Eberhardt and Kissick et al. characterized CD8+ T cells in patients with human papillomavirus (HPV)-positive HNSCC and identified a substantial proportion of HPV E2-, E5- and E6-specific CD8+ T cells in tumors, but not peripheral blood. Single-cell sequencing revealed 3 transcriptionally distinct subsets: stem-like cells expressing high levels of TCF7 and other stemness-associated genes; transitory cells expressing effector molecules; and terminally differentiated cells expressing high levels of TIM-3 and effector molecules. These subsets shared TCR clonotypes, and pseudotime analysis suggested the progression from stem-like to transitory to terminally differentiated states.
Contributed by Shishir Pant
ABSTRACT: T cells are important in tumour immunity but a better understanding is needed of the differentiation of antigen-specific T cells in human cancer(1,2). Here we studied CD8 T cells in patients with human papillomavirus (HPV)-positive head and neck cancer and identified several epitopes derived from HPV E2, E5 and E6 proteins that allowed us to analyse virus-specific CD8 T cells using major histocompatibility complex (MHC) class I tetramers. HPV-specific CD8 T cells expressed PD-1 and were detectable in the tumour at levels that ranged from 0.1% to 10% of tumour-infiltrating CD8 T lymphocytes (TILs) for a given epitope. Single-cell RNA-sequencing analyses of tetramer-sorted HPV-specific PD-1(+) CD8 TILs revealed three transcriptionally distinct subsets. One subset expressed TCF7 and other genes associated with PD-1(+) stem-like CD8 T cells that are critical for maintaining T cell responses in conditions of antigen persistence. The second subset expressed more effector molecules, representing a transitory cell population, and the third subset was characterized by a terminally differentiated gene signature. T cell receptor clonotypes were shared between the three subsets and pseudotime analysis suggested a hypothetical differentiation trajectory from stem-like to transitory to terminally differentiated cells. More notably, HPV-specific PD-1(+)TCF-1(+) stem-like TILs proliferated and differentiated into more effector-like cells after in vitro stimulation with the cognate HPV peptide, whereas the more terminally differentiated cells did not proliferate. The presence of functional HPV-specific PD-1(+)TCF-1(+)CD45RO(+) stem-like CD8 T cells with proliferative capacity shows that the cellular machinery to respond to PD-1 blockade exists in HPV-positive head and neck cancer, supporting the further investigation of PD-1 targeted therapies in this malignancy. Furthermore, HPV therapeutic vaccination efforts have focused on E6 and E7 proteins; our results suggest that E2 and E5 should also be considered for inclusion as vaccine antigens to elicit tumour-reactive CD8 T cell responses of maximal breadth.
Author Info: (1) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. C
Author Info: (1) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. Centre for Vaccinology, University Hospitals Geneva, Geneva, Switzerland. Division of General Pediatrics, Department of Pediatrics, Gynecology & Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland. (2) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. Winship Cancer Institute of Emory University, Atlanta, GA, USA. Department of Urology, Emory University School of Medicine, Atlanta, GA, USA. (3) Winship Cancer Institute of Emory University, Atlanta, GA, USA. Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA, USA. (4) Department of Urology, Emory University School of Medicine, Atlanta, GA, USA. (5) Department of Urology, Emory University School of Medicine, Atlanta, GA, USA. (6) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA. Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (7) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. (8) Winship Cancer Institute of Emory University, Atlanta, GA, USA. Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA. (9) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. Department of Immunology, Sungkyunkwan University School of Medicine, Suwon, South Korea. (10) Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA. (11) Division of General Pediatrics, Department of Pediatrics, Gynecology & Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland. Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA. (12) Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA. Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA. (13) Winship Cancer Institute of Emory University, Atlanta, GA, USA. Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA. (14) Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA. (15) Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA. Department of Medicine, University of California, San Diego, La Jolla, CA, USA. (16) Winship Cancer Institute of Emory University, Atlanta, GA, USA. Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA. (17) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. andreas.wieland@emory.edu. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. andreas.wieland@emory.edu. (18) Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA. rahmed@emory.edu. Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. rahmed@emory.edu. Winship Cancer Institute of Emory University, Atlanta, GA, USA. rahmed@emory.edu.
