Unbiased single-cell TCR analysis reveals infrequent tumor-reactivity among T cells infiltrating human cancers
Sander Kelderman1,*, Wouter Scheper1,*, Carsten Linnemann1, Gavin Bendle1, Marije de Rooij1, Christian Hirt1, Gemma Kenter2, Willemien van Driel2, Henry Zijlmans2, Petur Snaebjornsson3, Marja Nieuwland4, Roel Kluin4, Ron Kerkhoven4, John Haanen1, Ton Schumacher1
1Division of Immunology, 2Department of Gynecology, 3Department of Pathology, 4Central Genomics Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
*Both authors contributed equally.
In many tumor types, infiltration by T cells is interpreted as a sign of immune recognition, and there is a growing interest in strategies that aim to reinvigorate the antitumor activity of such T cells. A key assumption behind such efforts is that the T cell receptor (TCR) repertoire carried by these cells is intrinsically tumor-reactive. However, the tumor recognition potential of the intratumoral TCR repertoire has not been established in an unbiased manner for human cancers. To address this issue, we have developed a high-throughput screening platform that combines next-generation sequencing of paired TCR a and b chains from single intratumoral CD8+ T cells with functional testing of the obtained TCRs against autologous tumor material. Using this platform, we analyzed whether the intratumoral TCR repertoire in ovarian cancer and colorectal cancer – two tumor types for which T cell infiltrates form a positive prognostic marker – is commonly tumor reactive. Reconstruction and functional analysis of single T cell-derived TCRs (N = 80) isolated from four patients indicates that only a small and variable fraction of tumor-infiltrating CD8+ T cells is intrinsically reactive against the autologous tumor. These data uncover the need for immunotherapeutic strategies that focus not only on stimulating the activity of tumor-resident T cells, but also on the mobilization of a tumor-specific T cell repertoire.