Browse
Submit Data
Database
Help
Login

Dataset Information

223 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Combinatorial flexibility of cytokine during Human T helper cells differentiation

ABSTRACT: Transcriptional analysis of human T cells differentiated in 4 T Helper context ( Th0, Th1, Th2 and Th17) in the presence or not of Interferon alpha We analyzed the transcriptomic profiles of 4 human naives T cells diferentiated in Th0, Th1, Th2 and Th17 in the presence or not of Interferon Alpha. Microarray analyses were performed in 2 time points : 1/ after Day 5 of polarization (= Day5); 2/ after Day 5+ four hours of re-stimulation (=Day 5+ 4H restim) in 3 different donors.

ORGANISM(S): Homo sapiens

SUBMITTER: Antonio Cappuccio Takeshi Satoh Maximilien Grandclaudon Carolina Martinez-Cingolani Vassili Soumelis Nicolas Servant Nicolas Manel Maxime Touzot

PROVIDER: E-GEOD-54627 | ArrayExpress | 2014-05-29

SECONDARY ACCESSION(S): GSE54627PRJNA237221

REPOSITORIES: GEO, ArrayExpress

ACCESS DATA

Json Xml

Publications

Combinatorial flexibility of cytokine function during human T helper cell differentiation.

Touzot Maxime M Grandclaudon Maximilien M Cappuccio Antonio A Satoh Takeshi T Martinez-Cingolani Carolina C Servant Nicolas N Manel Nicolas N Soumelis Vassili V

Nature communications 20140528

In an inflammatory microenvironment, multiple cytokines may act on the same target cell, creating the possibility for combinatorial interactions. How these may influence the system-level function of a given cytokine is unknown. Here we show that a single cytokine, interferon (IFN)-alpha, can generate multiple transcriptional signatures, including distinct functional modules of variable flexibility, when acting in four cytokine environments driving distinct T helper cell differentiation programs ...[more]

PMID: 24865484

Similar Datasets

Regulation of T cell cytokine expression by Tet2-mediated DNA demethylation [gene expression]

Project description:T cell function is regulated by epigenetic mechanisms. 5-methylcytosine (5mC) conversion to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (Tet) proteins was identified to mediate DNA demethylation. Here, we characterize the genome-wide distribution of 5hmC in T cells using DNA immunoprecipitation coupled with high-throughput DNA sequencing. 5hmC marks signature genes associated with effector cell differentiation in the putative regulatory elements. Moreover, Tet2 protein is recruited to 5hmC-containing regions, dependent on lineage-specific transcription factors. Deletion of the Tet2 gene in T cells decreased their cytokine expression, associated with reduced p300 recruitment. In vivo, Tet2 plays a critical role in the expression of cytokine genes. Collectively, our findings for the first time demonstrate a key role of Tet-mediated active DNA demethylation in T cells. A total of 8 samples were analyzed. The expression patterns in Tet2 wild-type and deficient Th1 and Th17 cells were analyzed.

2015-04-12 | E-GEOD-66944 | ArrayExpress

Expression and functions of long noncoding RNAs during human T helper cell differentiation

Project description:To improve our understanding of lncRNA expression in T cells, we used whole genome sequencing (RNA-seq) to identify lncRNAs expressed in human T cells and those selectively expressed in T cells differentiated under TH1, TH2, or TH17 polarizing conditions. The majority of these lineage-specific lncRNAs are co-expressed with lineage-specific protein-coding genes. These lncRNAs are predominantly intragenic with co-expressed protein-coding genes and are transcribed in sense and antisense orientations with approximately equal frequencies. Further, genes encoding TH lineage specific mRNAs are not randomly distributed across the genome but are highly enriched in the genome in genomic regions also containing genes encoding TH lineage-specific lncRNAs. Our analyses also identify a cluster of antisense lncRNAs transcribed from the RAD50 locus that are selectively expressed under TH2 polarizing conditions and co-expressed with IL4, IL5 and IL13 genes. Depletion of these lncRNAs via selective siRNA treatment demonstrates the critical requirement of these lncRNAs for expression of the TH2 cytokines, IL-4, IL-5 and IL-13. Collectively, our analyses identify new lncRNAs expressed in a TH lineage specific manner and identify a critical role for a cluster of lncRNAs for expression of genes encoding TH2 cytokines. Human peripheral blood mononuclear cells (PBMC) were cultured under TH1, TH2, and TH17 polarizing conditions. TH1, TH2, and TH17 primary and effector cultures were isolated and poly(A)+ and total RNA sequencing performed.

