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Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease

ABSTRACT: Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease

PROVIDER: PRJNA667340 | ENA |

REPOSITORIES: ENA

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Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Whole mucosa]

Project description:Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Whole mucosa]

| PRJNA667343 | ENA

Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Microdissected IEC]

Project description:Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Microdissected IEC]

| PRJNA667344 | ENA

Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Whole mucosa]

Project description:Background and Aims: The pathophysiology of the diarrhoea-predominant inflammatory bowel disease collagenous colitis (CC) is poorly described. Our aim was to use RNA sequencing of colonic biopsies from patients with active CC, CC in remission, refractory CC, ulcerative colitis (UC), and controls to gain insight into CC pathophysiology, identify additional genetic signatures linked to CC, and uncover targets for future therapeutic agents. Methods: We performed whole transcriptome sequencing of CC colonic samples from patients before and during treatment with the corticosteroid drug budesonide, steroid-refractory patients, UC and healthy controls (n=9-13). Bulk mucosa and laser-captured microdissected intestinal epithelial cell gene expression was functionally analyzed by gene-set enrichment and gene-set variation analyses to identify statistically significant pathways and cells, respectively, that change in CC. Leading genes and cells were validated using reverse transcription quantitative PCR and/or immunohistochemistry. Finally, we compared CC transcriptome with that from UC samples. Results: We identified an activation of the adaptive immune response to bacteria in active CC compared to that in remission that could be mediated by dendritic cells. However, a unique signature of genes related to the immune response and DNA transcription remain dysregulated after achieving remission. Budesonide-refractory CC patients fail to restore normal gene expression, which results in a transcriptomic profile close to UC. Intestinal epithelial CC cells displayed an impaired cell proliferation and increased antigen presentation. Conclusion: Our study confirmed previous findings from GWAS and immunological studies related to CC pathogenesis and describes novel genes, pathways and cells that might contribute to the pathophysiology of CC, ongoing epithelial damage, and complications associated with CC.

2021-05-03 | GSE159008 | GEO

Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Microdissected IEC]

2021-05-03 | GSE159007 | GEO

Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-05-03 | GSE159010 | GEO

Expression profiling in inflammatory bowel disease

Project description:The series was designed to identify new genes involved in the pathophysiology of inflammatory bowel disease (Crohn's disease and ulcerative colitis). This series represents a group of 31 samples, subdivided into 3 groups: 1) Normal controls: 11 samples; 2) patients with Crohn's diseases: 10 samples; 3) patients with ulcerative colitis: 10 samples. Each sample originated from a different patient or normal control, in total n=31 individuals were examined. Keywords = Inflammatory bowel disease Keywords = Crohn's disease Keywords = ulcerative colitis Keywords = expression screening Keywords = expression profiling Keywords: other

2005-08-11 | GSE1710 | GEO

Deep metaproteomics of inflammatory bowel diseases

Project description:Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is associated with a loss or an imbalance of host-microbe interactions. Depletion-assisted deep metaproteomics was employed to reveal disease-specific networks of host-microbial protein associations in IBD.

2023-06-28 | PXD043380 |

RNA-sequencing of inflamed intestinal mucosa of inflammatory bowel disease patients

Project description:Studying differences in responders and non-responders to therapy in inflammatory bowel disease (IBD) patients (crohn's disease and ulcerative colitis)

2019-01-24 | E-MTAB-7604 | biostudies-arrayexpress

Transcription profiling of mucosa from human patients with irritable bowel syndrome or ulcerative colitis

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

2007-10-02 | E-GEOD-2461 | biostudies-arrayexpress

Short Noncoding RNAs as predictive biomarkers for the development from Inflammatory Bowel Disease Unclassified to Crohn’s Disease or Ulcerative Colitis

Project description:To find predictive biomarkers for the development from inflammatory bowel disease unclassified (IBDU) to Crohn's disease(CD) or ulcerative colitis (UC), we performed short non-coding RNA profiling on IBDU patient samples at the time of diagnostic endoscopy.

2024-03-04 | GSE228622 | GEO

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