Microarray analysis of colonic mucosal biopsies from healthy controls and patients with active ulcerative colitis
Ontology highlight
ABSTRACT: Expression data was used to evaluate changes to the transcriptional signatures across the healthy and inflamed colon. A comparison between healthy controls and active ulcerative colitis signatures was also made. Mucosal biopsy specimens were harvested at four anatomical locations within the colon from healthy volunteers and patients with active ulcerative colitis. specimens were fixed in RNA later for 24 hours at room temperature and stored at -80C for a further 24 hours prior to RNA extraction and microarray analysis.
Project description:Expression data was used to evaluate changes to the transcriptional signatures across the healthy and inflamed colon. A comparison between healthy controls and active ulcerative colitis signatures was also made.
Project description:Ulcerative Colitis is an autoimmune inflammatory bowel disease that causes chronic inflammation in the colon and the rectum. Althoung extensively researched, the underlying molecular mechanisms of Ulcerative Colitis remain elusive. Especially, there is a lack of understanding about regulatory non-coding miRNA expression during Ulcerative Colitis. Therefore, we performed high-throughput miRNA profiling of colon tissue biopsies from XX patients with active Ulcerative Colitis, XX patients with quiescent Ulcerative Colitis and XX Symptomatic Control individuals.
Project description:Ulcerative Colitis is an autoimmune inflammatory bowel disease that causes chronic inflammation in the colon and the rectum. Althoung extensively researched, the underlying molecular mechanisms of Ulcerative Colitis remain elusive. Especially, there is a lack of understanding about regulatory non-coding miRNA expression during Ulcerative Colitis in a cell type-specific context. Therefore, we performed high-throughput miRNA profiling of Fluorescence Activated Cell Sorting (FACS)-enriched CD66a+ and CD44+ colonic epithelial cell populations from colon tissue biopsies of 16 patients with active Ulcerative Colitis, 15 patients with quiescent Ulcerative Colitis and 17 Symptomatic Control individuals.
Project description:To clarify the pathological significance of CGRP in ulcerative colitis, we generated knockout mice for CGRPα and CGRPβ and analyzed colon proteome data from DDS drinking water ulcerative colitis model mice. In addition, to confirm changes in the colon over time, the colon of wild-type mice after DDS drinking was harvested over time and used for proteome data.
Project description:This scRNA-seq dataset of five human subjects with ulcerative colitis (derived from colonic lamina propria samples), was analyzed and published as part of a larger manuscript (Mitsialis, V et al, "“Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease” in Gastroenterology), which reported immune signatures of blood and intestinal tissue differentiating ulcerative colitis from Crohn's disease from non-IBD human subjects using mass cytometry as well as scRNA-seq.
Project description:PL8177 is a potent and selective agonist of the melanocortin 1 receptor (MC1R). PL8177 has shown efficacy in reversing intestinal inflammation in a cannulated rat ulcerative colitis model. To facilitate oral delivery, a novel, polymer-encapsulated formulation of PL8177 was developed and tested in dextran sulfate sodium induced rat ulcerative colitis model. Rats treated with 50 µg oral PL8177 demonstrated significantly lower macroscopic colon damage scores and improvement in colon weight, stool consistency, and fecal occult blood vs the vehicle without active drug. We used single nuclei RNA sequencing of colon tissues to characterize the mechanism of action and identify relative cell population and key gene expression changes between treated, healthy and vehicle.
Project description:Hypothesis: Gene expression differences in biopsies from patients with inflammatory bowel disease can be used to identify molecular heterogeneity within patients with active disease. Methods: Patients with a diagnosis of Crohn's disease, ulcerative colitis or normal healthy controls (with or without infectious colitis) underwent ileocolonoscopy. In healthy controls, biopsies were taken in the sigmoid colon (n=21), ascending/descending colon (n=25) and the terminal ileum (n=12). In patients with Crohn's disease, biopsies were taken in the ascending/descending colon (n=107) and terminal ileum (n=70) in uninflamed areas in all patients; in patients with mucosal lesions, additional biopsies were taken in inflamed regions of the ascending/descending colon (n=35) and terminal ileum (n=55). In ulcerative colitis patients, paired uninflamed sigmoid (n=48) and inflamed sigmoid biopsies (n=46) were taken. Biopsies were placed in RNAlater at the clinical site, frozen and shipped to Genentech, where they were disrupted using TissueLyzer beads, then RNA was isolated using RNeasy columns. RNA was hybridized to Agilent human 4x44kv1 arrays, dual channel, using universal reference.
Project description:Gene expression profiles were performed to compare the difference in sigmoid colon biopsies between from healthy control and patients with ulcerative colitis. Keywords: disease signature
Project description:Purpose: The objective of this study is to compare the transcriptome profile of intestinal epithelial organoids cultivated from distal colon tissue of patients with ulcerative colitis vs organoids cultivate from non-matched and otherwise healthy patient colon
Project description:Transcriptional profiling of colon epithelial biopsies from ulcerative colitis patients and healthy control donors. Study aims to survey and analyze variation from disease in different GI regions. Keywords: disease state analysis