue. In the offspring, we have repeated ultrasounds during pregnancy, cord blood, and anthropometrics up to 4 years of age. We have quantified DNA methylation in peripheral blood leukocytes in nearly all eligible women from the STORK Groruddalen study, to minimize the risk of selection bias. Genetic principal components distinctly separated Europeans and South Asian women, which fully corresponded with the self-reported ethnicity. Technical validation of 4 CpG sites from the methylation bead chip showed good agreement with bisulfite pyrosequencing. We plan to study associations between DNA methylation and cardiometabolic traits and outcomes.

• Böttcher, Yvonne (2020). Epigenetische Mechanismen bei Adipositas: Finetuning der Genaktivität durch DNA-Methylierung - Bertram-Preis 2020 - eine Kurzübersicht der Preisträgerin Yvonne Böttcher. Diabetologie und Stoffwechsel. ISSN 1861-9002. 15(6), p. 443–446. doi: 10.1055/a-1247-1099. Full text in Research Archive
• Opsahl, Julia; Moen, Gunn-Helen Øiseth; Qvigstad, Elisabeth; Böttcher, Yvonne; Birkeland, Kåre Inge & Sommer, Christine (2020). Epigenetic signatures associated with maternal body mass index or gestational weight gain: a systematic review. Journal of Developmental Origins of Health and Disease. ISSN 2040-1744. doi: 10.1017/S2040174420000811. Full text in Research Archive
• Breitfeld, Jana; Kehr, Stephanie; Müller, Luise; Stadler, Peter F.; Böttcher, Yvonne & Blüher, Matthias [Show all 8 contributors for this article] (2020). Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity. Frontiers in Endocrinology. 11. doi: 10.3389/fendo.2020.00138. Full text in Research Archive Show summary

  Subcutaneous (sc) and visceral (vis) adipose tissue (AT) contribute to the variability in pathophysiological consequences of obesity and adverse fat distribution. To gain insights into the molecular mechanisms distinguishing vis and sc fat, we compared the transcriptome during differentiation of immortalized adipocytes from murine epididymal (epi) and inguinal (ing) AT. RNA was extracted on different days of adipogenesis (−2, 0, 2, 4, 6, 8) and analyzed using Clariom™ D mouse assays (Affymetrix) covering >214,900 transcripts in >66,100 genes. Transcript Time Course Analysis revealed 137 differentially expressed genes. The top genes with most divergent expression dynamics included developmental genes like Alx1, Lhx8, Irx1/2, Hoxc10, Hoxa5/10, and Tbx5/15. According to pathway analysis the majority of the genes were enriched in pathways related to AT development. Finally, in paired samples of human vis and sc AT (N = 63), several of these genes exhibited depot-specific variability in expression which correlated closely with body mass index and/or waist-to-hip ratio. In conclusion, intrinsically programmed differences in gene expression patterns during adipogenesis suggest that fat depot specific regulation of adipogenesis contributes to individual risk of obesity.

• Shamsi, Farnaz; Xue, Ruidan; Huang, Tian Lian; Lundh, Morten; Liu, Yang & Leiria, Luiz O. [Show all 26 contributors for this article] (2020). FGF6 and FGF9 regulate UCP1 expression independent of brown adipogenesis. Nature Communications. 11(1), p. 1–16. doi: 10.1038/s41467-020-15055-9. Full text in Research Archive Show summary

  Uncoupling protein-1 (UCP1) plays a central role in energy dissipation in brown adipose tissue (BAT). Using high-throughput library screening of secreted peptides, we identify two fibroblast growth factors (FGF), FGF6 and FGF9, as potent inducers of UCP1 expression in adipocytes and preadipocytes. Surprisingly, this occurs through a mechanism independent of adipogenesis and involves FGF receptor-3 (FGFR3), prostaglandin-E2 and interaction between estrogen receptor-related alpha, flightless-1 (FLII) and leucine-rich-repeat-(in FLII)-interacting-protein-1 as a regulatory complex for UCP1 transcription. Physiologically, FGF6/9 expression in adipose is upregulated by exercise and cold in mice, and FGF9/FGFR3 expression in human neck fat is significantly associated with UCP1 expression. Loss of FGF9 impairs BAT thermogenesis. In vivo administration of FGF9 increases UCP1 expression and thermogenic capacity. Thus, FGF6 and FGF9 are adipokines that can regulate UCP1 through a transcriptional network that is dissociated from brown adipogenesis, and act to modulate systemic energy metabolism.

