The effect of LAIR-1 ligation on naïve CD8 T cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE228709 | GEO | 2024/01/24
REPOSITORIES: GEO
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Project description:Histone methylations play a major role in regulating the chromatin state and gene expression, yet little is known about their involvement in differential gene expression and function of memory CD8 T cells. Here, we report a genome-wide analysis of two histone H3 methylations (H3K4me3 and H3K27me3) and gene expression in naïve, central (TCM) and effector (TEM) memory CD8 T cells. Analysis of 16,314 annotated genes in CD8 T cell subsets revealed that gene expression were positively correlated with the levels of H3K4me3 and negatively correlated with the levels of H3K27me3 in these gene loci. The correlation between differential H3K4me3 orH3K27me3 levels with gene expressions in memory CD8 T cells displayed four distinct modes: repressive, active, poised, and bivalent, reflecting their complex regulation and different function of these genes. Furthermore, accessible chromatin states of different gene loci were preferentially influenced by different histone modifications as demonstrated here high levels of H3K9ac found in active gene loci without high levels of H3K4me3. These findings reveal a histone methylation based complex regulation of differential gene expression in memory CD8 T cells. Thus, change of chromatin structure mediated by histone methylation may serve a fundamental basis for the rapid transcriptional response of memory CD8 T cells. Keywords: Histone methylations, chromatin state, CD8 memory T cells Enriched naïve and memory CD8 T cells were purified into CD8+CD45RA+CD62L+ naïve T cells, CD8+CD45RA-CD62L+ central memory T cells (TCM), and CD8+CD45RA-CD62L- effector memory T cells (TEM) by a cell sorter (MoFlo; Dako Cytomation, Carpentaria, CA). Triplicates of each cell type were either used right away or incubated with anti-CD3 and anti-CD28 Ab (anti-CD3/CD28) coupled magnetic beads (Invitrogen) at the cell:bead ratio of 1:1 for 16 hours in RPMI-1640 with 10% Fetal bovine serum and penicillin (10 U/ml)/streptomycin (10 ug/ml) (Invitrogen). The freshly isolated and 16 hr stimulated cells from several donors as a pool were used for gene expression microarray analysis. All sample data was normalized to a standard control RNA labeled and hybed along with each sample and all data from the 3 replicates was averaged.
2009-03-06 | E-GEOD-14422 | biostudies-arrayexpress
Project description:IFN alpha mediated gene expression pattern. The effect of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs. This analysis examined the effects of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs. Magnetically sorted untouched CD8+CD45R0- T cells from three different donors were unstimulated or stimulated with IFNa2b or with anti-CD3/CD28 Beads alone or along with IFNa2b or IFNa5 for 48 hours. Individual mRNA samples were analyzed using HG-U133A 2.0 array gene chips. Keywords: Gene expression analysis after different stimulation Magnetically sorted untouched CD8+CD45R0-T cells from three different donors (named A, B and C) unstimulated or stimulated with IFN alpha 2b or with anti-CD3/CD28 beads alone or along with IFN alpha 2b or IFN alpha 5 for 48 hours.
2010-07-23 | E-GEOD-17301 | biostudies-arrayexpress
Project description:Using a CRISPR/Cas9-based approach, we engineered human primary CD4+ and CD8+ T cells in which a bait protein (LAT, SLP76, VAV1 or ZAP70) was tagged with an affinity Twin-Strep-tag (OST), with the purpose of determining by quantitative mass spectrometry the composition and dynamics of the signalosome assembling around each of these signaling proteins prior to and following T cell activation. Affinity purification of the OST tagged protein was performed using Streptactin beads, from T cells left non-stimulated, or stimulated for 30s, 60s, 120s, or 300s with anti-CD3 and anti-CD28 antibodies. Each AP-MS purification is associated with a corresponding control (purification from non-edited WT CD4+ or CD8+ T cells, cultured and stimulated in the same conditions). The number of replicate biological experiments was n=3 for all time-points, and each sample was analyzed twice by single-run nano LC-MS.
