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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE52746 | GEO | 2014/04/08

SECONDARY ACCESSION(S): PRJNA229963

REPOSITORIES: GEO

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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

Expression data from antigen-specific CD4+T cells from peripheral blood of patietns with CD and healthy controls.

2016-07-27 | GSE70469 | GEO

Expression data from antigen-specific CD4+T cells from peripheral blood of patietns with CD and healthy controls.

Project description:Crohn's Disease (CD) is a chronic inflammatory disease of the intestinal tract. We performed a whole-genome transcriptional analysis using sorted commensal antigen-specific CD4+T cells from peripheral blood of CD patients and from healthy controls. Peripheral blood sorted FlaX, Fla2 and YidX-specific CD4+T cells from Crohn's disease patients and 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.

2016-07-27 | E-GEOD-70469 | biostudies-arrayexpress

Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC

Project description:Colon gene expression in human IBD. The three major clinical subsets of Inflammatory Bowel Disease (IBD) include colon-only Crohn's Disease (CD), ileo-colonic CD, and Ulcerative Colitis (UC). These experiments tested differential colon gene expression in these three types of IBD, relative to healthy control samples, and the local degree of mucosal inflammation as measured by the CD Histological Index of Severity (CDHIS). Colon biopsy samples were obtained from IBD patients at diagnosis and during therapy, and healthy controls. The global pattern of gene expression was determined using GeneSpring software, with a focus upon candidate genes identified in a recent genome wide association study in pediatric onset IBD. Data suggested that two of these candidate genes are up regulated in pediatric IBD, partially influenced by local mucosal inflammation. These experiments tested differential colon gene expression in healthy, CD, and UC samples for candidate genes identified in a recent pediatric onset IBD genome wide association study. Keywords: Single time point in CD and UC and healthy controls.

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Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC

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Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease

Project description:This study aimed at genome-wide gene expression analysis of colonic biopsies from confirmed cases of intestinal tuberculosis (ITB) and Crohn's disease (CD) in comparison to controls. Further, to evaluate the role of T regulatory cells, Foxp3 mRNA expression was quantified in serum as well as colonic biopsies of patients with intestinal tuberculosis, Crohn's disease and controls. Paired samples, i.e. serum and colonic biopsies, were taken from 33 study subjects, which included patients with ITB and CD, and controls. RNA extraction was done and stringent quality checks performed. Human whole genome gene expression microarray analysis was performed on the Illumina HumanWG-6 Bead Chip with six total RNA samples of the 3 groups in duplicates. Real-time PCR for FOXP3 mRNA expression was analyzed in serum samples (4-CD, 5-ITB, 4-controls) and colonic biopsy samples (4-CD, 5-ITB, 4-controls).

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Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease

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Developing biomarkers incorporating high throughput RNA, DNA, small RNA sequencing and protein expression in Inflammatory Bowel Disease using formalin-fixed, paraffin-embedded (FFPE) tissue samples.

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

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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.

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