Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N=190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P<1x10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions. We characterised genome-wide DNA methylation in two independent cohorts. Cohort one comprised 48 adipocyte samples (24 subcutaneous and 24 visceral) from people with extreme obesity and 48 adipocyte samples from healthy controls (24 subcutaneous and 24 visceral) analysed using the Illumina Infinium HumanMethylation450 BeadChip (Discovery Cohort). Cohort two comprised 48 adipocyte samples (24 subcutaneous and 24 visceral) from people with extreme obesity and 48 adipocyte samples from healthy controls (24 subcutaneous and 24 visceral) analysed using the Illumina Infinium EPIC BeadChip (Replication Cohort). Adipocytes were isolated from fresh whole subcutaneous and visceral adipose tissue samples using collagenase digestion and flotation, and stored at -80C, prior to DNA extraction and bisulfite conversion with 0.2-0.5-mcg of genomic DNA.