Gene expression analysis of rectal mucosa in chronic irritable bowel syndrome (IBS) compared to healthy volunteers (HV)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE36701 | GEO | 2012/07/13
SECONDARY ACCESSION(S): PRJNA153623
REPOSITORIES: GEO
Similar Datasets
Project description:An investigation of gene expression changes in rectal biopsies from donors with IBS compared to controls to begin to understand this complex syndrome. To further investigate differences between IBS groups (constipation and diarrhoea predominant) (part1) and how IBS relates to bacterial infection (part2) with biopsies taken 6 months after Campylobacter jejuni infection. Part1: 18 Constipation predominant IBS subjects (IBS-C) and 27 diarrhoea predominant IBS subjects (IBS-D) compared to 21 healthy volunteers (HV). Part2: 21 Campylobacter jejuni infection (PIBD, PIBS, PINIBS) compared to 19 healthy volunteers (HV). PIBD = post Campylobacter infection with IBS (within 6 months) PIBS = post infection IBS (unknown time point and organism) PINIBS = post Campylobacter infection with no resulting IBS
2012-07-12 | E-GEOD-36701 | biostudies-arrayexpress
Project description:Micro-inflammation and gut dysfunction are features of diarrhea-irritable bowel syndrome (d-IBS) patients, although the underlying interacting molecular mechanisms remain mostly unknown. Therefore, we aimed to identify critical networks and signaling pathways active in chronic diarrhea-associated inflammation. Experiment Overall Design: Healthy volunteers and d-IBS patients were studied. Jejunal biopsies were subjected to chip analysis (Affymetrix Human Genome U133 Plus 2.0 GeneChips).
2009-02-21 | E-GEOD-14841 | biostudies-arrayexpress
Project description:We conducted a microarray study of sigmoid mucosal gene expression in pilot sample of Rome III+ IBS patients and age and sex-matched HCs. This sample was balanced by sex, free of active psychiatric disease and had limited use of medications. Rome III+ IBS patients and HCs ages 18-55 were recruited primarily by community advertisement. Bowel habit subtypes (IBS with diarrhea (IBS-D), constipation (IBS-C) and mixed pattern (IBS-M)) were based on the Rome III criteria. The diagnosis was confirmed by a clinician with expertise in IBS. Rome III+a IBS patients and HCs ages 18-55 were recruited primarily by community advertisement. Bowel habit subtypes (IBS with diarrhea (IBS-D), constipation (IBS-C) and mixed pattern (IBS-M)) were based on the Rome III criteria. The diagnosis was confirmed by a clinician with expertise in IBS. HCs had no personal or family history of IBS or other chronic pain conditions. Additional exclusion criteria for all subjects included: infectious or inflammatory disorders, active psychiatric illness over the past 6 months as assessed by structured clinical interview for the DSM-IV (MINI),b use of corticosteroids in the past six months, use of narcotics, antidepressants or other medications that could affect neuroendocrine function in the past two months, or current tobacco or alcohol abuse. Participants were compensated. Our goal was to evaluate women during the follicular phase or days 4-14 of their menstrual cycle if on oral contraceptive pills. Phase was determined by date of last menstrual period and progesterone levels. The study was approved by the UCLA Institutional Review Board, and all subjects signed a written informed consent prior to start of study. IBS symptom severity over the prior week was assessed with a numeric rating scale (0-20).c Current anxiety and depression symptoms were measured with the Hospital Anxiety and Depression (HAD) scale.d Sigmoid biopsies (30cm from the anal verge) were obtained by flexible sigmoidoscopy following tap water enemas. Specimens were immediately flash frozen in liquid nitrogen. RNA was extracted with TRIzol. Sigmoid biopsies (30cm from the anal verge) were obtained by flexible sigmoidoscopy following tap water enemas. Specimens were immediately flash frozen in liquid nitrogen. Differential expression analysis was done on mRNA only (\\ormalized_Unfiltered_mRNAonly.txt\\) using limma[1]. Weighted gene coexpression network analysis (WGCNA[2]) was done using all targets after removing those on X and Y chromosomes and filtered by mean raw signal >200. 1. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3. 2. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.\
2018-06-03 | E-MTAB-5811 | biostudies-arrayexpress
Project description:Purposes: To investigate the epigenetic mechanism of IBS-D(Irritable Bowel Syndrome with Diarrhea) by tRF & tiRNA sequencing in intestinal biopsies of IBS-D patients and healthy volunteers Methods: Five IBS-D and five healthy volunteers were screened, and biopsies were taken under colonoscopy. Small RNA sequencing was performed on Illumina NexSeq instrument Results:If P < 0.05, fold change > 1.5 as the cutoff, there were 14 up-regulated tRFs & tiRNAs and 14 down-regulated tRFs & tiRNAs. Conclusions:There were 14 up-regulated tRFs & tiRNAs and 14 down-regulated tRFs & tiRNAs in intestinal tissues of IBS-D .
