Elucidating the Epigenetic Landscape of Type 2 Diabetes: A Multi-Omics Analysis Revealing Novel CpG Sites and Their Association with Cardiometabolic Traits

Abstract Type 2 Diabetes (T2D) is a complex, multifactorial disease with a significant global health burden. Genome-Wide Association Studies (GWAS) have identified numerous genetic variants associated with T2D, yet understanding their functional mechanisms remains challenging due to the polygenic nature of the disease and the prevalence of non-coding region variants. This study leverages a multi-omics approach integrating methylome-wide association studies (MWAS), Mendelian Randomization (MR), and functional analyses in human pancreatic cells and mouse models to elucidate the functional consequences of genetic variants on T2D. Using summary statistics calculated from large-scale GWAS for T2D and a DNA methylation (DNAm) prediction model, our MWAS tested the association of DNAm at CpGs in whole blood with T2D across the genome. We identified 87 significant and independent CpG sites associated with T2D risk in Europeans, including 13 novel CpG sites located in or near genes not previously associated with T2D, with these results being replicated in an additional dataset. Our analyses also revealed a significant overlap of these CpGs with cardiometabolic traits, underscoring the interconnectedness of metabolic diseases. Additionally, we demonstrated trans-ethnic effects of significant CpGs in East Asians, highlighting their global relevance. Functional analyses in human pancreatic alpha and beta cells identified potential regulatory roles of these CpGs in gene expression, particularly in genes involved in glucose metabolism. Notably, differential expression of the PPP1R3B gene, regulated by a significant CpG, between T2D cases and normal controls was observed in both alpha and beta cells, with mouse models confirming its role in glucose homeostasis. Our findings provide new insights into the epigenetic architecture of T2D, revealing novel genetic susceptibilities and highlighting potential targets for therapeutic intervention.