REFERENCES
1. Coley WB. The treatment of malignant tumors by repeated inoculations of erysipelas. With a report of ten original cases. 1893. Clin Orthop Relat Res 1991;(262):3-11.
2. Parish CR. Cancer immunotherapy: the past, the present and the future. Immunol Cell Biol 2003;81:106-13.
3. Riera Romo M, Pérez-Martínez D, Castillo Ferrer C. Innate immunity in vertebrates: an overview. Immunology 2016;148:125-39.
4. Litman GW, Rast JP, Fugmann SD. The origins of vertebrate adaptive immunity. Nat Rev Immunol 2010;10:543-53.
5. Xing Y, Hogquist KA. T-Cell tolerance: central and peripheral. Cold Spring Harb Perspect Biol 2012;4:a006957.
6. Whitton JL, editor. Antigen Presentation. Berlin, Heidelberg: Springer; 1998; doi: 10.1007/978-3-642-72045-1.
7. van Endert P, editor. Antigen Processing: Methods and Protocols. Totowa, NJ: Humana Press; 2013; doi: 10.1007/978-1-62703-218-6.
8. Roche PA, Furuta K. The ins and outs of MHC class II-mediated antigen processing and presentation. Nat Rev Immunol 2015;15:203-16.
9. Shah DK. T-cell development in thymus. British Society for Immunology. Available from:https://www.immunology.org/public-information/bitesized-immunology/immune-development/t-cell-development-in-thymus. [Last accessed on 29 Jul 2017].
10. Crespo J, Sun H, Welling TH, Tian Z, Zou W. T cell anergy, exhaustion, senescence, and stemness in the tumor microenvironment. Curr Opin Immunol 2013;25:214-21.
11. Walker LSK, Sansom DM. Confusing signals: recent progress in CTLA-4 biology. Trends Immunol 2015;36:63-70.
12. Manz BN, Jackson BL, Petit RS, Dustin ML, Groves J. T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters. Proc Natl Acad Sci U S A 2011;108:9089-94.
13. Reinherz EL. αβ TCR-mediated recognition: relevance to tumor-antigen discovery and cancer immunotherapy. Cancer Immunol Res 2015;3:305-12.
14. Meydan C, Otu HH, Sezerman OU. Prediction of peptides binding to MHC class I and II alleles by temporal motif mining. BMC Bioinformatics 2013;14 Suppl 2:S13.
16. Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. Tissue Antigens 2010;75:291-455.
17. Ghattaoraya GS, Dundar Y, González-Galarza FF, Maia MHT, Santos EJM, da Silva ALS, McCabe A, Middleton D, Alfirevic A, Dickson R, Jones AR. A web resource for mining HLA associations with adverse drug reactions: HLA-ADR. Database (Oxford) 2016;2016:baw069.
18. Robinson J, Soormally AR, Hayhurst JD, Marsh SGE. The IPD-IMGT/HLA database -new developments in reporting HLA variation. Hum Immunol 2016;77:233-7.
19. Arstila TP, Casrouge A, Baron V, Even J, Kanellopoulos J, Kourilsky P. A direct estimate of the human αβ T cell receptor diversity. Science 1999;286:958-61.
20. Davis MM, Tato CM, Furman D. Systems immunology: just getting started. Nat Immunol 2017;18:725-32.
21. Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, Bolotin DA, Lukyanov S, Bogdanova EA, Mamedov IZ, Lebedev YB, Chudakov DM. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. J Immunol 2014;192:2689-98.
22. Qi Q, Liu Y, Cheng Y, Glanville J, Zhang D, Lee JY, Olshen RA, Weyand CM, Boyd SD, Goronzy JJ. Diversity and clonal selection in the human T-cell repertoire. Proc Natl Acad Sci U S A 2014;111:13139-44.
23. Derhovanessian E, Solana R, Larbi A, Pawelec G. Immunity, ageing and cancer. Immun Ageing 2008;5:11.
24. Elias R, Karantanos T, Sira E, Hartshorn KL. Immunotherapy comes of age: immune aging & checkpoint inhibitors. J Geriatr Oncol 2017;8:229-35.
26. Wucherpfenning KW, Strominger JL. Molecular mimicry in T cell-mediated autoimmunity: viral peptides activate human T cell clones specific for myelin basic protein. Cell 1995;80:695-705.
27. Cole DK, Bulek AM, Dolton G, Schauenberg AJ, Szomolay B, Rittase W, Trimby A, Jothikumar P, Fuller A, Skowera A, Rossjohn J, Zhu C, Miles JJ, Peakman M, Wooldridge L, Rizkallah PJ, Sewell AK. Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. J Clin Invest 2016;126:2191-204.
28. Kumar A, Delogu F. Dynamical footprint of cross-reactivity in a human autoimmune T-cell receptor. Sci Rep 2017;7:42496.
29. 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;42:1405-16.
30. Yager EJ, Ahmed M, Lanzer K, Randall TD, Woodland DL, Blackman MA. Age-associated decline in T cell repertoire diversity leads to holes in the repertoire and impaired immunity to influenza virus. J Exp Med 2008;205:711-23.
31. Wölfl M, Rutebemberwa A, Mosbruger T, Mao Q, Li H, Netski D, Ray SC, Pardoll D, Sidney J, Sette A, Allen T, Kuntzen T, Kavanagh DG, Kuball J, Greenberg PD, Cox AL. Hepatitis C virus immune escape via exploitation of a hole in the T cell repertoire. J Immunol 2008;181:6435-46.
32. Vatti A, Monsalve DM, Pacheco Y, Chang C, Anaya JM, Gershwin ME. Original antigenic sin: a comprehensive review. J Autoimmun 2017;83:12-21.
33. Joffre OP, Segura E, Savina A, Amigorena S. Cross-presentation by dendritic cells. Nat Rev Immunol 2012;12:557-69.
34. Fehres CM, Unger WWJ, Garcia-Vallejo JJ, van Kooyk Y. Understanding the biology of antigen cross-presentation for the design of vaccines against cancer. Front Immunol 2014;5:149.
36. Caza T, Landas S. Functional and phenotypic plasticity of CD4+ T cell subsets. Biomed Res Int 2015;2015:521957.
37. van de Berg PJ, van Leeuwen EM, ten Berge IJ, van Lier R. Cytotoxic human CD4+ T cells. Curr Opin Immunol 2008;20:339-43.
38. Takeuchi A, Saito T. CD4 CTL, a cytotoxic subset of CD4+ T cells, their differentiation and function. Front Immunol 2017;8:194.
