The transcriptional signature of mucosa of patients with ulcerative colitis (UC) in remission reveals long-lasting changes in the epithelial barrier which persist once the inflammatory response has resolved. In order to investigate if these changes are caused by primary defects in the epithelial cells, we generated in vitro epithelial organoid cultures (EpOCs) from colon samples of non-IBD controls and UC patients. After induction of differentiation, total RNA was extracted from both EpOCs and differentiated EpOCs (d-EpOCs) and used for hybridization on Affymetrix microarray.
Overall design
Colon samples from non-IBD controls and UC patients were collected. Both surgical and biopsy samples for non-IBD controls, and only biopsy samples for UC patients, were considered. Non-IBD controls were those subjects undergoing surgery for colorectal cancer, colonoscopy for mild gastrointestinal symptoms, or a screening for CRC and who presented no lesions during examination. Inclusion criteria for UC patients at the time of colonoscopy were: age between 18 and 80, diagnosis at least 5 years before inclusion, and exclusion of colitis-associated dysplasia or neoplasia. Endoscopic activity of UC at the time of colonoscopy was categorized according to the Mayo endoscopy subscore. Active disease was defined as Mayo endoscopic subscore of ≥1; quiescent disease was defined as a Mayo score of 0. Only samples from UC patients with inactive or mildly active disease were included in the generation of epithelial organoid cultures (EpOCs). Once expanded, EpOCs were induced to differentiate into the different epithelial lineages (d-EpOCs). Finally, a total of 19 human samples were analysed: 11 from non-IBD controls and 8 from UC patients. From these samples 19 EpOCs and 17 d-EpOCs were generated. RNA was then extracted and used for hybridization on Affymetrix microarrays.
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