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

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.

Integrated analysis of genome-wide genetic and epigenetic association data for identification of disease mechanisms

“…These included the HLA region (P = 2.6 × 10 −4 ), in consistency with the findings of the original studies. 3 The association of GAD2 with T1D in the Raykan et al EWAS data was also confirmed by the combined effect analysis (P = 0.0014), but it was not found to be significantly associated with T1D in the WTCCC GWAS data (P = 0.50). Through assessment of combined effects, additional genetic loci were identified to be associated with T1D epigenetically, with PGM1 (Phosphoglucomutase 1) as the most interesting candidate, whose encoded protein is one of the PGM isozymes, which catalyze the transfer of phosphate between the 1 and 6 positions of glucose, and is therefore an important component in the breakdown and synthesis of glucose.…”

“…1,2 Although a large number of epigenome-wide association studies (EWAS) have to date been performed to identify such DNA methylation modifications in the genome, the results were only confirmed by independent replications in two cases. 3,4 In the first case, Rakyan et al 3 identified disease-associated methylation signals from a genome-wide DNA methylation scan of purified CD14+ monocytes from 15 T1D-discordant monozygotic twin pairs. Some of the association signals were not only replicated but also demonstrated to be present before disease diagnosis, thus indicating an etiological role of the epigenetic variations.…”

“…Some of the association signals were not only replicated but also demonstrated to be present before disease diagnosis, thus indicating an etiological role of the epigenetic variations. 3 Liu et al 4 identified two clusters within the major histocompatibility complex (MHC) region to be associated with risk of RA from genome-wide DNA methylation variations of a total of 354 cases and 337 controls, with both clusters showing evidence of association at replication.…”

“…3,4 In other words, both DNA sequence variations and DNA methylation variations in certain regions in the genome were found to be important for the etiology of the diseases. This observation leads to a more general question of to what extent environmental factors, through epigenetic changes, affect the same genomic regions and biological pathways that have been identified via genetic association studies.…”

Effects of early-life environment and epigenetics on cardiovascular disease risk in children: highlighting the role of twin studies

“…To our knowledge, only one EWAS of a CVD-related phenotype has been performed in twins. Using DNA methylation profiles of purified CD14+ monocytes from 15 type 1 diabetes-discordant pairs of MZ twin children (77), this study revealed the presence of 132 genomic locations that differed in DNA methylation in all twins with type 1 diabetes. Genes associated with these CpGs were enriched in those involved in immune function including HLA-related genes (HLA-DQB1) and regulatory factor X-associated protein (RFXAP), both previously associated with type 1 diabetes in genetic studies, and the proinflammatory cytokine tumor necrosis factor.…”