• Keller, Maria; Gebhardt, Claudia; Huth, Sandra; Schleinitz, Dorit; Heyne, Henrike O. & Scholz, Markus [Show all 10 contributors for this article] (2020). Genetically programmed changes in transcription of the novel progranulin regulator. Journal of Molecular Medicine. ISSN 0946-2716. 98(8), p. 1139–1148. doi: 10.1007/s00109-020-01942-7. Full text in Research Archive Show summary

  Progranulin is a glycoprotein marking chronic inflammation in obesity and type 2 diabetes. Previous studies suggested PSRC1 (proline and serine rich coiled-coil 1) to be a target of genetic variants associated with serum progranulin levels. We aimed to identify potentially functional variants and characterize their role in regulation of PSRC1. Phylogenetic module complexity analysis (PMCA) prioritized four polymorphisms (rs12740374, rs629301, rs660240, rs7528419) altering transcription factor binding sites with an overall score for potential regulatory function of Sall > 7.0. The effects of these variants on transcriptional activity and binding of transcription factors were tested by luciferase reporter and electrophoretic mobility shift assays (EMSA). In parallel, blood DNA promoter methylation of two regions was tested in subjects with a very high (N = 100) or a very low (N = 100) serum progranulin. Luciferase assays revealed lower activities in vectors carrying the rs629301-A compared with the C allele. Moreover, EMSA indicated a different binding pattern for the two rs629301 alleles, with an additional prominent band for the A allele, which was finally confirmed with the supershift for the Yin Yang 1 transcription factor (YY1). Subjects with high progranulin levels manifested a significantly higher mean DNA methylation (P < 1 × 10−7) in one promoter region, which was in line with a significantly lower PSRC1 mRNA expression levels in blood (P = 1 × 10−3). Consistently, rs629301-A allele was associated with lower PSRC1 mRNA expression (P < 1 × 10−7). Our data suggest that the progranulin-associated variant rs629301 modifies the transcription of PSRC1 through alteration of YY1 binding capacity. DNA methylation studies further support the role of PSRC1 in regulation of progranulin serum levels.

• Keller, Maria; Meir, Anat Yaskolka; Bernhart, Stephan H.; Gepner, Yftach; Shelef, Ilan & Schwarzfuchs, Dan [Show all 17 contributors for this article] (2020). DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial. Genome Medicine. 12:97, p. 1–18. doi: 10.1186/s13073-020-00794-7. Full text in Research Archive Show summary

  Background One of the major challenges in obesity treatment is to explain the high variability in the individual’s response to specific dietary and physical activity interventions. With this study, we tested the hypothesis that specific DNA methylation changes reflect individual responsiveness to lifestyle intervention and may serve as epigenetic predictors for a successful weight-loss. Methods We conducted an explorative genome-wide DNA methylation analysis in blood samples from 120 subjects (90% men, mean ± SD age = 49 ± 9 years, body mass-index (BMI) = 30.2 ± 3.3 kg/m2) from the 18-month CENTRAL randomized controlled trial who underwent either Mediterranean/low-carbohydrate or low-fat diet with or without physical activity. Results Analyses comparing male subjects with the most prominent body weight-loss (responders, mean weight change − 16%) vs. non-responders (+ 2.4%) (N = 10 each) revealed significant variation in DNA methylation of several genes including LRRC27, CRISP2, and SLFN12 (all adj. P < 1 × 10−5). Gene ontology analysis indicated that biological processes such as cell adhesion and molecular functions such as calcium ion binding could have an important role in determining the success of interventional therapies in obesity. Epigenome-wide association for relative weight-loss (%) identified 15 CpGs being negatively correlated with weight change after intervention (all combined P < 1 × 10− 4) including new and also known obesity candidates such as NUDT3 and NCOR2. A baseline DNA methylation score better predicted successful weight-loss [area under the curve (AUC) receiver operating characteristic (ROC) = 0.95–1.0] than predictors such as age and BMI (AUC ROC = 0.56). Conclusions Body weight-loss following 18-month lifestyle intervention is associated with specific methylation signatures. Moreover, methylation differences in the identified genes could serve as prognostic biomarkers to predict a successful weight-loss therapy and thus contribute to advances in patient-tailored obesity treatment.

