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

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

PROVIDER: PRJNA667343 | ENA |

REPOSITORIES: ENA

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

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

| PRJNA667340 | 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

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

Proteomic Analysis of rattus norvegicus colonic mucosa following acupuncture treatment for irritable bowel syndrome with diarrhea by label-free LC–MS/MS

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

Differential genetic influences over colorectal cancer risk and gene expression in large bowel mucosa

Project description:Site-specific variation in colorectal cancer (CRC) incidence, biology and prognosis are poorly understood. We sought to determine whether common genetic variants influencing CRC risk might exhibit topographical differences on CRC risk through regional differences in effects on gene expression in the large bowel mucosa. We conducted a site-specific genetic association study (10,630 cases, 31,331 controls) to identify whether established risk variants exert differential effects on risk of proximal, compared to distal CRC. We collected normal colorectal mucosa and blood from 481 subjects and assessed mucosal gene expression using Illumina HumanHT-12v4 arrays in relation to germline genotype. Expression quantitative trait loci (eQTLs) were explored by anatomical location of sampling. Normal colorectal mucosa was analyzed from both CRC patients and healthy controls.

2021-04-29 | GSE161023 | GEO

Distinct transcriptomic signature of mRNA and microRNA in ulcerative colitis and irritable bowel syndrome

Project description:Background: Ulcerative colitis (UC) and irritable bowel syndrome (IBS) are both chronic bowel diseases involving stress. To identify genes differentially expressed in UC and IBS, and to determine whether psychological stress can influence those gene expressions, we conducted this pilot study. Methods: Patients of UC, irritable bowel syndrome (IBS) and normal controls (NC) (n=5 in each group) were recruited. Perceived stress scale (PSS) was adopted to assess psychological stress level. Sigmoid mucosa samples were collected during colonoscopy. Differentially expressed genes (DEGs) of both mRNA and microRNA (DEG-mRNA and DEG-miRNA) were identified by RNA-Seq and microarray, respectively. Weighted gene co-expression network analysis (WGCNA), gene ontology, and microRNA target analysis were performed to identify regulatory relationships and pathways involved. Pearson correlation was performed to identify the relationship between DEGs and PSS score.

2024-11-01 | GSE160900 | GEO

Functional Proteomic Profiling of Secreted Serine Proteases in Health and Inflammatory Bowel Disease

Project description:Dysregulated proteolysis plays a pivotal role in the pathophysiology of inflammatory bowel disease. Nonetheless, the identity of overactive proteases released by human colonic mucosa remains unknown. Herein, we employed a serine protease-targeted activity-based probe (ABP) coupled with mass spectral analysis to identify active forms of proteases secreted by the colonic mucosa of healthy volunteers and inflammatory bowel disease patients. With this approach, we identified seven active serine proteases: cathepsin G, plasma kallikrein, plasmin, tryptase, chymotrypsin-like elastase 3A, aminopeptidase B, and thrombin. Furthermore, cathepsin G and thrombin were overactive in supernatants from inflammatory bowel disease patients once compared to healthy volunteers.

2018-05-18 | PXD009450 | Pride

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