Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome

References

• Sette A, Sidney J. HLA supertypes and supermotifs: a functional perspective on HLA polymorphism. Curr Opin Immunol. 1998;10(4):478–482. doi:10.1016/S0952-7915(98)80124-6.
   PubMed Web of Science ®Google Scholar
• Lennerz V, Fatho M, Gentilini C, Frye RA, Lifke A, Ferel D, Wölfel C, Huber C, Wölfel T. The response of autologous T cells to a human melanoma is dominated by mutated neoantigens. Proc Natl Acad Sci U S A. 2005;102(44):16013–16018. doi:10.1073/pnas.0500090102.
   PubMed Web of Science ®Google Scholar
• Matsushita H, Vesely MD, Koboldt DC, Rickert CG, Uppaluri R, Magrini VJ, Arthur CD, White JM, Chen Y-S, Shea LK, et al. Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature. 2012;482(7385):400–404. doi:10.1038/nature10755.
   PubMed Web of Science ®Google Scholar
• Heemskerk B, Kvistborg P, Schumacher TNM. The cancer antigenome. Embo J. 2013;32(2):194–203. doi:10.1038/emboj.2012.333.
   PubMed Web of Science ®Google Scholar
• Lu Y-C, Yao X, Li YF, El-Gamil M, Dudley ME, Yang JC, Almeida JR, Douek DC, Samuels Y, Rosenberg SA, et al. Mutated PPP1R3B is recognized by T cells used to treat a melanoma patient who experienced a durable complete tumor regression. J Immunol. 2013;190(12):6034–6042. doi:10.4049/jimmunol.1202830.
   PubMed Web of Science ®Google Scholar
• Robbins PF, Lu Y-C, El-Gamil M, Li YF, Gross C, Gartner J, Lin JC, Teer JK, Cliften P, Tycksen E, et al. Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells. Nat Med. 2013;19(6):747–752. doi:10.1038/nm.3161.
   PubMed Web of Science ®Google Scholar
• van Rooij N, van Buuren MM, Philips D, Velds A, Toebes M, Heemskerk B, Lja VD, Behjati S, Hilkmann H, El Atmioui D, et al. Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J Clin Oncol. 2013;31(32):e439–42. doi:10.1200/JCO.2012.47.7521.
   PubMed Web of Science ®Google Scholar
• Wick DA, Webb JR, Nielsen JS, Martin SD, Kroeger DR, Milne K, Castellarin M, Twumasi-Boateng K, Watson PH, Holt RA, et al. Surveillance of the tumor mutanome by T cells during progression from primary to recurrent ovarian cancer. Clin Cancer Res. 2014;20(5):1125–1134. doi:10.1158/1078-0432.CCR-13-2147.
   PubMed Web of Science ®Google Scholar
• Chowell D, Morris LGT, Grigg CM, Weber JK, Samstein RM, Makarov V, Kuo F, Kendall SM, Requena D, Riaz N, et al. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science. 2017 Dec 7;80:eaao4572.doi:10.1126/science.aao4572.
   Google Scholar
• Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, et al. MHC-I genotype restricts the oncogenic mutational landscape. Cell. 2017;171(6):1272–1283.e15. doi:10.1016/j.cell.2017.09.050.
   PubMed Web of Science ®Google Scholar
• Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A, Kloetzel PM, Stumpf MPH, Heck AJR, Mishto M. A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science. 2016;354(6310):354–358. doi:10.1126/science.aaf4384.
   PubMed Web of Science ®Google Scholar
• Granados DP, Laumont CM, Thibault P, Perreault C. The nature of self for T cells-a systems-level perspective. Curr Opin Immunol. 2015;34:1–8. doi:10.1016/j.coi.2014.10.012.
   PubMed Web of Science ®Google Scholar
• Schreiber RD, Old LJ, Smyth MJ. Cancer immunoediting: integrating immunity’s roles in cancer suppression and promotion. Science. 2011;331(6024):1565–1570. doi:10.1126/science.1203486.
   PubMed Web of Science ®Google Scholar
• Eichmann M, de Ru A, van Veelen PA, Peakman M, Kronenberg-Versteeg D. Identification and characterisation of peptide binding motifs of six autoimmune disease-associated human leukocyte antigen-class I molecules including HLA-B*39:06. Tissue Antigens. 2014;84(4):378–388. doi:10.1111/tan.12413.
   PubMedGoogle Scholar
• Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, et al. The SysteMHC Atlas project. Nucleic Acids Res. 2018;46(D1):D1237–D1247. doi:10.1093/nar/gkx664.
   PubMed Web of Science ®Google Scholar
• González-Galarza FF, Takeshita LYC, Santos EJM, Kempson F, Maia MHT, da Silva ALS, Teles e Silva AL, Ghattaoraya GS, Alfirevic A, Jones AR, et al. Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. Nucleic Acids Res. 2015;43(D1):D784–D788. doi:10.1093/nar/gku1166.
   PubMed Web of Science ®Google Scholar
• Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, et al. The immune landscape of cancer. Immunity. 2018;48(4):812–830.e14. doi:10.1016/j.immuni.2018.03.023.
   PubMed Web of Science ®Google Scholar
• Gragert L, Madbouly A, Freeman J, Maiers M. Six-locus high resolution HLA haplotype frequencies derived from mixed-resolution DNA typing for the entire US donor registry. Hum Immunol. 2013;74(10):1313–1320. doi:10.1016/J.HUMIMM.2013.06.025.
   PubMed Web of Science ®Google Scholar
• Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics. 2014;30(23):1–7. doi:10.1093/bioinformatics/btu548.
