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Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [RNA-seq II]

ABSTRACT: In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection. Flow cytometric analysis indicated that EGR2 is expressed selectively within the progenitor exhausted subset, however a subpopulation of progenitor exhausted cells did not express in EGR2. To define the differences between the EGR2+ and EGR2- progenitor exhausted cells, GFP+ and GFP- polyclonal progenitor exhausted (ie. CD44int-hiPD-1+Slamf6+Tim3-) CD8+ T cells were sorted from Egr2-GFP reporter mice at day 20 p.i. with chronic LCMV-Cl13, and analysed by RNAseq. The resulting data demonstrated that GFP- progenitor cells have a more differentiated phenotype.

ORGANISM(S): Mus musculus

PROVIDER: GSE152849 | GEO | 2021/03/02

REPOSITORIES: GEO

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Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [scRNAseq]

Project description:In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection. We conducted scRNAseq analysis on sorted virus-specific tetramer+ CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from either littermate control or EGR2 T cell conditional knock-out mice. Cells were labelled with hashtags and mixed prior to multiplexed analysis. The resulting data demonstrated that the exhausted cell subsets within EGR2 KO CD8+ T cells have an effector-like phenotype, suggesting that EGR2 stabilises the exhausted state.

2021-03-02 | GSE154143 | GEO

Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [ATACseq]

Project description:In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection. Flow cytometric and scRNAseq analysis indicated that EGR2 deficient CD8+ T cells had an abnormal effector-like phenotype. To examine whether this was due to epigenetic alterations, we conducted ATACseq analysis on sorted virus-specific tetramer+ CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from either littermate control or EGR2 T cell conditional knock-out mice. The resulting data demonstrated that there were substantial epigenetic changes within EGR2 KO CD8+ T cells, suggesting that EGR2 stabilises the exhausted epigenetic state.

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Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [RNA-seq I]

Project description:In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection. Flow cytometric analysis indicated that EGR2 deficient CD8+ T cells had a block in differentiation and failed to undergo terminal exhaustion. To confirm this at a whole transcriptome level, we conducted RNAseq analysis on sorted splenic virus-specific tetramer+ CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from either littermate control or EGR2 T cell conditional knock-out mice. The resulting data demonstrated that there was a global loss of the terminally exhausted gene signature within EGR2 KO CD8+ T cells. This suggests that EGR2 promotes terminal CD8+ T cell exhaustion.

2021-03-02 | GSE134689 | GEO

Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [CHIP-seq]

Project description:In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection. Flow cytometric and RNAseq analysis indicated that EGR2 deficient CD8+ T cells had a block in differentiation and failed to undergo terminal exhaustion. To examine the direct gene targets of EGR2 during exhaustion, we conducted ChIPseq analysis on enriched bulk splenic CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from C57BL/6J mice. The resulting data demonstrated that EGR2 directly controls expression of key gene targets, including Pdcd1, Tigit, Cxcr5, Tcf7, Bach2 and Bcl6.

2021-03-02 | GSE134708 | GEO

RNA-seq analysis of CD8 tumour infiltrating lymphocytes from GFP-Egr2 Knockin and hCD2-Cre Egr2loxP/loxP Egr3-/- mice

Project description:To determine the effect of Egr2 and Egr3 on tumour infiltrating lymphocyte gene expression, GFP-Egr2 knockin (Egr2 Kin) and hCD2-Cre Egr2loxP/loxP Egr3-/- (Egr2/3 DKO) mice were inoculated with MC38 or B16 tumour cells. Fourteen days later, GFP-Egr2high and Egr2-/-Egr3-/- CD8+ tumour infiltrating lymphocytes were isolated from Egr2 Kin and Egr2/3 DKO mice, respectively, and analysed by RNA-seq.

