An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss

Abstract

Background: Environmental factors can influence obesity by epigenetic mechanisms. Adipose tissue plays a key role in obesity-related metabolic dysfunction, and gastric bypass provides a model to investigate obesity and weight loss in humans.

Results: Here, we investigate DNA methylation in adipose tissue from obese women before and after gastric bypass and significant weight loss. In total, 485,577 CpG sites were profiled in matched, before and after weight loss, subcutaneous and omental adipose tissue. A paired analysis revealed significant differential methylation in omental and subcutaneous adipose tissue. A greater proportion of CpGs are hypermethylated before weight loss and increased methylation is observed in the 3' untranslated region and gene bodies relative to promoter regions. Differential methylation is found within genes associated with obesity, epigenetic regulation and development, such as CETP, FOXP2, HDAC4, DNMT3B, KCNQ1 and HOX clusters. We identify robust correlations between changes in methylation and clinical trait, including associations between fasting glucose and HDAC4, SLC37A3 and DENND1C in subcutaneous adipose. Genes investigated with differential promoter methylation all show significantly different levels of mRNA before and after gastric bypass.

Conclusions: This is the first study reporting global DNA methylation profiling of adipose tissue before and after gastric bypass and associated weight loss. It provides a strong basis for future work and offers additional evidence for the role of DNA methylation of adipose tissue in obesity.

Figure 1

Global DNA methylation in human adipose tissue plotted by gene region. Gene regions are based on Illumina 450 K beadchip annotation. Data are presented as mean +/− standard deviation. *Significant difference between average DNA methylation before and after weight loss, Bonferroni adjusted P <0.05. TSS proximal promoter defined as 200 bp (TSS200) or 1,500 bp (TSS1500) upstream of the transcription start site. UTR: untranslated region. Ab – subcutaneous adipose, Om – omentum before (pre) and after (post) gastric bypass and weight-loss.

Figure 2

Heatmap of hierarchical clustering for differentially methylated CpG sites in omentum (A) and subcutaneous adipose (B). CpG sites passing a relaxed (P <1 × 10⁻⁵) are represented. Dark blue to white indicates hypermethylation through hypomethylation. OP1 and OP2 indicate samples taken before and after gastric bypass, respectively; numeral indicates samples from individuals 1 to 15.

Figure 3

Genome-wide differential methylation in subcutaneous adipose. Difference in methylation (∆beta) for all CpG sites passing Bonferroni correction is plotted. ∆beta is weighted by t-statistic such that distance from central core (grey) indicates increasing levels of statistical significance. Red dots represent CpG sites hypermethylated and blue dots CpG sites hypomethylated, respectively, before weight loss. Chromosomes are shown clockwise from 1 through X.

Figure 4

An example DMR upstream of miR-199A1. Location and orientation of miR-199A1 within DMN2, as well as CpG sites upstream of the miRNA are shown above. The bottom panel shows average beta values across the DMR on chromosome 19 for: healthy whole blood (light grey dotted), subcutaneous adipose before weight loss (blue), subcutaneous adipose after weight loss (green), and healthy subcutaneous adipose (black dotted).

Figure 5

Correlations between Illumina 450 K array data and pyrosequence analysis. Representative data for a single CpG site in four genes are shown. Red indicates samples taken before and blue after gastric bypass. Illumina probe IDs are indicated after gene names.