Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer

Nature. 2021 Sep;597(7875):279-284. doi: 10.1038/s41586-021-03862-z. Epub 2021 Sep 1.


T cells are important in tumour immunity but a better understanding is needed of the differentiation of antigen-specific T cells in human cancer1,2. 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alphapapillomavirus / immunology*
  • Alphapapillomavirus / isolation & purification
  • CD8-Positive T-Lymphocytes / classification
  • CD8-Positive T-Lymphocytes / cytology*
  • CD8-Positive T-Lymphocytes / immunology*
  • CD8-Positive T-Lymphocytes / metabolism
  • Cancer Vaccines / immunology
  • Cell Differentiation
  • Cell Proliferation
  • DNA-Binding Proteins / immunology
  • Head and Neck Neoplasms / immunology*
  • Head and Neck Neoplasms / virology*
  • Humans
  • Lymphocytes, Tumor-Infiltrating / classification
  • Lymphocytes, Tumor-Infiltrating / cytology
  • Lymphocytes, Tumor-Infiltrating / immunology*
  • Lymphocytes, Tumor-Infiltrating / metabolism
  • Oncogene Proteins, Viral / immunology
  • Papillomavirus Infections / immunology
  • Papillomavirus Infections / virology
  • Papillomavirus Vaccines / immunology
  • Programmed Cell Death 1 Receptor / metabolism*
  • RNA-Seq
  • Receptors, Antigen, T-Cell / immunology
  • Single-Cell Analysis
  • Stem Cells / cytology*
  • Stem Cells / immunology
  • T Cell Transcription Factor 1 / metabolism
  • T-Lymphocytes / immunology
  • Transcription, Genetic


  • Cancer Vaccines
  • DNA-Binding Proteins
  • E2 protein, Human papillomavirus type 16
  • Oncogene Proteins, Viral
  • PDCD1 protein, human
  • Papillomavirus Vaccines
  • Programmed Cell Death 1 Receptor
  • Receptors, Antigen, T-Cell
  • T Cell Transcription Factor 1
  • TCF7 protein, human
  • oncogene protein E5, Human papillomavirus type 16