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Gene expression in CD8+ T cells derived from Nrdp1+/+ and Nrdp1-/- mice

ABSTRACT: The purpose of this study was to determine which genes are differentially regulated by the E3 ligase Nrdp1 in CD8+ T cells after treatments with anti-CD3/CD28 Abs. The results demonstrate increased induction of cytotoxicity-associated genes in Nrdp1-/- mice than in Nrdp1+/+ mice after activation. Thus Nrdp1 may be involved in the regulation of TCR signaling.

ORGANISM(S): Mus musculus

PROVIDER: GSE70393 | GEO | 2015/08/03

SECONDARY ACCESSION(S): PRJNA288506

REPOSITORIES: GEO

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Gene expression in CD8+ T cells derived from Nrdp1+/+ and Nrdp1-/- mice

Project description:The purpose of this study was to determine which genes are differentially regulated by the E3 ligase Nrdp1 in CD8+ T cells after treatments with anti-CD3/CD28 Abs. The results demonstrate increased induction of cytotoxicity-associated genes in Nrdp1-/- mice than in Nrdp1+/+ mice after activation. Thus Nrdp1 may be involved in the regulation of TCR signaling. Naive CD8+ T cells derived spleens of Nrdp1+/+ and Nrdp1-/- mice were either untreated or treated with immobilized anti-CD3 (5 μg/ml) and soluble anti-CD28 (1 μg/ml) Abs for 4h or 8h. Equal amounts of RNA were assayed for gene expression using Affymetrix mouse 430 2.0 arrays.

2015-08-03 | E-GEOD-70393 | biostudies-arrayexpress

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Project description:To understand the function of Riplet in effector CD8 T cells, we have employed whole genome microarray expression profiling of effector CD8 T cells from wild-type (WT) and Riplet knockout (KO) mice. Naive CD8 T cells isolated from splenocytes in WT and Riplet KO mice were stimulated with anti-CD3 and anti-CD28 Abs and after resting culture, restimulated with anti-CD3 Ab in vitro and mRNA was isolated.

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Microarray analysis of WT and Tfap4-KO CD8 T cells during early activation

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2014-07-13 | E-GEOD-58078 | biostudies-arrayexpress

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Project description:To broadly assess which pathways FRCs regulate in CD8+ T cells, we sorted CD8+ T cells for RNA-seq following activation in whole splenocyte mixtures via soluble anti-CD3/CD28 for 48 hours (Stim), activated with anti-CD3/CD28 in the presence of Nos2–/– FRCs (FRC) or activated with anti-CD3/CD28 plus 100 ng/ml recombinant IL-6 (IL-6). Here we demonstrate that FRC-derived signals, including IL-6, act in concert with TCR signaling and co-stimulation to promote the expression of MYC and HIF-1-dependent glycolytic genes and vital pro-survival genes (encoding BCL-2 family members, inhibitors of apoptosis [IAPs] members and Cflar) in activated CD8+ T cells.

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Project description:TC-510 is a novel cell therapy that consists of autologous genetically engineered T cells expressing two synthetic constructs: first, a single-domain antibody that recognizes human Mesothelin, fused to the CD3-epsilon subunit which, upon expression, is incorporated into the endogenous T cell receptor (TCR) complex and second, a PD-1:CD28 switch receptor, which is expressed on the surface of the T cell, independently from the TCR. The PD-1:CD28 switch receptor comprises the PD-1 extracellular domain fused to the CD28 intracellular domain via a transmembrane domain. Thus, the switch is designed to produce a costimulatory signal upon engagement with PD-L1 on cancer cells.

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Mus musculus primary CD4+ T cell di-glycine remnant and whole cell proteomics

Project description:It is known that ubiquitination is important for T cell receptor (TCR) signaling during T cell activation but the breadth of ubiquitination events triggered during TCR signaling is not completely understood. This dataset utilizes di-glycine remnant profiling combined with mass spectrometry to identify a global landscape of ubiquitination events downstream of the TCR and to quantify changes ubiquitin abundance in response to TCR stimulation. Additionally, whole cell proteomics data were generated to measure protein abundances during TCR stimulation. Mouse primary T cells were isolated, proliferated and either remained resting or stimulated with CD3/CD28 to activate downstream signaling through the TCR and co-stimulatory pathways. Di-glycine remnant profiling and whole cell proteomics was performed on rested cells and cells that had undergone CD3/CD28 TCR stimulation for 4 hours. These data were analyzed to identify the ubiquitination events during TCR activation and to quantify the change in peptide-based ubiquitin abundance and total protein abundance over the course of the 4 hour TCR stimulation. Integration of di-glycine and whole cell proteomics was used to generate protein-specific predictions of whether ubiquitination events downstream of TCR signaling lead to a decrease in associated protein abundance. The analysis of these data suggests that T cell activation leads to an increase in ubiquitination that is not associated with proteasomal or lysosomal degradation.

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ATAC-seq profiling of in vitro FRC-conditioned, IL6-conditioned or control (anti-CD3/CD28)-stimulated CD8+ T cells

Project description:To broadly assess which pathways FRCs regulate in CD8+ T cells, we sorted CD8+ T cells for ATAC-seq following activation in whole splenocyte mixtures via soluble anti-CD3/CD28 (0.25μg/ml) for 48 hours (Stim), activated with anti-CD3/CD28 in the presence of Nos2–/– FRCs (FRC) or activated with anti-CD3/CD28 plus 100 ng/ml recombinant IL-6 (IL-6). Here we demonstrate that FRC-derived signals, including IL-6, act in concert with TCR signaling and co-stimulation to remodel chromatin and render essential transcription factor binding motifs accessible in activated CD8+ T cells. Signals from FRCs led to increased binding regions for MYC, HIF-1α and HIF-1β, which are known to promote metabolic pathways following T cell activation. Additionally, FRC-derived signals promoted activity of transcription factors that regulate survival and memory programs in T lymphocytes such as BATF and BACH2.

2019-10-14 | GSE136903 | GEO

RNA sequencing analysis of anti-CD3/CD28 stimulated wild type-OT1 (WT) and Lrch1-/- -OT1 (KO) CD8+ T cells

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2020-07-29 | GSE150634 | GEO

Proteome of CD4 T cells activated through the TCR in the presence of IL2 and IL12 - Part 1

Project description:To activate primary T cells, lymph nodes were removed and disaggregated. Cells were cultured in RPMI 1640 containing L-glutamine, 10% FBS, 50 μM β-mercaptoethanol and penicillin/streptomycin. Cells were stimulated with 1 μg/ml of the CD3 monoclonal antibody (2C11) and 2 μg/ml anti-CD28 (37.51) in the presence of cytokines IL12 (10 ng/ml) and 20 ng/ml IL2 (20 ng/ml). Cells were stimulated for 24 hours. Live TCR activated CD4+ cells were sorted for CD4+ and CD45.1+ expression and DAP1 exclusion prior to collection for proteomics processing. Mice were “wild-type” (ie non-TCR transgenic) from OT-2 CD45.1 expressing C57bl6 background maintained in-house line.

2019-03-29 | PXD012052 | Pride

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Project description:The aim of the project is to determine the binding sites of Ikaros in CD4+ T cells. To perform this, CD4 naive T cells (CD4 TN; d0) either rested or activated with anti-CD3+anti-CD28 Abs for 1 day (Th0 d1) were subjected to a ChIP using anti-Ikaros Ab followed by high throughput sequencing.

2021-04-26 | GSE157811 | GEO

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