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Gene expression profile of CD4+ T-cells restimulated by anti-CD3 and anti-ICOS compared to anti-CD3 alone

ABSTRACT: Engagement of the ICOS receptor represents a key event in a process that culminates in Bcl6 expression and acquisition of the TFH and TFR phenotype. To better understand the essentials of ICOS-mediated signaling pathway, we profiled the changes in gene expression elicited after co-ligation of ICOS and CD3 compared with CD3 ligation alone. Naïve CD4+ T-cells were purified from single cell suspensions of B6 spleen and stimulated with anti-CD3 and anti-CD28 for 2d followed by resting overnight before 20 min of incubation with anti-CD3 and/or anti-ICOS and cross-linking with goat anti-hamster Ab for 8h. RNA was prepared, amplified, labeled and hybridized to Mouse Gene 1.0 ST Array (Affymetrix), in quadruplicates for anti-CD3 ligation and duplicates for anti-CD3/ anti-ICOS co-ligation.

ORGANISM(S): Mus musculus

SUBMITTER: Jianmei Leavenworth

PROVIDER: E-GEOD-61284 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profile of CD4+ T-cells restimulated by anti-CD3 and anti-ICOS compared to anti-CD3 alone

Project description:Engagement of the ICOS receptor represents a key event in a process that culminates in Bcl6 expression and acquisition of the TFH and TFR phenotype. To better understand the essentials of ICOS-mediated signaling pathway, we profiled the changes in gene expression elicited after co-ligation of ICOS and CD3 compared with CD3 ligation alone.

2014-09-23 | GSE61284 | GEO

RNA-seq of purified T cells treated with KY1044 + anti-CD3 against anti-CD3 treated controls

Project description:KY1044 is a human monoclonal IgG1 that selectively binds to Inducible T cell CO-stimulator (ICOS). The co-stimulatory effect of KY1044-stimulated human T cells was analysed by RNA sequencing (RNA seq). Purified pre-activated (ICOS+ve) T cells were stimulated with either KY1044 and anti-CD3 or anti-CD3 alone and cells were harvested for RNA seq after 6hrs. Kallisto transcript abundance are provided in the absence of raw sequence reads.

2020-09-01 | E-MTAB-9500 | biostudies-arrayexpress

Transcription profiling of human peripheral blood monocytes from a patient with a heterozygous deletion of the CARMA1 gene cultured with anti-CD3, anti-CD3 and anti-CD28 or lipopolysaccharide

Project description:PBMCs were isolated from whole blood taken from one patient and one healthy control. Cells were cultured in media (RPMI) alone, with 1µg/ml anti-CD3, with 1µg/ml anti-CD3 & 1µg/ml anti-CD28 or with 0.5ng/ml LPS. Cells were harvested after 24 or 48 hours, RNA isolated using Trizol, purified using RNeasy columns and labelled using Illumina TotalPrep RNA Amplificiation kit (Applied Biosystems) before hybridisation to Illumina HumanRef-8 arrays.

2022-04-01 | E-MTAB-101 | biostudies-arrayexpress

Transcription profiling of mouse T-cells from wildtype and Gfi1 knockout mice activated by anti-CD3 plus anti-CD28 for 0 to 24h

Project description:To compare the transcriptomes of T-cells from Gfi1-knockout cells with wildtype cells, spleenocytes from wildtype and Gfi-knockout C57Bl/6 mice were isolated using panT-cell kit in an AutoMACS device (Miltenyi). Cells were cultured with anti-CD3 plus anti-CD28 antibodies (2 Âµg antibody/ml) for the indicated time period. Total RNAs was isolated and subjected to microarray analysis on Affymetrix MOE430A_2.0 arrays. Experiment Overall Design: 8 samples, 1 replicate per group

2008-10-18 | E-GEOD-4940 | biostudies-arrayexpress

Expression data from human peripheral blood lymphocytes stimulated with anti-CD3 and anti-CD28 antibodies.

Project description:Peripheral blood lymphocytes were separated in the Ficoll gradient and subjected for stimulation with anti-CD3 and anti-CD28 antiobodies upon time (6h, 12h and 18h). Next, total RNA was isolated and trenscriptional analysis of stimulated cells was performed. 11 total samples were analysed. Analysis was performed using samples from two healthy donors and one sample from patient. Unstimulated samples were used as a controls.

