An Epigenome-Wide Study to Identify DNA Methylation that Associates with Obesity

Obesity is a chronic disease which is often accompanied by low-grade inflammation. Epigenetic association studies have identified cytosine-phosphate-guanine (CpG) sites at which differential DNA methylation, which can affect gene expression, associates with obesity as measured by BMI. However, the extent to which these associations transfer to diverse populations, such as American Indians who have a high prevalence of obesity, remains unclear. In the current study, we conducted a genome-wide analysis to identify CpG sites at which methylation associates with BMI in Pima Indians. DNA methylation was measured on the Illumina Infinium HumanMethylation450 BeadChip. We analyzed 423,311 CpG sites in peripheral blood leukocyte samples from 399 nondiabetic Pima Indians (mean [± SD] age = 13.1±5.9 years). 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 of genome-wide significance in the discovery cohort (FDR p ≤0.05) were analyzed for replication in two existing datasets of diabetic Pima Indians (N = 320, age = 35.5±11.3; N = 183, age = 53.6±11.9). 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.