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GFP-Egr2 ChIP-seq analysis of CD4 T cells

Project description:Identification of Egr2 binding sites in CD4 T cells from GFP-Egr2 knockin (Egr2 Kin) mice by GFP-Egr2 ChIP-seq

2020-07-19 | E-MTAB-7797 | biostudies-arrayexpress

Identification of a T-bet hi Quiescent Exhausted CD8 T Cell Subpopulation That Can Differentiate into TIM3 + CX3CR1 + Effectors and Memory-like Cells

Project description:Persistent Ag induces a dysfunctional CD8 T cell state known as "exhaustion" characterized by PD-1 expression. Nevertheless, exhausted CD8 T cells retain functionality through continued differentiation of progenitor into effector cells. However, it remains ill-defined how CD8 T cell effector responses are sustained in situ. In this study, we show using the mouse chronic lymphocytic choriomeningitis virus infection model that CX3CR1+ CD8 T cells contain a T-bet-dependent TIM3-PD-1lo subpopulation that is distinct from the TIM3+CX3CR1+PD-1+ proliferative effector subset. The TIM3-CX3CR1+ cells are quiescent and express a low but significant level of the transcription factor TCF-1, demonstrating similarity to TCF-1hi progenitor CD8 T cells. Furthermore, following the resolution of lymphocytic choriomeningitis virus viremia, a substantial proportion of TCF-1+ memory-like CD8 T cells show evidence of CX3CR1 expression during the chronic phase of the infection. Our results suggest a subset of the CX3CR1+ exhausted population demonstrates progenitor-like features that support the generation of the CX3CR1+ effector pool from the TCF-1hi progenitors and contribute to the memory-like pool following the resolution of viremia.

2021-04-13 | GSE148497 | GEO

ChIP-seq analysis of wild-type or PAC1-/- T cells with anti-H3K27-ac

Project description:To analyze the effects of PAC1 on acetylation of H3K27 in exhausted CD8+ T cells, we isolated CD8+ T cells from spleen of wild-type or PAC1-/- mice post LCMV Cl13 infection and performed ChIP-seq with anti-H3K27-ac.

2019-12-22 | GSE141261 | GEO

Defining memory-like CD8 T cells that respond to PD-1 therapy in chronic viral infection

Project description:Chronic viral infections are characterized by a state of CD8 T cell dysfunction termed exhaustion. A better understanding of the mechanisms that regulate CD8 T cell responses during chronic infection is required to improve immunotherapies that restore function in exhausted CD8 T cells. Here we identify a novel population of virus-specific CD8 T cells with a T follicular helper (Tfh)-like signature in mice chronically infected with lymphocytic choriomeningitis virus (LCMV). These Tfh-like CD8 T cells expressed the programmed cell death-1 (PD-1) inhibitory receptor but at the same time also expressed co-stimulatory molecules and had a gene signature that was related to CD8 T cell memory precursor cells and hematopoietic stem cells (HSC). These Tfh-like CD8 T cells acted as stem cells during chronic infection undergoing self-renewal and also differentiating into the terminally exhausted CD8 T cells that were present in both lymphoid and non-lymphoid tissues. The Tfh-like CD8 T cells were found only in lymphoid tissues and resided predominantly in the T cell zones along with naÃ¯ve CD8 T cells. Interestingly, the proliferative burst after PD-1 blockade came almost exclusively from this Tfh-like CD8 T cell subset. Importantly, the transcription factor TCF1 played a cell intrinsic and essential role in the generation of Tfh-like CD8 T cells. Taken together, our study identifies Tfh-like CD8 T cells as the critical subset for maintaining the pool of virus-specific CD8 T cells during chronic infection and as the cells that proliferate after PD-1 blockade. These findings provide a better understanding of T cell exhaustion and have implications towards optimizing PD-1 directed immunotherapy. 8 samples isolated from CD8 T-cells in LCMV clone 13 GK1.5 infected mice (2 naÃ¯ve, 3 CXCR5+Tim3-, 3 CXCR5-Tim3+) cells were analyzed

2016-08-02 | E-GEOD-84105 | biostudies-arrayexpress

The Transcriptome of over expressed SLAMF6 isoform-3 in activated Jurkat cell line

Project description:SLAMF6 is a homotypic receptor of the Ig-superfamily associated with progenitor exhausted T cells. In humans, SLAMF6 has three splice isoforms involving its V-domain.We KO isoform 1 of SLAMF6 in a Jurkat cell line and harvest this cell line RNA using Bulk-RNA-Seq after activation in 5 time points. Comparing the results to WT Jurkat cell line, we analyzed the transcriptional landscape and showed that after activation SLAMF6 isoform 3 is the prominent expressed isoform, and that the KO Jurkat cells have a stronger cytotoxic phenotype.

2020-11-05 | GSE160817 | GEO

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