Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA305704 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The transcriptional signature of mucosa of patients with ulcerative colitis (UC) in remission reveals long-lasting changes in the epithelial barrier which persist once the inflammatory response has resolved. In order to investigate if these changes are caused by primary defects in the epithelial cells, we generated in vitro epithelial organoid cultures (EpOCs) from colon samples of non-IBD controls and UC patients. After induction of differentiation, total RNA was extracted from both EpOCs and differentiated EpOCs (d-EpOCs) and used for hybridization on Affymetrix microarray.
2016-11-02 | GSE75916 | GEO
Project description:Colon epithelial organoid lines were developed from pediatric patients with endoscopically active ulcerative colitis, inactive ulcerative colitis, and those without endoscopic or histologic evidence of colon inflammation (non-IBD controls). From each organoid line, RNA was processed from undifferentiated organoids (spheroids) and parallel organoids differentiated for 3 days (colonoids). Paired-end sequencing of poly-A enriched RNA libraries was carried out on the Illumina NovaSeq PE150 platform and the reads were aligned to the human reference hg38 genome. To determine differentially expressed genes, transcripts with Log2FC ≥ ±1, FDR P ≤ 0.1 were considered statistically significant.
2025-09-19 | GSE276170 | GEO
Project description:Altered function of the intestinal epithelium has been considered to play a key role in CD pathogenesis, however exact mechanisms that contribute towards lifelong relapsing mucosal inflammation remain ill defined. DNA methylation (DNAm) is a key epigenetic mechanism known to determine cellular identity by regulating gene transcription with alterations increasingly being implicated in IBD pathogenesis. We generated 312 intestinal epithelial organoids (IEOs) from mucosal stem cells obtained from 168 patients diagnosed with CD, non-IBD/healthy controls and Ulcerative colitis (UC). Genome wide epigenetic profiling of IEOs and primary purified epithelium revealed highly stable, CD associated loss of DNAm in MHC-I related genes which correlated with increased gene expression. Related Single Cell Portal accession number: SCP1884 Related Gene Expression Omnibus accession numbers: GSE57945, GSE75214
2024-03-31 | E-MTAB-12841 | biostudies-arrayexpress
Project description:We used microarrays to identify mucosal gene signatures predictive of response to infliximab (IFX) in patients with inflammatory bowel disease (IBD) and to gain more insight into the pathogenesis of IBD. Keywords: drug response and treatment effect Mucosal biopsies were obtained at endoscopy in actively inflamed mucosa from 61 IBD patients (24 ulcerative colitis (UC), 19 Crohnâs colitis (CDc) and 18 Crohnâs ileitis (CDi)), refractory to corticosteroids and/or immunosuppression, before and 4-6 weeks after (except for 1 CDc patient) their first infliximab infusion and in normal mucosa from 12 control patients (6 colon and 6 ileum). The patients were classified for response to infliximab based on endoscopic and histologic findings at 4-6 weeks after first infliximab treatment. Total RNA was isolated from intestinal mucosal biopsies, labelled and hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays.
2009-11-02 | E-GEOD-16879 | biostudies-arrayexpress
Project description:The pathogenesis of Inflammatory Bowel Disease (IBD) is a multifactorial process characterized by inflammation and damage to the intestinal barrier, which is made up of intestinal epithelial cells (IECs). Since IBD is a remitting and relapsing disease, we postulated that epigenetic memory exists in IECs following an inflammatory encounter. The objective of this study was to uncover the mechanisms of a retained altered IEC epigenetic landscape in the context of IBD. We have generated adult stem cell organoids (containing all epithelial cell lineages) from patients with Ulcerative Colitis (UC); two organoid lines per patient were propagated: 1) from a site of active inflammation and from the same patient, and 2) a never inflamed region. We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and bulk RNA-seq on each organoid line. Established bioinformatic pipelines were used to determine significantly different chromatin accessibility and differentially expressed genes. Functional significance of the open chromatin regions was assessed by pathway and motif analysis. Treatment with TNF-alpha (10 and 100ng/ml) for 24 hours on the organoids was performed to determine re-activation of pro-inflammatory genes. This study shows for the first time that epithelial cells derived from organoids of IBD patients retain an epigenetic memory of the prior inflammatory state.
