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Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

Nature volume 482, pages 400–404 (2012)Cite this article

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Abstract

Cancer immunoediting, the process by which the immune system controls tumour outgrowth and shapes tumour immunogenicity, is comprised of three phases: elimination, equilibrium and escape1,2,3,4,5. Although many immune components that participate in this process are known, its underlying mechanisms remain poorly defined. A central tenet of cancer immunoediting is that T-cell recognition of tumour antigens drives the immunological destruction or sculpting of a developing cancer. However, our current understanding of tumour antigens comes largely from analyses of cancers that develop in immunocompetent hosts and thus may have already been edited. Little is known about the antigens expressed in nascent tumour cells, whether they are sufficient to induce protective antitumour immune responses or whether their expression is modulated by the immune system. Here, using massively parallel sequencing, we characterize expressed mutations in highly immunogenic methylcholanthrene-induced sarcomas derived from immunodeficient Rag2−/− mice that phenotypically resemble nascent primary tumour cells1,3,5. Using class I prediction algorithms, we identify mutant spectrin-β2 as a potential rejection antigen of the d42m1 sarcoma and validate this prediction by conventional antigen expression cloning and detection. We also demonstrate that cancer immunoediting of d42m1 occurs via a T-cell-dependent immunoselection process that promotes outgrowth of pre-existing tumour cell clones lacking highly antigenic mutant spectrin-β2 and other potential strong antigens. These results demonstrate that the strong immunogenicity of an unedited tumour can be ascribed to expression of highly antigenic mutant proteins and show that outgrowth of tumour cells that lack these strong antigens via a T-cell-dependent immunoselection process represents one mechanism of cancer immunoediting.

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Figure 1: Unedited MCA-induced sarcomas d42m1 and H31m1 genomically resemble carcinogen-induced human cancers.
Figure 2: Affinity value profiles of predicted MHC class I epitopes from tumour-specific mutations.
Figure 3: Identification of mutant spectrin-β2 as an authentic antigen of an unedited tumour.
Figure 4: Mutant spectrin-β2 is a major rejection antigen of d42m1.

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References

  1. Shankaran, V. et al. IFNγ and lymphocytes prevent primary tumour development and shape tumour immunogenicity. Nature 410, 1107–1111 (2001)

    Article  ADS  CAS  Google Scholar 

  2. Dunn, G. P., Bruce, A. T., Ikeda, H., Old, L. J. & Schreiber, R. D. Cancer immunoediting: from immunosurveillance to tumor escape. Nature Immunol. 3, 991–998 (2002)

    Article  CAS  Google Scholar 

  3. Koebel, C. M. et al. Adaptive immunity maintains occult cancer in an equilibrium state. Nature 450, 903–907 (2007)

    ADS  CAS  Google Scholar 

  4. Vesely, M. D., Kershaw, M. H., Schreiber, R. D. & Smyth, M. J. Natural innate and adaptive immunity to cancer. Annu. Rev. Immunol. 29, 235–271 (2011)

    Article  CAS  Google Scholar 

  5. Schreiber, R. D., Old, L. J. & Smyth, M. J. Cancer immunoediting: integrating immunity’s roles in cancer suppression and promotion. Science 331, 1565–1570 (2011)

    Article  ADS  CAS  Google Scholar 

  6. Futreal, P. A. et al. A census of human cancer genes. Nature Rev. Cancer 4, 177–183 (2004)

    CAS  Google Scholar 

  7. Chen, A. C. & Herschman, H. R. Tumorigenic methylcholanthrene transformants of C3H/10T1/2 cells have a common nucleotide alteration in the c-Ki-ras gene. Proc. Natl Acad. Sci. USA 86, 1608–1611 (1989)

    Article  ADS  CAS  Google Scholar 

  8. Tuveson, D. A. et al. Endogenous oncogenic K-ras(G12D) stimulates proliferation and widespread neoplastic and developmental defects. Cancer Cell 5, 375–387 (2004)

    Article  CAS  Google Scholar 

  9. Kirsch, D. G. et al. A spatially and temporally restricted mouse model of soft tissue sarcoma. Nature Med. 13, 992–997 (2007)

    Article  CAS  Google Scholar 

  10. Ley, T. J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66–72 (2008)

    Article  ADS  CAS  Google Scholar 

  11. Ding, L. et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464, 999–1005 (2010)

    Article  ADS  CAS  Google Scholar 

  12. Shah, S. P. et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809–813 (2009)

    Article  ADS  CAS  Google Scholar 

  13. Lee, W. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473–477 (2010)

    Article  ADS  CAS  Google Scholar 

  14. Pleasance, E. D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184–190 (2010)

    Article  ADS  CAS  Google Scholar 

  15. Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nature Genet. 43, 464–469 (2011)

