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 N6-methyladenosine (m6A) influences various aspects of RNA metabolism, however the m6A 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 m6A 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 m6A 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 m6A in human adipose tissue in paired samples of SAT and OVAT. We show an overall high overlap in m6A sites between individuals and depots, but also distinct depot-specific differences. We identify 339 target genes showing depot-specific m6A 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 m6A in non-adipocyte cells in OVAT compared to SAT. Mechanistically, we show for selected targets that m6A affects RNA lifetime in pre-adipocyte cell culture models. Importantly, m6A 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 m6A methylation, with potential as biomarkers in metabolic disease. Our findings underscore the regulatory role of m6A 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.