Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11906-11915. doi: 10.1073/pnas.1818488116. Epub 2019 May 22.

Abstract

γδ T lymphocytes represent ∼1% of human peripheral blood mononuclear cells and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current single-cell RNA sequencing (scRNA-seq) studies do not identify γδ T lymphocytes because their transcriptomes at the single-cell level are unknown. Here we show that high-resolution clustering of large scRNA-seq datasets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their T cell receptor (TCR)Vδ1 and TCRVδ2 subsets in large datasets from complex cell mixtures. In t-distributed stochastic neighbor embedding plots from blood and tumor samples, the few γδ T lymphocytes appear collectively embedded between cytotoxic CD8 T and NK cells. Their TCRVδ1 and TCRVδ2 subsets form close yet distinct subclusters, respectively neighboring NK and CD8 T cells because of expression of shared and distinct cytotoxic maturation genes. Similar pseudotime maturation trajectories of TCRVδ1 and TCRVδ2 γδ T lymphocytes were discovered, unveiling in both subsets an unattended pool of terminally differentiated effector memory cells with preserved proliferative capacity, a finding confirmed by in vitro proliferation assays. Overall, the single-cell transcriptomes of thousands of individual γδ T lymphocytes from different CMV+ and CMV- donors reflect cytotoxic maturation stages driven by the immunological history of donors. This landmark study establishes the rationale for identification, subtyping, and deep characterization of human γδ T lymphocytes in further scRNA-seq studies of complex tissues in physiological and disease conditions.

Keywords: cancer; human immunology; single-cell RNA-sequencing; transcriptome; γδ T lymphocyte.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Base Sequence
  • CD8-Positive T-Lymphocytes / immunology
  • Cell Proliferation / physiology
  • Cells, Cultured
  • Humans
  • Immunologic Memory / immunology
  • Killer Cells, Natural / immunology
  • Leukocytes, Mononuclear / immunology
  • Receptors, Antigen, T-Cell, gamma-delta / immunology*
  • Sequence Analysis, RNA / methods
  • T-Lymphocyte Subsets / immunology*
  • Transcriptome / immunology

Substances

  • Receptors, Antigen, T-Cell, gamma-delta