Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigens

Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23662-23670. doi: 10.1073/pnas.1906026116. Epub 2019 Nov 4.


The impact of intratumoral heterogeneity (ITH) and the resultant neoantigen landscape on T cell immunity are poorly understood. ITH is a widely recognized feature of solid tumors and poses distinct challenges related to the development of effective therapeutic strategies, including cancer neoantigen vaccines. Here, we performed deep targeted DNA sequencing of multiple metastases from melanoma patients and observed ubiquitous sharing of clonal and subclonal single nucleotide variants (SNVs) encoding putative HLA class I-restricted neoantigen epitopes. However, spontaneous antitumor CD8+ T cell immunity in peripheral blood and tumors was restricted to a few clonal neoantigens featuring an oligo-/monoclonal T cell-receptor (TCR) repertoire. Moreover, in various tumors of the 4 patients examined, no neoantigen-specific TCR clonotypes were identified despite clonal neoantigen expression. Mature dendritic cell (mDC) vaccination with tumor-encoded amino acid-substituted (AAS) peptides revealed diverse neoantigen-specific CD8+ T responses, each composed of multiple TCR clonotypes. Isolation of T cell clones by limiting dilution from tumor-infiltrating lymphocytes (TILs) permitted functional validation regarding neoantigen specificity. Gene transfer of TCRαβ heterodimers specific for clonal neoantigens confirmed correct TCR clonotype assignments based on high-throughput TCRBV CDR3 sequencing. Our findings implicate immunological ignorance of clonal neoantigens as the basis for ineffective T cell immunity to melanoma and support the concept that therapeutic vaccination, as an adjunct to checkpoint inhibitor treatment, is required to increase the breadth and diversity of neoantigen-specific CD8+ T cells.

Keywords: CD8+ T cells; cancer vaccine; dendritic cells; melanoma; neoantigen.

Publication types

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

MeSH terms

  • Amino Acid Substitution
  • Antigens, Neoplasm / genetics
  • Antigens, Neoplasm / immunology*
  • CD8-Positive T-Lymphocytes / immunology*
  • Cancer Vaccines / immunology
  • Clone Cells
  • DNA, Neoplasm / genetics
  • Dendritic Cells / immunology
  • HLA Antigens / immunology
  • Humans
  • Lung Neoplasms / immunology
  • Lung Neoplasms / secondary
  • Lymphocytes, Tumor-Infiltrating / immunology*
  • Melanoma / genetics
  • Melanoma / immunology*
  • Melanoma / secondary
  • Polymorphism, Single Nucleotide
  • Receptors, Antigen, T-Cell, alpha-beta / genetics
  • Receptors, Antigen, T-Cell, alpha-beta / immunology
  • Retroperitoneal Neoplasms / immunology
  • Retroperitoneal Neoplasms / secondary
  • Sequence Analysis, DNA
  • T-Cell Antigen Receptor Specificity
  • T-Lymphocyte Subsets / immunology*
  • Tumor Escape
  • Vaccination


  • Antigens, Neoplasm
  • Cancer Vaccines
  • DNA, Neoplasm
  • HLA Antigens
  • Receptors, Antigen, T-Cell, alpha-beta