39. Ley K. The second touch hypothesis: T cell activation, homing and polarization. version 2. F1000 Research 2014;3:37.
40. Crome SQ, Nguyen LT, Lopez-Verges S, Yang SYC, Martin B, Yam JY, Johnson DJ, Nie J, Pniak M, Yen PH, Milea A, Sowamber R, Katz SR, Bernardini MQ, Clarke BA, Shaw PA, Lang PA, Berman HK, Pugh TJ, Lanier LL, Ohashi PS. A distinct innate lymphoid cell population regulates tumor-associated T cells. Nat Med 2017;23:368-75.
42. Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science 2017;357:eaal2380.
43. Thomas F, Fisher D, Fort P, Marie J-P, Daoust S, Roche B, Grunau C, Cosseau C, Mitta G, Baghdiguian S, Rousset F, Lassus P, Assenat E, Grégoire D, Missé D, Lorz A, Billy F, Vainchenker W, Delhommeau F, Koscielny S, Itzykson R, Tang R, Fava F, Ballesta A, Lepoutre T, Krasinska L, Dulic V, Raynaud P, Blache P, Quittau-Prevostel C, Vignal E, Trauchessec H, Perthame B, Clairambault J, Volpert V, Solary E, Hibner U, Hochberg ME. Applying ecological and evolutionary theory to cancer: a long and winding road. Evol Appl 2013;6:1-10.
44. Davis A, Gao R, Navin N. Tumor evolution: linear, branching, neutral or punctuated? Biochim Biophys Acta 2017;1867:151-61.
45. Paguirigan AL, Smith J, Meshinchi S, Carroll M, Maley C, Radich JP. Single-cell genotyping demonstrates complex clonal diversity in acute myeloid leukemia. Sci Transl Med 2015;7:281re2.
46. Sun R, Hu Z, Sottoriva A, Graham TA, Harpak A, Ma Z, Fischer JM, Shibata D, Curtis C. Between-region genetic divergence reflects the mode and tempo of tumor evolution. Nat Genet 2017;49:1015-24.
47. Aktipis CA, Kwan VSY, Johnson KA, Neuberg SL, Maley CC. Overlooking evolution: a systematic analysis of cancer relapse and therapeutic resistance research. PLoS One 2011;6:e26100.
49. Weinberg RA. The biology of cancer. Second edition. New York: Garland Science, Taylor & Francis Group; 2014.
50. Abbas AK, Lichtman AH, Pillai S. Cellular and molecular immunology. Philadelphia, PA: Elsevier Saunders; 2015.
51. Rezaei N, editor. Cancer Immunology. Berlin, Heidelberg: Springer Berlin Heidelberg; 2015.
52. Sell S. Cancer immunotherapy: breakthrough or "deja vu, all over again"? Tumor Biol 2017;39:1010428317707764.
53. Korman AJ, Peggs KS, Allison JP. Checkpoint blockade in cancer immunotherapy. Adv Immunol 2006;90:297-339.
54. Palucka K, Banchereau J. Cancer immunotherapy via dendritic cells. Nat Rev Cancer 2012;12:265-77.
55. Gardner T, Elzey B, Hahn NM. Sipuleucel-T (Provenge) autologous vaccine approved for treatment of men with asymptomatic or minimally symptomatic castrate-resistant metastatic prostate cancer. Hum Vaccines Immunother 2012;8:534-9.
56. Rosenberg SA, Restifo NP. Adoptive cell transfer as personalized immunotherapy for human cancer. Science 2015;348:62-8.
58. Gross G, Waks T, Eshhar Z. Expression of immunoglobulin-T-cell receptor chimeric molecules as functional receptors with antibody-type specificity. Proc Natl Acad Sci U S A 1989;86:10024-8.
59. Longoria TC, Eskander RN. Immunotherapy in endometrial cancer - an evolving therapeutic paradigm. Gynecol Oncol Res Pract 2015;2:11.
60. Page DB, Bourla AB, Daniyan A, Naidoo J, Smith E, Smith M, Friedman C, Khalil DN, Funt S, Shoushtari AN, Overwijk WW, Sharma P, Callahan MK. Tumor immunology and cancer immunotherapy: summary of the 2014 SITC primer. J Immunother Cancer 2015;3:25.
61. van Rooij N, van Buuren MM, Philips D, Velds A, Toebes M, Heemskerk B, van Dijk LJ, Behjati S, Hilkmann H, El Atmioui D, Nieuwland M, Stratton MR, Kerkhoven RM, Kesmir C, Haanen JB, Kvistborg P, Schumacher TN. Tumor exome analysis reveals neoantigen-specific t-cell reactivity in an ipilimumab-responsive melanoma. J Clin Oncol 2013;31:e439-42.
62. Hoos A, Eggermont AMM, Janetzki S, Hodi FS, Ibrahim R, Anderson A, Humphrey R, Blumenstein B, Old L, Wolchok J. Improved endpoints for cancer immunotherapy trials. J Natl Cancer Inst 2010;102:1388-97.
63. Bates SE, Berry DA, Balasubramaniam S, Bailey S, LoRusso PM, Rubin EH. Advancing clinical trials to streamline drug development. Clin Cancer Res 2015;21:4527-35.
65. Kato S, Goodman A, Walavalkar V, Barkauskas DA, Sharabi A, Kurzrock R. Hyperprogressors after immunotherapy: analysis of genomic alterations associated with accelerated growth rate. Clin Cancer Res 2017;23:4242-50.
66. Tedeschi B. Cancer researchers worry immunotherapy may hasten growth of tumors in some patients. Available from: https://www.statnews.com/2017/04/03/immunotherapy-cancer-tumor-growth/. [Last accessed on 15 Dec 2017].
67. Galon J, Pagès F, Marincola FM, Angell HK, Thurin M, Lugli A, Zlobec I, Berger A, Bifulco C, Botti G, Tatangelo F, Britten CM, Kreiter S, Chouchane L, Delrio P, Arndt H, Asslaber M, Maio M, Masucci GV, Mihm M, Vidal-Vanaclocha F, Allison JP, Gnjatic S, Hakansson L, Huber C, Singh-Jasuja H, Ottensmeier C, Zwierzina H, Laghi L, Grizzi F, Ohashi PS, Shaw PA, Clarke BA, Wouters BG, Kawakami Y, Hazama S, Okuno K, Wang E, O'Donnell-Tormey J, Lagorce C, Pawelec G, Nishimura MI, Hawkins R, Lapointe R, Lundqvist A, Khleif SN, Ogino S, Gibbs P, Waring P, Sato N, Torigoe T, Itoh K, Patel PS, Shukla SN, Palmqvist R, Nagtegaal ID, Wang Y, D'Arrigo C, Kopetz S, Sinicrope FA, Trinchieri G, Gajewski TF, Ascierto PA, Fox BA. Cancer classification using the Immunoscore: a worldwide task force. J Transl Med 2012;10:205.
