Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis

Epigenetics. 2017 Aug;12(8):591-606. doi: 10.1080/15592294.2017.1334023. Epub 2017 May 30.

Abstract

Aberrant DNA methylation patterns have been reported in inflamed tissues and may play a role in disease. We studied DNA methylation and gene expression profiles of purified intestinal epithelial cells from ulcerative colitis patients, comparing inflamed and non-inflamed areas of the colon. We identified 577 differentially methylated sites (false discovery rate <0.2) mapping to 210 genes. From gene expression data from the same epithelial cells, we identified 62 differentially expressed genes with increased expression in the presence of inflammation at prostate cancer susceptibility genes PRAC1 and PRAC2. Four genes showed inverse correlation between methylation and gene expression; ROR1, GXYLT2, FOXA2, and, notably, RARB, a gene previously identified as a tumor suppressor in colorectal adenocarcinoma as well as breast, lung and prostate cancer. We highlight targeted and specific patterns of DNA methylation and gene expression in epithelial cells from inflamed colon, while challenging the importance of epithelial cells in the pathogenesis of chronic inflammation.

Keywords: DNA methylation; inflammatory bowel disease; intestinal epithelial cell; transcriptome; ulcerative colitis.

MeSH terms

  • Adult
  • Colitis, Ulcerative / genetics*
  • Colitis, Ulcerative / metabolism
  • DNA Methylation*
  • Female
  • Hepatocyte Nuclear Factor 3-beta / genetics
  • Hepatocyte Nuclear Factor 3-beta / metabolism
  • Humans
  • Intestinal Mucosa / metabolism*
  • Male
  • Middle Aged
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Receptor Tyrosine Kinase-like Orphan Receptors / genetics
  • Receptor Tyrosine Kinase-like Orphan Receptors / metabolism
  • Receptors, Retinoic Acid / genetics
  • Receptors, Retinoic Acid / metabolism
  • Transcriptome

Substances

  • FOXA2 protein, human
  • Nuclear Proteins
  • PRAC1 protein, human
  • Receptors, Retinoic Acid
  • retinoic acid receptor beta
  • Hepatocyte Nuclear Factor 3-beta
  • ROR1 protein, human
  • Receptor Tyrosine Kinase-like Orphan Receptors