• Opsahl, Julia Onsrud; Moen, Gunn-Helen; Qvigstad, Elisabeth; Böttcher, Yvonne; Birkeland, Kåre I. & Sommer, Christine (2020). Epigenetic signatures associated with maternal body mass index or gestational weight gain: A systematic review. Journal of Developmental Origins of Health and Disease. ISSN 2040-1744. p. 1–11. doi: 10.1017/S2040174420000811. Full text in Research Archive Show summary

  Abstract Maternal body mass index (BMI) and gestational weight gain (GWG) impacts both the mother’s and the child’s health, and epigenetic modifications have been suggested to mediate some of these effects in offspring. This systematic review aimed to summarize the current literature on associations between maternal BMI and GWG and epigenetic marks. We performed systematic searches in PubMed and EMBASE and manual searches of reference lists. We included 49 studies exploring the association between maternal BMI and/or GWG and DNA methylation or miRNA; 7 performed in maternal tissues, 13 in placental tissue and 38 in different offspring tissues. The most consistent findings were reported for the relationship between maternal BMI, in particular pre-pregnant BMI, and expression of miRNA Let-7d in both maternal blood and placental tissue, methylation of the gene HIF3A in umbilical cord blood and umbilical tissue, and with expression in the miR-210 target gene, BDNF in placental tissue and cord blood. Correspondingly, methylation of BDNF was also found in placental tissue and cord blood. The current evidence suggests that maternal BMI is associated with some epigenetic signatures in the mother, the placenta and her offspring, which could indicate that some of the effects proposed by the Developmental Origins of Health and Disease-hypothesis may be mediated by epigenetic marks. In conclusion, there is a need for large, well-designed studies and meta-analyses that can clarify the relationship between BMI, GWG and epigenetic changes.

• Rohde, Kerstin; Rønningen, Torunn; Poulsen, Lars La Cour; Keller, Maria; Blüher, Matthias & Böttcher, Yvonne (2020). Role of the DNA repair genes H2AX and HMGB1 in human fat distribution and lipid profiles. BMJ Open Diabetes Research & Care. 8(1), p. 1–7. doi: 10.1136/bmjdrc-2019-000831. Full text in Research Archive Show summary

  Introduction Regional fat distribution strongly relates to metabolic comorbidities. We identified the DNA repair genes H2AX and HMGB1 to be differentially expressed between human subcutaneous (SAT) and omental visceral adipose tissue (OVAT) depots. As increased DNA damage is linked to metabolic disease, we here sought to analyze whether depot-specific H2AX and HMGB1 expression is related to anthropometric and metabolic profiles of obesity. We further tested for different H2AX mRNA regulatory mechanisms by analyzing promoter DNA methylation and genotyped rs7350 in the H2AX locus. Research design and methods Gene expression (OVAT n=48; SAT n=55) and DNA promoter methylation data (OVAT and SAT n=77) were extracted from an existing dataset as described elsewhere. Genotype data for the 3’untranslated region (3’UTR) H2AX variant rs7350 were generated by using the TaqMan genotyping system in 243 subjects of the same cohort. Statistical analyses were done using SPSS statistics software 24 and GraphPad Prism 6. Results We identified H2AX being higher (p=0.002) and HMGB1 being less expressed (p=0.0001) in OVAT compared with SAT. Further, we observed positive interdepot correlations of OVAT and SAT for both HMGB1 (p=1×10 –6 ) and H2AX mRNA levels (p=0.024). Depot-specific associations were observed for both genes’ methylation levels with either high density lipoprotein cholesterol, low density lipoprotein cholesterol, triglycerides and/or with OVAT/SAT-ratio (all p&lt;0.05). A significantly lower level of total cholesterol in minor A-Allele carriers of rs7350 compared with AG and GG carriers (p=0.001) was observed. Additionally, subjects carrying the A-allele showed lower SAT HMGB1 expression level (p=0.030). Conclusion Our results suggest a fat depot-specific regulation of H2AX and HMGB1 potentially mediated by both DNA methylation and genetic variation. Rs7350, DNA methylation and/or mRNA levels of H2AX and HMGB1 are related to lipid parameters. Further studies are warranted to evaluate the functional role of the DNA repair genes H2AX and HMGB1 in obesity and fat distribution.