2023-11-04 | GSE166405 | GEO
Project description:A subset of post-infection irritable bowel syndrome (PI-IBS) patients have elevated, or high fecal proteolytic activity (PA). Fecal PA has been shown to correlate with increased symptom severity as well as lower quality of life scores, increased fecal output and increased intestinal permeability. To address the underlying mechanisms of barrier disruption as a consequence of high fecal PA, colonic biopsies were collected from healthy individuals PI-IBS patients (n=11). Individuals diagnosed with PI-IBS were further divided in to 2 subgroups, high PA and low PA as defined by the PA in matched fecal samples. RNA was extracted from the biopsies for bulk RNA sequencing to understand transcriptional differences between healthy and high PA PI-IBS patients as well as high PA and Low PA PI-IBS patients.
2021-12-31 | GSE168759 | GEO
Project description:Micro-inflammation and gut dysfunction are features of diarrhea-irritable bowel syndrome (d-IBS) patients, although the underlying interacting molecular mechanisms remain mostly unknown. Therefore, we aimed to identify critical networks and signaling pathways active in chronic diarrhea-associated inflammation. Keywords: Comparison of gene expression
2009-02-14 | GSE14841 | GEO
Project description:Patients with chronic illnesses such as Irritable Bowel Syndrome (IBS) or Inflammatory Bowel Disease (IBD) often have reduced quality of life. IBS is characterized by abdominal pain/discomfort associated with altered bowel function, such as diarrhea or constipation, without gross structural changes or inflammation [1]; IBD is characterized by gross inflammation in the gastrointestinal (GI) tract which can result in symptoms such as abdominal pain, cramping, diarrhea and bloody stools. IBS and IBD can profoundly affect quality of life and are influenced by stress and resiliency.The impact of mind-body interventions (MBIs) on IBS and IBD patients has not previously been examined. In this study IBS and IBD patients were enrolled in a 9-week relaxation response based mind-body group intervention (RR-MBI), focusing on elicitation of the RR and cognitive skill building. We performed Peripheral blood transcriptome analysis to identify genomic correlates of the RR-MBI.
2015-03-12 | GSE66824 | GEO
Project description:Irritable bowel syndrome (IBS) is a highly prevalent disorder of the gastrointestinal tract characterized by abdominal pain, bloating, and disturbed bowel function. Here we report on the analysis of microarray expression profiles of sigmoid colon mucosal biopsies from IBS patients and healthy control subjects. Two samples were collected from each individual. From 10 individuals, a third sample was collected 2-3 months after the initial collection. The repeat samples were used to assess the robustness of the expression profiles over different locations within the colon and over time. This analysis revealed a number of differentially expressed genes in IBS patients, which point to functional alterations of specific components of the host defence system and the immune response. This is in support of an important role for peripheral gastrointestinal changes underlying the aetiology of IBS. Two gene probe sets with the most strikingly increased expression in mucosal colon biopsies of IBS patients represent a gene that is, as yet, uncharacterised (DKFZP564O0823). We propose to rename this gene IBS1. We also report on the identification of specific sets of gene probes on the microarray, so-called molecular signatures, which enable the distinction of IBS patients from healthy controls. The expression profiles in IBS are consistent across different sites within the sigmoid colon and are stable over time.
2007-11-24 | E-TABM-176 | biostudies-arrayexpress
Project description:Irritable bowel syndrome (IBS) patients often experience meal associated symptoms. Our objective was to determine small intestinal mechanisms of lipid-induced symptoms and rectal hypersensitivity in IBS based on RNA-seq.
2022-02-28 | GSE166869 | GEO
Project description:Increased numbers of mast cells and their products have been linked to symptom onset and severity in patients with chronic diarrhea and abdominal pain. Although mast-cell inhibition ameliorates clinical manifestations and reduces mucosal inflammation, underlying molecular mechanisms remain unknown. Experiment Overall Design: Diarrhea-irritable bowel syndrome (d-IBS) patients were studied at baseline, or 6 months after natural evolution (control) or oral cromoglycate treatment. Jejunal biopsies were subjected to chip analysis (Affymetrix Human Genome U133 Plus 2.0 GeneChips).
2009-02-21 | E-GEOD-14842 | biostudies-arrayexpress