    Article  CAS  Google Scholar 

  16. Puente, X. S. et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101–105 (2011)

    Article  CAS  Google Scholar 

  17. Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191–196 (2010)

    Article  ADS  CAS  Google Scholar 

  18. Boon, T., Coulie, P. G., Van den Eynde, B. J. & van der Bruggen, P. Human T cell responses against melanoma. Annu. Rev. Immunol. 24, 175–208 (2006)

    Article  CAS  Google Scholar 

  19. Segal, N. H. et al. Epitope landscape in breast and colorectal cancer. Cancer Res. 68, 889–892 (2008)

    Article  CAS  Google Scholar 

  20. Nielsen, M. et al. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 12, 1007–1017 (2003)

    Article  CAS  Google Scholar 

  21. van der Bruggen, P. et al. A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science 254, 1643–1647 (1991)

    Article  ADS  CAS  Google Scholar 

  22. Khong, H. T. & Restifo, N. P. Natural selection of tumor variants in the generation of “tumor escape” phenotypes. Nature Immunol. 3, 999–1005 (2002)

    Article  CAS  Google Scholar 

  23. Dunn, G. P., Old, L. J. & Schreiber, R. D. The three Es of cancer immunoediting. Annu. Rev. Immunol. 22, 329–360 (2004)

    Article  CAS  Google Scholar 

  24. DuPage, M., Mazumdar, C., Schmidt, L. M., Cheung, A. F. & Jacks, T. Expression of tumour-specific antigens underlies cancer immunoediting. Nature doi:10.1038/nature10803 (this issue).

  25. Yewdell, J. W. Confronting complexity: real-world immunodominance in antiviral CD8+ T cell responses. Immunity 25, 533–543 (2006)

    Article  CAS  Google Scholar 

  26. Prehn, R. T. & Main, J. M. Immunity to methylcholanthrene-induced sarcomas. J. Natl. Cancer Inst. 18, 769–778 (1957)

    CAS  PubMed  Google Scholar 

  27. Old, L. J. & Boyse, E. A. Immunology of experimental tumors. Annu. Rev. Med. 15, 167–186 (1964)

    Article  CAS  Google Scholar 

  28. Huang, S. et al. Immune response in mice that lack the interferon-γ receptor. Science 259, 1742–1745 (1993)

    Article  ADS  CAS  Google Scholar 

  29. Muller, U. et al. Functional role of type I and type II interferons in antiviral defense. Science 264, 1918–1921 (1994)

    Article  ADS  CAS  Google Scholar 

  30. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

    Article  CAS  Google Scholar 

  31. Koboldt, D. C. et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25, 2283–2285 (2009)

    Article  CAS  Google Scholar 

  32. Ning, Z., Cox, A. J. & Mullikin, J. C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725–1729 (2001)

    Article  CAS  Google Scholar 

  33. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)

    Article  Google Scholar 

  34. Robinson, J. T. et al. Integrative genomics viewer. Nature Biotechnol. 29, 24–26 (2011)

    Article  CAS  Google Scholar 

  35. Felsenstein, J. Phylogeny Inference Package. Cladistics 5, 164–166 (1989)

    Google Scholar 

  36. Ranganath, S. et al. GATA-3-dependent enhancer activity in IL-4 gene regulation. J. Immunol. 161, 3822–3826 (1998)

    CAS  PubMed  Google Scholar 

  37. Dighe, A. S., Richards, E., Old, L. J. & Schreiber, R. D. Enhanced in vivo growth and resistance to rejection of tumor cells expressing dominant negative IFNγ receptors. Immunity 1, 447–456 (1994)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to J. Archambault for expert technical assistance, T. H. Hansen (Washington University) for providing MHC class I antibodies, S. Horvath and P. M. Allen (Washington University) for synthesizing MHC class I peptides, the National Institutes of Health (NIH) Tetramer Core Facility for producing MHC class I tetramers, and T. S. Stappenbeck (Washington University) for technical help in recovering frozen tumour samples. We also thank E. Unanue, P. M. Allen and J. Bui for criticisms and comments, all members of the Schreiber laboratory for discussions, and the many members of The Genome Institute at Washington University School of Medicine, especially L. Ding for her insights into our analytical approaches. This work was supported by grants to R.D.S. from the National Cancer Institute, the Ludwig Institute for Cancer Research, the Cancer Research Institute, and the WWW.W Foundation; and to E.R.M. from the National Human Genome Research Institute. M.D.V. is supported by a pre-doctoral fellowship from the Cancer Research Institute. J.P.A. is supported by the Howard Hughes Medical Institute and the Ludwig Center for Cancer Immunotherapy; M.J.S. by the National Health and Medical Research Council of Australia (NH&MRC) and from the Association for International Cancer Research; and L.J.O. by the Ludwig Institute for Cancer Research and the Cancer Research Institute.

