Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Boyko Kabakchiev

PROVIDER: E-GEOD-65270 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Morgan Xochitl C XC Kabakchiev Boyko B Waldron Levi L Tyler Andrea D AD Tickle Timothy L TL Milgrom Raquel R Stempak Joanne M JM Gevers Dirk D Xavier Ramnik J RJ Silverberg Mark S MS Huttenhower Curtis C

Genome biology 20150408

<h4>Background</h4>Pouchitis is common after ileal pouch-anal anastomosis (IPAA) surgery for ulcerative colitis (UC). Similar to inflammatory bowel disease (IBD), both host genetics and the microbiota are implicated in its pathogenesis. We use the IPAA model of IBD to associate mucosal host gene expression with mucosal microbiomes and clinical outcomes. We analyze host transcriptomic data and 16S rRNA gene sequencing data from paired biopsies from IPAA patients with UC and familial adenomatous p ...[more]

PMID: 25887922

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Dataset Information

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

Publications

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

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