Towards a better cancer precision medicine: Systems biology meets immunotherapy

Hanahan, 2000, The hallmarks of cancer, Cell, 100, 57, 10.1016/S0092-8674(00)81683-9 Hanahan, 2011, Hallmarks of cancer: the next generation, Cell, 144, 646, 10.1016/j.cell.2011.02.013 Foo, 2014, Evolution of acquired resistance to anti-cancer therapy, J Theor Biol, 355, 10, 10.1016/j.jtbi.2014.02.025 Martin, 2013, Mathematical modeling of immune kinetics in advanced cancer through meta-analyses of complete response rates: immune synchronisation emerges as the likely key determinant of clinical response, J Immunother Cancer, 1, 150, 10.1186/2051-1426-1-S1-P150 Du, 2015, Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies, Oncogene, 34, 3215, 10.1038/onc.2014.291 Sieuwerts, 2016, Predicting first line tamoxifen response of recurrent ER+ breast cancer patients based on transcriptional activity of signaling pathways [abstract], AACR Cancer Res, 76 Boland, 2016, Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms, Wiley Interdiscip Rev Syst Biol Med, 8, 104, 10.1002/wsbm.1323 Werner, 2014, Cancer systems biology: a peek into the future of patient care?, Nat Rev Clin Oncol, 11, 167, 10.1038/nrclinonc.2014.6 National Cancer Institute. The Cancer Genome Atlas. http://cancergenome.nih.gov/. International Cancer Genome Consortium. http://icgc.org. Collins, 2015, A new initiative on precision medicine, N Engl J Med, 372, 793, 10.1056/NEJMp1500523 Rosenberg, 2011, Durable complete responses in heavily pretreated patients with metastatic melanoma using T-cell transfer immunotherapy, Clin Cancer Res, 17, 4550, 10.1158/1078-0432.CCR-11-0116 Hodi, 2010, Improved survival with ipilimumab in patients with metastatic melanoma, N Engl J Med, 363, 711, 10.1056/NEJMoa1003466 Schumacher, 2015, Neoantigens in cancer immunotherapy, Science, 348, 69, 10.1126/science.aaa4971 Reck, 2016, Pembrolizumab versus chemotherapy for PD-L1-positive non-small-cell lung cancer, N Engl J Med, 375, 1823, 10.1056/NEJMoa1606774 Snyder, 2014, Genetic basis for clinical response to CTLA-4 blockade in melanoma, N Engl J Med, 371, 2189, 10.1056/NEJMoa1406498 Van Allen, 2015, Genomic correlates of response to CTLA-4 blockade in metastatic melanoma, Science, 350, 207, 10.1126/science.aad0095 Hugo, 2016, Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma, Cell, 165, 35, 10.1016/j.cell.2016.02.065 Robert, 2014, CTLA4 blockade broadens the peripheral T-cell receptor repertoire, Clin Cancer Res, 20, 2424, 10.1158/1078-0432.CCR-13-2648 Tumeh, 2014, PD-1 blockade induces responses by inhibiting adaptive immune resistance, Nature, 515, 568, 10.1038/nature13954 Schreiber, 2011, Cancer immunoediting: integrating immunity's roles in cancer suppression and promotion, Science, 331, 1565, 10.1126/science.1203486 Blankenstein, 2012, The determinants of tumour immunogenicity, Nat Rev Cancer, 12, 307, 10.1038/nrc3246 Rizvi, 2015, Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer, Science, 348, 124, 10.1126/science.aaa1348 Le, 2015, PD-1 blockade in tumors with mismatch-repair deficiency, N Engl J Med, 372, 2509, 10.1056/NEJMoa1500596 Tran, 2014, Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer, Science, 344, 641, 10.1126/science.1251102 Tran, 2015, Immunogenicity of somatic mutations in human gastrointestinal cancers, Science, 350, 1387, 10.1126/science.aad1253 Lu, 2016, Cancer immunotherapy targeting neoantigens, Semin Immunol, 28, 22, 10.1016/j.smim.2015.11.002 Hundal, 2016, pVAC-Seq: a genome-guided in silico approach to identifying tumor neoantigens, Genome Med, 8, 11, 10.1186/s13073-016-0264-5 Hackl, 2016, Computational genomics tools for dissecting tumour-immune cell interactions, Nat Rev Genet, 17, 441, 10.1038/nrg.2016.67 Carreno, 2015, Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells, Science, 348, 803, 10.1126/science.aaa3828 Robbins, 2013, Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells, Nat Med, 19, 747, 10.1038/nm.3161 Gros, 