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Integrated Analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells

ABSTRACT: Integrated Analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells

PROVIDER: PRJNA380408 | ENA |

REPOSITORIES: ENA

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Integrated analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells [diseased subjects]

Project description: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.

2017-11-11 | GSE96665 | GEO

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells.

Project description:BACKGROUND:Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota. Our goal is to characterize and infer relationships between mucosal T cells, the host tissue environment, and microbial communities in patients with IBD who will serve as basis for mechanistic studies on human IBD. METHODS:We characterized mucosal CD4 T cells using flow cytometry, along with matching mucosal global gene expression and microbial communities data from 35 pinch biopsy samples from patients with IBD. We analyzed these data sets using an integrated framework to identify predictors of inflammatory states and then reproduced some of the putative relationships formed among these predictors by analyzing data from the pediatric RISK cohort. RESULTS: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. These SAA1-linked microbial and transcriptome interactions were further reproduced with data from the pediatric IBD RISK cohort. CONCLUSIONS:This study identifies expression of SAA1 as an important link between mucosal T cells, microbial communities, and their tissue environment in patients with IBD. A combination of T cell effector function data, gene expression and microbial profiling can distinguish between intestinal inflammatory states in IBD regardless of disease types.

| S-EPMC5613756 | biostudies-literature

Integrated Analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-11-12 | GSE97012 | GEO

Comparative transcriptome analysis of Th22 and Th17 cells

Project description:Microarray was used to delineate the global gene expression profile underlying the specific developmental program of two divergent antigen-specific T helper subsets (Th22 versus Th17) by identifying upregulation or downregulation of key lineage-determining transcription factors, cytokines, chemokines and other genes that govern their functional attributes. To identify factors that might distinguish the Th22 and Th17 developmental programs, comparative global transcriptome analysis between these 2 subsets was performed. Naïve splenic CD4+ T cells from OT-II-transgenic mice were isolated and grown in vitro under T-helper lineage-specific conditions in the presence of cognate antigen (ovalbumin) to identify their distinctive global gene-regulation profiles.

2013-01-29 | E-GEOD-42332 | biostudies-arrayexpress

Comparative transcriptome analysis of Th22 and Th17 cells

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2022-04-12 | GSE182767 | GEO

Th17, Th22 and Treg cells are enriched in the healthy human cecum

Project description:Dysregulation of CD4+ T cell populations leads to intestinal inflammation, but the regional differences of these T cell populations remained unclear in the healthy population. We first used flow cytometry to show that Th17 and Th22 cells are specifically enriched in the human cecum, while Th1 and Th2 cells do not differ regionally. We subsequently performed transcriptional profiling and found that Th17 was positively associated with the expression of RETN and negatively associated with TFF1, suggesting that the differential enrichment of Th17 cells in the healthy human cecum was underlined by the metabolic differences in this environment. Transcriptional profiling with microarray on human intestinal pinch biopsies obtained from different sites of the healthy colon.

2014-02-22 | E-GEOD-55258 | biostudies-arrayexpress

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Th22 cells form a distinct T helper lineage from Th17 cells in vitro with unique transcriptional properties and Tbet-dependent Th1 plasticity

Project description:To determine the transcriptional profile of Th22 cells and allow comparative analysis with Th17 cells

2017-01-16 | GSE92610 | GEO

Th17, Th22 and Treg cells are enriched in the healthy human cecum

2014-02-22 | GSE55258 | GEO