2015-04-23 | E-GEOD-66261 | ArrayExpress

Transcription profiling of mouse spleen CD4+ CD44Low CD62LHigh cells stimulated with anti-CD3 or anti-CD28 in the presence or absence of hTGFb-1 and mouse IL-6

Project description:Mouse spleen CD4+CD44LowCD62LHigh cells were stimulated with 2ug/ml anti-CD3(eBioscience), 2ug/ml anti-CD28 (eBioscience) in the presence (Th17 condition) or absence (Th0 condition) of hTGFb-1 (1ng/ml eBioscience), mouse IL-6(10ng/ml eBioscience). Cells were collected after 24 hourÕs culture using RNAeasy columns (Qiagen) for total RNA isolation. Isolated total RNA from Th0 and Th17 conditioned cells were submitted for the microarray gene transcription comparison analysis using Affymetrix Mouse 430A 2.0 array chips.

2008-12-21 | E-TABM-583 | ArrayExpress

miRNA-seq study between Th0 and Th17 cells

Project description:To explore the differences in miRNA profiles, naive CD4+CD62L+ helper T cells were sorted by magnetic cell sorting from spleens of female C57BL/6 mice and were induced to differentiate into Th1 or Th17 cells, then total RNA was extracted and miRNA-seq were conducted. The results showed that many microTNAs presented a different expression pattern between Th1 and Th17 cells, which prompted us to further study their roles in Th117 differenciation. miRNA profiles of Th0 and Th17 cells were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500

2016-07-30 | E-GEOD-80834 | ArrayExpress

A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-12 | E-GEOD-60680 | ArrayExpress

Expression data from mouse differentiated T helper cell lineages

Project description:Microarray data on TH cell subsets from WT C57BL/6 and Bhlhe40 KO mice We used microarrays to detail the global programme of gene expression in polarized TH cell lineages Purified naïve CD4 T cells from spleen were polarized in vitro and then activated with PMA/Ionomycin prior to microarray analysis

2014-03-26 | E-GEOD-49166 | ArrayExpress

Analysis of gene expression in different T cell clones

Project description:The aim was to analyze the expression of genes in T cell clones having different functional profiles (Th1, Th0, Th17, Th2) obtained from the same individual. Keywords: Gene expression, T cell clones, Th17 characterisation The T cell clones were derived according to well known protocol, using different cytokines, and classified on the basis of their ability to produce cytokines. Once characterized for their production of IL-4, IL-12, gamma-IFN, IL-13, IL-1, they were used to prepare microarray experiments.

2008-05-30 | E-GEOD-11553 | ArrayExpress

The polycomb protein Ezh2 regulates differentiation and plasticity of CD4 T helper type-1 and type-2 cells.

Project description:Following antigen encounter by CD4 T cells, polarizing cytokines induce the expression of master regulators that control differentiation. Inactivation of the histone methyltransferase Ezh2 was found to specifically enhance T-helper (Th)1 and Th2 cell differentiation and plasticity. Ezh2 directly bound and facilitated correct expression of Tbx21 and Gata3 in differentiating Th1 and Th2 cells, accompanied by substantial tri-methylation at lysine 27 of histone 3 (H3K27-Me3). In addition, Ezh2 deficiency resulted in spontaneous generation of discrete IFN-γ and Th2 cytokine-producing populations in non-polarizing cultures, and under these conditions IFN-γ expression was largely dependent on enhanced expression of the transcription factor Eomesodermin. In vivo, Loss of Ezh2 caused increased pathology in a model of allergic asthma and resulted in progressive accumulation of memory phenotype Th2 cells. This study establishes a functional link between Ezh2 and transcriptional regulation of lineage-specifying genes in terminally differentiated CD4 T cells. Wild type and Ezh2 knock out unpolarized Th cells, Th1 cells and Th2 cells are profiled for mRNA expression

2013-09-11 | E-GEOD-50729 | ArrayExpress

Defining a Th9 transcriptome

Project description:Microarray analyses were performed to compare gene expression in cultured mouse Th9, Th2 and Treg cells and resting versus activated Th9 cells. Three replicates were analyzed for each culture condition; Th9 unstim, Th2 unstim, Treg unstim, Th9 stim

2014-03-26 | E-GEOD-44937 | ArrayExpress

The polycomb protein Ezh2 regulates differentiation and plasticity of CD4 T helper type-1 and type-2 cells [ChIP-seq]

2013-09-24 | E-GEOD-51079 | ArrayExpress

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
GPMDB

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS

ArrayExpress
ExpressionAtlas

Information

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