Description

Unbiased single-cell TCR analysis reveals infrequent tumor-reactivity among T cells infiltrating human cancers

Sander Kelderman^1,*, Wouter Scheper^1,*, 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.