68. Gnjatic S, Bronte V, Brunet LR, Butler MO, Disis ML, Galon J, Hakansson LG, Hanks BA, Karanikas V, Khleif SN, Kirkwood JM, Miller LD, Schendel DJ, Tanneau I, Wigginton JM, Butterfield LH. Identifying baseline immune-related biomarkers to predict clinical outcome of immunotherapy. J Immunother Cancer 2017;5:44.
69. Zitvogel L, Galluzzi L, Smyth MJ, Kroemer G. Mechanism of action of conventional and targeted anticancer therapies: reinstating immunosurveillance. Immunity 2013;39:74-88.
70. O'Donnell JS, Massi D, Teng MWL, Mandala M. PI3K-AKT-mTOR inhibition in cancer immunotherapy, redux. Semin Cancer Biol 2017; doi: 10.1016/j.semcancer.2017.04.015.
71. Casey SC, Baylot V, Felsher DW. MYC: master regulator of immune privilege. Trends Immunol 2017;38:298-305.
72. Bracci L, Schiavoni G, Sistigu A, Belardelli F. Immune-based mechanisms of cytotoxic chemotherapy: implications for the design of novel and rationale-based combined treatments against cancer. Cell Death Differ 2014;21:15-25.
73. Tey SK. Adoptive T-cell therapy: adverse events and safety switches. Clin Transl Immunol 2014;3:e17.
74. Bertrand A, Kostine M, Barnetche T, Truchetet ME, Schaeverbeke T. Immune related adverse events associated with anti-CTLA-4 antibodies: systematic review and meta-analysis. BMC Med 2015;13:211.
75. Villadolid J, Amin A. Immune checkpoint inhibitors in clinical practice: update on management of immune-related toxicities. Transl Lung Cancer Res 2015;4:560-75.
76. Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ, Zhang W, Luoma A, Giobbie-Hurder A, Peter L, Chen C, Olive O, Carter TA, Li S, Lieb DJ, Eisenhaure T, Gjini E, Stevens J, Lane WJ, Javeri I, Nellaiappan K, Salazar AM, Daley H, Seaman M, Buchbinder EI, Yoon CH, Harden M, Lennon N, Gabriel S, Rodig SJ, Barouch DH, Aster JC, Getz G, Wucherpfennig K, Neuberg D, Ritz J, Lander ES, Fritsch EF, Hacohen N, Wu CJ. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 2017;547:217-21.
77. Pappalardo F, Chiacchio F, Motta S. Cancer vaccines: state of the art of the computational modeling approaches. Biomed Res Int 2013;2013:106407.
78. Andor N, Maley CC, Ji HP. Genomic instability in cancer: teetering on the limit of tolerance. Cancer Res 2017;77:2179-85.
79. Coulie PG, Van den Eynde BJ, van der Bruggen P, Boon T. Tumour antigens recognized by T lymphocytes: at the core of cancer immunotherapy. Nat Rev Cancer 2014;14:135-46.
80. Guo C, Manjili MH, Subjeck JR, Sarkar D, Fisher PB, Wang XY. Therapeutic cancer vaccines: past, present, and future. Adv Cancer Res 2013;119:421-75.
81. Melief CJM, Hall T van, Arens R, Ossendorp F, van der Burg SH. Therapeutic cancer vaccines. J Clin Invest 2015;125:3401-12.
82. Gubin MM, Artyomov MN, Mardis ER, Schreiber RD. Tumor neoantigens: building a framework for personalized cancer immunotherapy. J Clin Invest 2015;125:3413-21.
83. Slovin SF, Keding SJ, Ragupathi G. Carbohydrate vaccines as immunotherapy for cancer. Immunol Cell Biol 2005;83:418-28.
84. Neefjes J, Ovaa H. A peptide's perspective on antigen presentation to the immune system. Nat Chem Biol 2013;9:769-75.
85. Melief CJM, van der Burg SH. Immunotherapy of established (pre)malignant disease by synthetic long peptide vaccines. Nat Rev Cancer 2008;8:351-60.
86. Kumai T, Kobayashi H, Harabuchi Y, Celis E. Peptide vaccines in cancer—old concept revisited. Curr Opin Immunol 2017;45:1-7.
88. Sayour EJ, Mitchell DA. Manipulation of innate and adaptive immunity through cancer vaccines. J Immunol Res 2017;2017:3145742.
89. Kramps T, Elbers K, editors. RNA Vaccines. New York, NY: Springer New York; 2017; doi: 10.1007/978-1-4939-6481-9.
91. Beitelshees M, Li Y, Pfeifer BA. Enhancing vaccine effectiveness with delivery technology. Curr Opin Biotechnol 2016;42:24-9.
92. Yang Y, Hou J, Lin Z, Zhuo H, Chen D, Zhang X, Chen Y, Sun B. Attenuated listeria monocytogenes as a cancer vaccine vector for the delivery of CD24, a biomarker for hepatic cancer stem cells. Cell Mol Immunol 2014;11:184-96.
93. Cawood R, Hills T, Wong SL, Alamoudi AA, Beadle S, Fisher KD, Fisher KD, Seymour LW. Recombinant viral vaccines for cancer. Trends Mol Med 2012;18:564-74.
94. Swartz MA, Hirosue S, Hubbell JA. Engineering approaches to immunotherapy. Sci Transl Med 2012;4:148rv9.
95. Mehta NK, Moynihan KD, Irvine DJ. Engineering new approaches to cancer vaccines. Cancer Immunol Res 2015;3:836-43.
96. Francis DM, Thomas SN. Progress and opportunities for enhancing the delivery and efficacy of checkpoint inhibitors for cancer immunotherapy. Adv Drug Deliv Rev 2017;114:33-42.
98. Backert L, Kohlbacher O. Immunoinformatics and epitope prediction in the age of genomic medicine. Genome Med 2015;7:119.
99. Segal NH, Parsons DW, Peggs KS, Velculescu V, Kinzler KW, Vogelstein B, Allison JP. Epitope landscape in breast and colorectal cancer. Cancer Res 2008;68:889-92.
100. Nielsen M, Lundegaard C, Lund O, Keşmir C. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 2005;57:33-41.
101. Snyder A, Chan TA. Immunogenic peptide discovery in cancer genomes. Curr Opin Genet Dev 2015;30:7-16.
102. Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B. The immune epitope database (IEDB) 3.0. Nucleic Acids Res 2015;43:D405-12.
