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Etrolizumab-s fails to control E-Cadherin-dependent co-stimulation of highly stimulated cytotoxic T cells associated with Crohn’s disease

ABSTRACT: To interrogate the potential of αEβ7 integrin as a target in Crohn’s disease (CD), we single cell RNA-sequenced T cells from a patient with CD and a non-IBD control

ORGANISM(S): Homo sapiens

PROVIDER: GSE252122 | GEO | 2023/12/28

REPOSITORIES: GEO

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Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies:

Project description:Ulcerative colitis (UC) and Crohn’s disease (CD) are inflammatory bowel diseases (IBD) with variable, overlapping clinical features and complex pathophysiologies. To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies to estabolish 36 expression profiles, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls. Keywords: RNA

2007-03-01 | GSE6731 | GEO

Differences in tissue populations following hematopoietic stem cell transplantation in Crohn’s disease patients

Project description:Treatment of severely refractory Crohn’s disease (CD) patients remains a clinical challenge. Recent studies show the efficacy of autologous hematopoietic stem cell transplant (HSCT) in these severely compromised patients. HSCT is thought to eliminate auto-reactive cells; however, no specific studies of immune reconstitution in CD patients are available. We studied a group of CD patients (n=18) receiving autologous HSCT and non-IBD patients (n=19) to elucidate the mechanism of interaction with the microorganisms.

2020-10-22 | GSE139179 | GEO

Genome-wide analysis of DNA methylation profile provides clinical implication of Crohn’s Disease

Project description:Inflammatory bowel disease (IBD) is known to be caused by a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interaction with environmental, particularly epigenetic, factors can have a significant contribution during the development of IBD. Although many studies, particularly genome-wide association studies (GWAS), have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease (CD), the role of epigenetic changes in the development of complications arising from CD is poorly understood. Here, we employed an unbiased approach to define DNA methylation alteration in CD patients using the HumanMethylation450K BeadChip platform. Compared to normal controls, the majority of differential DNA methylation in CD patient samples was in the promoter, intergenic, and gene body regions. The DNA methylation profile in CD revealed 134 probes (23 hypermethylated and 111 hypomethylated probes) that were differentially methylated. We validated the methylation levels of 19 genes that showed hypermethylation in CD patients compared with normal control. Technical validation was performed using quantitative MSP analysis and we finally identified that the Fragile Histidine Triad (FHIT) genes were hypermethylated in a disease-specific manner. Gene network analysis of the hypermethylated candidates suggested putative molecular interactions relevant to IBD pathology. Overall, our DNA methylation profile identifies newly hypermethylated genes in CD, as well as the gene network associated with disease development, which can provide new therapeutic targets.

2017-12-25 | GSE105798 | GEO

RNA-seq of nonstenotic and stenotic areas of patients with Crohn’s disease

Project description:Fibrostenotic disease is a common complication in Crohn’s disease (CD). We performed bulk RNA sequencing (n=16) of paired intestinal biopsies taken from nonstenotic and stenotic areas of patients with CD (n=8).

2023-04-26 | E-MTAB-12788 | biostudies-arrayexpress

Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease

Project description:In this study, we performed single-cell transcriptional profiling of human embryonic and fetal gut samples obtained from 9 human embryos spanning ages 6-10 PCW and three regions (duo-jejunum, ileum and colon). Additionally, we profile mucosal biopsies from the terminal ileum of healthy children aged 4-12 years (n = 8) as well as a group of children newly diagnosed with Crohn’s disease (CD) (n = 7), a common form of IBD. Tissue samples were treated using an enzymatic dissociation protocol and single cell suspensions were then processed using the 3’v2 10x Genomics Chromium workflow. In a subset of samples, the intestinal epithelial cell fraction was enriched by performing magnetic bead sorting for EPCAM. In total, we generate single cell transcriptomes of ~90,000 primary human intestinal cells providing a rich resource and detailed roadmap. Using this data as well as scRNAseq profiles of human fetal gut derived organoids we describe embryonic and fetal epithelium composition, trace their differentiation dynamics and signaling partners, and provide links to regenerating Crohn’s disease epithelium.

2020-12-22 | E-MTAB-8901 | biostudies-arrayexpress

The Gut Microbiota Metabolite Succinate promotes Adipose Tissue Browning in Crohn’s Disease

Project description:In Crohn’s disease (CD), microbe-host interactions are altered, with changes in microbial’s communities and barrier defects leading to translocation of microbes to surrounding adipose tissue (AT). We evaluated the presence of beige AT depots in CD and questioned whether succinate and/or bacterial translocation promotes white-to-beige transition in adipocytes.

2022-09-14 | PXD030520 | Pride

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 | iProX

Assessing Cellular and Transcriptional diversity of IIeal Mucosa amongst Treatment Naïve and Treated Crohn’s disease

Project description:Crohn’s disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. We used single cell RNA sequencing (scRNAseq) to define the cellular and transcriptional activity of the mucosa at different stages of disease progression in CD.

2022-10-18 | GSE202052 | GEO

Expression Profiles of Circular RNAs in colon biopsies from Crohn’s Disease Patients by Microarray Analysis

Project description:To investigate the expression profiles of circRNAs in colon tissues of the patients with Crohn’s Disease(CD) , ulcerative colitis (UC) and healthy controls (HC), we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs in colon tissues of CD,UC and HC.

2019-05-30 | GSE131911 | GEO

Mediators in Crohn’s disease influence the gene expression profiles of mesenchymal progenitor cells differentiated into the osteoblastic lineage.

Project description:Crohn’s disease (CD) is associated with a higher prevalence of osteoporosis, a complication that is increasingly recognised as a significant cause of morbidity. Its pathogenesis is still controversial, but activity of CD is thought to be one contributing factor.

2012-03-16 | GSE20941 | GEO

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