• Rohde, Kerstin; Keller, Maria; Poulsen, Lars La Cour; Rønningen, Torunn; Stumvoll, Michael & Tonjes, Anke [Show all 11 contributors for this article] (2019). (Epi)genetic regulation of CRTC1 in human eating behaviour and fat distribution. EBioMedicine. 44, p. 476–488. doi: 10.1016/j.ebiom.2019.05.050. Full text in Research Archive Show summary

  Background In brain, CREB-regulated transcription co-activator 1 (CRTC1) is involved in metabolic dysregulation. In humans a SNP in CRTC1 was associated to body fat percentage and two SNPs affected RNA Pol II binding and chromatin structure, implying epigenetic regulation of CRTC1. We sought to understand the relevance of CRTC1 SNPs, DNA methylation and expression in human eating behaviour and its relationship to clinical variables of obesity in blood and adipose tissue. Methods 13 CRTC1 SNPs were included to analyze eating behaviour. For rs7256986, follow up association analyses were applied on DNA methylation, CRTC1 expression and clinical parameters. Linear regression was used throughout the study adjusted for age, sex and BMI. Besides data extraction from previous work, rs7256986 was de-novo genotyped and DNA methylation was evaluated by using pyrosequencing. Findings We found several SNPs in the CRTC1 locus nominally associated with human eating behaviour or 2hr postprandial insulin levels and observed a correlation with alcohol and coffee intake (all P < 0.05). G-allele carriers of rs7256986 showed slightly increased hip circumference. We showed that rs7256986 represents a methylation quantitative trait locus (meQTL) in whole blood and adipose tissue. The presence of the SNP and/or DNA methylation correlated with CRTC1 gene expression which in turn, related to BMI and fat distribution. Interpretation Our data support the known role of CRCT1 regulating energy metabolism in brain. Here, we highlight relevance of CRTC1 regulation in blood and adipose tissue. Fund IFB AdiposityDiseases (BMBF); n609020-Scientia Fellows; Helse-SørØst; DFG: CRC 1052/1 and/2; Kompetenznetz Adipositas, German Diabetes Association.

• Keller, Maria; Klos, Matthias; Rohde, Kerstin; Krüger, Jacqueline; Kurze, Tabea & Dietrich, Arne [Show all 14 contributors for this article] (2018). DNA methylation of SSPN is linked to adipose tissue distribution and glucose metabolism. The FASEB Journal. ISSN 0892-6638. 32(12), p. 6898–6910. doi: 10.1096/fj.201800528R. Full text in Research Archive Show summary

  DNA methylation is a crucial epigenetic mechanism in obesity and fat distribution. We explored the Sarcospan (SSPN) gene locus by using genome-wide data sets comprising methylation and expression data, pyrosequencing analysis in the promoter region, and genetic analysis of an SNP variant rs718314, which was previously reported to associate with waist-to-hip ratio. We found that DNA methylation influences several clinical variables related to fat distribution and glucose metabolism, while SSPN mRNA levels showed directionally opposite effects on these traits. Complete DNA methylation of the SSPN promoter construct suppressed the gene expression of firefly luciferase in MCF7 cells. Moreover, rs718314 was associated with waist and with DNA methylation at CpG sites. Our data strongly support the role of the SSPN locus in body fat composition and glucose homeostasis, and suggest that this is most likely the result of changes in DNA methylation of SSPN in adipose tissue.

