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| Status |
Public on Jan 27, 2015 |
| Title |
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Kabakchiev B, Morgan XC, Waldron L, Tyler A, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C |
| Citation(s) |
25887922 |
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| Submission date |
Jan 26, 2015 |
| Last update date |
Jul 26, 2018 |
| Contact name |
Boyko Kabakchiev |
| Organization name |
Mount Sinai Hospital
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| Department |
Samuel Lunenfeld Research Institute
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| Lab |
Silverberg Lab
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| Street address |
60 Murray Street, Room L3-004
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 3L9 |
| Country |
Canada |
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| Platforms (1) |
| GPL6244 |
[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (273)
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| Relations |
| BioProject |
PRJNA273579 |
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