2026-02-28 | GSE282442 | GEO
Project description:The pathogenesis of Inflammatory Bowel Disease (IBD) is a multifactorial process characterized by inflammation and damage to the intestinal barrier, which is made up of intestinal epithelial cells (IECs). Since IBD is a remitting and relapsing disease, we postulated that epigenetic memory exists in IECs following an inflammatory encounter. The objective of this study was to uncover the mechanisms of a retained altered IEC epigenetic landscape in the context of IBD. We have generated adult stem cell organoids (containing all epithelial cell lineages) from patients with Ulcerative Colitis (UC); two organoid lines per patient were propagated: 1) from a site of active inflammation and from the same patient, and 2) a never inflamed region. We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and bulk RNA-seq on each organoid line. Established bioinformatic pipelines were used to determine significantly different chromatin accessibility and differentially expressed genes. Functional significance of the open chromatin regions was assessed by pathway and motif analysis. Treatment with TNF-alpha (10 and 100ng/ml) for 24 hours on the organoids was performed to determine re-activation of pro-inflammatory genes. This study shows for the first time that epithelial cells derived from organoids of IBD patients retain an epigenetic memory of the prior inflammatory state.
2026-02-28 | GSE282444 | GEO
Project description:'Illumina Infinium HumanMethylation450 BeadChip data from CD326+ sorted colonic epithelial cells of mucosal biopsies from treatment-naive paediatric IBD patients (Crohn''s Disease or Ulcerative Colitis) or age-matched controls AC= ascending colon, PSC=sigmoid colon'
2015-09-15 | E-MTAB-3709 | biostudies-arrayexpress
Project description:Expression data of butyrate stimulated epithelial organoid cultures generated from intestinal mucosa
| PRJNA509201 | ENA
Project description:The joint disease rheumatoid arthritis (RA) is characterized by persistent synovitis, leading to cartilage damage, bone erosion, and ultimately impaired joint function. The disease affects 0.5 to 1.0% of adults in developed countries, and is three times more frequent in women than in men. A number of autoantibodies can be detected in RA patient’s serum targeting the patient’s own proteins. Several of these proteins, including rheumatoid factor, can also be detected in patients suffering from other autoimmune diseases, including the inflammatory bowel diseases (IBD). IBD and RA share several genetic risk logi, an altered gut microbiota, and environmental risk factors. Articular involvement is the most common extra-intestinal manifestation in patients diagnosed with IBD, with a prevalence between 17 to 39%. Additionally, methotrexate (MTX) is the most frequently prescribed immunosuppressive drug for RA and the second most for the IBD, indicating close similarities between the two diseases. We, therefore, characterized the protein content (the proteome) of the colon mucosa of gastrointestinal healthy RA patients, to investigate if we could detect IBD-related changes. The LC-MS/MS analysis was conducted as part of a previous study (ProteomeXChange submission PXD001608), enabling a comparison between the two datasets, containing the colon mucosal proteome of 11 RA patients, 10 IBD (ulcerative colitis) patients, and 10 controls. This data submission covers the triplicate proteome analysis of the colon mucosa of 11 gastrointestinal healthy RA patients.
2016-09-26 | PXD003082 | Pride
Project description:The etiology of the inflammatory bowel diseases, including ulcerative colitis, remains incomplete, but recent findings points to the involvement of complex host-microbial interactions. We hypothesized that an analysis of the proteins on the host-microbial interacting surface, the intestinal mucosa, could reveal novel insights into the diseases. Mucosal colonic biopsies were extracted by standard colonscopy from sigmoideum from 10 ulcerative colitis patients from non-inflammed tissue and 10 controls. The biopsies were immediately following extraction snap-frozen for protein analysis and the protein content of the biopsies was characterized by high-throughput quantative gel-free proteomics.
2015-05-26 | PXD001608 | Pride