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Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [splicing]

ABSTRACT: Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [splicing]

PROVIDER: PRJNA823721 | ENA |

REPOSITORIES: ENA

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Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [Costimulation CD8 Repeat]

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Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [CRISPR]

Project description:Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [CRISPR]

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Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [Costimulation CD8 Repeat]

Project description:Here, we provide a dataset from a repeat RNA-seq from mouse antigen-specific CD8+ T cells in naïve, antigen-primed, and antigen-primed plus costimulated states. These were used to measure splicing changes between groups and compare levels of RNA Binding Protein transcript expression.

2022-04-08 | GSE200237 | GEO

Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [splicing]

Project description:Here, we provide deep RNA-seq from mouse antigen-specific CD8+ T cells in naïve, antigen-primed, and antigen-primed plus costimulated states. This was used to measure splicing changes between groups.

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Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [Costimulated CD8]

Project description:Here, we provide RNA-seq from mouse antigen-specific CD8+ T cells in naïve, antigen-primed, and antigen-primed plus costimulated states. This was used to compare levels of RNA Binding Protein transcript expression.

2022-04-08 | GSE200236 | GEO

Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [CRISPR]

Project description:Here we provide a dataset of deep RNA sequencing from mouse CD8+ T cell CRISPR-mediated knockout of RBP Tardbp after adoptive transfer and antigen+costimulatory stimulus (in mice) which we show is critical for optimal CD8+ T effector function.

2022-04-08 | GSE200238 | GEO

CD28-CBCA driven PKM splicing licenses CD8 T cell glycolysis and effector function

Project description:T cells stimulated in the absence of CD28 costimulation are functionally anergic, characterized by reduced glucose metabolism and ability to produce effector cytokines. Surprisingly, previous studies have shown relatively few CD28-specific changes in gene transcription upon costimulation. Using mice expressing mutations in the CD28 cytoplasmic tail, we show a major effect of CD28 costimulation is alternative splicing of numerous genes including the glycolytic enzyme pyruvate kinase (Pkm), which is preferentially spliced from Pkm1 to Pkm2 upon stimulation. PKM2 is dispensable for T cell activation, but necessary for CD8+ T cells to utilize aerobic glycolysis, produce effector cytokines, and provide anti-tumor immunity. Mechanistically, CD28 regulates expression of the Cap-Binding Complex adaptor protein ARS2, which binds Pkm splicing factors and facilitates their interaction with the elongating transcript. Data suggest a major function of CD28 costimulation is control of RNA biogenesis in support of T cell transcriptome remodeling and acquisition of effector function.

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Gene expression signature of in vitro activated CD8 T cells in response to antigen and B7-1 alone or along with IL-21

Project description:Differentiation of naive CD8 T cells into cytotoxic effector cells requires three distinct signals- antigen (signal 1), costimulation -B7-1 (signal 2) and cytokine, either interleukin-12, interferon-a/b, or IL-21 (signal 3). Interaction of naive CD8 T cells with antigen and B7-1 programs cell division and proliferation whereas the presence of cytokines- IL-12, IFNa/b or IL-21 promote survival, differentiation and memory establishment. In the absence of signal 3, the cells interacting with antigen/B7-1 undergo tolerance induction. Previous work had analyzed the regulation of mRNA expression changes induced by IL-12 and IFN-a and cells stimulated with antigen, B7-1 and cytokine by comparing mRNA expression levels in naïve CD8 T cells, cells stimulated with 2 signals (antigen and B7-1) (Agarwal, P.A., A. Raghavan, S.L. Nandiwada, J.M. Curtsinger, P.R. Bohjanen, D.L. Mueller and M.F. Mescher. Gene regulation and chromatin remodeling by IL-12 and Type I interferon in programming for CD8 T cell effector function and memory. J. Immunol. 183:1695-1704 (2009). PMCID: PMC2893405). That microarray data was deposited in the NCI GEO database and can be found at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc_GSE15930. The objective of the current study was to carry out the same analysis to determine IL-21-dependent changes in mRNA expression in CD8 T cells responding to antigen and B7-1-dependent costimulation in the absence or presence of IL-21.

2015-09-30 | GSE70136 | GEO

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