Blood-Derived DNA Methylation Biomarkers Predict Diabetic Kidney Disease and Map to Epigenomic Remodeling in Renal Cells

Diabetic kidney disease (DKD) is a leading cause of end-stage kidney disease in type 1 diabetes (T1D); however, albuminuria and estimated glomerular filtration rate (eGFR) lack the precision necessary for early prognostication. We sought blood-derived DNA methylation biomarkers that predict DKD progression and reflect renal epigenomic remodeling. In the PROFIL cohort, we performed high-depth genome-wide methylation sequencing of leukocyte DNA from 101 adults with T1D and 20 control participants without diabetes, stratified by Kidney Disease: Improving Global Outcomes (KDIGO) risk and observed for a median of 5.6 years. Differentially methylated regions were identified across baseline KDIGO strata and prioritized based on hypomethylation, four or more CpGs per region, and discrimination between KDIGO categories; their associations with eGFR decline and rising albumin excretion were then evaluated. From these candidates, we derived a four-locus methylation risk score (MRS; SLC4A4, FSTL4, ICA1, and PTK2), validated by targeted assays in an independent subset of 330 participants with T1D with low or moderate KDIGO risk at baseline. Those with T1D showed global loss of 5-methylcytosine, with hypomethylated regions enriched at regulatory sites. In the discovery cohort, the combined MRS plus clinical model discriminated baseline KDIGO moderate- and high/very-high-risk strata (areas under the curve 0.91 and 0.86, respectively). In the independent validation cohort, the four-locus MRS predicted DKD progression within baseline low- and moderate-risk categories and improved risk stratification beyond clinical covariates, including eGFR and albumin excretion. In human podocytes, high glucose induced locus-specific hypomethylation, altered chromatin binding, and increased expression of MRS genes. These findings support a four-locus MRS for earlier, mechanistically grounded DKD risk stratification in T1D.