Epigenome-wide association study of incident type 2 diabetes in Black and White participants from the Atherosclerosis Risk in Communities Study

Abstract

ABSTRACTDNA methylation studies of incident type 2 diabetes in US populations are limited, and to our knowledge none included individuals of African descent living in the US. We performed an epigenome-wide association analysis of blood-based methylation levels at CpG sites with incident type 2 diabetes using Cox regression in 2,091 Black and 1,029 White individuals from the Atherosclerosis Risk in Communities study. At an epigenome-wide significance threshold of 10−7, we detected 7 novel diabetes-associated CpG sites inC1orf151(cg05380846: HR= 0.89,p= 8.4 × 10−12),ZNF2(cg01585592: HR= 0.88,p= 1.6 × 10−9),JPH3(cg16696007: HR= 0.87,p= 7.8 × 10−9),GPX6(cg02793507: HR= 0.85,p= 2.7 × 10−8and cg00647063: HR= 1.20,p= 2.5 × 10−8), chr17q25 (cg16865890: HR= 0.8,p= 6.9 × 10−8), and chr11p15 (cg13738793: HR= 1.11,p= 7.7 × 10−8). The CpG sites atC1orf151,ZNF2, JPH3andGPX6, were identified in Black adults, chr17q25 was identified in White adults, and chr11p15 was identified upon meta-analyzing the two groups. The CpG sites atJPH3andGPX6were likely associated with incident type 2 diabetes independent of BMI. All the CpG sites, except atJPH3, were likely consequences of elevated glucose at baseline. We additionally replicated known type 2 diabetes-associated CpG sites including cg19693031 atTXNIP, cg00574958 atCPT1A, cg16567056 atPLBC2, cg11024682 atSREBF1, cg08857797 atVPS25, and cg06500161 atABCG1, 3 of which were replicated in Black adults at the epigenome-wide threshold. We observed modest increase in type 2 diabetes variance explained upon addition of the significantly associated CpG sites to a Cox model that included traditional type 2 diabetes risk factors and fasting glucose (increase from 26.2% to 30.5% in Black adults; increase from 36.9% to 39.4% in White adults). We examined if groups of proximal CpG sites were associated with incident type 2 diabetes using a gene-region specific and a gene-region agnostic differentially methylated region (DMR) analysis. Our DMR analyses revealed several clusters of significant CpG sites, including a DMR consisting of a previously discovered CpG site atADCY7and promoter regions ofTP63which were differentially methylated across all race groups. This study illustrates improved discovery of CpG sites/regions by leveraging both individual CpG site and DMR analyses in an unexplored population. Our findings include genes linked to diabetes in experimental studies (e.g.,GPX6,JPH3,andTP63), and future gene-specific methylation studies could elucidate the link between genes, environment, and methylation in the pathogenesis of type 2 diabetes.