Background: 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). Pioneering work in other barrier tissues revealed that epithelial cells retain epigenetic marks of inflammatory encounters long after resolution. This is referred to as epigenetic memory, which is an altered epigenetic landscape of a cell in response to a stimulus that not only indicates its state at that time but persists and a memory of this exposure is retained. 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. Methods: We have generated adult stem cell organoids (containing all epithelial cell lineages) from Mayo Clinic patients with Ulcerative Colitis (UC) and healthy controls. Two organoid lines per patient were propagated: 1) from a site of active inflammation and from the same patient, 2) a never inflamed region. We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and bulk RNA-seq on each organoid line, along with single cell multiomics on a subset. 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. Chromatin immunoprecipitation (ChIP-seq) data was generated to confirm protein interactions with DNA. Results: Regions of increased chromatin accessibility (open chromatin) were enriched in organoids from inflamed areas compared to never inflamed regions. Open chromatin regions are associated with proinflammatory genes, which were not concomitantly upregulated in expression. This suggests that an epigenetic memory is retained in IECs derived from an inflammatory milieu but propagated in the absence of inflammatory stimuli. Intestinal stem cells from inflamed regions show alterations in gene expression at both the bulk and single cell level. Motif analysis for accessibility peaks in UC inflamed organoids showed an enrichment of the AP-1 family of transcription factors and chromatin remodelers (SMARCA4). ChIP-seq analysis confirmed that these open chromatin domains are driven by AP-1 factors. Conclusions: This study shows for the first time that epithelial cells of the IBD patient retain an epigenetic memory of the prior inflammatory state. The results from this work raise the possibility that retained accessible chromatin domains post-inflammation could heighten the potential for relapse. Funding by the AGA Research Scholar Award and KL2 TR002379.

Rohini Mopuri

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