Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

ABSTRACT: Management of terminal ileal Crohn's disease (CD) is difficult due to fibrotic prognosis and failure to achieve mucosal healing. A limited number of synchronous analyses have been conducted on the transcriptome and microbiome in unpaired terminal ileum tissues. Therefore, our study focused on the transcriptome and mucosal microbiome in terminal ileal tissues of CD patients with the aim of determining the role of cross-talk between the microbiome and transcriptome in the pathogenesis of terminal ileal CD. Mucosa-attached microbial communities were significantly associated with segmental inflammation status. Interaction-related transcription factors (TFs) are the panel nodes for crosstalk between the gene patterns and microbiome for terminal ileal CD. The transcriptome and microbiome in terminal ileal CD can be different related to local inflammatory status, and specific differentially expressed genes (DEGs) may be targeted for mucosal healing. TFs connect gene patterns with the microbiome by reflecting environmental stimuli and signals from microbiota.

ORGANISM(S): Homo sapiens

PROVIDER: GSE171244 | GEO | 2021/04/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

Project description:Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

| PRJNA718848 | ENA

Microarray analysis from paired biopsies from ileal pouch-anal anastomosis surgery patients with ulcerative colitis and familial adenomatous polyposis

Project description:Pouchitis is a common complication for ulcerative colitis (UC) patients with ileal pouch-anal anastomosis (IPAA) surgery. Similarly to IBD, both innate host factors such as genetics, and environmental stimuli including the tissue-associated microbiome have been implicated in the pathogenesis. In this study, we make use of the IPAA model of inflammatory bowel disease (IBD) to carry out a study associating mucosal host gene expression with the microbiome and corresponding clinical outcomes. In order to determine how host gene expression might influence, or be influenced by the tissue associated microbiome, we analyzed 205 IPAA patients with biopsies collected from the pouch and afferent limb for host transcriptomics and 16S rDNA gene sequencing. Metadata included antibiotic use, inflammation score, and clinical classification. To achieve power for a genome-wide microbiome-transcriptome association study, we used principal component analysis to reduce OTUs and host transcripts to eigengenes and eigenclades explaining 50% of observed variance. These were subsequently tested for significant covariation with one another and/or outcome using multivariate linear modeling.

2015-01-27 | E-GEOD-65270 | biostudies-arrayexpress

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

2015-01-27 | GSE65270 | GEO

16S V3-V4 -based microbial profiling of matched healthy and inflamed ileal mucosa from patients affected by Crohn’s disease

Project description:Crohn’s Disease (CD) pathogenesis is still unclear. Disorders in the mucosal immunoregulation and its crosstalk with the microbiota may represent an important component in tissue injury. We aimed to characterize the molecular immune response distribution within the ileal layers ( mucosa, submucosa and serosa) and to evaluate the correlated microbiota in pathological/healthy settings comparing first surgery/relapse clinical conditions.

2021-11-22 | GSE162844 | GEO

16S V3-V4 -based microbial profiling of matched healthy and inflamed ileal mucosa from patients affected by Crohn’s disease (set 2)

2022-07-21 | GSE198329 | GEO

Core Ileal Transcriptome in Pediatric Crohn Disease

Project description:We report the global pattern of ileal gene expression in a cohort of 359 treatment-naïve pediatric Crohn Disease, Ulcerative Colitis patients and controls. We focus on genes with consistent altered expression in inflamed and unaffected ileum of CD [ileal-involved CD (iCD) and non-invloved ileal CD (cCD)], but not in the ileum of ulcerative colitis or control.

2014-07-24 | GSE57945 | GEO

Common and distinct pathophysiological processes associated to ileal and colonic ulcers in Crohn’s disease

Project description:Based on genetic risk factors and natural history, Crohn’s disease (CD) can be separated in two entities, an ileal and a colonic disease. Protein based-approaches are needed to elucidate whether such subphenotypes are related to distinct pathophysiological processes. In this work, we compared the proteome of ulcer edge to the one of paired control tissue in ileum and colon of CD patients. We revealed that ileal and colonic ulcer edge can be distinguished by a differential distribution of epithelial–mesenchymal transition proteins, neutrophil degranulation proteins and ribosomal proteins. In ileal and colonic ulcer edge, we found a quasi-systematic increase of the proteins implicated in the pathway of protein processing in endoplasmic reticulum and a quasi-systematic decrease of mitochondrial proteins. Our study provides for the first time protein-based evidences showing partly distinct pathophysiological processes associated to ileal and colonic ulcer edge in CD. This could constitute a first step toward the development of gut segment-specific diagnostic markers and therapeutics.

2019-07-15 | PXD012284 | Pride

Gene expression data from human intestinal biopsies

Project description:Anti-TNFα therapy induces mucosal healing in a large proportion of Crohn’s disease (CD) patients, but the mechanisms underlying this process are not fully elucidated. To this end we examined molecular effects of adalimumab treatment in CD. CD patients (n=10) underwent ileocolonoscopy were sampled for mucosal biopsies before and after three months of adalimumab treatment. Collected material was analyzed using transcriptome microarray analysis. All patients were responders and eight patients reached clinical remission. Mucosal transcriptome analyses demonstrated that anti-inflammatory and tissue-repair gene-sets were upregulated in inflamed mucosa, in addition to proinflammatory and tissue-destruction-related genes. After treatment, genes promoting inflammation or tissue-destruction were downregulated. , and these genes are primarily expressed in innate leukocytes and stromal cells. Expression of anti-inflammatory and tissue-repair-related genes was also downregulated, but to a lesser degree. Of note, various parts of the colon displayed distinct gene-expression profiles. Adalimumab operates by down-shifting several proinflammatory arms of both the innate and adaptive immune-system, but does not disturb regulatory T-cells. Anti-inflammatory and tissue-repair machineries are upregulated already during active inflammation, but are not effective until proinflammatory drivers have been silenced.

2020-05-11 | GSE98820 | GEO

Crohn’s Disease Differentially Affects Region Specific Composition and Aerotolerance Profiles of Mucosally-Adherent Bacteria

Project description:BACKGROUND: The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn’s disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen has been proposed as a contributor to CD dybiosis. METHODS: 16S rRNA data was generated using colonic and ileal mucosal from patients with CD and without inflammatory bowel diseases (nonIBD). We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes. RESULTS: Bacterial diversity decreased in CD in both ileum and colon. Aerotolerance profiles significantly differed between intestinal segments in nonIBD, though both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundance of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, though specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected pre-operative tissues of patients that developed disease recurrence across two independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera. CONCLUSIONS: Mucosally adherent bacteria in colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.

2020-04-15 | GSE147600 | GEO

Mucosal miRNA expression profiling in ileum of patients with Crohn's disease

Project description:In this study, we investigated miRNA expression profiles in ileal mucosa from CD patients in different settings (post-operative recurrent (POR) CD, newly diagnosed CD and late stage CD)) and controls.

2019-03-01 | GSE102127 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data