An Epigenome-Wide Association Study of DNA Methylation and Proliferative Retinopathy Over 28 Years in Type 1 Diabetes

Purpose To perform a prospective epigenome-wide association study (EWAS) of DNA methylation (DNAm) and 28-year proliferative diabetic retinopathy (PDR) incidence in type 1 diabetes (T1D). Design Prospective observational cohort study. Participants The Pittsburgh Epidemiology of Diabetes Complications study of childhood-onset (<17 years) T1D. Methods Stereoscopic fundus photographs were taken in fields 1, 2, and 4 at baseline, 2, 4, 6, 8, 16, 23, and 28 years after DNAm measurements. The photos were graded using the modified Airlie House System. In those free of PDR at baseline (n=265, mean T1D duration 18 years at baseline), whole blood DNAm (EPIC array) at 683,597 CpGs was analyzed in Cox models for time to event. Associations between significant CpGs and clinical risk factors were assessed; genetic variants associated with DNAm were identified (meQTLs). Mendelian Randomization (MR) was used to examine evidence of causal associations between DNAm and PDR. Post-hoc regional and functional analyses were performed. Main Outcome Measures PDR was defined as the first instance of a grade of ≥60 in at least one eye or pan-retinal photocoagulation for PDR. Follow-up time was calculated from the study visit at which DNAm data were available (baseline) until PDR incidence or censoring (31 December 2018 or last follow-up). Results PDR incidence was 53% over 28-years’ follow-up. Greater DNAm of cg27512687 (KIF16B) was associated with reduced PDR incidence (p=6.3x10-9, FDR<0.01); 113 cis-meQTLs (p<5x10-8) were identified. MR analysis using the sentinel meQTL as the instrumental variable supported a potentially causal association between cg27512687 and PDR. Cg27512687 was also associated with lower pulse rate and albumin excretion rate and higher eGFR but its association with PDR remained independently significant after adjustment for those factors. In regional analyses, DNAm of FUT4, FKBP1A, and RIN2 was also associated with PDR incidence. Conclusions DNAm of KIF16B, FUT4, FKBP1A, and RIN2 was associated with PDR incidence, supporting roles for epigenetic regulation of iron clearance, developmental pathways, and autophagy in PDR pathogenesis. Further study of those loci may provide insight into novel targets for interventions to prevent or delay PDR in T1D.