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Whole-transcriptome quantitative analysis of WT versus Ikzf4-/- CD4+ T cells cultured in Th1-polarizing conditions

ABSTRACT: Purpose: To evaluate transcriptome-wide alterations in CD4+ T cells cultured under Th1-polarizing conditions in the absence of the Ikaros zinc finger transcription factor Eos via RNA-seq analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE147428 | GEO | 2020/03/24

REPOSITORIES: GEO

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Transcriptomic analysis of WT versus Ikzf4-/- CD4+ T cells cultured in Th2-polarizing conditions

Project description:The Ikaros zinc finger transcription factor Eos has been commonly implicated in regulatory T cells to promote their immunosuppressive functions. Paradoxically, a new role is emerging for Eos in promoting pro-inflammatory responses of conventional CD4+ T cells in the dysregulated setting of autoimmunity. Even so, the precise role of Eos in regulating the differentiation and function of healthy effector CD4+ T cell subsets remains unclear. Here, we find that Eos is a positive regulator of CD4+ T helper 2 (TH2) cells—effector T cells implicated in the induction of allergic asthma. Using murine in vitro TH2 cells and an in vivo house dust mite asthma model, we found that Eos-deficient T cells had reduced expression of key TH2 transcription factors, effector cytokines, and differentiation receptors. Mechanistically, among various TH2-polarizing pathways, the IL-2/STAT5 axis and its downstream TH2 gene targets emerged as one of the most significantly downregulated networks in Eos deficiency. Using in vitro TH2 cells and overexpression of Eos zinc-finger-domain mutants, we discovered that Eos forms a novel complex with and supports the tyrosine-phosphorylated signaling activity of STAT5. Overall, these data define a novel regulatory mechanism whereby Eos promotes IL-2/STAT5 activity to facilitate TH2 differentiation.

2023-02-01 | GSE216737 | GEO

Effect of SGC0946 and SGC0649 on CD4+ T cells under Th1 polarizing conditions

Project description:Comparison between naïve CD4+ mouse T cells and either bona fide IFNg+ and IFNg- CD4+ T cells after culturing under Th1 polarizing conditions in the presence of either the epigenetic probe SGC0946 or SGC0649

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Whole-transcriptome quantitative analysis of WT versus Ikzf4-/- CD4+ T cells cultured in Th1-polarizing conditions

Project description:Whole-transcriptome quantitative analysis of WT versus Ikzf4-/- CD4+ T cells cultured in Th1-polarizing conditions

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ATAC-seq analysis of WT versus Ikzf3-/- CD4+ T cells cultured in Th1-polarizing or Tfh-polarizing conditions

Project description:Effective immunity to viruses such as influenza and SARS-CoV-2 requires the generation of CD4+ T cell subsets that coordinate complementary aspects of the immune response. These include T follicular helper (TFH) and T helper 1 (TH1) cells, which promote humoral and cell-mediated helper responses, respectively. A third population, CD4+ cytotoxic T lymphocytes (CD4-CTLs) facilitates clearance of infection via mechanisms normally associated with CD8+ T cells, including perforin-mediated destruction of infected cells. Here, we identify the transcription factor Aiolos as a reciprocal regulator of TFH and CD4-CTL responses. We demonstrate that Aiolos deficiency compromises TFH differentiation and antibody production during influenza infection. Conversely, we find that CD4+ T cells acquire a cytotoxic-like program in the absence of Aiolos, including increased expression of the CTL-associated transcription factors Eomes and Blimp-1. We further show that while Aiolos positively regulates the TFH transcriptional regulators Zfp831, Tcf-1 and Bcl-6, it also directly represses expression of IL-2Ra and IL-2/STAT5-driven expression of the cytotoxic gene program. Thus, our findings identify Aiolos as a pivotal regulator of TFH and CD4-CTL differentiation and highlight its potential as a therapeutic target for the manipulation of CD4+ T cell humoral and cytotoxic responses.

2023-02-01 | GSE203064 | GEO

Whole-transcriptome quantitative analysis of WT versus Ikzf3-/- CD4+ T cells cultured in Th1-polarizing or Tfh-polarizing conditions

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WT versus Ikzf3-/- CD4+ T cells cultured in Th1-polarizing or Tfh-polarizing conditions

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

2023-02-01 | GSE203066 | GEO

Effect of SGC0946 and SGC0649 on CD4+ T cells under Th1 polarizing conditions

Project description:Effect of SGC0946 and SGC0649 on CD4+ T cells under Th1 polarizing conditions

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Transcriptional modifications driven by STING activation in polarizing TH1 and Th9 cells

Project description:Transcriptional modifications driven by STING activation in polarizing TH1 and Th9 cells

| PRJNA613701 | ENA

Eomes+ natural Th1 (nTh1) T cells share functional features with classical Th1 (cTh1) cells.

Project description:Identification of intrathymic Eomes+ natural Th1 cells creates a novel idea that there is more than one way for the generation of innate CD4 T cells. To more deeply characterize this type of innate T cells, we compared the gene expression profile between nTh1 cells generated in CIITAtg mice and classic Th1 cells differentiated from naive CD4 T cells in Th1-polarizing condition.

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Transcriptional modifications driven by STING activation in polarizing TH1 and Th9 cells

Project description:We assessed the global transcriptional changes driven by STING activation with the cyclic dinucleotide 2'3'-cGAMP TH1 and TH9 cells polarized in vitro for 16h and 48h. Our data indicated that STING activation led to an upregulation of Type I Interferon, Interferon Stimulated Genes and pro-inflammatory molecule production that was maintained over time. Furthermore, not only STING activation enhanced the transcription of TH1 and TH9 main effector cytokines (respectively Ifng and Il9) but they also also globally enhanced their differentiation programs.

2022-02-18 | GSE147300 | GEO

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