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Gene expression profiling in Treg cells deficient or mutant in candidate FoxP3 cofactors

ABSTRACT: The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability.

ORGANISM(S): Mus musculus

PROVIDER: GSE40273 | GEO | 2012/08/23

SECONDARY ACCESSION(S): PRJNA173378

REPOSITORIES: GEO

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Gene expression profiling in Treg cells deficient or mutant in candidate FoxP3 cofactors

Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. To study the impact of deficiency of candidate FoxP3 cofactors (Xbp1, Eos, Gata1) on the expression of the Treg transcriptional signature, gene expression profiles were generated from purified splenic CD4+CD25hi Tregs of these mutant or knockout mice and their wildtype littermates.

2012-08-23 | E-GEOD-40273 | biostudies-arrayexpress

Gene profiling data of CD4+ T cells transduced with FOXP3 and candidate cofactors

Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. To study the impact of FoxP3 and its candidate cofactors (Eos, Gata1, Helios, Irf4, Lef1, Satb1, Xbp1) on the expression of the Treg transcriptional signature, CD4+ conventional T cells (Tconv) activated with anti-CD3+CD28 beads were retrovirally transduced with cDNAs encoding FOXP3, candidate TFs, or a combination of FOXP3 and candidate TFs. After 3 days in culture, the transduced cells were sorted into Trizol, and RNA was purified, labeled and hybridized to Affymetrix arrays.

2012-08-23 | E-GEOD-40274 | biostudies-arrayexpress

Gene profiling data of CD4+ T cells transduced with FOXP3 and candidate cofactors

2012-08-23 | GSE40274 | GEO

Gene profiling data of CD4+ T cells doubly transduced with EOS+LEF1 or GATA1+SATB1

Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. To study the impact of the combination of two transcription factors on the expression of the Treg transcriptional signature, CD4+ Tconv cells activated with anti-CD3+CD28 beads were retrovirally transduced with cDNAs encoding EOS and LEF1, or GATA1 and SATB1. The cells were then sorted into Trizol, and RNA was purified, labeled and hybridized to Affymetrix arrays.

2012-08-23 | E-GEOD-40277 | biostudies-arrayexpress

Gene profiling data of CD4+ T cells transduced with FOXP3 and GATA1, then sorted into different fractions, based on the expression of Thy1.1 (FOXP3)

Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. To study the impact of FOXP3 alone or together with GATA1 on the expression of the Treg transcriptional signature, we sorted and profiled matched bins of FOXP3-transduced cells bearing various levels of FOXP3, alone or co-transduced with GATA1, chosen as a representative of the quintet factors.

2012-08-23 | E-GEOD-40276 | biostudies-arrayexpress

Gene profiling data of CD4+ T cells doubly transduced with EOS+LEF1 or GATA1+SATB1

2012-08-23 | GSE40277 | GEO

Gene profiling data of CD4+ T cells transduced with FOXP3 and GATA1, then sorted into different fractions, based on the expression of Thy1.1 (FOXP3)

2012-08-23 | GSE40276 | GEO

Genome-wide maps of FoxP3 binding in transduced CD4+ T cells

2012-08-23 | GSE40238 | GEO

Genome-wide maps of FoxP3 binding in transduced CD4+ T cells

Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. We used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to assess how cofactors affect the genome-wide localization of FoxP3. Chromatin was prepared from primary CD4+ Tconv cells transfected with FLAG-FoxP3 alone or together with GATA1, immunoprecipitated with anti-FLAG, and the bound DNA determined by Illumina deep sequencing. Immunoprecipitation with anti-PolII, or whole cell extract, provided genome-wide controls for transcriptional start sites (TSSd) or for sequencing non-homogeneity, respectively.

2012-08-23 | E-GEOD-40238 | biostudies-arrayexpress

Transcription profiling of mouse naive CD4+CD25-CD62Lhi T cells and nTreg cells with Eos knock-down

Project description:Eos expression in Treg cells have been documented by several microarrays including ours. We hypothesized that Eos facilitates Foxp3- dependent gene repression in Regulatory T cells. In order to investigate the role of Eos in mediating the Foxp3-dependent gene silencing program, we utilized lentiviral shRNA knockdown of Eos in natural Tregs isolated from the periphery of Balb/C mice. A renilla luciferase (RL) gene specific shRNA lentivirus was used as a control for the transduction of cells. The transcriptional profile of naive T cells, natural Tregs, Eos knockdown Tregs, and control shRNA knockdown Tregs was compared using Agilent 4x 44K whole mouse genome array. The goal of this microarray is to document the global effect of the loss of Eos expression on the transcriptional profile of natrual Treg cells. Experiment Overall Design: Eos knock-down (si-Eos) was mediated by Lentivirus expressing GFP as a reporter of transduction and sorting marker. Renilla luciferase specific shRNA lentiviral transduction was carried out in parallel as a control. NaÃ¯ve (CD4+CD25-CD62Lhi) T cells and nTreg cells were freshly isolated from Balb/C mice.

2009-10-16 | E-GEOD-17166 | biostudies-arrayexpress

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