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Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples.

ABSTRACT: Gene expression patterns of Crohn's disease (CD) and ulcerative colitis (UC) colonic specimens were analyzed using whole-genome microarrays. Healthy control samples were included in order to detect gene expression changes associated with CD or UC. CD and UC samples were also compared in order to identify the molecular mechanisms that distinguish both fenotypes of inflammatory bowel disease.

ORGANISM(S): Homo sapiens

PROVIDER: GSE36807 | GEO | 2013/09/23

SECONDARY ACCESSION(S): PRJNA156835

REPOSITORIES: GEO

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Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples.

Project description:Gene expression patterns of Crohn's disease (CD) and ulcerative colitis (UC) colonic specimens were analyzed using whole-genome microarrays. Healthy control samples were included in order to detect gene expression changes associated with CD or UC. CD and UC samples were also compared in order to identify the molecular mechanisms that distinguish both fenotypes of inflammatory bowel disease. Total RNA obtained from intestinal biopsies were analyzed using whole-genome microarrays.

2013-09-23 | E-GEOD-36807 | biostudies-arrayexpress

MicroRNA expression in human colon: Crohn's disease versus ulcerative colitis

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

Gene expression analysis of omental and mesenteric adipose tissue in Crohn's disease and ulcerative colitis

Project description:Our hypothesis is that in IBD patients intestinal bacteria translocation into the intra-abdominal fat depots affects adipocyte morphology and gene expression. The study aimed to study adipocyte gene expression of omental (OM) and mesenteric (MES) adipose tissue of ulcerative colitis (UC) and crohn's disease (CD). Total RNA was extracted from isolated adipocytes from omental and mesenteric adipose tissue of CD and UC patients. Microarray experiments were performed in duplicates of 4 different pools of RNAs extracted from adipocytes isolated from OM and MES of UC patients (n=5) and CD patients (n=5) respectively.

2013-05-09 | E-GEOD-46754 | biostudies-arrayexpress

Transcription profiling of peripheral blood samples from patients with Crohn's disease (CD) and Ulcerative colitis (UC) .

Project description:The whole-genome oligonucleotide microarray analysis of peripheral blood samples can contribute to the determination of distant blood markers of local pathophysiological alterations in colorectal diseases. These markers can lead to alternative screening procedures. Total RNA was extracted from peripheral blood samples of patients with Ulcerative colitis (UC) and Crohn's disease (CD) and hybridized on Affymetrix HGU133 Plus 2.0 microarrays

2009-05-19 | E-GEOD-11499 | biostudies-arrayexpress

Gene expression analysis of omental and mesenteric adipose tissue in Crohn's disease and ulcerative colitis

2013-05-09 | GSE46754 | GEO

Short Noncoding RNAs as predictive biomarkers for the development from Inflammatory Bowel Disease Unclassified to Crohn’s Disease or Ulcerative Colitis

Project description:To find predictive biomarkers for the development from inflammatory bowel disease unclassified (IBDU) to Crohn's disease(CD) or ulcerative colitis (UC), we performed short non-coding RNA profiling on IBDU patient samples at the time of diagnostic endoscopy.

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Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn's disease and healthy individuals

Project description:This study employs spectroscopy-based metabolic profiling of fecal extracts from healthy subjects and patients with active or inactive ulcerative colitis (UC) and Crohn's disease (CD) to substantiate the potential use of spectroscopy as a non-invasive diagnostic tool and to characterize the fecal metabolome in inflammatory bowel disease (IBD). Stool samples from 113 individuals (UC 48, CD 44, controls 21) were analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy (Bruker 600 MHz, Bruker BioSpin, Rheinstetten, Germany). Data were analyzed with principal component analysis and orthogonal-projection to latent structure-discriminant analysis using SIMCA-P plus 12 and MATLAB. Significant differences were found in the metabolic profiles making it possible to differentiate between active IBD and controls and between UC and CD. The metabolites holding differential power primarily belonged to a range of amino acids, microbiota-related short chain fatty acids, and lactate suggestive of an inflammation-driven malabsorption and dysbiosis of the normal bacterial ecology. However, removal of patients with intestinal surgery and anti-TNF-alpha antibody treatment eliminated the discriminative power regarding UC versus CD. This study consequently demonstrates that 1H NMR spectroscopy of fecal extracts is a potential non-invasive diagnostic tool and able to characterize the inflammation-driven changes in the metabolic profiles related to malabsorption and dysbiosis. Intestinal surgery and medication are to be accounted for in future studies, as it seems to be factors of importance in the discriminative process.

