Abstract
Recent data indicate that endogenous mutated cancer proteins can be processed and presented as HLA binding peptides, leading to their recognition in vivo as “non-self.” Targeting such neoantigens would enable immune cells to distinguish between normal and cancerous cells, avoiding the risk of autoimmunity. So far, discovery of such neoantigens relies mainly on prediction-based interrogation of the “mutanome” using genomic information as input, followed by highly laborious and time-consuming T cell screening assays. Currently, mass spectrometry is the only unbiased methodology to comprehensively interrogate the naturally presented repertoire of HLA binding peptides, including peptides derived from tumor-associated antigens and post-translational modified peptides. This chapter describes a detailed protocol for in-depth and accurate mass spectrometry based immunopeptidomics, enabling the direct identification of tissue-derived neoantigens extracted from human tumors.
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References
Grupp SA, Kalos M, Barrett D et al (2013) Chimeric antigen receptor-modified T cells for acute lymphoid leukemia. N Engl J Med 368(16):1509–1518
Hodi FS, O’Day SJ, McDermott DF et al (2010) Improved survival with ipilimumab in patients with metastatic melanoma. N Engl J Med 363(8):711–723
Kantoff PW, Higano CS, Shore ND et al (2010) Sipuleucel-T immunotherapy for castration-resistant prostate cancer. N Engl J Med 363(5):411–422
Rosenberg SA, Yang JC, Sherry RM et al (2011) Durable complete responses in heavily pretreated patients with metastatic melanoma using T-cell transfer immunotherapy. Clin Cancer Res 17(13):4550–4557
Walter S, Weinschenk T, Stenzl A et al (2012) Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival. Nat Med 18(8):1254–1261
Wolchok JD, Kluger H, Callahan MK et al (2013) Nivolumab plus ipilimumab in advanced melanoma. N Engl J Med 369(2):122–133
Larkin J, Chiarion-Sileni V, Gonzalez R et al (2015) Combined Nivolumab and Ipilimumab or monotherapy in untreated melanoma. N Engl J Med 373(1):23–34
Schadendorf D, Hodi FS, Robert C et al (2015) Pooled analysis of long-term survival data from phase II and phase III trials of Ipilimumab in unresectable or metastatic melanoma. J Clin Oncol 33(17):1889–1894
Borghaei H, Paz-Ares L, Horn L et al (2015) Nivolumab versus docetaxel in advanced nonsquamous non-small-cell lung cancer. N Engl J Med 373(17):1627–1639
Powles T, Eder JP, Fine GD et al (2014) MPDL3280A (anti-PD-L1) treatment leads to clinical activity in metastatic bladder cancer. Nature 515(7528):558–562
Le DT, Uram JN, Wang H et al (2015) PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med 372(26):2509–2520
Castle JC, Kreiter S, Diekmann J et al (2012) Exploiting the mutanome for tumor vaccination. Cancer Res 72(5):1081–1091
Brown SD, Warren RL, Gibb EA et al (2014) Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res 24(5):743–750
Rizvi NA, Hellmann MD, Snyder A et al (2015) Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348(6230):124–128
Snyder A, Makarov V, Merghoub T et al (2014) Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 371(23):2189–2199
Neefjes J, Jongsma ML, Paul P et al (2011) Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol 11(12):823–836
Bassani-Sternberg M, Coukos G (2016) Mass spectrometry-based antigen discovery for cancer immunotherapy. Curr Opin Immunol 41:9–17
Bassani-Sternberg M, Braunlein E, Klar R et al (2016) Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat Commun 7:13404
Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ et al (2015) Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol Cell Proteomics 14(3):658–673
Carreno BM, Magrini V, Becker-Hapak M et al (2015) Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science 348(6236):803–808
Gubin MM, Zhang X, Schuster H et al (2014) Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature 515(7528):577–581
Kalaora S, Barnea E, Merhavi-Shoham E et al (2016) Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens. Oncotarget 7(5):5110–5117
Yadav M, Jhunjhunwala S, Phung QT et al (2014) Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 515(7528):572–576
Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11(12):2301–2319
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372
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Bassani-Sternberg, M. (2018). Mass Spectrometry Based Immunopeptidomics for the Discovery of Cancer Neoantigens. In: Schrader, M., Fricker, L. (eds) Peptidomics. Methods in Molecular Biology, vol 1719. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7537-2_14
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DOI: https://doi.org/10.1007/978-1-4939-7537-2_14
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