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P728 Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis

A. Barnicle*1, C. Seoighe2, A. Golden3, J. Greally3, L. Egan1

1NUI Galway, Clinical Pharmacology, Galway, Ireland, 2NUI Galway, School of Mathematics, Statistics and Applied Mathematics, Galway, Ireland, 3Albert Einstein College of Medicine, Centre of Epigenomics and Department of Genetics, New York, United States


DNA methylation acts as a key epigenetic mechanism, a means by which cells regulate the transcription of genes. It is fundamental to the dynamic regulation of gene expression and cell differentiation in specific cell and tissue types. In previous work, we showed that exposure of epithelium to the pro-inflammatory cytokine IL-6 results in increased methylation of DNA, via the stabilization enzyme DNMT1. However, whether prolonged exposure of colonic epithelium to inflammation in the disease setting of UC is associated with altered DNA methylation is not known. This study in ulcerative colitis (UC) patients aimed to identify potential epigenomic dysregulation occurring in intestinal epithelial cells between affected (inflamed) and unaffected (non-inflamed) areas of the colon.


Genome-wide DNA methylation (HELP-tagging assay) and transcriptome profiling (Human Transcriptome Array 2.0) of purified epithelial cells (Chelation, Flow Cytometry) from human subjects (n = 13) with non-neoplastic sub-total UC was performed.


In total, 577 differentially methylated sites mapping to 210 unique protein-coding genes were identified. We observed significant hypermethylation in the presence of inflammation at promoter regions of genes associated with embryonic development and regionalisation, most notably at members of the homeotic HOXB gene family. Using genome-wide gene expression data generated from the same pure epithelial cell isolates, 73 differentially expressed transcripts, corresponding to 62 known unique protein-coding genes were identified. We recognised increased gene expression in the presence of inflammation at HOXB13, as well as prostate cancer susceptibility candidates PRAC1 and PRAC2. Using integrative analysis, we distinguished 4 genes showing inverse correlation between DNA methylation and gene expression levels. These genes were ROR1, GXYLT2, FOXA2 and most notably RARB, a gene previously identified as a tumour suppressor in colorectal adenocarcinoma, as well as in breast, lung, and prostate cancer.


Results obtained highlight distinct patterns of DNA methylation and gene expression in the presence of non-cancerous UC. The interplay between genetic and epigenetic signatures in the pathway of colitis-associated carcinogenesis needs to be explored in further studies. However, this integrative epigenomic dataset will enhance our understanding of the role played by epithelial cells in UC pathophysiology, potentially gaining insight into the molecular mechanism underlying the progression of UC to colitis-associated cancer.