RNA sequencing analysis of gene expression profiles in WT and Etv5-deficient TFH cells
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ABSTRACT:
PROVIDER: PRJNA1035785 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26669414_1.fastq.gz | Fastqsanger.gz | |||
| SRR26669414_2.fastq.gz | Fastqsanger.gz | |||
| SRR26669415_1.fastq.gz | Fastqsanger.gz | |||
| SRR26669415_2.fastq.gz | Fastqsanger.gz | |||
| SRR26669416_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The aim of this study is compare the gene expression profiles between wild-type (WT) and Etv5-deficient follicular helper T (TFH) cells to identify the molecular mechanism of how ETV5 promotes the TFH cell differentiation. Methods: TFH cells (CD4+CD44+CXCR5+PD-1+) from the spleen of WT and Etv5f/f;Cd4-Cre mice immunized with OVA in alum for 7 days were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol (GeneAll) according to the manufacturer’s instruction. The library for RNA sequencing was generated using the Truseq stranded mRNA library prep kit (Illumina), and sequencing was performed with Novaseq 6000 (Illumina). Results: Reads were mapped to the mouse reference genome (mm10) with Tophat (v2.0.13), and the aligned results were analyzed with Cuffdiff (v2.2.0) for differentially expressed genes (DEGs). A total of 92 genes were differentially expressed in Etv5-deficient TFH cells (46 genes upregulated and 46 genes downregulated) when compare with WT TFH cells (fold change > 2 and P-value < 0.05). Conclusions: Our study presents the first comparative gene expression analysis of TFH cells from control and T cell-specific Etv5-deficient mice. Since ETV5 usually acts as a transcription activator, we focused on the downregulated genes in Etv5-deficient TFH cells. Through this study, we identified the candidate genes that are targeted by ETV5 for TFH cell differentiation.
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Project description:CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation. Analysis of in vivo antigen-specific (LCMV-specific, SMARTA TCR transgenic) WT and Sh2d1a-/- follicular helper CD4 T cells (CXCR5high),versus non-follicular helper CD4 T cells (CXCR5low), eight days after viral infection.
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Project description:To better understand how Chi3l1 regulates the TFH response, we analyzed the transcriptome of CXCR5+PD1+CD4+Lin- TFH cells from msLNs of WT and Chi3l1-/- mice on D14 post H. pylori infection.
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Project description:Differential gene expression profile of Tfh and non-Tfh cells from both Wt and miR-155-/- mice spleens.
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Project description:Transcriptome analysis of Chi3l1-deficient TFH cells
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Project description:CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation. Analysis of in vivo polyclonal GC Tfh vs Tfh vs Non-Tfh eight days after LCMV viral infection. Analysis of in vivo follicular helper CD4 T cells (CXCR5high GL7low), versus germinal center follicular helper CD4 T cells (CXCR5hi GL7hi), versus non-follicular helper CD4 T cells (CXCR5low) eight days after viral infection.
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Project description:Gene Expression in COP1-ETV1-ETV5-cJun deficient mouse brain
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Project description:Follicular helper T (Tfh) cells access the B cell follicle to promote antibody responses, and are particularly important for germinal center (GC) reactions. However, the molecular mechanisms of how Tfh cells are physically associated with GCs are incompletely understood. Here we report that the sphingosine-1-phosphate receptor 2 (S1PR2) gene is highly expressed in a subpopulation of Tfh cells that localizes in GCs. S1PR2-deficient Tfh cells exhibited reduced accumulation in GCs due to their impaired retention. T cells deficient in both S1PR2 and CXCR5 were ineffective in supporting GC responses compared to T cells deficient only in CXCR5. These results suggest that S1PR2 and CXCR5 cooperatively regulate localization of Tfh cells in GCs to support GC responses. Venus-high Tfh, Venus-low Tfh, PD1-intermediate Th, PD1-low Th and naïve CD4+ T cells were sorted on FACSAria from immunized S1pr2V/+ mice or control mice for RNA extraction and hybridization on Affimetrix microarrays.
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