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Identification of human CD4+ TEM and TEMRA cell-specific gene markers

ABSTRACT: Memory T cells mount an accelerated response upon antigen re-challenge but are heterogeneous in phenotype and function. Therefore, traditionally memory T cells were classified into central memory (TCM), effector memory (TEM) and terminally differentiated effector memory (TEMRA) cells based on the expression of lymph node homing receptors and CD45 splice variants. However, findings on functional heterogeneity even within these subsets demonstrated the need for more suitable markers to match phenotype and function during T cell differentiation. To improve functional classification of human CD4+ memory T cells we applied bulk and single gene expression profiling and identified a set of surface markers, KLRB1, KLRG1, GPR56 and KLRF1, which facilitate classification into subsets with “low”, “high” or “exhausted” cytokine production. Highest level production of multiple cytokines was observed in T cells co-expressing KLRB1 with KLRG1 and/or GPR56 while additional KLRF1 expression was associated with a decline in cytokine production. The superiority of using KLRF1 expression to define exhausted cytokine producers compared to classical TEMRA identification was best exemplified for intrahepatic T cells in patients with inflammatory liver diseases. These data open up new opportunities for monitoring and treatment of chronic inflammatory diseases driven by cytokine producing CD4+ memory T cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE102005 | GEO | 2019/04/09

REPOSITORIES: GEO

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Project description:The goal of this study is to compare the transcriptional program and the TCR sequences of different subsets of CD8 T cells purified from the peripheral blood of 3 patienst with Amyotrophic Lateral Sclerosis 4 (ALS4) and 3 age-matched controls (unreleated). Peripheral blood mononuclear cells (PBMCs) were purified from 3 ALS4 patients and 3 age-matched healthy controls.By combining RNA and surface protein expression followed by multidimensional reduction using the Uniform Manifold Approximation and Projection (UMAP), we could identified 9 clusters corresponding to different CD8 T cell subsets: naïve/naïve like (clusters 0, 2, 5, 8), central memory (cluster 7), effector memory (clusters 4 and 6), TEMRA (clusters 1 and 3), and mucosal associated invariant T (MAIT) cells (cluster 9). ALS4 patients exhibited a higher proportion of TEMRA, and a decreased frequency of effector/effector memory cells, as compared to controls. Downregulation of IL7R and CCR7, and upregulation of GZMM and GZMB (encoding for Granzyme M and B, respectively), KLRB1 (Killer Cell Lectin Like Receptor B1), NKG7 (Natural Killer Cell Granule Protein 7), FGFBP2 (Fibroblast Growth Factor Binding Protein 2) and CCL4 (Chemokine (C-C motif) ligands 4), all of which correlate with a TEMRA phenotype are among the top deregulated genes in ALS4 CD8 T cells. The proportion of naïve cells seemed to be increased as well; however only 1 patient has an abnormal high frequency of CCR7+CD45RA+CD28+ cells, while the TEMRA signature was consistent among all 3 ALS4 donors. More than 90% of expanded clones (≥5) are TEMRA cells in ALS4 patients, in comparison to ~ 60% in healthy controls. By matching UMAP coordinates from RNA and TCR analyses, we observed a colocalization between the most expanded clones, i.e. CD8 T cells in which the same TCR sequence was shared by more than 20 cells, and the TEMRA subset that we found enriched in patients. We quantified this clonal expansion and found that over half of all TEMRA cells comprised of highly expanded clones in patients. Hyperexpanded (>100 clones) TEMRA cells were detected in 2 of the 3 patients, with one clone reaching as high as 407 cells. No hyperexpanded clones were found in other CD8 T cell subsets or in control patients. Comparison of surface protein expression from our CITE-seq analysis in “Low” and “High” (>20) expanded clones from ALS4 patients revealed a stronger TEMRA phenotype in the latter, as indicated by CD27 downregulation and CD45RA and CD57 upregulation.

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Identification of human CD4+ TEM and TEMRA cell-specific gene markers

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