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

Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis.

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a Clinical Pharmacology, School of Medicine, National University of Ireland , Galway , Ireland.
b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland.
c Center of Epigenomics and Department of Genetics (Division of Computational Genetics) , Albert Einstein College of Medicine, Morris Park Avenue , Bronx , NY , USA.
d Department of Mathematical Sciences , Yeshiva University , 2495 Amsterdam Avenue, New York , NY , USA.


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.


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

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