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Author notes

  1. Hirokazu Matsushita

    Present address: Present address: Department of Immunotherapeutics (Medinet), The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.,

  2. Hirokazu Matsushita and Matthew D. Vesely: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA,

    Hirokazu Matsushita, Matthew D. Vesely, Charles G. Rickert, Cora D. Arthur, J. Michael White, Yee-Shiuan Chen, Lauren K. Shea & Robert D. Schreiber

  2. The Genome Institute, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA,

    Daniel C. Koboldt, Vincent J. Magrini, Jasreet Hundal, Michael C. Wendl, Ryan Demeter, Todd Wylie & Elaine R. Mardis

  3. Department of Otolaryngology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA,

    Ravindra Uppaluri

  4. Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA,

    Vincent J. Magrini, Michael C. Wendl & Elaine R. Mardis

  5. Department of Immunology, Ludwig Center for Cancer Immunotherapy, Memorial Sloan-Kettering Cancer Center, New York, 10021, New York, USA

    James P. Allison

  6. Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, 10021, New York, USA

    James P. Allison

  7. Cancer Immunology Program, Peter MacCallum Cancer Centre, East Melbourne, 3002 Victoria, Australia,

    Mark J. Smyth

  8. Department of Pathology, University of Melbourne, Parkville, 2010 Victoria, Australia,

    Mark J. Smyth

  9. New York Branch of The Ludwig Institute for Cancer Research at Memorial Sloan-Kettering Cancer Center, New York, 10021, New York, USA

    Lloyd J. Old

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Contributions

H.M. and M.D.V. were involved in all aspects of this study including planning and performing experiments, analysing and interpreting data, and writing the manuscript. C.G.R., R.U., C.D.A., J.M.W., Y.-S.C. and L.K.S. also performed experiments and analysed data. V.J.M., R.D. and members of The Genome Institute performed Illumina library preparation, cDNA capture and sequencing as well as validation Roche/454 pyrosequencing and 3730 sequencing. D.C.K. analysed and interpreted sequencing data from this study and previously published cancer genome data. J.H. and T.W. analysed cDNA CapSeq data for potential MHC class I epitopes. M.C.W. performed the phylogenetic analysis on the tumour cells. J.P.A., M.J.S. and L.J.O. interpreted data and contributed to the preparation of the final manuscript. E.R.M. and R.D.S oversaw all the work performed, planned experiments, interpreted data and wrote the manuscript.

Corresponding author

Correspondence to Robert D. Schreiber.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains: 1 Supplementary Figures 1-11 with legends, which include supporting experiments demonstrating the immunogenic behavior of H31m1 and d42m1, that mutant spectrin-β2 is the major rejection antigen of d42m1 sarcoma cells, that spectrin-β2 is not epigenetically silenced, and that escape tumours of d42m1 emerge via an immunoselection process that favors outgrowth of cells lacking mutant spectrin-β2; and 2 Supplementary Table 5, which lists both wild type and mutant epitopes predicted by Immune Epitope Database and Analysis Resource for misssense mutations that are present in d42m1 regressor tumours (d42m1 parental, d42m1-T1, d42m1-T2, and d42m1-T9) and absent in d42m1 progressor tumours (d42m1-T3, d42m1-T10, d42m1-es1, d42m1-es2, and d42m1-es3) - see separate files for Supplementary Tables 1-4. (PDF 1461 kb)

Supplementary Table 1

This table lists all the single nucleotide variants (SNVs) for H31m1 and the d42m1 tumour tumours as detected by cDNA capture sequencing. These include missense, nonsense, nonstop, splice site, silent, and RNA gene mutations. (XLS 4994 kb)

Supplementary Table 2

This table compares all the missense mutations in H31m1 and d42m1 parental tumour cells. Missense mutations are organized as either shared between H31m1 and d42m1 or unique to each individual sarcoma cell line. (XLS 1072 kb)

Supplementary Table 3

This table lists all the mutated genes in H31m1 and d42m1 parental tumour cells and whether these genes are among the list of known human cancer genes (Cancer Gene Census; http://www.sanger.ac.uk/genetics/CGP/Census/). (XLS 261 kb)

Supplementary Table 4

This table lists validation sequencing by Roche/454 pyrosequencing and Applied Biosystems/3730 sequencing in tumour cells and normal cells and lists the primer sets used for this analysis. (XLS 53 kb)

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Matsushita, H., Vesely, M., Koboldt, D. et al. Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature 482, 400–404 (2012). https://doi.org/10.1038/nature10755

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