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Proceedings of the National Academy of Sciences of the United States of America
06 11, 2019;116 (24): 11906-11915.

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

Gabriele Pizzolato, Hannah Kaminski, Marie Tosolini, Don-Marc Franchini, Fréderic Pont, Fréderic Martins, Carine Valle, Delphine Labourdette, Sarah Cadot, Anne Quillet-Mary, Mary Poupot, Camille Laurent, Loic Ysebaert, Serena Meraviglia, Francesco Dieli, Pierre Merville, Pierre Milpied, Julie Déchanet-Merville, Jean-Jacques Fournié
Author Information
  1. Gabriele Pizzolato: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  2. Hannah Kaminski: University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, F-33076 Bordeaux, France.
  3. Marie Tosolini: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  4. Don-Marc Franchini: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  5. Fréderic Pont: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  6. Fréderic Martins: Institut des Maladies Métaboliques et Cardiovasculaires, INSERM UMR1048, 31432 Toulouse, France.
  7. Carine Valle: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  8. Delphine Labourdette: Plateforme GeT, Genotoul, 31100 Toulouse, France.
  9. Sarah Cadot: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  10. Anne Quillet-Mary: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France. ORCID
  11. Mary Poupot: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  12. Camille Laurent: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  13. Loic Ysebaert: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
  14. Serena Meraviglia: Department of Biopathology and Medical Biotechnologies, University of Palermo, 90133 Palermo, Italy.
  15. Francesco Dieli: Department of Biopathology and Medical Biotechnologies, University of Palermo, 90133 Palermo, Italy. ORCID
  16. Pierre Merville: University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, F-33076 Bordeaux, France.
  17. Pierre Milpied: Aix Marseille University, CNRS, INSERM, Centre d' Immunologie de Marseille-Luminy, 13007 Marseille, France.
  18. Julie Déchanet-Merville: University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, F-33076 Bordeaux, France.
  19. Jean-Jacques Fournié: Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France; jean-jacques.fournie@inserm.fr.
PMID: 31118283 DOI: 10.1073/pnas.1818488116

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 -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

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MeSH Term

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

Chemicals

Receptors, Antigen, T-Cell, gamma-delta
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GEN: GEND000096 (Single cell RNAseq of human TCRVdelta 1 and TCRVdelta 2 gammadelta T lymphocytes purified from healthy adults blood)

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