Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [RNA-seq]

The pathogenesis of Inflammatory Bowel Disease (IBD) is a multifactorial process characterized by inflammation and damage to the intestinal barrier, which is made up of intestinal epithelial cells (IECs). Since IBD is a remitting and relapsing disease, we postulated that epigenetic memory exists in IECs following an inflammatory encounter. The objective of this study was to uncover the mechanisms of a retained altered IEC epigenetic landscape in the context of IBD. We have generated adult stem cell organoids (containing all epithelial cell lineages) from patients with Ulcerative Colitis (UC); two organoid lines per patient were propagated: 1) from a site of active inflammation and from the same patient, and 2) a never inflamed region. We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and bulk RNA-seq on each organoid line. Established bioinformatic pipelines were used to determine significantly different chromatin accessibility and differentially expressed genes. Functional significance of the open chromatin regions was assessed by pathway and motif analysis. Treatment with TNF-alpha (10 and 100ng/ml) for 24 hours on the organoids was performed to determine re-activation of pro-inflammatory genes. This study shows for the first time that epithelial cells derived from organoids of IBD patients retain an epigenetic memory of the prior inflammatory state.