• Rohde, Kerstin; Keller, Maria; Poulsen, Lars La Cour; Blüher, Matthias; Kovacs, Peter & Böttcher, Yvonne (2018). Genetics and epigenetics in obesity. Metabolism: Clinical and Experimental. ISSN 0026-0495. 92, p. 37–50. doi: 10.1016/j.metabol.2018.10.007. Full text in Research Archive Show summary

  Obesity is among the most threatening health burdens worldwide and its prevalence has markedly increased over the last decades. Obesity maybe considered a heritable trait. Identifications of rare cases of monogenic obesity unveiled that hypothalamic circuits and the brain-adipose axis play an important role in the regulation of energy homeostasis, appetite, hunger and satiety. For example, mutations in the leptin gene cause obesity through almost unsuppressed overeating. Common (multifactorial) obesity, most likely resulting from a concerted interplay of genetic, epigenetic and environmental factors, is clearly linked to genetic predisposition by multiple risk variants, which, however only account for a minor part of the general BMI variability. Although GWAS opened new avenues in elucidating the complex genetics behind common obesity, understanding the biological mechanisms relative to the specific risk contributing to obesity remains poorly understood. Non-genetic factors such as eating behavior or physical activity strongly modulate the individual risk for developing obesity. These factors may interact with genetic predisposition for obesity through epigenetic mechanisms. Thus, here, we review the current knowledge about monogenic and common (multifactorial) obesity highlighting the important recent advances in our knowledge on how epigenetic regulation is involved in the etiology of obesity.

• Loffler, Antje; Luck, Tobias; Then, Francisca S; Luck-Sikorski, Claudia; Pabst, Alexander & Kovacs, Peter [Show all 16 contributors for this article] (2017). Effects of psychological eating behaviour domains on the association between socio-economic status and BMI. Public Health Nutrition (PHN). ISSN 1368-9800. 20(15), p. 2706–2712. doi: 10.1017/S1368980017001653. Full text in Research Archive Show summary

  Objective The current study investigates potential pathways from socio-economic status (SES) to BMI in the adult population, considering psychological domains of eating behaviour (restrained eating, uncontrolled eating, emotional eating) as potential mediators stratified for sex. Design Data were derived from the population-based cross-sectional LIFE-Adult-Study. Parallel-mediation models were conducted to obtain the total, direct and indirect effects of psychological eating behaviour domains on the association between SES and BMI for men and for women. Setting Leipzig, Germany. Subjects We studied 5935 participants aged 18 to 79 years. Results Uncontrolled eating mediated the association between SES and BMI in men only and restrained eating in both men and women. Emotional eating did not act as mediator in this relationship. The total effect of eating behaviour domains on the association between SES and BMI was estimated as β=−0·03 (se 0·02; 95 % CI −0·062, −0·003) in men and β=−0·18 (se 0·02; 95 % CI −0·217, −0·138) in women. Conclusions Our findings do not indicate a strong overall mediation effect of the eating behaviour domains restrained eating, uncontrolled eating and emotional eating on the association between SES and BMI. Further research on other pathways of this association is strongly recommended. Importantly, our findings indicate that, independent from one’s social position, focusing on psychological aspects in weight reduction might be a promising approach. COPYRIGHT: © The Authors 2017

• Blüher, Susann; Käpplinger, Jakob; Herget, Sabine; Reichardt, Sandra; Böttcher, Yvonne & Grimm, Andrea [Show all 8 contributors for this article] (2017). Cardiometabolic risk markers, adipocyte fatty acid binding protein (aFABP) and the impact of high-intensity interval training (HIIT) in obese adolescents. Metabolism: Clinical and Experimental. ISSN 0026-0495. 68, p. 77–87. doi: 10.1016/j.metabol.2016.11.015. Full text in Research Archive
• Drabe, Mandy; Rullmann, Michael; Luthardt, Julia; Böttcher, Yvonne; Regenthal, Ralf & Plötz, Tanja [Show all 17 contributors for this article] (2017). Serotonin transporter gene promoter methylation status correlates with in vivo prefrontal 5-HTT availability and reward function in human obesity. Translational Psychiatry. 7:e1167(7), p. 1–7. doi: 10.1038/tp.2017.133. Full text in Research Archive Show summary

