Metabolic memory, initiated by hyperglycemia at diabetes onset, contributes to long-term vascular complications. While prior studies in type 1 diabetes have linked this legacy effect to CpG methylation changes, its epigenetic basis in type 2 diabetes (T2D), which comprises over 90% of diabetes cases remains largely underexplored.

Peripheral blood mononuclear cells were collected from normoglycemic individuals, newly diagnosed T2D patients, and long-duration T2D patients. A subset received follow-up treatment with sodium-glucose co-transporter-2 inhibitors (SGLT2i). Genome-wide DNA methylation profiling was performed using reduced representation bisulfite sequencing, covering around 4 million CpG sites enriched at 20,000 promoters. A custom computational pipeline was developed to classify methylation dynamics into reversible, persistent, or deteriorating loci across disease stages and treatment responses.

We identified two distinct waves of methylation reduction corresponding to early and chronic phases of T2D. Newly diagnosed patients exhibited epialleles with methylation patterns that gradually normalized over time, whereas long-duration diabetes generated additional, persistent epigenetic alterations. Notably, SGLT2i therapy significantly restored methylation profiles across both footprint types, suggesting a potential for epigenetic reversal.

This study is the first to delineate dual epigenetic footprints of metabolic memory in T2D and demonstrate their partial reversibility through SGLT2i treatment. These findings offer mechanistic insights into the legacy effect and support the development of personalized epigenetic strategies for mitigating diabetic complications.