Genome-wide Analysis Reveals DNA Methylation Alterations in Obesity Associated with High Risk of Colorectal Cancer

Abstract

Obesity is a high risk factor for colorectal cancer (CRC). The contribution of underlying epigenetic mechanisms to CRC and the precise targets of epigenetic alterations during cancer development are largely unknown. Several types of epigenetic processes have been described, including DNA methylation, histone modification, and microRNA expression. To investigate the relationship between obesity and CRC, we studied both obese and CRC patients, focusing on genome-wide peripheral blood DNA methylation alterations. Our results show abnormal distributions of overlapping differentially methylated regions (DMRs) such as hypermethylated CpG islands, which may account for epigenetic instability driving cancer initiation in obesity patients. Furthermore, functional analysis suggests that altered DNA methylation of extracellular (e.g., O-glycan processing) and intracellular components contribute to activation of oncogenes (e.g. KRAS and SCL2A1) and suppression of tumor suppressors (e.g. ARHGEF4, EPHB2 and SOCS3), leading to increased oncogenic potency. Our study demonstrates how DNA methylation changes in obesity contribute to CRC development, providing direct evidence of an association between obesity and CRC. It also reveals the diagnostic potential of using DNA methylation as an early risk evaluation to detect patients with high risk for CRC.

Figure 1

Association of differentially methylated CpGs (DMCs) in obesity and CRC. (A) Venn-diagram of DMCs generated from CRC vs. Control and Obesity vs. Control genes; (B) Scatter plot displaying the methylation differences in overlapping DMCs and the distribution of these DMCs partitioned by hyper-/hypomethylated CpGs in CRC and obesity; (C) Number of hyper-/hypomethylated CpGs in CRC and obesity. The Chi-Square test was used to determine a potential significant relationship between obesity and CRC.

Figure 2

Association of differentially methylated regions (DMRs) in obesity and CRC. (A) Venn-diagram of the DMRs generated from CRC vs. Control and Obesity vs. Control genes; (B) Scatter plot displaying the mean methylation difference of overlapping DMRs and the distribution of these DMRs partitioned by hyper-/hypomethylated DMRs in CRC and obesity. (C) Number of hyper-/hypomethylated DMRs in CRC and obesity.

Figure 3

Bar plots of the number of cancer-specific, obesity-specific, overlapping DMRs by gene subregions (A–C) and CpG islands (D–F).

Figure 4

Mean methylation levels of relevant DMRs. (A) Summary of 12 overlapping major DMRs; (B–M) Box plots of methylation level of individual DMRs in three different gene groups. Each dot represents the mean methylation level of the specific DMR for each individual subject.

Figure 5

Heatmap displays mean row-centered log-CPM (log2-counts per million) values of the representative genes selected in Fig. 4 in two replicas of HCT116 and DKO cell line.