Microarray analysis of the effects of IL-2 signaling on in vitro activated WT CD8 T cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE58077 | GEO | 2014/07/13
SECONDARY ACCESSION(S): PRJNA248825
REPOSITORIES: GEO
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Project description:Interleukin 2 (IL-2) promotes proliferation and differentiation of CD8+ T cells in vitro and in vivo. To define gene expression regulated by IL-2, we purified naive CD8+ T cells, activated them for 2 days followed by treatment with recombinant IL-2 or with neutralizing antibody against IL-2 and compared gene expression between the two treatments. Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel), amplified using a PicoSL RNA amplification kit (Nugen) and biotinylated with Encore biotin module (Nugen). Labeled RNA was hybridized to Mouse Gene 1.0ST microarrays (Affymetrix) according to the manufacturer’s instruction.
2014-07-13 | E-GEOD-58077 | biostudies-arrayexpress
Project description:Interleukin 6 (IL-6) is a pleiotropic cytokine with diverse roles in homeostasis, inflammation, and cancer. Here we performed transcriptional profiling of OT-I CD8+ T cells activated in the presence or absence of IL-6. In this study, splenocytes from wild type C57BL/6J mice were incubated with SIINFEKL peptide for two days to activate OT-I CD8+ T cells. SIINFEKL was then withdrawn, T cells were rested in medium with IL-2 for three days, and CD8+ T cells were restimulated with anti-CD3 + anti-CD28 antibodies and purified by FACS for RNA sequencing analysis on day 7. Throughout this culture period, some cells were treated with anti-IL6R antibody (clone MR16-1, 5 ug/ml), isotype control antibody (5 ug/ml), recombinant IL-6 (10 ng/ml), or recombinant hyper-IL-6 (IL-6 linked to IL6R; 20 ng/ml). Experimental conditions were run in triplicate, for a total of 15 samples. Conclusion: Neutralization of endogenous IL-6 signaling (with anti-IL6R antibody) enhances effector differentiation of CD8+ T cells, while addition of exogenous IL-6 or hyper-IL-6 suppresses effector differentiation.
2022-11-04 | GSE151157 | GEO
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 or interferon-a/b (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 or IFNa/b promote survival, differentiation and memory establishment. In the absence of signal 3, the cells interacting with antigen/B7-1 undergo tolerance induction. The objective of this study was to elucidate the mechanisms how the provision of signal 3 promotes differentiation and averts tolerance induction in CD8 T cells. Trichostatin A is a pharmacological agent that inhibits histone deacetylase activity, hence regulating chromatin structure and gene expression and differentiation in many cell types. Gene signature profiles of IL-12, IFNa/b and trichostatin A stimulated cells were compared to elucidate the molecular mechanisms of gene regulation. Oligonucleotide microarray analysis is carried out to determine the extent and molecular nature of the CD8 T cell differentiation program induced by IL-12 or IFNa/b in concert with antigen and B7-1 signal.
2009-07-22 | GSE15930 | GEO
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
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 or interferon-a/b (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 or IFNa/b promote survival, differentiation and memory establishment. In the absence of signal 3, the cells interacting with antigen/B7-1 undergo tolerance induction. The objective of this study was to elucidate the mechanisms how the provision of signal 3 promotes differentiation and averts tolerance induction in CD8 T cells. Trichostatin A is a pharmacological agent that inhibits histone deacetylase activity, hence regulating chromatin structure and gene expression and differentiation in many cell types. Gene signature profiles of IL-12, IFNa/b and trichostatin A stimulated cells were compared to elucidate the molecular mechanisms of gene regulation. Oligonucleotide microarray analysis is carried out to determine the extent and molecular nature of the CD8 T cell differentiation program induced by IL-12 or IFNa/b in concert with antigen and B7-1 signal. Experiment Overall Design: The programming for development of function and memory in presence of signal 3 occurs over three days of initial stimulation, and antigen-B7 and IL-12 or IFNa/b must be present for most of this period to achieve maximal responses. We analyzed gene expression in highly purified naive CD8 T cells at 0, 24, 48 and 72h of in vitro culture stimulated with antigen-B7 and with or without IL-12 or IFNa/b to tease apart gene expression profiles of naive, 2-signal and 3-signal stimulated cells over the course of 3-days. Gene expression of cells stimulated with trichostatin A for 72hr were compared with IL-12 or IFNa/b stimulated cells. 20 arrays.
2009-08-01 | E-GEOD-15930 | biostudies-arrayexpress
Project description:murine naive CD8+ T-cell samples for control or treated with 100ng/ml of IL-15 and/or IL-21 for 4 hours Keywords: other
2004-12-11 | GSE2059 | GEO
Project description:Effects of IL-4 on CD8 T cells functions are largely unknown. IL-4 induces survival and proliferation of CD8 T cells, but several studies suggest that IL-4 could also affect several functions of CD8 T cells such as cytotoxicity. Our team has shown that IL-4 repress the expression of Ccl5 in vitro. To define more precisely the impact of IL-4 on CD8 T cells, we performed a whole genome expression microarray analysis of naive and memory CD8 T cells cultured in presence or absence of IL-4. This approach allowed us to define the IL4-gene-expression signature on CD8 T cells. 18 samples were processed. Two populations of F5 naive CD8 T cells were FACS-sorted: samples from each population were incubated 20 hours with IL-7 in presence or absence of IL-4. Thus, a total of 6 “Naive” samples were processed. In addition, 4 populations of F5 TIM memory CD8 T cells were FACS-sorted: samples from 2 of these populations were incubated 20 hours in presence of IL-7 and/or IL-4, or in medium alone. Thus, 12 “Memory” samples were processed.
2011-09-27 | E-GEOD-32423 | biostudies-arrayexpress
Project description:Interleukin 6 (IL-6) is a pleiotropic cytokine with diverse roles in homeostasis, inflammation, and cancer. To identify genes regulated by short-term IL-6 treatment, we performed RNAseq profiling of naïve murine CD8+ T cells stimulated for 4 hours with recombinant mouse IL-6 in the presence or absence of anti-CD3/CD28 antibodies. We found that IL-6 controls expression of diverse regulators of T cell differentiation and function, including repression of co-stimulatory receptors, induction of co-inhibitory receptors, and induction of transcription factors important for memory formation and T cell quiescence.
2022-11-04 | GSE199045 | GEO
Project description:To investigate the role of cBAF in regulation of Tbet binding, polyclonal naive CD8 T cells were stimulated for 48h with anti-CD3, CD28, and hIL-2. Cells were then treated with DMSO, ACBI1, or BRM014 for 6 hours, and treated with recombinant mouse IL-12 for the last two hours of inhibitor treatment. Chromatin accessibility profiling was performed via ATAC-seq.
2023-06-13 | GSE228193 | GEO
Project description:The epigenetic modifier TET2 plays a role in cell fate decisions in hematopeotic stem cells and CD4+ Th1 and Th17 differentiation. Here, we demonstrate that loss of TET2 promotes CD8+ memory differentiation following acute viral infection with LCMV-Armstrong. To identify early gene expression changes following TCR activation in WT versus TET2cKO CD8+ T cells, we isolated naive CD8+ T cells and activated them for three days with anti-CD3/CD28+IL-2 and performed microarray analysis.
2017-02-22 | GSE95147 | GEO