Genome-Wide Analysis of DNA Methylation Differences in Muscle and Fat from Monozygotic Twins Discordant for Type 2 Diabetes

Abstract

BackgroundMonozygotic twins discordant for type 2 diabetes constitute an ideal model to study environmental contributions to type 2 diabetic traits. We aimed to examine whether global DNA methylation differences exist in major glucose metabolic tissues from these twins.Methodology/Principal FindingsSkeletal muscle (n = 11 pairs) and subcutaneous adipose tissue (n = 5 pairs) biopsies were collected from 53–80 year-old monozygotic twin pairs discordant for type 2 diabetes. DNA methylation was measured by microarrays at 26,850 cytosine-guanine dinucleotide (CpG) sites in the promoters of 14,279 genes. Bisulfite sequencing was applied to validate array data and to quantify methylation of intergenic repetitive DNA sequences. The overall intra-pair variation in DNA methylation was large in repetitive (LINE1, D4Z4 and NBL2) regions compared to gene promoters (standard deviation of intra-pair differences: 10% points vs. 4% points, P<0.001). Increased variation of LINE1 sequence methylation was associated with more phenotypic dissimilarity measured as body mass index (r = 0.77, P = 0.007) and 2-hour plasma glucose (r = 0.66, P = 0.03) whereas the variation in promoter methylation did not associate with phenotypic differences. Validated methylation changes were identified in the promoters of known type 2 diabetes-related genes, including PPARGC1A in muscle (13.9±6.2% vs. 9.0±4.5%, P = 0.03) and HNF4A in adipose tissue (75.2±3.8% vs. 70.5±3.7%, P<0.001) which had increased methylation in type 2 diabetic individuals. A hypothesis-free genome-wide exploration of differential methylation without correction for multiple testing identified 789 and 1,458 CpG sites in skeletal muscle and adipose tissue, respectively. These methylation changes only reached some percentage points, and few sites passed correction for multiple testing.Conclusions/SignificanceOur study suggests that likely acquired DNA methylation changes in skeletal muscle or adipose tissue gene promoters are quantitatively small between type 2 diabetic and non-diabetic twins. The importance of methylation changes in candidate genes such as PPARGC1A and HNF4A should be examined further by replication in larger samples.

Use of Blood as a Surrogate Model for the Assessment of Visceral Adipose Tissue Methylation Profiles Associated with the Metabolic Syndrome in Men

“…Using a cohort showing minimal overlap with previously assessed cohort (N=2) [15], our goal was to investigate whether blood methylation levels may serve as surrogate of VAT methylation levels in the context of an analysis of the determinants of obesity-related metabolic complications. Previous studies assessed methylation levels in paired tissues but few performed inter-tissue analysis in the context of cardiovascular disease risk factors or epigenetic epidemiology [18,20,21,31,32]. Testing mean methylation level differences between VAT and blood, the present study reports high correlation levels across tissues.…”

“…However, analyses on such relevant tissues samples are sometimes impossible or extremely difficult to collect. As a result, most genome-wide methylation profiles in humans have been performed on DNA extracted from blood, a readily accessible tissue, and tissue-specific DNA methylation was noted for various genes [16][17][18]. In addition, the relative accessibility of blood offers the possibility of prospective sampling and makes it attractive for the study of dynamic epigenetic changes [19].…”

Young men with low birthweight exhibit decreased plasticity of genome-wide muscle DNA methylation by high-fat overfeeding

“…The involvement of tissue-specific DNA methylation in the pathogenesis of type 2 diabetes is supported by several studies [2][3][4]. Maternal diet and/or the intrauterine environment may influence DNA methylation in the offspring, possibly affecting phenotypes and disease risk Electronic supplementary material The online version of this article (doi:10.1007/s00125-014-3198-8) contains peer-reviewed but unedited supplementary material, which is available to authorised users.…”

Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood

“…Many studies to date have investigated methylation in single tissue types. For example, epigenome-wide association studies (EWAS) have reported that epigenetic alterations in adipose tissue are associated with metabolic process-related phenotypes such as type 2 diabetes, 5,6 and may be modulated by physical activity. 7,8 EWAS using blood DNA methylation showed associations of DNA methylation with immune-related conditions such as rheumatoid arthritis 9 and clinical parameters such as immunoglobulin E concentration.…”