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Series GSE96665 Query DataSets for GSE96665
Status Public on Nov 11, 2017
Title Integrated analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells [diseased subjects]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota. Our goal is to characterize the relationships between mucosal T cells, the host tissue environment and microbial communities in IBD patients to identify new therapeutic targets. We identified 26 predictors from our combined data set that were effective in distinguishing between regions of the intestine undergoing active inflammation and regions that were normal. Network analysis on these 26 predictors revealed SAA1 as the most connected node linking the abundance of the genus Bacteroides with the production of IL17 and IL22 by CD4+ T cells. The SAA1-linked microbial and transcriptome interactions were further validated with data from the pediatric IBD RISK cohort. This study identifies expression of SAA1 as an important link between mucosal T cells, microbial communities and their tissue environment in IBD patients. A combination of FACS, gene expression and microbial profiling can distinguish between intestinal inflammatory states in IBD regardless of disease types.
Overall design We characterized mucosal CD4+ T cells using flow cytometry (FACS), along with matching mucosal global gene expression and microbial communities data from 35 pinch biopsy samples from IBD patients. We analyzed these data sets using an integrated framework to identify predictors of inflammatory states and then validated the putative relationship networks by analyzing data from the pediatric RISK cohort.
Contributor(s) Tang MS, Leung JM, Gundra UM, Loke P
Citation(s) 28806280
Submission date Mar 15, 2017
Last update date Nov 27, 2018
Contact name Mei San Tang
Organization name Washington University in St Louis
Department Pathology & Immunology
Street address 660 S Euclid, Campus Box 8118
City Saint Louis
State/province MO
ZIP/Postal code 63108
Country USA
Platforms (1)
GPL13607 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
Samples (41)
GSM2537668 10I-CD-Active-Ileum-1
GSM2537669 10N-CD-Normal-Sigmoid-1
GSM2537670 11I-CD-Active-Sigmoid-2
This SubSeries is part of SuperSeries:
GSE97012 Integrated Analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells
BioProject PRJNA379314

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE96665_RAW.tar 133.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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