2017-02-07 | MTBLS237 | MetaboLights

Transcription profiling of CD8 T-cells predicts disease course in Crohn's disease and ulcerative colitis

Project description:The natural history of Crohn's disease (CD) and ulcerative colitis (UC) is variable. In patients with frequently-relapsing/steroid-refractory disease, sustained remission is more likely if immunomodulators are introduced earlier. However, many patients experience quiescent disease without immunomodulators, and should not be unnecessarily immunosuppressed. Previous attempts to stratify treatment from diagnosis have failed because disease course cannot be reliably predicted. We performed whole genome expression analysis of peripheral CD8 and CD4 T-cells isolated from patients with active, untreated CD or UC. Patients were prospectively managed by clinicians blinded to the microarray results. Analysis of CD8 T-cell gene-expression data revealed two distinct subgroups within each disease cohort, which did not correlate with any contemporaneous laboratory or clinical data. There was considerable overlap in the genes that were differentially expressed between the subgroups in each disease. Patients belonging to one of the subgroups (termed IBD1) experienced significantly more aggressive disease than those in the other (termed IBD2) in both diseases. This was characterised by a greater need to escalate treatment with immunomodulators or surgery in response to relapsing or chronically active disease. Furthermore, this subgroup more frequently required additional interventions due to the initial escalation failing to maintain disease remission. Similar association with disease behaviour could not be demonstrated with CD4 T-cell gene-expression analysis, nor with previously described methods of predicting outcome. Our findings demonstrate that gene-expression profiling of CD8 T-cells at diagnosis can stratify patients with CD or UC according to subsequent disease behaviour and represents a significant step towards personalised therapy.

2011-07-19 | E-MTAB-331 | biostudies-arrayexpress

Differential early pathogenic changes in human ileal gene expression in Crohn's disease and ulcerative colitis

Project description:The aim of this study is to identify early pathogenic changes in ileal gene expression that precede the development of macroscopic disease in inflammatory bowel diseases (IBDs). We focused on two IBD phenotypes that were unlikely to overlap: 1) ileal Crohn‚Äôs disease (CD) patients undergoing initial ileocolic resection of diseased ileum; and 2) ulcerative colitis (UC) patients undergoing total colectomy. The Control patients were those patients without IBD undergoing initial right hemicolectomy or total colectomy. In order to identify early pathogenic changes in the human ileum in inflammatory bowel diseases, we analyzed 99 two-color whole human genome expression profiles (Agilent 4410A) of a test human ileal cRNA probe vs. a common reference human ileal RNA from a Control patient (N17). A minimum of four biopsies were taken from the macroscopically disease-unaffected proximal ileal margin of freshly resected specimens from 47 ileal Crohn's disease patients undergoing initial ileocolic resection, 27 ulcerative colitis patients undergoing total colectomy and 25 Control patients undergoing either right hemicolectomy or total colectomy. The test and common reference probes were synthesized using the Agilent Low Input Linear Amplification Kit. Hybridization was carried out in DNA hybridization chambers, washed and scanned on an Axon GenePix 4000B scanner. The preprocessing, filtering and normalization of the array data was carried out using the R package LIMMA.

2010-09-26 | E-GEOD-24287 | biostudies-arrayexpress

Differential pathogenic Th17 profile in mesenteric lymph nodes of Crohn's disease and ulcerative colitis patients

Project description:The drug targets IL23 and IL12 regulate pathogenicity and plasticity of intestinal Th17 cells in Crohn’s disease (CD) and ulcerative colitis (UC), the two most common inflammatory bowel diseases (IBD). However, studies examining Th17 dysregulation in mesenteric lymph nodes (mLNs) of these patients are rare. We showed that in mLNs, CD could be distinguished from UC by increased frequencies of CCR6+CXCR3-RORg+Tbet-CD4+ (Th17) memory T cells enriched in CD62Llow effector memory T cells (TEM), and their differentially expressed molecular profile. Th17 TEM cells (expressing IL17A, IL17F, RORC and STAT3) displayed a higher pathogenic/cytotoxic (IL23R, IL18RAP, and GZMB, CD160, PRF1) gene signature in CD relative to UC, while non-pathogenic/regulatory genes (IL9, FOXP3, CTLA4) were more elevated in UC. In both CD and UC, IL12 but not IL23, augmented IFNg expression in Th17 TEM and switched their molecular profile towards an ex-Th17 (Th1*)-biased transcriptomic signature (increased IFNG, and decreased TCF7, IL17A), suggesting that Th17 plasticity occurs in mLNs before their recruitment to inflamed colon. We propose that differences observed between Th17 cell frequencies and their molecular profile in CD and UC might have implications in understanding disease pathogenesis, and thus, therapeutic management of patients with IBD.

2019-05-17 | GSE131359 | GEO

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