Identification of Type 1 Diabetes–Associated DNA Methylation Variable Positions That Precede Disease Diagnosis

TLDR

Monozygotic twin discordance for childhood‑onset type 1 diabetes is about 50%, indicating both genetic and non‑genetic factors contribute, yet the non‑genetic component remains poorly defined. The authors aimed to test whether epigenetic variation underlies the non‑genetic component of type 1 diabetes by conducting an epigenome‑wide association study. They profiled genome‑wide DNA methylation in CD14+ monocytes from 15 discordant MZ twin pairs and generated additional datasets to assess temporal enrichment of T1D‑associated methylation variable positions before and at diagnosis and in autoantibody‑positive, disease‑free individuals. The study identified 132 T1D‑associated methylation variable positions that differ in direction between twins, were validated in an independent cohort, and were enriched in singletons before and at diagnosis and in autoantibody‑positive, disease‑free individuals, indicating they arise early in disease etiology.

Abstract

Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is ∼50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. We generated genome-wide DNA methylation profiles of purified CD14+ monocytes (an immune effector cell type relevant to T1D pathogenesis) from 15 T1D–discordant MZ twin pairs. This identified 132 different CpG sites at which the direction of the intra-MZ pair DNA methylation difference significantly correlated with the diabetic state, i.e. T1D–associated methylation variable positions (T1D–MVPs). We confirmed these T1D–MVPs display statistically significant intra-MZ pair DNA methylation differences in the expected direction in an independent set of T1D–discordant MZ pairs (P = 0.035). Then, to establish the temporal origins of the T1D–MVPs, we generated two further genome-wide datasets and established that, when compared with controls, T1D–MVPs are enriched in singletons both before (P = 0.001) and at (P = 0.015) disease diagnosis, and also in singletons positive for diabetes-associated autoantibodies but disease-free even after 12 years follow-up (P = 0.0023). Combined, these results suggest that T1D–MVPs arise very early in the etiological process that leads to overt T1D. Our EWAS of T1D represents an important contribution toward understanding the etiological role of epigenetic variation in type 1 diabetes, and it is also the first systematic analysis of the temporal origins of disease-associated epigenetic variation for any human complex disease.