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

Abstract

Purpose: To perform a prospective epigenome-wide association study 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 (EDC) 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 of 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 (methylation quantitative trait loci [meQTLs]). Mendelian randomization was used to examine evidence of causal associations between DNAm and PDR. Post hoc regional and functional analyses were performed.

Main outcome measures: Proliferative diabetic retinopathy was defined as the first instance of a grade of ≥ 60 in at least 1 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 (December 31, 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 = 6.3 × 10^-9; false discovery rate [FDR]: < 0.01); 113 cis-meQTLs (P < 5 × 10^-8) were identified. Mendelian randomization 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 estimated glomerular filtration rate, 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: DNA methylation 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.

Financial disclosures: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Keywords: DNA methylation; Epigenetics; Proliferative diabetic retinopathy; Retina; Type 1 diabetes.

Figure 2

LocusZoom plots of genetic variants significantly associated with methylation of cg27512687 in the Epidemiology of Diabetes Complications cohort (panel A) and variants annotated as eQTLs in GTEx in the same genomic region (panel B).

Figure 3

Reactome Functional Interaction network of loci with significant CpGs or differentially methylated regions associated with 28-year proliferative retinopathy incidence in the Epidemiology of Diabetes Complications cohort. Candidate loci are indicated in black font (red font indicates linker genes used only to construct the network). Categories of significantly enriched (false discovery rate < 0.05) Reactome pathways for each module are noted. Solid line = involved in same reaction as inputs or are components of a shared complex, → = activator or catalyst, --| = inhibitor, dashed line = predicted interaction.