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Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

Nature Medicine volume 25, pages 89–94 (2019)Cite this article

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Abstract

Infiltration of human cancers by T cells is generally interpreted as a sign of immune recognition, and there is a growing effort to reactivate dysfunctional T cells at such tumor sites1. However, these efforts only have value if the intratumoral T cell receptor (TCR) repertoire of such cells is intrinsically tumor reactive, and this has not been established in an unbiased manner for most human cancers. To address this issue, we analyzed the intrinsic tumor reactivity of the intratumoral TCR repertoire of CD8+ T cells in ovarian and colorectal cancer—two tumor types for which T cell infiltrates form a positive prognostic marker2,3. Data obtained demonstrate that a capacity to recognize autologous tumor is limited to approximately 10% of intratumoral CD8+ T cells. Furthermore, in two of four patient samples tested, no tumor-reactive TCRs were identified, despite infiltration of their tumors by T cells. These data indicate that the intrinsic capacity of intratumoral T cells to recognize adjacent tumor tissue can be rare and variable, and suggest that clinical efforts to reactivate intratumoral T cells will benefit from approaches that simultaneously increase the quality of the intratumoral TCR repertoire.

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Fig. 1: Overview and functional validation of TCR profiling technology.
Fig. 2: Analysis of tumor reactivity of intratumoral CD8+ T cells in OVC patient OVC21.
Fig. 3: Assessment of tumor reactivity of CD8+ TILs in patients with ovarian and colorectal cancer.

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Data availability

DNA and RNA sequencing data have been deposited in the European Genome-phenome Archive under accession code EGAS00001003119 and are subject to a controlled Data Access Agreement. These data are available from the corresponding authors to any party able to comply with the associated Data Access Agreement.

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Acknowledgements

We thank M. van Zon, N. Bakker, and N. van Rooij for handling of patient material; A. Pfauth for flow cytometric support; S. Reijm for technical assistance; D. Thommen for critical reading of the manuscript; R. van Kerkhoven and M. Nieuwland for support with next generation sequencing; B. Thijssen for helpful discussion on Bayesian analysis; L. Wessels for discussions; the NKI-AVL Core Facility Molecular Pathology & Biobanking for supplying NKI-AVL Biobank material and laboratory support; H. Spits and R. Schotte (AIMM Therapeutics) for sharing reagents for B cell immortalization; K. van de Vijver for histological support; and M. Kranendonk for critical reading of the manuscript and histological support. This work was supported by the Dutch Cancer Society Queen Wilhelmina Award NKI 2013−6122, EU H2020 grant 633592 (APERIM), and the K.G. Jebsen Foundation (T.N.S.), Krebsliga Beider Basel (C.H.), and BC Cancer Foundation (B.H.N.).

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Author notes

  1. These authors contributed equally: W. Scheper, S. Kelderman.

Authors and Affiliations

  1. Division of Molecular Oncology & Immunology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands

    Wouter Scheper, Lorenzo F. Fanchi, Riccardo Mezzadra, Maarten Slagter & Ton N. Schumacher

  2. Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands

    Sander Kelderman, Carsten Linnemann, Gavin Bendle, Marije A. J. de Rooij, Krijn Dijkstra, Emile E. Voest & John B. A. G. Haanen

  3. Department of Biomedicine, University of Basel, Basel, Switzerland

    Christian Hirt

  4. Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands

    Maarten Slagter

  5. Central Genomics Facility, the Netherlands Cancer Institute, Amsterdam, the Netherlands

    Roelof J. C. Kluin

  6. Division of Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands

    Petur Snaebjornsson

  7. Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada

    Katy Milne & Brad H. Nelson

  8. Department of Gynecologic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands

    Henry Zijlmans & Gemma Kenter

  9. Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands

    Emile E. Voest & John B. A. G. Haanen

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Contributions

W.S. and S.K. designed, performed, analyzed, and interpreted experiments and wrote the manuscript. L.F.F., M.A.J.d.R., and C.H. performed experiments. C.L. and G.B. helped develop the single-cell TCR sequencing protocol. M.S. performed the likelihood of tumor reactivity analysis. R.M. generated TCRα/β-deficient Jurkat cells. K.D. and E.E.V. provided essential assistance with the generation of tumor organoids. R.J.C.K. analyzed TCR sequencing data. P.S. and K.M. provided assistance with immunohistochemistry. B.H.N., H.Z., G.K., and J.B.A.G.H. provided patient material. T.N.S. supervised the project, designed and interpreted experiments, and wrote the manuscript. All authors reviewed the manuscript.

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Correspondence to Ton N. Schumacher.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10

Reporting Summary

Supplementary Table 1

Patient information

Supplementary Table 2

Tumor variants

Supplementary Table 3

Predicted neoantigens

Supplementary Table 4

TCR sequencing data

Supplementary Table 5

Primer sequences

Supplementary Table 6

CMV and EBV epitopes

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Scheper, W., Kelderman, S., Fanchi, L.F. et al. Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers. Nat Med 25, 89–94 (2019). https://doi.org/10.1038/s41591-018-0266-5

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