  A polymorphism in the promoter region of the human serotonin transporter (5-HTT)-coding SLC6A4 gene (5-HTTLPR) has been implicated in moderating susceptibility to stress-related psychopathology and to possess regulatory functions on human in vivo 5-HTT availability. However, data on a direct relation between 5-HTTLPR and in vivo 5-HTT availability have been inconsistent. Additional factors such as epigenetic modifications of 5-HTTLPR might contribute to this association. This is of particular interest in the context of obesity, as an association with 5-HTTLPR hypermethylation has previously been reported. Here, we tested the hypothesis that methylation rates of 14 cytosine–phosphate–guanine (CpG) 5-HTTLPR loci, in vivo central 5-HTT availability as measured with [11C]DASB positron emission tomography (PET) and body mass index (BMI) are related in a group of 30 obese (age: 36±10 years, BMI>35 kg/m2) and 14 normal-weight controls (age 36±7 years, BMI<25 kg/m2). No significant association between 5-HTTLPR methylation and BMI overall was found. However, site-specific elevations in 5-HTTLPR methylation rates were significantly associated with lower 5-HTT availability in regions of the prefrontal cortex (PFC) specifically within the obese group when analyzed in isolation. This association was independent of functional 5-HTTLPR allelic variation. In addition, negative correlative data showed that CpG10-associated 5-HTT availability determines levels of reward sensitivity in obesity. Together, our findings suggest that epigenetic mechanisms rather than 5-HTTLPR alone influence in vivo 5-HTT availability, predominantly in regions having a critical role in reward processing, and this might have an impact on the progression of the obese phenotype.

• Haertle, Larissa; Maierhofer, Anna; Bock, Julia; Lehnen, Harald; Böttcher, Yvonne & Blüher, Matthias [Show all 11 contributors for this article] (2017). Hypermethylation of the non-imprinted maternal MEG3 and paternal MEST alleles is highly variable among normal individuals. PLOS ONE. 12(8). doi: 10.1371/journal.pone.0184030. Full text in Research Archive Show summary

  Imprinted genes show parent-specific activity (functional haploidy), which makes them particularly vulnerable to epigenetic dysregulation. Here we studied the methylation profiles of oppositely imprinted genes at single DNA molecule resolution by two independent parental allele-specific deep bisulfite sequencing (DBS) techniques. Using Roche (GSJunior) next generation sequencing technology, we analyzed the maternally imprinted MEST promoter and the paternally imprinted MEG3 intergenic (IG) differentially methylated region (DMR) in fetal cord blood, adult blood, and visceral adipose tissue. Epimutations were defined as paternal or maternal alleles with >50% aberrantly (de)methylated CpG sites, showing the wrong methylation imprint. The epimutation rates (range 2–66%) of the paternal MEST and the maternal MEG3 IG DMR allele, which should be completely unmethylated, were significantly higher than those (0–15%) of the maternal MEST and paternal MEG3 alleles, which are expected to be fully methylated. This hypermethylation of the non-imprinted allele (HNA) was independent of parental origin. Very low epimutation rates in sperm suggest that HNA occurred after fertilization. DBS with Illumina (MiSeq) technology confirmed HNA for the MEST promoter and the MEG3 IG DMR, and to a lesser extent, for the paternally imprinted secondary MEG3 promoter and the maternally imprinted PEG3 promoter. HNA leads to biallelic methylation of imprinted genes in a considerable proportion of normal body cells (somatic mosaicism) and is highly variable between individuals. We propose that during development and differentiation maintenance of differential methylation at most imprinting control regions may become to some extent redundant. The accumulation of stochastic and environmentally-induced methylation errors on the non-imprinted allele may increase epigenetic diversity between cells and individuals.

