Genomic definition of multiple ex vivo Treg sub-phenotypes
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE20366 | GEO | 2010/03/02
SECONDARY ACCESSION(S): PRJNA125463
REPOSITORIES: GEO
Similar Datasets
Project description:Regulatory T (Treg) cells that express the FoxP3 transcription factor are essential for lymphoid homeostasis and immune tolerance to self. Other non-immunological functions of Treg cells, such as controlling metabolic function in adipose tissue, are also emerging. Treg cells originate primarily in the thymus, but can also be elicited from conventional T cells by in vivo exposure to low-dose antigen or homeostatic expansion, or by activation in the presence of TGFβ in vitro. Treg cells are characterized by a distinct transcriptional signature controlled in part, but not solely, by FoxP3. For a better perspective on transcriptional control in Treg cells, we compared gene expression profiles of a broad panel of Treg cells from various origins or anatomical locations. Treg cells generated by different means form different sub-phenotypes identifiable by particular combinations of transcripts, none of which fully encompass the entire Treg signature. Molecules involved in Treg effector function, chemokine receptors, and the transcription factors that control them are differentially represented in these subphenotypes. Treg cells from the gut proved dissimilar to cells elicited by exposure to TGFβ, but instead they resembled a CD103+Klrg1+ subphenotype preferentially generated in response to lymphopenia. All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and replicates or triplicates were generated for all groups. RNA from 1-5 x 104 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.
2010-03-09 | E-GEOD-20366 | biostudies-arrayexpress
Project description:Regulatory T (Treg) cells actively control pathological immune responses and immunotherapeutic strategies triggering an increase in the number and/or the function of endogenous Treg cells emerge as a promising therapeutic strategy in autoimmune diseases to restore tolerance. A remarkable heterogeneity in peripheral Treg cells has been evidenced and underscored the need to better characterize them and compare their suppressive function to determine which Treg subset will be optimally suitable for a given clinical situation. We demonstrated that repetitive injections of immature dendritic cells (DC) expand FoxP3-negative CD49b+ Treg cells that display an effector memory phenotype. Transcriptome analysis of ex-vivo isolated Treg-expanded by DC injections contains multiple transcripts of the canonical Treg signature shared mainly by CD25+ but also by other Treg subphenotypes. We provided an in-depth characterization of the CD49b+ Treg cells phenotype underscoring their similarities with CD25+ Treg cells and highlighting some specific expression pattern for several markers including LAG3, KLRG1, CD103, ICOS, CTLA-4 and GZB. Comparison of their suppressive mechanism in vitro and in vivo with that of FoxP3-positive Treg cells provide evidence of their potent suppressive activity in vivo, partly dependent on IL-10 secretion. Altogether our results underscore the therapeutic potential of IL-10 secreting CD49b+ Treg cells in arthritis and strongly suggest that expression of several canonical markers and suppressive function could be FoxP3-independent All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and two to three replicates were generated for all groups. RNA from 2.5-10 x 105 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays.
2015-12-10 | E-GEOD-68621 | biostudies-arrayexpress
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
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
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
Project description:Regulatory T (Treg) cells actively control pathological immune responses and immunotherapeutic strategies triggering an increase in the number and/or the function of endogenous Treg cells emerge as a promising therapeutic strategy in autoimmune diseases to restore tolerance. A remarkable heterogeneity in peripheral Treg cells has been evidenced and underscored the need to better characterize them and compare their suppressive function to determine which Treg subset will be optimally suitable for a given clinical situation. We demonstrated that repetitive injections of immature dendritic cells (DC) expand FoxP3-negative CD49b+ Treg cells that display an effector memory phenotype. Transcriptome analysis of ex-vivo isolated Treg-expanded by DC injections contains multiple transcripts of the canonical Treg signature shared mainly by CD25+ but also by other Treg subphenotypes. We provided an in-depth characterization of the CD49b+ Treg cells phenotype underscoring their similarities with CD25+ Treg cells and highlighting some specific expression pattern for several markers including LAG3, KLRG1, CD103, ICOS, CTLA-4 and GZB. Comparison of their suppressive mechanism in vitro and in vivo with that of FoxP3-positive Treg cells provide evidence of their potent suppressive activity in vivo, partly dependent on IL-10 secretion. Altogether our results underscore the therapeutic potential of IL-10 secreting CD49b+ Treg cells in arthritis and strongly suggest that expression of several canonical markers and suppressive function could be FoxP3-independent
2015-12-10 | GSE68621 | GEO
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
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
Project description:CD4+Foxp3+ regulatory T cells (Treg) are essential for immune homeostasis and maintenance of self-tolerance. They are produced in the thymus and also generated de novo in the periphery in a TGFB dependent manner. Foxp3+ Treg are also required to achieve tolerance to transplanted tissues when induced by co-receptor or costimulation blockade. Using TCR transgenic mice to avoid issues of autoimmune pathology we show that Foxp3 expression is necessary and sufficient for tissue tolerance by coreceptor blockade. Moreover, the known need in tolerance induction for TGFB signalling to T cells, can wholly be explained by its role in induction of Foxp3, as such signalling proved dispensable for the suppressive process. We analysed the relative contribution of TGFB and Foxp3 on the transcriptome of TGFB induced Treg. TGFB elicited a large set of downregulated signature genes. The number of genes uniquely modulated due to the influence of Foxp3 alone was surprisingly limited. Retroviral conditional Foxp3 expression proved sufficient to confer transplant-suppressive potency on CD4+ T cells, and was lost once nuclear Foxp3 expression was extinguished. Thus despite the large genetic influence of TGFB exposure on iTreg the crucial Foxp3 influenced signature independent of TGFB is small. These data support a dual role for TGFB and Foxp3 in induced tolerance, where TGFB stimulates Foxp3 expression whose sustained expression is associated with acquisition of tolerance 21 samples were analyzed. 5 replicates of Marilyn.Foxp3hCD2 activated (HY)(Untreated) and TGFB-induced (HYT) cells sorted as CD4+hCD2+ and CD4+hCD2- and 3 replicates of Marilyn.Foxp3-/- activated and TGFβ-experienced (but Foxp3-) cells sorted as CD4+CD2. Pairwise comparisons were generated for the Marilyn Foxp3hCD2 UT versus TGFB induced populations and also for the Marilyn Foxp3-/- UT versus the TGFB experienced cells sorted as CD4+CD2
2012-10-03 | E-GEOD-39529 | biostudies-arrayexpress
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.
2012-08-23 | GSE40238 | GEO