   PubMed Web of Science ®Google Scholar
• Liu J, Lichtenberg TM, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, et al. An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics. Cell. 2018;173(2):400–416.e11. doi:10.1016/j.cell.2018.02.052.
   PubMed Web of Science ®Google Scholar
• Calis JJA, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol. 2013;9(10):e1003266. doi:10.1371/journal.pcbi.1003266.
   PubMed Web of Science ®Google Scholar
• Nielsen M, Andreatta M. NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med. 2016;8(1):33. doi:10.1186/s13073-016-0288-x.
   PubMedGoogle Scholar
• Lund O, Nielsen M, Kesmir C, Petersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, et al. Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics. 2004;55(12):797–810. doi:10.1007/s00251-004-0647-4.
   PubMed Web of Science ®Google Scholar
• Bjerregaard A-M, Nielsen M, Jurtz V, Barra CM, Hadrup SR, Szallasi Z, Eklund AC. An analysis of natural T cell responses to predicted tumor neoepitopes. Front Immunol. 2017;8:1566. doi:10.3389/fimmu.2017.01566.
   PubMed Web of Science ®Google Scholar
• Borbulevych OY, Baxter TK, Yu Z, Restifo NP, Baker BM. Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design. J Immunol. 2005;174(8):4812–4820. doi:10.4049/JIMMUNOL.174.8.4812.
   PubMed Web of Science ®Google Scholar
• Harndahl M, Rasmussen M, Roder G, Dalgaard Pedersen I, Sørensen M, Nielsen M, Buus S. Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur J Immunol. 2012;42(6):1405–1416. doi:10.1002/eji.201141774.
   PubMed Web of Science ®Google Scholar
• Degano M, Garcia KC, Apostolopoulos V, Rudolph MG, Teyton L, Wilson IA. A functional hot spot for antigen recognition in a superagonist TCR/MHC complex. Immunity. 2000;12(3):251–261.
   PubMed Web of Science ®Google Scholar
• Sharma AK, Kuhns JJ, Yan S, Friedline RH, Long B, Tisch R, Collins EJ. Class I major histocompatibility complex anchor substitutions alter the conformation of T cell receptor contacts. J Biol Chem. 2001;276(24):21443–21449. doi:10.1074/jbc.M010791200.
   PubMed Web of Science ®Google Scholar
• Tsukahara T, Kawaguchi S, Torigoe T, Asanuma H, Nakazawa E, Shimozawa K, Nabeta Y, Kimura S, Kaya M, Nagoya S, et al. Prognostic significance of HLA class I expression in osteosarcoma defined by anti-pan HLA class I monoclonal antibody, EMR8–5. Cancer Sci. 2006;97(12):1374–1380. doi:10.1111/j.1349-7006.2006.00317.x.
   PubMed Web of Science ®Google Scholar
• Bijen CBM, Bantema-Joppe EJ, de Jong RA, Leffers N, Mourits MJE, Eggink HF, van der Zee AGJ, Hollema H, de Bock GH, Nijman HW. The prognostic role of classical and nonclassical MHC class I expression in endometrial cancer. Int J Cancer. 2010;126(6):1417–1427. doi:10.1002/ijc.24852.
   PubMed Web of Science ®Google Scholar
• Dunn GP, Bruce AT, Ikeda H, Old LJ, Schreiber RD. Cancer immunoediting: from immunosurveillance to tumor escape. Nat Immunol. 2002;3(11):991–998. doi:10.1038/ni1102-991.
   PubMed Web of Science ®Google Scholar
• Frankild S, de Boer RJ, Lund O, Nielsen M, Kesmir C. Amino acid similarity accounts for T cell cross-reactivity and for “Holes” in the T cell repertoire Zhang L, editor. PLoS ONE. 2008;3(3):e1831. doi:10.1371/journal.pone.0001831.
   PubMed Web of Science ®Google Scholar
• Yadav M, Jhunjhunwala S, Phung QT, Lupardus P, Tanguay J, Bumbaca S, Franci C, Cheung TK, Fritsche J, Weinschenk T, et al. Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature. 2014;515(7528):572–576. doi:10.1038/nature14001.
   PubMed Web of Science ®Google Scholar
• Bristol JA, Schlom J, Abrams SI. Development of a murine mutant ras CD8+ CTL peptide epitope variant that possesses enhanced MHC class I binding and immunogenic properties. J Immunol. 1998;160:2433–2441.
   PubMed Web of Science ®Google Scholar
• Kim Y, Sidney J, Buus SS, Sette A, Nielsen M, Peters B. Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. BMC Bioinformatics. 2014;15(1):241. doi:10.1186/1471-2105-15-241.
   PubMedGoogle Scholar
• Paul S, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A. HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. J Immunol. 2013;191(12):5831–5839. doi:10.4049/jimmunol.1302101.
   PubMed Web of Science ®Google Scholar
• Sette A, Vitiello A, Reherman B, Fowler P, Nayersina R, Kast WM, Melief CJ, Oseroff C, Yuan L, Ruppert J, et al. The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes. J Immunol. 1994;153(12):5586–5592.
   PubMed Web of Science ®Google Scholar
• Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, Nelson BH, Holt RA. Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 2014;24(5):743–750. doi:10.1101/gr.165985.113.
   PubMed Web of Science ®Google Scholar
• Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160(1–2):48–61. doi:10.1016/j.cell.2014.12.033.
   PubMed Web of Science ®Google Scholar
• Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan MD, et al. Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines. Cell Syst. 2018;6(3):271–281.e7. doi:10.1016/j.cels.2018.03.002.
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. doi:10.1093/bioinformatics/btp352.
   PubMed Web of Science ®Google Scholar