• Wheeler, Eleanor; Leong, Aaron; Liu, Ching-Ti; Hivert, Marie-France; Strawbridge, Rona J. & Podmore, Clara [Show all 215 contributors for this article] (2017). Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. PLoS Medicine. ISSN 1549-1277. doi: 10.1371/journal.pmed.1002383. Full text in Research Archive Show summary

  <b>Background:</b> <br> Glycated hemoglobin (HbA1c) is used to diagnose type 2 diabetes (T2D) and assess glycemic control in patients with diabetes. Previous genome-wide association studies (GWAS) have identified 18 HbA1c-associated genetic variants. These variants proved to be classifiable by their likely biological action as erythrocytic (also associated with erythrocyte traits) or glycemic (associated with other glucose-related traits). In this study, we tested the hypotheses that, in a very large scale GWAS, we would identify more genetic variants associated with HbA1c and that HbA1c variants implicated in erythrocytic biology would affect the diagnostic accuracy of HbA1c. We therefore expanded the number of HbA1c-associated loci and tested the effect of genetic risk-scores comprised of erythrocytic or glycemic variants on incident diabetes prediction and on prevalent diabetes screening performance. Throughout this multiancestry study, we kept a focus on interancestry differences in HbA1c genetics performance that might influence race-ancestry differences in health outcomes. <br><b>Methods & findings: </b> <br> Using genome-wide association meta-analyses in up to 159,940 individuals from 82 cohorts of European, African, East Asian, and South Asian ancestry, we identified 60 common genetic variants associated with HbA1c. We classified variants as implicated in glycemic, erythrocytic, or unclassified biology and tested whether additive genetic scores of erythrocytic variants (GS-E) or glycemic variants (GS-G) were associated with higher T2D incidence in multiethnic longitudinal cohorts (N = 33,241). Nineteen glycemic and 22 erythrocytic variants were associated with HbA1c at genome-wide significance. GS-G was associated with higher T2D risk (incidence OR = 1.05, 95% CI 1.04–1.06, per HbA1c-raising allele, p = 3 × 10−29); whereas GS-E was not (OR = 1.00, 95% CI 0.99–1.01, p = 0.60). In Europeans and Asians, erythrocytic variants in aggregate had only modest effects on the diagnostic accuracy of HbA1c. Yet, in African Americans, the X-linked G6PD G202A variant (T-allele frequency 11%) was associated with an absolute decrease in HbA1c of 0.81%-units (95% CI 0.66–0.96) per allele in hemizygous men, and 0.68%-units (95% CI 0.38–0.97) in homozygous women. The G6PD variant may cause approximately 2% (N = 0.65 million, 95% CI0.55–0.74) of African American adults with T2D to remain undiagnosed when screened with HbA1c. Limitations include the smaller sample sizes for non-European ancestries and the inability to classify approximately one-third of the variants. Further studies in large multiethnic cohorts with HbA1c, glycemic, and erythrocytic traits are required to better determine the biological action of the unclassified variants.<br> <b>Conclusions: </b> <br> As G6PD deficiency can be clinically silent until illness strikes, we recommend investigation of the possible benefits of screening for the G6PD genotype along with using HbA1c to diagnose T2D in populations of African ancestry or groups where G6PD deficiency is common. Screening with direct glucose measurements, or genetically-informed HbA1c diagnostic thresholds in people with G6PD deficiency, may be required to avoid missed or delayed diagnoses.

