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Single Cell Analysis of CD8+ T-cells with Aging

ABSTRACT: CD8+ T cells play essential roles in combatting infection and cancers. The major subsets of CD8+ T cells such as naïve, effector, and memory carry out distinct functions. Although the defined subsets are known to be heterogeneous, the precise composition of these subsets and their functional alterations have not been thoroughly determined. Here, we used single cell RNA sequencing (scRNAseq) and multicolor immunophenotyping to analyze the composition of CD8+ T cells. From scRNAseq analysis of isolated CD8+ T cells from 16 healthy donors, we analyzed 80,775 cells and identified a total of 13 subpopulations of CD8+ T cells including naïve, central and effector memory cells and terminally differentiated effector memory cells (EMRA). In parallel, our multi-color (16 antibody-panel) immunophenotyping analysis by flow cytometry of CD8+ T cells from 165 donors also divided CD8+ T cells into 11 major subpopulations. The majority of the subpopulations identified by these two methods were their age-related changes in percentage. Together, our findings reveal previously unidentified subpopulations of CD8+ T cells, their distinct transcriptional profiles and changes with age.

ORGANISM(S): Homo sapiens

PROVIDER: GSE136184 | GEO | 2022/06/28

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.

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Single Cell Analysis of CD8+ T-cells with Aging

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