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

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

Pizzolato G1,2,3,4,5,6,7,8,9,10, Kaminski H11,12, Tosolini M1,2,3,4,5,6,7, Franchini DM1,2,3,4,5,6,7, Pont F1,7, Martins F13,14, Valle C1,2,3,4,5,6,7, Labourdette D14,15, Cadot S1,2,3,4,5,6,7, Quillet-Mary A1,2,3,4,5,6,7, Poupot M1,2,3,4,5,6,7, Laurent C1,2,3,4,5,6,7, Ysebaert L1,2,3,4,5,6,7, Meraviglia S9,10, Dieli F9,10, Merville P11,12, Milpied P16, Déchanet-Merville J11, Fournié JJ17,2,3,4,5,6,7.

Author information

1
Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France.
2
Toulouse University, 31000 Toulouse, France.
3
ERL 5294 CNRS, 31024 Toulouse, France.
4
Institut Universitaire du Cancer-Oncopole de Toulouse, 31100 Toulouse, France.
5
Laboratoire d'Excellence 'TOUCAN', Toulouse, France.
6
Programme Hospitalo, Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France.
7
Institut Carnot Lymphome CALYM, 69495 Lyon-Pierre Bénite, France.
8
Humanitas University, 20089 Rozzano (MI), Italy.
9
Department of Biopathology and Medical Biotechnologies, University of Palermo, 90133 Palermo, Italy.
10
Central Laboratory of Advanced Diagnosis and Biomedical Research, University of Palermo, 90133 Palermo, Italy.
11
University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, F-33076 Bordeaux, France.
12
Service de Néphrologie et Transplantation Rénale, Centre Hospitalo-Universitaire de Bordeaux, 33000 Bordeaux, France.
13
Institut des Maladies Métaboliques et Cardiovasculaires, INSERM UMR1048, 31432 Toulouse, France.
14
Plateforme GeT, Genotoul, 31100 Toulouse, France.
15
Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France.
16
Aix Marseille University, CNRS, INSERM, Centre d' Immunologie de Marseille-Luminy, 13007 Marseille, France.
17
Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France; jean-jacques.fournie@inserm.fr.

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

PMID:
31118283
PMCID:
PMC6576116
[Available on 2019-11-22]
DOI:
10.1073/pnas.1818488116

Conflict of interest statement

The authors declare no conflict of interest.

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