• Rohde, Kerstin; Klos, Matthias; Hopp, Lydia; Liu, Xuanshi; Keller, Maria & Stumvoll, Michael [Show all 15 contributors for this article] (2017). IRS1 DNA promoter methylation and expression in human adipose tissue are related to fat distribution and metabolic traits. Scientific Reports. 7:12369, p. 1–10. doi: 10.1038/s41598-017-12393-5. Full text in Research Archive Show summary

  The SNP variant rs2943650 near IRS1 gene locus was previously associated with decreased body fat and IRS1 gene expression as well as an adverse metabolic profile in humans. Here, we hypothesize that these effects may be mediated by an interplay with epigenetic alterations. We measured IRS1 promoter DNA methylation and mRNA expression in paired human subcutaneous and omental visceral adipose tissue samples (SAT and OVAT) from 146 and 41 individuals, respectively. Genotyping of rs2943650 was performed in all individuals (N = 146). We observed a significantly higher IRS1 promoter DNA methylation in OVAT compared to SAT (N = 146, P = 8.0 × 10−6), while expression levels show the opposite effect direction (N = 41, P = 0.011). OVAT and SAT methylation correlated negatively with IRS1 gene expression in obese subjects (N = 16, P = 0.007 and P = 0.010). The major T-allele is related to increased DNA methylation in OVAT (N = 146, P = 0.019). Finally, DNA methylation and gene expression in OVAT correlated with anthropometric traits (waist- circumference waist-to-hip ratio) and parameters of glucose metabolism in obese individuals. Our data suggest that the association between rs2943650 near the IRS1 gene locus with clinically relevant variables may at least be modulated by changes in DNA methylation that translates into altered IRS1 gene expression.

• Weiner, Juliane; Rohde, Kerstin; Krause, Kerstin; Zieger, Konstanze; Klöting, Nora & Kralisch, Susan [Show all 11 contributors for this article] (2017). Brown adipose tissue (BAT) specific vaspin expression is increased after obesogenic diets and cold exposure and linked to acute changes in DNA-methylation. Molecular Metabolism. 6(6), p. 482–493. doi: 10.1016/j.molmet.2017.03.004. Full text in Research Archive Show summary

  Objective Several studies have demonstrated anti-diabetic and anti-obesogenic properties of visceral adipose tissue-derived serine protease inhibitor (vaspin) and so evoked its potential use for treatment of obesity-related diseases. The aim of the study was to unravel physiological regulators of vaspin expression and secretion with a particular focus on its role in brown adipose tissue (BAT) biology. Methods We analyzed the effects of obesogenic diets and cold exposure on vaspin expression in liver and white and brown adipose tissue (AT) and plasma levels. Vaspin expression was analyzed in isolated white and brown adipocytes during adipogenesis and in response to adrenergic stimuli. DNA-methylation within the vaspin promoter was analyzed to investigate acute epigenetic changes after cold-exposure in BAT. Results Our results demonstrate a strong induction of vaspin mRNA and protein expression specifically in BAT of both cold-exposed and high-fat (HF) or high-sugar (HS) fed mice. While obesogenic diets also upregulated hepatic vaspin mRNA levels, cold exposure tended to increase vaspin gene expression of inguinal white adipose tissue (iWAT) depots. Concomitantly, vaspin plasma levels were decreased upon obesogenic or thermogenic triggers. Vaspin expression was increased during adipogenesis but unaffected by sympathetic activation in brown adipocytes. Analysis of vaspin promoter methylation in AT revealed lowest methylation levels in BAT, which were acutely reduced after cold exposure. Conclusions Our data demonstrate a novel BAT-specific regulation of vaspin gene expression upon physiological stimuli in vivo with acute epigenetic changes that may contribute to cold-induced expression in BAT. We conclude that these findings indicate functional relevance and potentially beneficial effects of vaspin in BAT function.

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• Cayir, Akin & Böttcher, Yvonne (2025). Protocol for single-base quantification of RNA m5C by pyrosequencing. Elsevier. doi: 10.1016/j.xpro.2025.104099. Full text in Research Archive Show summary

  5-methylcytosine (m5C) is a common RNA modification found in both coding and non-coding RNAs. Here, we present a protocol for RNA-m5C-pyroseq for quantitative, single-nucleotide resolution analysis of RNA methylation. We describe steps for designing primers for the target region of RNA, performing bisulfite conversion of RNA, and using pyrosequencing to measure RNA methylation in cytosine. We then detail procedures for all the steps, including RNA isolation, bisulfite conversion, cDNA synthesis, PCR, gel electrophoresis, and pyrosequencing.

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