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High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma

Nature Medicine volume 21, pages 81–85 (2015)Cite this article

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A Corrigendum to this article was published on 06 October 2016

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Abstract

Tumor-specific neo-antigens that arise as a consequence of mutations1,2 are thought to be important for the therapeutic efficacy of cancer immunotherapies3,4,5. Accumulating evidence suggests that neo-antigens may be commonly recognized by intratumoral CD8+ T cells3,4,5,6,7, but it is unclear whether neo-antigen–specific CD4+ T cells also frequently reside within human tumors. In view of the accepted role of tumor-specific CD4+ T-cell responses in tumor control8,9,10, we addressed whether neo-antigen–specific CD4+ T-cell reactivity is a common property in human melanoma.

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Figure 1: Detection of neo-antigen–specific CD4+ T cells in human melanoma lesions.
Figure 2: Characterization of neo-antigen–specific CD4+ T cells in human melanoma lesions.
Figure 3: Identification and characterization of neo-antigen–reactive CD4+ T cells in T-cell products used for adoptive T-cell therapy.
Figure 4: Mutational load and neo-antigen–specific CD4+ T-cell reactivity in melanoma patients.

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  • 18 August 2016

    In the version of this article initially published, the article did not mention some restrictions on the availability of reagents. The following text has been added to the HTML and PDF versions of the paper: “The retroviral vectors containing BCL-6 and BCL-xL have been generated by a for-profit company, AIMM Therapeutics, which makes the plasmids available. Obtaining the plasmids requires an MTA (http://www.aimmtherapeutics.com/partnering/academic-collaboration/) that includes financial obligations.” The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We are grateful to A. Pfauth, F. van Diepen and C. Bachas for flow cytometric support; W. van de Kasteele and T. de Jong for technical assistance; N. van Rooij and B. Heemskerk for handling of patient material; and R. Kluin, M. Nieuwland and R. van Kerkhoven for support with next generation sequencing. We thank G. Bendle and P. Kvistborg for critical reading of the manuscript, and members from the Schumacher and Haanen laboratories for useful discussions. This work was supported by Worldwide Cancer Research grant 14-0321 (to C.L. and T.N.M.S.), the PhD Fellowship Program of Boehringer Ingelheim Fonds–Foundation for Basic Research in Biomedicine (to C.L.), Dutch Cancer Society grants: UVA 2010-4822 (to H.S.), NKI 2012-5463 (to J.B.A.G.H., S.H.v.d.B. and T.N.M.S.) and UL 2012-5544 (to E.M.E.V.), The Wellcome Trust Research Training Fellowship for Clinicians (to S.B.), The Wellcome Trust Grant WT098051 (to M.R.S.), the Anticancer Fund (to E.M.E.V., M.V.) the K.G. Jebsen Foundation (to T.N.M.S.), EU FP7 SUPERSIST, and the Stand Up To Cancer–Cancer Research Institute Cancer Immunology Translational Cancer Research Grant (to T.N.M.S.). SU2C is a program of the Entertainment Industry Foundation administered by the American Association for Cancer Research.

Author information

Author notes

  1. Carsten Linnemann, Marit M van Buuren and Laura Bies: These authors contributed equally to this work.

  2. Hergen Spits and Sjoerd H van der Burg: These authors jointly supervised this work.

Authors and Affiliations

  1. Division of Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands

    Carsten Linnemann, Marit M van Buuren, Laura Bies, Jorg J A Calis, John B A G Haanen & Ton N M Schumacher

  2. Department of Clinical Oncology, Leiden University Medical Center, Leiden, the Netherlands

    Els M E Verdegaal, Marten Visser & Sjoerd H van der Burg

  3. AIMM Therapeutics B.V., Amsterdam, the Netherlands

    Remko Schotte & Hergen Spits

  4. Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom

    Sam Behjati & Michael R Stratton

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

    Arno Velds

  6. Peptide Synthesis Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands

    Henk Hilkmann & Dris el Atmioui

  7. Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands

    John B A G Haanen

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Contributions

C.L., M.M.v.B. and L.B. designed, performed, analyzed and interpreted experiments and wrote the paper. E.M.E.V. and M.V. designed, performed, analyzed, and interpreted the analysis of subject BO. R.S. generated BCL-6/BCL-XL–immortalized B-cell lines and provided essential culture reagents and advice for the development of the B-cell screening platform. J.J.A.C. developed bioinformatics scripts for TCR sequence identification in NGS data. H.H. and D.e.A. synthesized peptide libraries. S.B., M.R.S. and A.V. performed and analyzed exome and RNA sequencing and developed the pipeline for identification of somatic mutations. J.B.A.G.H. supervised the clinical treatment of NKI TIL patients, supplied patient material and provided clinical interpretation of results. H.S. developed the BCL-6/BCL-XL immortalization technology and provided essential culture reagents and advice for the development of the B-cell screening platform. S.H.v.d.B. supervised, analyzed and interpreted the analysis of subject BO. T.N.M.S. supervised the project, designed and interpreted all experiments, and wrote the paper.

Corresponding authors

Correspondence to Carsten Linnemann or Ton N M Schumacher.

Ethics declarations

Competing interests

The technology described in this manuscript is the subject of an EU patent application co-owned by NKI-AVL and AIMM Therapeutics B.V. Based on NKI-AVL policy on management of intellectual property, C.L., M.M.v.B., L.B. and T.N.M.S would be entitled to a portion of received royalty income. H.S. and R.S. own certificates of AIMM Therapeutics B.V. (minority stake). T.N.M.S. is a scientific advisor of AIMM Therapeutics B.V. and indirectly owns stock of AIMM Therapeutics B.V. (minority stake).

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Linnemann, C., van Buuren, M., Bies, L. et al. High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma. Nat Med 21, 81–85 (2015). https://doi.org/10.1038/nm.3773

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