Epigenetic modifications associated with intrauterine exposure to maternal type 2 diabetes.

National Institute Of Diabetes And Digestive And Kidney Diseases

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Abstract

Individuals exposed to maternal diabetes in utero are more likely to develop metabolic and cardiovascular diseases later in life. This may be partially attributable to epigenetic regulation of gene expression. To examine whether differential DNA methylation, a major source of epigenetic regulation, can be observed in offspring of mothers with type 2 diabetes (OMD) during the pregnancy as compared to offspring of mothers with no type 2 diabetes(OMND) during the pregnancy, we performed an epigenome-wide association study. A total of 423,311 cytosine-phosphate-guanine (CpG) sites were analyzed in 388 Native Americans, of which 187 were OMD and 201 were OMND. Forty-eight differentially methylated CpG sites (with empirical false discovery rate < 0.05), mapping to 29 genes and 10 intergenic regions, were identified. The gene with the strongest evidence was LHX3, where 6 CpG sites were hyper-methylated in OMD (P 1.1 10-5). Similarly, a CpG near PRDM16 was hyper-methylated in OMD (1.1% higher, P = 5.6 10-7), where hyper-methylation also predicted future diabetes risk (hazard ratio = 2.12, P = 9.7 10-5). Hyper-methylation near AK3L1 and hypo-methylation at PCDHGA4 and STC1 associated with exposure to diabetes in utero and decreased insulin secretory function among offspring with normal glucose tolerance. Analysis of all 29 genes in aggregate did not shown enrichment for any biologic pathway; however, literature searches provided evidences that several of these genes have a role in embryonic development and/or beta cell function. We conclude that intrauterine exposure to diabetes can affect methylation at multiple genomic sites. Methylation status at some of these sites can impair insulin secretion, increase body weight and increase risk of type 2 diabetes. We have also conducted a genome-wide analysis to identify CpG sites at which methylation associates with BMI in American Indians. DNA methylation in 399 peripheral blood leukocyte samples was measured on the Illumina Infinium HumanMethylation450 BeadChip, and 423,311 CpG sites were analyzed. Each subject's BMI (measured at the time of blood sampling) was natural logarithm transformed and tested for association with DNA methylation with adjustments for appropriate covariates. CpG sites that achieved genome-wide significance in the discovery cohort (FDR p 0.05) were analyzed for replication in two existing datasets of Pima Indians (N = 320, age = 35; N = 183, age = 53). Among 263 CpG sites that associated with BMI in the discovery cohort, 9 replicated (p 0.05 and consistent direction of effect) in both replication cohorts. These were located in 6 genes and 2 enhancer elements. Three of these CpG sites map to genes (AHRR, RPS6KA2 and LGALS3BP) where DNA methylation has previously been reported to associate with BMI in other populations. The epigenetic associations at the remaining genes (DUSP5, RRAS2, APOBR) and enhancer elements are novel. Several of these genes have known roles in inflammation (DUSP5, LGALS3BP, APOBR, RPS6KA2) or cell proliferation (RRAS2 and AHRR). Thus, the present study has validated that DNA methylation at some genes associates with obesity in different ethnic groups, and it identifies other genes that may have a larger effect in American Indians. Our previous studies have used DNA from peripheral blood to identify epigenetic changes due to in-utero glucose exposure, however, it is known that the epigenetic marks are more different between different tissue types from the same individual than they are in the same tissue from different individuals Therefore, to better understand and identify “epimutations” that play a role in type 2 diabetes pathogenesis, it is important to perform such studies in diabetes relevant tissue types such as pancreatic islets. This is now possible due to recent advances in induced pluripotent stem cell (iPSC) technology. We been using our iPSC-derived pancreatic islet-based model system to elucidate the effect of glucose exposure during pancreatic islet development (to mimic in-utero glucose exposure) and identify stable epigenetic and transcriptomic changes in pancreatic islets exposed to excess glucose during development. Preliminary results have identified a significant effect on insulin secretion and identified stable transcriptomic (bulk RNA-seq) and epigenomic changes (ATAC-seq) in pancreatic-islets exposed to excess glucose exposure during development. Importantly, epigenetic changes can be inherited mitotically in somatic cells, providing a potential mechanism by which environmental effects on the epigenome can have long-term effects on gene expression. Evidence from animal studies and limited human studies suggest that prenatal and early postnatal environmental exposure can result in stable, altered epigenetic programming which can predispose to adult-onset diseases like type 2 diabetes. Our recent studies have shown that iPSC-based modeling can faithfully capture tissue specific gene imprinting, which is primarily controlled by epigenetics (DNA methylation), suggesting an epigenetic memory in these blood-cell derived iPSCs. Therefore, to complement our studies of induced glucose exposure during iPSC-derived pancreatic-islet development, we are initiating a study which uses iPSCs generated from blood cells of Indigenous American individuals who were either off-springs of a diabetic pregnancy (OMD) or off-springs of a non-diabetic pregnancy (OFMD) and generate pancreatic islets to identify naïve epigenetic and transcriptomic differences.