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Series GSE48634 Query DataSets for GSE48634
Status Public on Sep 05, 2014
Title Mucosal transcriptomics implicates under expression of FAM5C in the pathogenesis of ulcerative colitis
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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 Crohn’s disease. Differential gene expression analysis was performed at each tissue location separately and results were then meta-analysed using Fisher’s 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.
 
Overall design 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.
 
Contributor(s) Smith PJ, Levine AP, Dunne J, Guilhamon P, Turmaine M, Sewell GW, Vega R, O'Shea NR, Paterson JC, Oukrif D, Beck S, Bloom SL, Novelli M, Rodriguez-Justo M, Smith AM, Segal AW
Citation(s) 25171508
Submission date Jul 09, 2013
Last update date Aug 13, 2018
Contact name Professor Anthony W Segal
E-mail(s) [email protected]
Phone +44 (0) 207 679 6175
Organization name Centre for Molecular Medicine
Department Division of Medicine
Lab Professor Segal Laboratory
Street address Rayne Building, 5 University Street
City London
ZIP/Postal code WC1E 6JF
Country United Kingdom
 
Platforms (1)
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Samples (171)
GSM1182596 Crohn's disease Ileal rectum P1
GSM1182597 Crohn's disease Ileocolonic rectum P2
GSM1182598 Crohn's disease Ileal rectum P3
Relations
BioProject PRJNA210877

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE48634_RAW.tar 26.2 Mb (http)(custom) TAR
GSE48634_non-normalized.txt.gz 30.3 Mb (ftp)(http) TXT
Processed data included within Sample table
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