103. Olsen LR, Tongchusak S, Lin H, Reinherz EL, Brusic V, Zhang GL. TANTIGEN: a comprehensive database of tumor T cell antigens. Cancer Immunol Immunother 2017;66:731-5.
104. Lund O, Karosiene E, Lundegaard C, Larsen MV, Nielsen M. Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players. In: van Endert P, editor. Antigen processing: methods and protocols. Humana Press, Totowa, NJ; 2013. pp. 247-60.
105. Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC. MuPeXI: prediction of neo-epitopes from tumor sequencing data. Cancer Immunol Immunother 2017;66:1123-30.
106. Schubert B, de la Garza L, Mohr C, Walzer M, Kohlbacher O. ImmunoNodes - graphical development of complex immunoinformatics workflows. BMC Bioinformatics 2017;18:242.
107. Kobayashi H, Wood M, Song Y, Appella E, Celis E. Defining promiscuous MHC class II helper T-cell epitopes for the HER2/neu tumor antigen. Cancer Res 2000;60:5228-36.
108. Stern LJ, Santambrogio L. The melting pot of the MHC II peptidome. Curr Opin Immunol 2016;40:70-7.
109. Hudrisier D, Gairin JE. Peptide-major histocompatibility complex class I complex: from the structural and molecular basis to pharmacological principles and therapeutic applications. In: Whitton JL, editor. Antigen presentation. Berlin, Heidelberg: Springer; 1998. pp. 75-97.
110. Faro J, Castro M, Molina-París C. A unifying mathematical framework for experimental TCR-pMHC kinetic constants. Sci Rep 2017;7:46741.
111. Yarchoan M, Johnson Iii BA, Lutz ER, Laheru DA, Jaffee EM. Targeting neoantigens to augment antitumour immunity. Nat Rev Cancer 2017;17:209-22.
113. Yadav M, Jhunjhunwala S, Phung QT, Lupardus P, Tanguay J, Bumbaca S, Franci C, Cheung TK, Fritsche J, Weinschenk T, Modrusan Z, Mellman I, Lill JR, Delamarre L. Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 2014;515:572-6.
114. Kowalewski DJ, Schuster H, Backert L, Berlin C, Kahn S, Kanz L, Salih HR, Rammensee HG, Stevanovic S, Stickel JS. HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL). Proc Natl Acad Sci U S A 2015;112:E166-75.
115. Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM. Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat Commun 2016;7:13404.
116. Bentzen AK, Marquard AM, Lyngaa R, Saini SK, Ramskov S, Donia M, Such L, Furness AJ, McGranahan N, Rosenthal R, Straten PT, Szallasi Z, Svane IM, Swanton C, Quezada SA, Jakobsen SN, Eklund AC, Hadrup SR. Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes. Nat Biotechnol 2016;34:1037-45.
117. Bunse L, Schumacher T, Sahm F, Pusch S, Oezen I, Rauschenbach K, Gonzalez M, Solecki G, Osswald M, Capper D, Wiestler B, Winkler F, Herold-Mende C, von Deimling A, Wick W, Platten M. Proximity ligation assay evaluates IDH1R132H presentation in gliomas. J Clin Invest 2015;125:593-606.
118. Schumacher T, Bunse L, Pusch S, Sahm F, Wiestler B, Quandt J, Menn O, Osswald M, Oezen I, Ott M, Keil M, Balß J, Rauschenbach K, Grabowska AK, Vogler I, Diekmann J, Trautwein N, Eichmüller SB, Okun J, Stevanović S, Riemer AB, Sahin U, Friese MA, Beckhove P, von Deimling A, Wick W, Platten M. A vaccine targeting mutant IDH1 induces antitumour immunity. Nature 2014;512:324-7.
119. Scheikl-Gatard T, Tosch C, Lemonnier F, Rooke R. Identification of new MUC1 epitopes using HLA-transgenic animals: implication for immunomonitoring. J Transl Med 2017;15:154.
120. Schmidt J, Guillaume P, Dojcinovic D, Karbach J, Coukos G, Luescher I. In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes. J Biol Chem 2017;292:11840-9.
121. Gros A, Parkhurst MR, Tran E, Pasetto A, Robbins PF, Ilyas S, Prickett TD, Gartner JJ, Crystal JS, Roberts IM, Trebska-McGowan K, Wunderlich JR, Yang JC, Rosenberg SA. Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nat Med 2016;22:433-8.
122. Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, Gill S, Harrington WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, Hsiao J, Gerath WFJ, Howell S, Merkel E, Ghandi M, Garraway LA, Root DE, Golub TR, Boehm JS, Hahn WC. Defining a cancer dependency map. Cell 2017;170:564-76.e16.
123. Uhlen M, Zhang C, Lee S, Sjöstedt E, Fagerberg L, Bidkhori G, Benfeitas R, Arif M, Liu Z, Edfors F, Sanli K, von Feilitzen K, Oksvold P, Lundberg E, Hober S, Nilsson P, Mattsson J, Schwenk JM, Brunnström H, Glimelius B, Sjöblom T, Edqvist PH, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F. A pathology atlas of the human cancer transcriptome. Science 2017;357:eaan2507.
124. Van Waes C, Monach PA, Urban JL, Wortzel RD, Schreiber H. Immunodominant deters the response to other tumor antigens thereby favoring escape: prevention by vaccination with tumor variants selected with cloned cytolytic T cells in vitro. Tissue Antigens 1996;47:399-407.
125. Kim A, Sadegh-Nasseri S. Determinants of immunodominance for CD4 T cells. Curr Opin Immunol 2015;34:9-15.
126. Macdonald IK, Harkiolaki M, Hunt L, Connelley T, Carroll AV, MacHugh ND, Graham SP, Jones EY, Morrison WI, Flower DR, Ellis SA. MHC class I bound to an immunodominant theileria parva epitope demonstrates unconventional presentation to T cell receptors. PLoS Pathog 2010;6:e1001149.
127. Hunt JD, Brown LE, Jackson DC. Antigenic competition. Chichester, UK: John Wiley & Sons, Ltd; 2001; doi: 10.1038/npg.els.0000948.
129. Palmowski M, Salio M, Dunbar RP, Cerundolo V. The use of HLA class I tetramers to design a vaccination strategy for melanoma patients. Immunol Rev 2002;188:155-63.
130. Slingluff CL. The present and future of peptide vaccines for cancer: single or multiple, long or short, alone or in combination? Cancer J 2011;17:343-50.