2013-02-25 | E-GEOD-29624 | biostudies-arrayexpress

Anti-CD3 therapy permits regulatory T cells to surmount T cell receptor-specified peripheral niche constraints

Project description:Treatment with anti-CD3 is a promising therapeutic approach for autoimmune diabetes, but its mechanism of action remains unclear. Foxp3+ regulatory T (Treg) cells may be involved, but the evidence has been conflicting, and there is great uncertainty as to possible mechanistic connections. We investigated this issue in mice derived from the NOD model, which were engineered mice in which Treg populations were perturbed, or could be manipulated by acute ablation or transfer. The data highlighted the involvement of Foxp3+ cells in anti-CD3 action. Rather than a generic influence on all Treg cells, the therapeutic effect seemed to involve an striking expansion of previously constrained Treg cell populations; this expansion occurred not through conversion from Foxp3- Tconv cells but from a dramatic proliferative expansion. We found that Treg cells are normally constrained by TCR-specific niches in secondary lymphoid organs, and that intraclonal competition restrains their possibility for conversion and expansion in the spleen and lymph nodes, much as niche competition limits their selection in the thymus. The strong perturbations induced by anti-CD3 overcame these niche limitations, in a process dependent on receptors for trophic cytokines, interleukin-2 receptor (IL-2R) and IL-7R. Keywords: Treatment response All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. RNA from 5 - 50 x 104 cells was amplified, labeled, and hybridized to Affymetrix M430v2. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

2010-07-29 | E-GEOD-22527 | biostudies-arrayexpress

Transcription profiling of mouse Itk-deficiency using CD3+ T-cells

Project description:The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-like T-cell development. We have characterized the transcriptome of Itk-deficient CD3+ T-cells, including CD4+ and CD8+ subsets, using Affymetrix microarrays. The largest difference between Itk-/- and Wt CD3+ T-cells was found in unstimulated cells, e.g. for killer cell lectin-like receptors. Compared to anti-CD3-stimulation, anti-CD3/CD28 significantly decreased the number of transcripts suggesting that the CD28 co-stimulatory pathway is mainly independent of Itk. The signatures of CD4+ and CD8+ T-cell subsets identified a greater differential expression than in total CD3+ cells. Cyclosporin (CsA)-treatment had a stronger effect on transcriptional regulation than Itk-deficiency, suggesting that only a fraction of TCR-mediated calcineurin/NFAT-activation is dependent on Itk. Bioinformatic analysis of NFAT-sites of the group of transcripts similarly regulated by Itk-deficiency and CsA-treatment, followed by chromatin-immunoprecipitation, revealed NFATc1-binding to the Bub1, IL7R, Ctla2a, Ctla2b, and Schlafen1 genes. Finally, to identify transcripts that are regulated by Tec-family kinases in general, we compared the expression profile of Itk-deficient T-cells with that of Btk-deficient B-cells and a common set of transcripts was found. Taken together, our study provides a general overview about the global transcriptional changes in the absence of Itk. Experiment Overall Design: CD3+ T-cells from pooled suspensions of spleen and lymph nodes of Wt and Itk knockout mice on C57BL/6 background were isolated after negative depletion. Unstimulated as well as stimulated T-cells were studied. Stimulations were done with anti-CD3 (1 mg/ml) with or without anti-CD28 (3 mg/ml) in the presence or absence of CsA (1 mg/ml) for 24 hrs. For each stimulus, at least duplicate samples were used.

2009-05-29 | E-GEOD-12464 | biostudies-arrayexpress

Expression data measured by microarray of CD4+ T cells from healthy individuals stimulated with anti-CD3/CD28 with or without IFNb or Th17 polarizing cytokines

Project description:Variation in individuals' adaptive immune response is believed to influence susceptibility to complex diseases in humans. The genetic basis of such variation is poorly understood. We measured gene expression from resting and activated CD4+ T cells derived from the peripheral blood of healthy individuals. We activated the primary T cells with anti-CD3/CD28 beads. We collected peripheral blood from each human donor. We isolated peripheral blood mononuclear cells by Ficoll, and negatively selected for CD4+ T cells using RosettaSep. We then either left cells unstimulated or stimulated them with beads conjugated with anti-CD3 and anti-CD28. Cells from 15 individuals were harvested at up to 3 time points (0hr, 4hr or 48hr), lysed and RNA isolated to be profiled on microarray.

2014-08-28 | E-GEOD-60235 | biostudies-arrayexpress

CD3/CD28 and IL-2 stimulated mouse CD8 T cells with or without anti-CD132 blocking antibody

Project description:Mouse CD8 T cells were isolated from total splenocytes from C57BL/6 mice by MACS separation. Cells were incubated for 48 h with CD3/CD28 DynaBeads and 50 ng/ml IL-2 for 48 h with or without 100 nm anti-CD132 blocking antibody. Cells were collected and RNA was isolated.

2015-03-23 | E-MTAB-2960 | biostudies-arrayexpress

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Project description:Primary non-expanded human T cell populations were isolated by leukapheresis from 10 healthy donors. Out of each donor > 95% pure CD4-positive Th cell and >95% pure regulatory T cell populations were purified. Two affymetrix exon arrays were hybridized from each donor both populations as resting, non-activated samples. In addition, samples were hybridized from each donor and both populations activated by anti-CD3/anti-CD28 treatment for 4hours and 16 hours.

2010-05-18 | E-TABM-779 | biostudies-arrayexpress

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