Epigenetic landscapes in human pancreatic islets reveal distinct drivers for adaptation to age and type 2 diabetes

Age is the strongest risk factor for type 2 diabetes, yet their independent contribution to pancreatic islet dysfunction remains unclear. We integrate DNA methylation, transcriptomic, and genotyping data from 144 islet donors. We identify 996 age- and 902 T2D-associated CpGs with minimal overlap, and 251 age- and 310 diabetes CpG target genes, usually distant from the CpG. Age-linked CpGs are enriched in promoters, form co-regulated gene modules, link to beta-cell function, including insulin secretion. Diabetes-associated CpGs are enriched in enhancer/non-regulatory regions, and modules suggest stress-induced epigenetic drift. CpG-gene associations are independent of genetic variation. Mendelian randomisation supports a causal role for age-associated CpGs regulating KLHL42, a T2D GWAS locus. A blood-based methylation risk score based on age-linked CpGs correlates with insulin secretion and improves diabetes classification when combined with genetic risk (AUC = 0.91). Altogether, age is associated with a coordinated epigenetic programme, whereas diabetes links to a heterogeneous, stress-related epigenetic signature. Age is the strongest risk factor for type 2 diabetes. Here, the authors show that aging and diabetes drive distinct epigenetic programmes in human pancreatic islets, with age‑linked DNA methylation coordinately regulating beta‑cell function, while diabetes associates with heterogeneous stress‑related epigenetic changes.