131. Kumai T, Fan A, Harabuchi Y, Celis E. Cancer immunotherapy: moving forward with peptide T cell vaccines. Curr Opin Immunol 2017;47:57-63.
132. Baxevanis CN, Voutsas IF, Tsitsilonis OE, Gritzapis AD, Sotiriadou R, Papamichail M. Tumor-specific CD4+ T lymphocytes from cancer patients are required for optimal induction of cytotoxic T cells against the autologous tumor. J Immunol 2000;164:3902-12.
133. Nakanishi Y, Lu B, Gerard C, Iwasaki A. CD8+ T lymphocyte mobilization to virus-infected tissue requires CD4+ T-cell help. Nature 2009;462:510-3.
134. Sun Z, Chen F, Meng F, Wei J, Liu B. MHC class II restricted neoantigen: a promising target in tumor immunotherapy. Cancer Lett 2017;392:17-25.
136. Quezada SA, Simpson TR, Peggs KS, Merghoub T, Vider J, Fan X, Blasberg R, Yagita H, Muranski P, Antony PA, Restifo NP, Allison JP. Tumor-reactive CD4+ T cells develop cytotoxic activity and eradicate large established melanoma after transfer into lymphopenic hosts. J Exp Med 2010;207:637-50.
137. Tran E, Turcotte S, Gros A, Robbins PF, Lu YC, Dudley ME, Wunderlich JR, Somerville RP, Hogan K, Hinrichs CS, Parkhurst MR, Yang JC, Rosenberg SA. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science 2014;344:641-5.
138. Sahin U, Derhovanessian E, Miller M, Kloke B-P, Simon P, Löwer M, Bukur V, Tadmor AD, Luxemburger U, Schrörs B, Omokoko T, Vormehr M, Albrecht C, Paruzynski A, Kuhn AN, Buck J, Heesch S, Schreeb KH, Müller F, Ortseifer I, Vogler I, Godehardt E, Attig S, Rae R, Breitkreuz A, Tolliver C, Suchan M, Martic G, Hohberger A, Sorn P, Diekmann J, Ciesla J, Waksmann O, Brück AK, Witt M, Zillgen M, Rothermel A, Kasemann B, Langer D, Bolte S, Diken M, Kreiter S, Nemecek R, Gebhardt C, Grabbe S, Höller C, Utikal J, Huber C, Loquai C, Türeci Ö. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature 2017;547:222-6.
139. Kreiter S, Vormehr M, van de Roemer N, Diken M, Löwer M, Diekmann J, Boegel S, Schrörs B, Vascotto F, Castle JC, Tadmor AD, Schoenberger SP, Huber C, Türeci Ö, Sahin U. Mutant MHC class II epitopes drive therapeutic immune responses to cancer. Nature 2015;520:692-6.
140. Young MRI. Cancer immunology with a focus on understudied cancers as targets for immunotherapy. Int J Mol Sci 2017;18:E127.
141. Baxevanis CN, Papamichail M, Perez SA. Prostate cancer vaccines: the long road to clinical application. Cancer Immunol Immunother 2015;64:401-8.
142. Roszik J, Haydu LE, Hess KR, Oba J, Joon AY, Siroy AE, Karpinets TV, Stingo FC, Baladandayuthapani V, Tetzlaff MT, Wargo JA, Chen K, Forget MA, Haymaker CL, Chen JQ, Meric-Bernstam F, Eterovic AK, Shaw KR, Mills GB, Gershenwald JE, Radvanyi LG, Hwu P, Futreal PA, Gibbons DL, Lazar AJ, Bernatchez C, Davies MA, Woodman SE. Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set. BMC Med 2016;14:168.
143. Campesato LF, Barroso-Sousa R, Jimenez L, Correa BR, Sabbaga J, Hoff PM, Reis LF, Galante PA, Camargo AA. Comprehensive cancer-gene panels can be used to estimate mutational load and predict clinical benefit to PD-1 blockade in clinical practice. Oncotarget 2015;6:34221-7.
144. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjörd JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinski M, Jäger N, Jones DT, Jones D, Knappskog S, Kool M, Lakhani SR, López-Otín C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt AN, Valdés-Mas R, van Buuren MM, van 't Veer L, Vincent-Salomon A, Waddell N, Yates LR; Australian Pancreatic Cancer Genome Initiative; ICGC Breast Cancer Consortium; ICGC MMML-Seq Consortium; ICGC PedBrain, Zucman-Rossi J, Futreal PA, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ, Stratton MR. Signatures of mutational processes in human cancer. Nature 2013;500:415-21.
145. Le DT, Durham JN, Smith KN, Wang H, Bartlett BR, Aulakh LK, Lu S, Kemberling H, Wilt C, Luber BS, Wong F, Azad NS, Rucki AA, Laheru D, Donehower R, Zaheer A, Fisher GA, Crocenzi TS, Lee JJ, Greten TF, Duffy AG, Ciombor KK, Eyring AD, Lam BH, Joe A, Kang SP, Holdhoff M, Danilova L, Cope L, Meyer C, Zhou S, Goldberg RM, Armstrong DK, Bever KM, Fader AN, Taube J, Housseau F, Spetzler D, Xiao N, Pardoll DM, Papadopoulos N, Kinzler KW, Eshleman JR, Vogelstein B, Anders RA, Diaz LA Jr. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science 2017;357:409-13.
146. Kloor M, Michel S, von Knebel Doeberitz M. Immune evasion of microsatellite unstable colorectal cancers. Int J Cancer 2010;127:1001-10.
147. Queirolo P, Spagnolo F. Atypical responses in patients with advanced melanoma, lung cancer, renal-cell carcinoma and other solid tumors treated with anti-PD-1 drugs: a systematic review. Cancer Treat Rev 2017;59:71-8.
148. Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE. Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer. Cancer Discov 2017;7:264-76.
149. Gulley JL, Madan RA, Pachynski R, Mulders P, Sheikh NA, Trager J, Drake CG. Role of antigen spread and distinctive characteristics of immunotherapy in cancer treatment. J Natl Cancer Inst 2017:109.
150. Seliger B. Molecular mechanisms of HLA class I-mediated immune evasion of human tumors and their role in resistance to immunotherapies. HLA 2016;88:213-20.
151. Khanna R. Tumour surveillance: missing peptides and MHC molecules. Immunol Cell Biol 1998;76:20-6.
152. Thor Straten P, Garrido F. Targetless T cells in cancer immunotherapy. J Immunother Cancer 2016;4:23.
153. Mahmoud F, Shields B, Makhoul I, Avaritt N, Wong HK, Hutchins LF, Shalin S, Tackett AJ. Immune surveillance in melanoma: from immune attack to melanoma escape and even counterattack. Cancer Biol Ther 2017;18:451-69.
