{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Thomas Langmann"],"disease":["Crohn's disease"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-1152"],"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 µg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Processing - 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. All diagnoses of IBD patients were based on classical clinical features, radiological, endoscopic and laboratory findings. IBD tissue biopsies from non-inflamed regions 10 cm distant from pathological areas were selected and sampled by a specialized gastroenterologist. To preserve the transcriptional profile of tissue specimens, biopsies were immediately stabilized in RNAlater solution and kept at â€\"80°C until isolation of RNA. Total RNA was extracted from the tissue biopsies according to the manufacturer's instructions using the RNeasy Protect Midi Kit (Qiagen). 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 to generate cRNA. Gene expression profiles were determined using Affymetrix HG-U133A and HG-U133B Gene Chips. Array scanning and expression analysis was performed using Microarray Analysis Suite 5.0 software. Each array was scaled to a target intensity of 100 (scaling to all probesets). Lot batch ="],"figure_sub":["MIAME Score","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Loss of intestinal mucosa integrity is an important factor in the pathogenesis of inflammatory bowel disease (IBD). The aim of this study was to characterize expression changes and allelic variants of genes related to intestinal epithelial barrier function in this disease. Therefore, ileal and colonic mucosal biopsies from nonaffected regions of patients with ulcerative colitis (UC) and Crohn's disease (CD), as well as non-IBD probands, were subjected to Affymetrix DNA-microarray analysis. Real-time reverse transcription polymerase chain reaction was used for verification in larger IBD sample numbers. Disturbed mRNA expression was identified for several mucin genes in both disease groups and tissues. A significant downregulation in the colon was obtained for MUC2 in CD and MUC12 in CD and UC. Expression analysis of all dysregulated mucins in a broad human tissue panel revealed dominant epithelial tissue-specific transcription. In silico analysis of the regulatory regions of these mucins indicated nuclear factor kappaB (NFkappaB) binding sites in each promoter. Furthermore, NFkappaB was overrepresented in mucin promoters and a component of a specific combination of transcription factors (composite module). In vivo stimulation experiments in the adenocarcinoma cell line LS174T showed inducible mucin expression by the cytokines tumor necrosis factor-alpha and transforming growth factor-beta, which could be blocked by NFkappaB signaling inhibitors. Allelic discrimination screening obtained statistically significant associations for the MUC2-V116M (P = 0.003) polymorphism with CD and for MUC4-A585S (P = 0.025), as well as MUC13-R502S (P = 0.0003) with UC. These data suggest that the disturbed expression of mucin genes and the connection to the NFkappaB pathway may influence the integrity of the intestine and therefore contribute to the pathophysiology of IBD."],"study_type":["transcription profiling by array"],"species":["Homo sapiens"],"pubmed_title":["Aberrant intestinal expression and allelic variants of mucin genes associated with inflammatory bowel disease"],"pubmed_authors":["Thomas Langmann","Moehle C, Ackermann N, Langmann T, Aslanidis C, Kel A, Kel-Margoulis O, Schmitz-Madry A, Zahn A, Stremmel W, Schmitz G"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling of human ileum and colonic tissues from patients with Crohns disease or ulcerative colitis","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 µg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling.","dates":{"release":"2007-08-03T00:00:00Z","modification":"2023-08-03T01:43:14.785Z","creation":"2022-03-15T07:42:40.208Z"},"accession":"E-GEOD-1152","cross_references":{"pubmed":["17058067"],"EFO":["EFO_0002768"],"doi":["17058067"]}}