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Expression data from CD28+/- resting CD8 T cells

ABSTRACT: Expression data from CD28+/- resting CD8 T cells

PROVIDER: PRJNA414963 | ENA |

REPOSITORIES: ENA

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Expression data from CD28+/- resting CD8 T cells

Project description:We used microarrays to detail the global programme of gene expression underlying the loss of CD28 co-receptor on primary human CD8+ T cells. We identified distinct classes of differentially regulated genes between sorted T cell subsets.

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Genome wide expression profiles (RNAseq) of human CD8+ T cells in resting, activated (CD3+CD28) and PD-1-stimulated cells (CD3+CD28+PD-L1-Fc) at diferent time points

Project description:Background: Binding of the programmed death-1 (PD-1) receptor to its ligands (PD-L1/2) transduces inhibitory signals that promote exhaustion of activated T cells. Blockade of the PD 1 pathway is widely used for cancer treatment, yet the inhibitory signals transduced by PD-1 in T cells remain elusive. Methods: Expression profiles of human CD8+ T cells in resting, activated (CD3+CD28) and PD-1-stimulated cells (CD3+CD28+PD-L1-Fc) conditions were evaluated by RNA-seq. Bioinformatic analyses were used to identify signaling pathways differentially regulated in PD 1-stimulated cells.

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CD28 region-capture HiC of resting and anti-CD3/CD28-stimuated Jurkat cells

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Profiling of Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD8+ T cells

Project description:Profiling of Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD8+ T cells

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ChIP-seq of resting and anti-CD3/CD28-stimuated Jurkat cells

Project description:To finely dissect the dynamic changes in the epigenome and chromatin state during T cell activation, we utilized the Jurkat cell line as a model and performed ChIP-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells, targeting various histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K27me3), RNA PolII, and CTCF.

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Differentiated expression profiling between CD8+CD28+ T cell subset and CD8+CD28- T cell subset using long non coding RNA microarray in five healthy Chinese nonagenarians

Project description:To obtain the differentiated profiling of long noncoding RNA expression between CD8+CD28+ T cell subset and CD8+CD28- T cell subset, we have detecte lncRNA profiling between within-individual T cell subsets to identify differentiated lncRNA profiling in five apperant healthy Chinese nenogenarians who were cytomegalovirus-seropositive carriers. Human peripheral blood monocytes from these apperantly healthy CMV-seropositive nonagenarians was gathered. CD8+CD28+ T cells and CD8+CD28- T cells were further isolated using flow cytometry. Differentiated lncRNA profiling was compared between CD8+CD28+ T cells and CD8+CD28- T cells using lncRNA microarry detection within-individually. 586 lncRNAs were found significantly upregulated while 1113 lncRNAs were found significantly downregulated comparing CD8+CD28+ T cells with CD8+CD28- T cells in these Chinese nonagenarians with CMV seropositivity. Expression of ENST00000446590,NR_121652,NR_045006,ENST00000428936,NR_110375 from this differentiated profiling which were identified as previously domumented ageing-related lncRNAs were quantified in the same RNA samples by real-time PCR, confirming lncRNAs take critical role in regulating T cell immunosenesence in healthy nonagenarian Chinese CMV carriers. Diffentiated lncRNA profiling was in-pair compared between total RNAs isolated from CD8+CD28+ T cells and CD8+CD28- T cells within-individually in Chinese nonagenarian CMV carriers.

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ATAC-seq of resting and anti-CD3/CD28-stimuated Jurkat cells

Project description:The majority of genetic risk variants associated with autoimmune diseases are located in chromatin regions that are accessible during T cell stimulation. To systematically investigate the dynamic changes in chromatin accessibility during T cell activation, we utilized the Jurkat cell line as a model and performed ATAC-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells.

2025-09-01 | GSE276690 | GEO

PD-1 blockade-unresponsive human tumor-infiltrating CD8+ T cells are marked by loss of CD28 expression and rescued by IL-15

Project description:Blockade of programmed death-1 (PD-1) reinvigorates exhausted CD8+ T cells, resulting in tumor regression in cancer patients. Recently, reinvigoration of exhausted CD8+ T cells following PD-1 blockade was shown to be CD28-dependent in mouse models. Herein, we examined the role of CD28 in anti-PD-1-induced human T-cell reinvigoration using tumor-infiltrating CD8+ T cells (CD8+ TILs) obtained from non-small cell lung cancer patients. Single cell analysis demonstrated a distinct expression pattern of CD28 between mouse and human CD8+ TILs. Furthermore, we found that human CD28+CD8+, but not CD28–CD8+ TILs, responded to PD-1 blockade irrespective of B7/CD28 blockade, indicating that CD28 co-stimulation in human CD8+ TILs is dispensable for PD-1 blockade-induced reinvigoration, and loss of CD28 expression rather serve as a marker of anti-PD-1-unresponsive CD8+ TILs. Transcriptionally and phenotypically, PD-1 blockade-unresponsive human CD28–PD-1+CD8+ TILs exhibited characteristics of terminally exhausted CD8+ T cells with low TCF1 expression. Notably, CD28–PD-1+CD8+ TILs had preserved machinery to respond to IL-15, and IL-15 treatment enhanced proliferation of CD28–PD-1+CD8+ TILs as well as CD28+PD-1+CD8+ TILs. Taken together, we demonstrate loss of CD28 expression as a marker of PD-1 blockade-unresponsive human CD8+ TILs with TCF1– signature and provide mechanistic insights into combining IL-15 with anti-PD-1.

2020-05-01 | GSE145896 | GEO

Gene expression in CD3/CD28 stimulated CD8 vs CD8 with various dosage of Cholesterol treatment

Project description:gene expression in in vitro diffrerentiated CD8 (CD3/CD28 stimulation ) T cells and CD8 T cells treated with Cholesterol

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Gene expression of resting memory, resting naive and in vitro activated memory CD8+CD127+ T cells from spleen and bone marrow (BM)

Project description:To understand differences between resting and activated memory CD8+ T cells, we compared the global gene expression of ex vivo isolated naive and spleen and BM memory cells to in vitro activated spleen and BM memory cells. Single cell suspension from the spleen and bones of aged C57BL/6 mice were prepared. Naive (CD44-CD127+) and memory (CD44+CD127+) CD8+CD3+ T cells were then cytometrically sorted. Sorted cells were either immediately processed for RNA preparation or were activated with anti-CD3 and anti-CD28 for 42-44 hours. Total RNA was extracted using the NucleoSpin RNA (Macherey-Nagel). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 M-BM-5g total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to MG_U430_2 GeneChips (Affymetrix) in triplicates. Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

2015-02-05 | E-GEOD-62691 | biostudies-arrayexpress

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