154. Gajewski TF, Woo S-R, Zha Y, Spaapen R, Zheng Y, Corrales L, Spranger S. Cancer immunotherapy strategies based on overcoming barriers within the tumor microenvironment. Curr Opin Immunol 2013;25:268-76.
155. Dilek N, Vuillefroy de Silly R, Blancho G, Vanhove B. Myeloid-derived suppressor cells: mechanisms of action and recent advances in their role in transplant tolerance. Front Immunol 2012;3:208.
157. Yang L, Zhang Y. Tumor-associated macrophages: from basic research to clinical application. J Hematol Oncol 2017;10:58.
158. Joyce JA, Fearon DT. T cell exclusion, immune privilege, and the tumor microenvironment. Science 2015;348:74-80.
159. Spranger S, Dai D, Horton B, Gajewski TF. Tumor-residing Batf3 dendritic cells are required for effector T cell trafficking and adoptive T cell therapy. Cancer Cell 2017;31:711-23.e4.
160. Buck MD, Sowell RT, Kaech SM, Pearce EL. Metabolic instruction of immunity. Cell 2017;169:570-86.
161. Chang C-H, Pearce EL. Emerging concepts of T cell metabolism as a target of immunotherapy. Nat Immunol 2016;17:364-8.
162. Schietinger A, Philip M, Krisnawan VE, Chiu EY, Delrow JJ, Basom RS, Lauer P, Brockstedt DG, Knoblaugh SE, Hämmerling GJ, Schell TD, Garbi N, Greenberg PD. Tumor-specific T cell dysfunction is a dynamic antigen-driven differentiation program initiated early during tumorigenesis. Immunity 2016;45:389-401.
163. Schietinger A, Greenberg PD. Tolerance and exhaustion: defining mechanisms of T cell dysfunction. Trends Immunol 2014;35:51-60.
164. Quezada SA, Peggs KS, Simpson TR, Allison JP. Shifting the equilibrium in cancer immunoediting: from tumor tolerance to eradication. Immunol Rev 2011;241:104-18.
166. Marcus A, Gowen BG, Thompson TW, Iannello A, Ardolino M, Deng W, Wang L, Shifrin N, Raulet DH. Recognition of tumors by the innate immune system and natural killer cells. Adv Immunol 2014;122:91-128.
167. Dahlberg CIM, Sarhan D, Chrobok M, Duru AD, Alici E. Natural killer cell-based therapies targeting cancer: possible strategies to gain and sustain anti-tumor activity. Front Immunol 2015;6:605.
168. Morvan MG, Lanier LL. NK cells and cancer: you can teach innate cells new tricks. Nat Rev Cancer 2016;16:7-19.
169. Ferlazzo G, Morandi B. Cross-talks between natural killer cells and distinct subsets of dendritic cells. Front Immunol 2014;5:159.
170. Cai X, Caballero-Benitez A, Gewe MM, Jenkins IC, Drescher CW, Strong RK, Spies T, Groh V. Control of tumor initiation by NKG2D naturally expressed on ovarian cancer cells. Neoplasia N Y N 2017;19:471-82.
171. Bruno A, Ferlazzo G, Albini A, Noonan DM. A think tank of TINK/TANKs: tumor-infiltrating/tumor-associated natural killer cells in tumor progression and angiogenesis. J Natl Cancer Inst 2014;106:dju200.
172. Dammeijer F, Lau SP, van Eijck CHJ, van der Burg SH, Aerts JGJV. Rationally combining immunotherapies to improve efficacy of immune checkpoint blockade in solid tumors. Cytokine Growth Factor Rev 2017;36:5-15.
173. Chen DS, Mellman I. Oncology meets immunology: the cancer-immunity cycle. Immunity 2013;39:1-10.
174. Accolla RS, Tosi G. Optimal MHC-II-restricted tumor antigen presentation to CD4+ T helper cells: the key issue for development of anti-tumor vaccines. J Transl Med 2012;10:154.
175. Seliger B, Kloor M, Ferrone S. HLA class II antigen-processing pathway in tumors: molecular defects and clinical relevance. Oncoimmunology 2017;6:e1171447.
176. Ehlers M, Kuebart A, Hautzel H, Enczmann J, Reis AC, Haase M, Allelein S, Dringenberg T, Schmid C, Schott M. Epitope-specific antitumor immunity suppresses tumor spread in papillary thyroid cancer. J Clin Endocrinol Metab 2017;102:2154-61.
177. Vesely MD, Schreiber RD. Cancer immunoediting: antigens, mechanisms, and implications to cancer immunotherapy. Ann N Y Acad Sci 2013;1284:1-5.
178. Zurrida S, Bassi F, Arnone P, Martella S, Del Castillo A, Ribeiro Martini R, Semenkiw ME, Caldarella P. The changing face of mastectomy (from mutilation to aid to breast reconstruction). Int J Surg Oncol 2011;2011:980158.
179. Dittmer J. Mechanisms governing metastatic dormancy in breast cancer. Semin Cancer Biol 2017;44:72-82.
182. Sosa MS, Bragado P, Aguirre-Ghiso JA. Mechanisms of disseminated cancer cell dormancy: an awakening field. Nat Rev Cancer 2014;14:611-22.
183. Eyles J, Puaux A-L, Wang X, Toh B, Prakash C, Hong M, Tan TG, Zheng L, Ong LC, Jin Y, Kato M, Prévost-Blondel A, Chow P, Yang H, Abastado JP. Tumor cells disseminate early, but immunosurveillance limits metastatic outgrowth, in a mouse model of melanoma. J Clin Invest 2010;120:2030-9.
184. Romero I, Garrido F, Garcia-Lora AM. Metastases in immune-mediated dormancy: a new opportunity for targeting cancer. Cancer Res 2014;74:6750-7.
185. Manjili MH. Tumor dormancy and relapse: from a natural byproduct of evolution to a disease state. Cancer Res 2017;77:2564-9.
186. Barkan D, Chambers AF. Prevention of conversion of tumor dormancy into proliferative metastases. In: Cote RJ, Datar RH, editors. Circulating tumor cells. Current cancer research. New York, NY: Springer New York; 2016. pp. 121-37.
187. Whiteside TL, Demaria S, Rodriguez-Ruiz ME, Zarour HM, Melero I. Emerging opportunities and challenges in cancer immunotherapy. Clin Cancer Res 2016;22:1845-55.