2022-01-10 | PXD024820 | Pride
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.
2021-01-27 | GSE160496 | GEO
Project description:Recent studies reported the inhibitory properties of LAIR-1 in different inflammatory diseases, including allergic and viral airway inflammation. However, the implication of LAIR-1 in ALI/ARDS remains unknown. Poly(I:C), a synthetic analog of (ds)RNA was administrated intranasally to mimic acute inflammation in viral infections and therefore induce experimental ALI/ARDS. RNA sequencing approach was used to explore and compare lung macrophage transcriptomic profiles in wild-type and LAIR-1 knock-out mice.
2023-09-01 | GSE216259 | GEO
Project description:Purified primary human CD8 T cells were stimulated in vitro in parallel using a magnetic bead conjugated to either anti-CD3/28 or anti-CD2/3/28 antibodies. Cells were cultured for 6 days in complete RPMI1640 and 10ng/ml IL2 and were harvested on day 6 and RNA was isolated for further labelling and hybridisation.
2015-08-12 | E-MTAB-3470 | biostudies-arrayexpress
Project description:Gene expression in CD3/CD28 stimulated CD8 vs CD8 with various dosage of Cholesterol treatment
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Project description:Type-2 innate lymphoid cells (ILC2s) are central players in type-2 asthma. They initiate eosinophil infiltration and airway hyperreactivity (AHR) through cytokine secretion. Leukocyte-associated immunoglobulin-like receptor 1 (LAIR-1) is an inhibitory receptor considered as immune checkpoint in different inflammatory diseases. Here we assessed the role of LAIR-1 in murine ILC2s. WT and LAIR-1 KO mice were intranasally challenged with IL-33 and pulmonary ILC2s were sorted to perform RNA sequencing. Our results unravel a novel regulatory axis in ILC2s with the capacity to reduce their activation.
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Project description:We report that the microRNA (miR)-31 confers CD8 T cell sensitivity to type I interferon (IFN) stimulation following CD3/CD28 engagement. Method: miR31 WT and KO CD8 T cells were stimulated with anti-CD3/CD28 beads for two days, then maintained in 10ng/mL IL-2 for a further 5 days. CD8 T cells were then stimulated with 20ng/mL IFN-beta for 0, 4, or 18h. Total RNA was isolated at each time point and sequenced. Results: Prior to IFN-beta stimulation, miR-31 KO CD8 T cells had a slightly increased effector program (cytotoxic granzymes) and decreased inhibitory program (Mt1/Maf). Stimulation with IFN-beta further enhanced this difference increasing a number of granzymes, Prf1 and Spp1 whilst also decreasing inhibitory genes (Mt1, Mt2, Maf, Ptger2). Conclusion: This study shows that miR-31 may lead to decreased effector function and increased inhibitory programs in CD8 T cells during chronic viral infections, in particular due to continued type I interferon stimulation.
2017-05-07 | GSE98615 | GEO
Project description:It is unknown whether human lung T cells recirculate or belong to a distinct tissue-specific population. This issue is important for understanding their role in protection against viral infection and their contribution to pathophysiology of lung diseases such as chronic obstructive pulmonary disease. By comparing transcriptional profiles of blood and lung CD8+ T cells, we aimed to reveal specific traits of lung CD8+ T cells. A total of 12 samples was analyzed: 10 patient samples (including 1 technical replicate) and 2 reference samples (including 1 technical replicate). Per patient (in total 3 patients), 3 paired samples were analyzed. These samples were non-naive peripheral blood CD8+ T cells (CD45R0+CD3+CD8+ T cells), memory-type lung CD8+ T cells (CD45R0+CD27+CD3+CD8+ T cells) and effector-type lung CD8+ T cells (CD45R0+CD27-CD3+CD8+ T cells). The reference population consisted of a mix of naive peripheral blood CD8+ T cells from 5 healthy donors.
2011-06-20 | E-GEOD-30027 | biostudies-arrayexpress