Transcription profiling of mucosa from human patients with irritable bowel syndrome or ulcerative colitis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Jorgen Olsen
PROVIDER: E-GEOD-2461 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:IBS: Patients who have undergone a diagnostic program for gastrointestinal symptoms and where the diagnosis irritable bowel syndrome was reached. UC: Patients with well-diagnosed ulcerative colitis Keywords: other
2005-04-01 | GSE2461 | GEO
Project description:The samples are a part of a study aiming at diagnosing ulcerative colitis from genome-wide gene expression analysis of the colonic mucosa. Colonic mucosal samples were collected as endoscopic pinch biopsies from ulcerative colitis patients and from control subjects. Samples with and without macroscopic signs of inflammation were collected from the patients. Experiment Overall Design: The series contain eight UC samples with macroscopic signs of inflammation, 13 UC smaples without macroscopic signs of inflammation, five control subjects.
2008-06-20 | E-GEOD-9452 | biostudies-arrayexpress
Project description:Objective Crohn’s Disease (CD) and Ulcerative Colitis (UC) are chronic inflammatory diseases of the gastrointestinal tract. Reliable diagnosis of these diseases requires a comprehensive examination of the patient, which include invasive endoscopy. This study assesses whether non-invasive LC-MS/MS based analysis of microbial and human proteins from feces may support the diagnosis of the diseases. Design In order to mimic a representative clinical background for this study, we investigated 17 healthy controls, 11 CD patients, 14 UC patients, also 13 Irritable Bowel Disease (IBS) patients, 8 Colon Adenoma (CA) patients, and 8 Gastric Carcinoma (GCA) patients. The proteins were extracted from the fecal samples with liquid phenol in a ball mill. Subsequently, the proteins were digested tryptically to peptides and analyzed by liquid chromatography coupled to an Orbitrap MS/MS. For protein identification and interpretation of taxonomic and functional results, the MetaProteomeAnalyzer software and the UniProtKB/SwissProt database and several metagenomes from human fecal samples were used. Results Cluster analysis and ANOSIM show a separation of healthy controls from patients with CD and UC as well as from patients with GCA. Among others, UC and CD correlated with an increase of neutrophil extracellular traps and immunoglobulins G (IgG) as well as a decrease of IgA. A specific marker metaprotein for CD was an increase of the human enzyme sucrose-isomaltase. IBS and CA patient’s fecal metaproteome showed only minor alterations. Conclusion Metaproteome analysis distinguished between patients with UC, CD and healthy controls and is therefore useful as a non-invasive tool for routine diagnostics in hospitals.
2019-03-11 | PXD010371 | Pride
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:A role for immunoproteasome in the regulation of intestinal permeability has been previously suggested both in mice during water avoidance stress (WAS) and in patients with irritable bowel syndrome (IBS). We thus aimed (i) to evaluate the colonic proteome in wild-type (wt) and β2i immunoproteasome subunit knock-out (β2i-/-) mice during WAS and (ii) to investigate the colonic expression of 49 ubiquitinated-proteins in diarrhea-predominant IBS patients (IBS-D).
2018-12-05 | PXD011199 | Pride
Project description:The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease pathogenesis has been difficult due to the apparent disconnect between animal and human studies and a lack of an integrated multi-omics view in the context of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases.
2020-03-13 | GSE146853 | 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:We report ileum gene expression of 37 controls and 158 patients with either Crohn's disease (n=112), ulcerative colitis (n=44), unclassifed IBD (1), or IBS (1). We contrast gene expression in African American (n=104) versus white (n=25) CD and UC patients.
2020-04-15 | GSE137344 | GEO
Project description:The role of environmental factors and gender disparities as determinants of health is incontrovertible. In the digestive sphere, it is noteworthy that one of the most prevalent diseases such as irritable bowel syndrome (IBS) has a predominance in females. The origin of IBS is related to mucosal microinflammation phenomena, psychosocial stress, and in the last years, alterations in gut microbiota. Recent observations from our group in healthy subjects, demonstrate that both chronic psychosocial stress, and female gender per se determine a significant intestinal epithelial barrier dysfunction in response to intercurrent stimuli, which, in susceptible individuals, could result in an early stage in the development of more lasting changes and the onset of clinical manifestations of IBS. Although the intimate mechanisms involved in stress-induced intestinal pathophysiology are not well known, diverse studies suggest that gut microbiota alteration, through epigenetic modifications of the main stress-mediators could be one of them. However, solid scientific evidence demonstrating the influence of stress on gut microbiota and epigenetics of the main stress-mediators is missing. Therefore, we want to investigate and characterize gender-dependent epigenetic modifications involved in intestinal barrier dysfunction in response to acute stress. The identification of gender-dependent abnormal epigenetic patterns related to female gender dysfunction can make a breakthrough in the understanding of the pathophysiology of the regulation of intestinal permeability, and promote positive diagnostic and therapeutic future progress in IBS.
2024-02-15 | E-MTAB-10158 | biostudies-arrayexpress
Project description:To investigate the molecular pathological mechanisms of irritable bowel syndrome with diarrhea (IBS-D) and elucidate the effects of acupuncture on IBS-D colonic mucosa protein abundance in rats, a label-free high-throughput liquid chromatography-tandem mass spectrometry (LC-MS)-based proteomics analysis was used to survey the global changes of colonic mucosa proteins between different groups. A Nano flow Ultimate 3000 HPLC (Dionex Corp, Sunnyvale, CA) coupled online to a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) was used in this project.
2022-10-14 | PXD025558 | Pride