Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA295143 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To evaluate the effects of induction treatment with an anti-TNF, golimumab (GLM), on gene expression in patients with moderately to severely active ulcerative colitis (UC), we performed mRNA microarray studies on colon biopsies from patients who participated in the PURSUIT-SC induction study and additional samples from 21 healthy subjects. Comparisons were conducted between baseline UC (n=87) and healthy (n=21), and week 6 (n=75) vs. baseline (n=87) prior to treatment. A significant difference was observed in mRNA expression between UC and healthy. Significant expression modulations were identified in patients who responded to GLM at week 6, but not GLM-treated non-responders or placebo-treated subjects.
2018-12-03 | GSE92415 | GEO
Project description:The samples are a part of a study aiming at diagnosing ulcerative colitis from genome-wide gene expression analysis of the colonic mucosa. Colonic mucosal samples were collected as endoscopic pinch biopsies from ulcerative colitis patients and from control subjects. Samples with and without macroscopic signs of inflammation were collected from the patients. Experiment Overall Design: The series contain eight UC samples with macroscopic signs of inflammation, 13 UC smaples without macroscopic signs of inflammation, five control subjects.
2008-06-20 | E-GEOD-9452 | biostudies-arrayexpress
Project description:Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission. We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls. Ulcerative colitis patients and non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria for UC patients were: age between 18 and 65, diagnosis of UC established at least 6 months before inclusion and exclusion of concomitant infection. Active disease was defined by endoscopic and histologic score: Mayo sub score >=2 and MATTS >=3 respectively . Inactive disease was also defined by endoscopic and histologic score: Mayo sub score =0 and MATTS <=2 respectively, and a remission state for a minimum of 5 month prior to biopsy collection, and remained inactive for at least 6 months after. Uninvolved mucosa from patients with active UC was defined as a colonic segment with completely normal endoscopic appearance, normal histology, and absence of any previous evidence of active disease. Finally, a total of 43 biopsies were analyzed: 13 healthy controls, 8 inactive UC, 7 non-involved active UC and 15 involved active UC.
2012-11-09 | E-GEOD-38713 | biostudies-arrayexpress
Project description:Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission. We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls.
2012-11-09 | GSE38713 | GEO
Project description:Gene expression profiles were performed to compare the difference in sigmoid colon biopsies between from healthy control and patients with ulcerative colitis. Experiment Overall Design: Total RNA was isolated sigmoid biopdy from 5 healthy and 6 UC patients. Pooled 5 ug total RNA equally for each group was used and followed the Affymetrix standard protocol for microarray.
2009-03-07 | E-GEOD-10791 | biostudies-arrayexpress
Project description:Microarrays were used to analyze the gene expression in endoscopic-derived intestinal mucosal biopsies from patients with inflammatory bowel disease (IBD) and controls Mucosal biopsies were obtained at endoscopy from the colon of 97 ulcerative colitis (UC), 8 Crohn's disease (CD) patients and 11 controls. The biopsies were taken at the most affected sites but at a distance of ulcerations. Disease activity was endoscopically assessed. Total RNA extracted from mucosal biopsies was used to analyze mRNA expression via Affymetrix Human Gene 1.0 ST arrays
2015-05-27 | E-GEOD-59071 | biostudies-arrayexpress
Project description:Analysis of miRNA expression in colon biopsies from Crohn's disease (CD), ulcerative colitis (UC), and non-inflammatory bowel disease (IBD) control subjects.
2014-12-31 | GSE53867 | GEO
Project description:Patient-derived intestinal organoids provide an excellent tool to unravel mechanisms underlying ulcerative colitis (UC). Fresh biopsies, to isolate crypts and culture organoids, were obtained from both inflamed and non-inflamed regions from eight patients with active UC (Mayo endoscopic subscore ≥2), and from eight non-IBD controls.To address the inflammatory character of ex vivo organoids, we compared the transcriptome of biopsies, crypts and organoids derived from inflamed, and non-inflamed regions and aimed to (re-)induce inflammation ex vivo.
2020-10-08 | E-MTAB-7860 | biostudies-arrayexpress
Project description:Background and aims: Mucosal abnormalities are potentially important in the primary pathogenesis of ulcerative colitis (UC). We investigated the mucosal transcriptomic expression profiles of biopsies from patients with UC and healthy controls (HC), taken from macroscopically non-inflamed tissue from the terminal ileum and three colonic locations with the objective of identifying abnormal molecules that might be involved in disease development. Methods: Whole-genome transcriptional analysis was performed on intestinal biopsies taken from 24 UC, 26 HC and 14 patients with CrohnM-bM-^@M-^Ys disease. Differential gene expression analysis was performed at each tissue location separately and results were then meta-analysed using FisherM-bM-^@M-^Ys method. Significantly differentially expressed genes were validated using qPCR. Gene location within the colon was determined using immunohistochemistry, subcellular fractionation, electron and confocal microscopy. DNA methylation was quantified by pyrosequencing. Results: Seven probes were abnormally expressed throughout the colon in UC patients with Family with sequence similarity member 5 C (FAM5C) being the most significantly underexpressed. Attenuated expression of FAM5C in UC was independent of inflammation, unrelated to phenotype or treatment, and remained low at rebiopsy approximately 23 months later. FAM5C is localised to the brush border of the colonic epithelium and expression is influenced by DNA methylation within its promoter. Conclusion: Genome-wide expression analysis of non-inflamed mucosal biopsies from UC patients identified FAM5C as significantly under-expressed throughout the colon in a major sub-set of patients with UC. Low levels of this gene could predispose to or contribute to the maintenance of the characteristic mucosal inflammation seen in this condition. Total RNA was extracted from the intestinal biopsies taken from macroscopically normal mucosa in the rectum, descending colon, ascending colon and terminal ileum in clinically quiescent Ulcerative colitis and Crohn's disease patients and compared to healthy controls. Normalized data for 26,261 probes out of 47,323 only. Criteria for inclusion not specified. The non-normalized matrix contains the complete non-normalized data for all probes.
2014-09-05 | E-GEOD-48634 | biostudies-arrayexpress
Project description:Dysregulated protease activity is often implicated in the initiation of inflammation and immune cell recruitment in gastrointestinal inflammatory diseases. Using N-terminomics/TAILS (terminal amine isotopic labeling of substrates), we compared proteases, along with their substrates and inhibitors, between colonic mucosal biopsies of healthy patients and those with ulcerative colitis (UC). Among the 1,642 N-termini enriched using TAILS, increased endogenous processing of proteins was identified in UC compared to healthy patients. Changes in the reactome pathways for proteins associated with metabolism, adherens junction proteins (E-cadherin, liver-intestinal cadherin, catenin alpha-1 and catenin delta-1) and neutrophil degranulation were identified between the two groups. Increased neutrophil infiltration and distinct proteases observed in ulcerative colitis may result in extensive break down, altered processing or increased remodeling of adherens junctions and other cellular functions. Analysis of the proteolytic preferred cleavage sites indicated that the majority of proteolytic activity and processing comes from host proteases, but that key microbial proteases may also play a role in maintaining homeostasis. Thus, the identification of distinct proteases and processing of their substrates improves the understanding of dysregulated proteolysis in normal intestinal physiology and ulcerative colitis.
2019-09-08 | PXD014479 | Pride