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Colon biopsies from Crohns patients and healthy controls

ABSTRACT: The aim of this study was to investigate differential intestinal gene expression in patients with Crohn's disease (CD) and controls. 172 biopsies from CD and control subjects were studied. Endoscopic biopsies were taken at ileocolonoscopy from five specific anatomical locations including the terminal ileum for RNA extraction.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20881 | GEO | 2010/07/19

SECONDARY ACCESSION(S): PRJNA124721

REPOSITORIES: GEO

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Colon biopsies from Crohns patients and healthy controls

Project description:The aim of this study was to investigate differential intestinal gene expression in patients with Crohn's disease (CD) and controls. 172 biopsies from CD and control subjects were studied. Endoscopic biopsies were taken at ileocolonoscopy from five specific anatomical locations including the terminal ileum for RNA extraction. Biopsies from one of four anatomic locations, from healthy controls and treated (with non-biologic standard of care) or untreated CD patients.

2010-07-19 | E-GEOD-20881 | biostudies-arrayexpress

Expression data from intestinal mucosa of patients with CD under anti-TNF-alpha therapy.

Project description:Crohn's Disease (CD) is a chronic inflammatory disease of the intestinal tract. We performed a whole-genome transcriptional analysis using colonic biopsies from CD patients before and after anti-TNF-α therapy. Involved colonic samples from Crohn's disease patients and healthy colonic samples from non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria for CD patients were: age between 18 and 70, diagnosis of CD established at least 4 months before inclusion and exclusion of concomitant infection. Active disease was defined by endoscopic and clinical score: endoscopic active disease was defined as a CD endoscopic index of severity (CDEIS) of 5 or more and the presence of large ulcers (> 0.5 cm diameter) in at least one of the explored segments. Clinical activity was defined as a CD activity index (CDAI) above 150. Finally, a total of 39 biopsies were analyzed: 17 healthy controls, 10 active CD without anti-TNF therapy, 5 active CD with anti-TNF therapy (non-responders) and 7 inactive CD with anti-TNF therapy (responders).

2014-04-08 | E-GEOD-52746 | biostudies-arrayexpress

Microarray gene expression analysis of pinch biopsies from terminal ileum of patients with active and inactive Crohn’s disease and healthy controls

Project description:Biopsies from six individuals of each of the categories active CD (CDA), inactive CD (CD) and healthy controls (N) were analyzed for gene expression using microarray. The biopsies were obtained by ileo-colonoscopy and snap-frozen in nitrogen before RNA-isolation. A gastrointestinal pathologist classified the biopsies into normal, chronic active or chronic inactive inflammation based on Hematoxylin-Eosin stain of tissue sections from adjacent biopsies. Samples with discrepancy between endoscopic and histologic diagnoses were excluded from the final analysis, and uploaded with "NaN". The patients with chronic inactive inflammation all previously had verified CD of the terminal ileum. Patients coming to endoscopy for other reasons than IBD and with normal endoscopic and histological findings served as controls.

2019-05-01 | E-MTAB-6593 | biostudies-arrayexpress

Microarray analysis of colonic mucosa biopsies in patients with inflammatory bowel disease

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

Characterization of H3K4me3 histone modifications in intestinal epithelial cells among healthy controls and newly-diagnosed pediatric Crohn's disease patients.

Project description:We report profiling of H3Kme3 histone modifications in intestinal epithelial cells from ileal endoscopic biopsies obtained from healthy controls and newly-diagnosed Crohn's disease (CD). We identified 1066 shared sites, corresponding to 1038 genes with increased H3K4me3 in CD, and 539 sites corresponding to 548 genes with reduced H3K4me3 in CD.

2018-10-30 | GSE117889 | GEO

Gene expression analysis in gut biopsies of Crohn's Disease patients and patients with Spondylarthropathy

Project description:A focussed microarray chip was constructed specifically for studying basal colonic gene expression in patients with Spondyloarthropathy (SpA) and Crohn's disease (CD) (ref: PMID 16476712). These focus microarrays were used 1) to study common changes in gene expression between SpA and CD, providing early markers in the follow-up study of patients with SpA and particularly these patients that evolve into clinically overt CD; and 2) to identify new candidate genes for CD by integrating gene expression data with genetic information. Keywords: Crohn's Disease, Spondylarthropathy, biopsies

2010-05-01 | GSE14442 | GEO

Transcriptomic profile of intestinal epithelial cells obtained from ileal endoscopic biopsies from newly-diagnosed, pediatric Crohn's disease patients and healthy controls.

Project description:Purpose: To uncover differentially-regulated transcripts and pathways/biological processes in newly-diagnosed, pediatric Crohn's disease in comparison to healthy controls. Methods: Intestinal epithelial cells were dissociated from ileal endoscopic biopsies, and stored at -80C in RNAlater. The polyA RNA fraction was purified, and single-end, 50 bp reads were sequenced and aligned to the Hg19 genome using the TopHat2 aligner. Differential analysis was performed using Bioconductor packages including edgeR, where significance was defined as p<0.05 and fold change>2. Results: We obtained 15788 reasonably-expressed transcripts that were included in differential analyses. Conclusions: Our study characterizes the dysregulation of intestinal epithelial cells in treatment-naïve Crohn's disease using RNA sequencing for transcriptomic profile of cells obtained through ileal endoscopic biopsies.

2018-10-30 | GSE117875 | GEO

Transcription profiling of human ileum and colonic tissues from patients with Crohns disease or ulcerative colitis

Project description:Samples for microarray analysis were derived from terminal ileum and colonic tissues from probands with Crohn's disease and Ulcerative Colitis and control patients, respectively. IBD tissue biopsies from non-inflamed regions 10 cm distant from pathological areas were selected. To minimize inter-individual differences in gene expression and to enrich for IBD-specific transcriptional events, 2.5 Âµg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling.

2007-08-03 | E-GEOD-1152 | biostudies-arrayexpress

Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies:

Project description:Ulcerative colitis (UC) and Crohn’s disease (CD) are inflammatory bowel diseases (IBD) with variable, overlapping clinical features and complex pathophysiologies. To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies to estabolish 36 expression profiles, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls. Keywords: RNA

2007-03-01 | GSE6731 | GEO

Gene expression analysis in gut biopsies of Crohn's Disease patients and patients with Spondylarthropathy

2010-05-01 | E-GEOD-14442 | biostudies-arrayexpress

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