188. Hoos A. Development of immuno-oncology drugs—from CTLA4 to PD1 to the next generations. Nat Rev Drug Discov 2016;15:235-47.
189. Sharma P, Allison JP. Immune checkpoint targeting in cancer therapy: toward combination strategies with curative potential. Cell 2015;161:205-14.
190. Hucl T, Gallmeier E, Kern SE. Distinguishing rational from irrational applications of pharmacogenetic synergies from the bench to clinical trials. Cell Cycle 2007;6:1336-41.
191. Khong H, Overwijk WW. Adjuvants for peptide-based cancer vaccines. J Immunother Cancer 2016;4:56.
192. Saxena M, Bhardwaj N. Turbocharging vaccines: emerging adjuvants for dendritic cell based therapeutic cancer vaccines. Curr Opin Immunol 2017;47:35-43.
193. Circelli L, Tornesello M, Buonaguro FM, Buonaguro L. Use of adjuvants for immunotherapy. Hum Vaccines Immunother 2017;13:1774-7.
194. Temizoz B, Kuroda E, Ishii KJ. Vaccine adjuvants as potential cancer immunotherapeutics. Int Immunol 2016;28:329-38.
195. Hodi FS, Chesney J, Pavlick AC, Robert C, Grossmann KF, McDermott DF, Linette GP, Meyer N, Giguere JK, Agarwala SS, Shaheen M, Ernstoff MS, Minor DR, Salama AK, Taylor MH, Ott PA, Horak C, Gagnier P, Jiang J, Wolchok JD, Postow MA. Combined nivolumab and ipilimumab versus ipilimumab alone in patients with advanced melanoma: 2-year overall survival outcomes in a multicentre, randomised, controlled, phase 2 trial. Lancet Oncol 2016;17:1558-68.
196. Wu Y, Shi H, Jiang M, Qiu M, Jia K, Cao T, Shang Y, Shi L, Jiang K, Wu H. The clinical value of combination of immune checkpoint inhibitors in cancer patients: a meta-analysis of efficacy and safety. Int J Cancer 2017;141:2562-70.
197. Schadendorf D, Wolchok JD, Hodi FS, Chiarion-Sileni V, Gonzalez R, Rutkowski P, Grob JJ, Cowey CL, Lao CD, Chesney J, Robert C, Grossmann K, McDermott D, Walker D, Bhore R, Larkin J, Postow MA. Efficacy and safety outcomes in patients with advanced melanoma who discontinued treatment with nivolumab and ipilimumab because of adverse events: a pooled analysis of randomized phase II and III trials. J Clin Oncol 2017;35:3807-14.
198. Emens LA, Ascierto PA, Darcy PK, Demaria S, Eggermont AMM, Redmond WL, Seliger B, Marincola FM. Cancer immunotherapy: opportunities and challenges in the rapidly evolving clinical landscape. Eur J Cancer 2017;81:116-29.
199. Dunn J, Rao S. Epigenetics and immunotherapy: the current state of play. Mol Immunol 2017;87:227-39.
200. Probst P, Kopp J, Oxenius A, Colombo MP, Ritz D, Fugmann T, Neri D. Sarcoma eradication by doxorubicin and targeted TNF relies upon CD8+ T-cell recognition of a retroviral antigen. Cancer Res 2017;77:3644-54.
201. Fessler JL, Gajewski TF. The microbiota: a new variable impacting cancer treatment outcomes. Clin Cancer Res 2017;23:3229-31.
202. Li CX, Yu B, Shi L, Geng W, Lin QB, Ling CC, Yang M, Ng KT, Huang JD, Man K. "Obligate" anaerobic Salmonella strain YB1 suppresses liver tumor growth and metastasis in nude mice. Oncol Lett 2017;13:177-83.
203. Mahoney KM, Rennert PD, Freeman GJ. Combination cancer immunotherapy and new immunomodulatory targets. Nat Rev Drug Discov 2015;14:561-84.
204. Jaini R, Rayman P, Cohen PA, Finke JH, Tuohy VK. Combination of sunitinib with anti-tumor vaccination inhibits T cell priming and requires careful scheduling to achieve productive immunotherapy. Int J Cancer 2014;134:1695-705.
205. Albiges L, Choueiri T, Escudier B, Galsky M, George D, Hofmann F, Lam T, Motzer R, Mulders P, Porta C, Powles T, Sternberg C, Bex A. A systematic review of sequencing and combinations of systemic therapy in metastatic renal cancer. Eur Urol 2015;67:100-10.
206. Moher D, Hopewell S, Schulz KF, Montori V, Gøtzsche PC, Devereaux PJ, Elbourne D, Egger M, Altman DG; Consolidated Standards of Reporting Trials Group. CONSORT 2010 explanation and elaboration: updated guidelines for reporting parallel group randomised trials. J Clin Epidemiol 2010;63:e1-37.
207. Simon R. Development and validation of biomarker classifiers for treatment selection. J Stat Plan Inference 2008;138:308-20.
208. Gridelli C, Ardizzoni A, Barberis M, Cappuzzo F, Casaluce F, Danesi R, Troncone G, De Marinis F. Predictive biomarkers of immunotherapy for non-small cell lung cancer: results from an Experts Panel Meeting of the Italian Association of Thoracic Oncology. Transl Lung Cancer Res 2017;6:373-86.
209. Altman DG, McShane LM, Sauerbrei W, Taube SE. Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): explanation and elaboration. PLoS Med 2012;9:e1001216.
210. Sekula P, Mallett S, Altman DG, Sauerbrei W. Did the reporting of prognostic studies of tumour markers improve since the introduction of REMARK guideline? A comparison of reporting in published articles. PLoS One 2017;12:e0178531.
211. Stroncek DF, Butterfield LH, Cannarile MA, Dhodapkar MV, Greten TF, Grivel JC, Kaufman DR, Kong HH, Korangy F, Lee PP, Marincola F, Rutella S, Siebert JC, Trinchieri G, Seliger B. Systematic evaluation of immune regulation and modulation. J Immunother Cancer 2017;5:21.
212. Haris M, Bagga P, Hariharan H, McGettigan-Croce B, Johnson LA, Reddy R. Molecular imaging biomarkers for cell-based immunotherapies. J Transl Med 2017;15:140.
213. Spitzer MH, Carmi Y, Reticker-Flynn NE, Kwek SS, Madhireddy D, Martins MM, Gherardini PF, Prestwood TR, Chabon J, Bendall SC, Fong L, Nolan GP, Engleman EG. Systemic immunity is required for effective cancer immunotherapy. Cell 2017;168:487-502.e15.
214. Loo K, Tsai KK, Mahuron K, Liu J, Pauli ML, Sandoval PM, Nosrati A, Lee J, Chen L, Hwang J, Levine LS, Krummel MF, Algazi AP, Alvarado MD, Rosenblum MD, Daud AI. Partially exhausted tumor-infiltrating lymphocytes predict response to combination immunotherapy. JCI Insight 2017;2:93433.
216. Gros A, Robbins PF, Yao X, Li YF, Turcotte S, Tran E, Wunderlich JR, Mixon A, Farid S, Dudley ME, Hanada K, Almeida JR, Darko S, Douek DC, Yang JC, Rosenberg SA. PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors. J Clin Invest 2014;124:2246-59.
217. Robert L, Tsoi J, Wang X, Emerson R, Homet B, Chodon T, Mok S, Huang RR, Cochran AJ, Comin-Anduix B, Koya RC, Graeber TG, Robins H, Ribas A. CTLA4 blockade broadens the peripheral t-cell receptor repertoire. Clin Cancer Res 2014;20:2424-32.
218. Akyüz N, Brandt A, Stein A, Schliffke S, Mährle T, Quidde J, Goekkurt E, Loges S, Haalck T, Ford CT, Asemissen AM, Thiele B, Radloff J, Thenhausen T, Krohn-Grimberghe A, Bokemeyer C, Binder M. T-cell diversification reflects antigen selection in the blood of patients on immune checkpoint inhibition and may be exploited as liquid biopsy biomarker. Int J Cancer 2017;140:2535-44.
219. Dziubianau M, Hecht J, Kuchenbecker L, Sattler A, Stervbo U, Rödelsperger C, Nickel P, Neumann AU, Robinson PN, Mundlos S, Volk HD, Thiel A, Reinke P, Babel N. TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell-related pathology. Am J Transplant 2013;13:2842-54.
220. Rosati E, Dowds CM, Liaskou E, Henriksen EKK, Karlsen TH, Franke A. Overview of methodologies for T-cell receptor repertoire analysis. BMC Biotechnol 2017;17:61.
221. Madi A, Poran A, Shifrut E, Reich-Zeliger S, Greenstein E, Zaretsky I, Arnon T, Laethem FV, Singer A, Lu J, Sun PD, Cohen IR, Friedman N. T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences. Elife 2017;6:e22057.
222. Emerson RO, DeWitt WS, Vignali M, Gravley J, Hu JK, Osborne EJ, Desmarais C, Klinger M, Carlson CS, Hansen JA, Rieder M, Robins HS. Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat Genet 2017;49:659-65.
223. Garner JP, Gaskill BN, Weber EM, Ahloy-Dallaire J, Pritchett-Corning KR. Introducing Therioepistemology: the study of how knowledge is gained from animal research. Lab Anim (NY) 2017;46:103-13.
224. Klevorn LE, Teague RM. Adapting cancer immunotherapy models for the real world. Trends Immunol 2016;37:354-63.
227. Hurez V, Padrón áS, Svatek RS, Curiel TJ. Considerations for successful cancer immunotherapy in aged hosts. Clin Exp Immunol 2017;187:53-63.
228. Institute of Medicine (US). Sharing clinical research data: workshop summary. Washington (DC): National Academies Press (US); 2013.
229. Klinke DJ 2nd. A multiscale systems perspective on cancer, immunotherapy, and interleukin-12. Mol Cancer 2010;9:242.
230. Palsson S, Hickling TP, Bradshaw-Pierce EL, Zager M, Jooss K, O'Brien PJ, Spilker ME, Palsson BO, Vicini P. The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. BMC Syst Biol 2013;7:95.
231. Narang V, Decraene J, Wong SY, Aiswarya BS, Wasem AR, Leong SR, Gouaillard A. Systems immunology: a survey of modeling formalisms, applications and simulation tools. Immunol Res 2012;53:251-65.
232. Scharovsky OG, Mainetti LE, Rozados VR. Metronomic chemotherapy: changing the paradigm that more is better. Curr Oncol 2009;16:7-15.
233. Romiti A, Falcone R, Roberto M, Marchetti P. Current achievements and future perspectives of metronomic chemotherapy. Invest New Drugs 2017;35:359-74.
235. Michor F, Beal K. Improving cancer treatment via mathematical modeling: surmounting the challenges is worth the effort. Cell 2015;163:1059-63.
236. dePillis LG, Eladdadi A, Radunskaya AE. Modeling cancer-immune responses to therapy. J Pharmacokinet Pharmacodyn 2014;41:461-78.
237. Konstorum A, Vella AT, Adler AJ, Laubenbacher RC. Addressing current challenges in cancer immunotherapy with mathematical and computational modelling. J R Soc Interface 2017;14:20170150.
238. Radunskaya A, Hook S. Modeling the kinetics of the immune response. In: d'Onofrio A, Cerrai P, Gandolfi A, editors. New challenges for cancer systems biomedicine. Milano: Springer Milan; 2012. pp. 267-82.
241. Transtrum MK, Qiu P. Bridging mechanistic and phenomenological models of complex biological systems. PLoS Comput Biol 2016;12:e1004915.
242. Wenbo L, Wang J. Uncovering the underlying mechanism of cancer tumorigenesis and development under an immune microenvironment from global quantification of the landscape. J R Soc Interface 2017;14:20170105.
243. d'Onofrio A, Gandolfi A, editors. Mathematical Oncology 2013. New York, NY: Springer New York; 2014.
244. Molina-París C, Lythe G, editors. Mathematical models and immune cell biology. New York, NY: Springer New York; 2011.
245. Bassaganya-Riera J, editor. Computational immunology. Cambridge, MA: Academic Press; 2016.
246. Kroer C, Sandholm T. Sequential planning for steering immune system adaptation. New York, USA: AAAI Press/International Joint Conferences on Artificial Intelligence; 2016.
247. Sandholm T. Steering evolution strategically: computational game theory and opponent exploitation for treatment planning, drug design, and synthetic biology. 2015. Available from: https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/view/10047. [Last accessed on 15 Dec 2017].
248. Zhao Y, Zeng D, Socinski MA, Kosorok MR. Reinforcement learning strategies for clinical trials in nonsmall cell lung cancer. Biometrics 2011;67:1422-33.
249. Wallace MP, Moodie EEM, Stephens DA. SMART thinking: a review of recent developments in sequential multiple assignment randomized trials. Curr Epidemiol Rep 2016;3:225-32.
250. Littman DR. releasing the brakes on cancer immunotherapy. Cell 2015;162:1186-90.