2016, Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients, Nat Med, 22, 433, 10.1038/nm.4051 McGranahan, 2016, Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade, Science, 351, 1463, 10.1126/science.aaf1490 Verdegaal, 2016, Neoantigen landscape dynamics during human melanoma-T cell interactions, Nature, 536, 91, 10.1038/nature18945 Polyakova, 2015, Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens, Expert Rev Proteomics, 12, 533, 10.1586/14789450.2015.1070100 Giannakis, 2016, Genomic correlates of immune-cell infiltrates in colorectal carcinoma, Cell Rep, 15, 857, 10.1016/j.celrep.2016.03.075 Morse, 2009, Countering tumor-induced immunosuppression during immunotherapy for pancreatic cancer, Expert Opin Biol Ther, 9, 331, 10.1517/14712590802715756 Fuertes Marraco, 2015, Inhibitory receptors beyond T cell exhaustion, Front Immunol, 6, 310, 10.3389/fimmu.2015.00310 Turley, 2015, Immunological hallmarks of stromal cells in the tumour microenvironment, Nat Rev Immunol, 15, 669, 10.1038/nri3902 Huang, 2012, Vascular normalizing doses of antiangiogenic treatment reprogram the immunosuppressive tumor microenvironment and enhance immunotherapy, Proc Natl Acad Sci U S A, 109, 17561, 10.1073/pnas.1215397109 Spranger, 2015, Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity, Nature, 523, 231, 10.1038/nature14404 Sweis, 2016, Molecular drivers of the non-t-cell-inflamed tumor microenvironment in urothelial bladder cancer, Cancer Immunol Res, 4, 563, 10.1158/2326-6066.CIR-15-0274 Rooney, 2015, Molecular and genetic properties of tumors associated with local immune cytolytic activity, Cell, 160, 48, 10.1016/j.cell.2014.12.033 Fridman, 2012, The immune contexture in human tumours: impact on clinical outcome, Nat Rev Cancer, 12, 298, 10.1038/nrc3245 Denkert, 2010, Tumor-associated lymphocytes as an independent predictor of response to neoadjuvant chemotherapy in breast cancer, J Clin Oncol, 28, 105, 10.1200/JCO.2009.23.7370 Oved, 2009, Predicting and controlling the reactivity of immune cell populations against cancer, Mol Syst Biol, 5, 265, 10.1038/msb.2009.15 Newman, 2015, Robust enumeration of cell subsets from tissue expression profiles, Nat Methods, 12, 453, 10.1038/nmeth.3337 Yoshihara, 2013, Inferring tumour purity and stromal and immune cell admixture from expression data, Nat Commun, 4, 2612, 10.1038/ncomms3612 Spitzer, 2015, IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system, Science, 349, 1259425, 10.1126/science.1259425 Mlecnik, 2016, The tumor microenvironment and Immunoscore are critical determinants of dissemination to distant metastasis, Sci Transl Med, 8, 327, 10.1126/scitranslmed.aad6352 Aryee, 2016, Modeling immune system-tumor interactions using humanized mice, J Immunol, 196, 10.4049/jimmunol.196.Supp.212.12 Zitvogel, 2016, Mouse models in oncoimmunology, Nat Rev Cancer, 16, 759, 10.1038/nrc.2016.91 Wilkie, 2013, A review of mathematical models of cancer-immune interactions in the context of tumor dormancy, Adv Exp Med Biol, 734, 201, 10.1007/978-1-4614-1445-2_10 Bianca, 2012, Mathematical modeling of the immune system recognition to mammary carcinoma antigen, BMC Bioinform, 13, S21, 10.1186/1471-2105-13-S17-S21 Kronik, 2010, Predicting outcomes of prostate cancer immunotherapy by personalized mathematical models, PLoS One, 5, e15482, 10.1371/journal.pone.0015482 Li, 2016, Landscape of tumor-infiltrating T cell repertoire of human cancers, Nat Genet, 48, 725, 10.1038/ng.3581 Keane, 2016, The T-cell receptor repertoire influences the tumor microenvironment and is associated with survival in aggressive B-cell lymphoma, Clin Cancer Res Page, 2016, Deep sequencing of T-cell receptor DNA as a biomarker of clonally expanded TILs in breast cancer after immunotherapy, Cancer Immunol Res, 4, 835, 10.1158/2326-6066.CIR-16-0013 Colli, 2016, Burden of nonsynonymous mutations among TCGA cancers and candidate immune checkpoint inhibitor responses, Cancer Res, 76, 3767, 10.1158/0008-5472.CAN-16-0170 Blank, 2016, Cancer immunology. The “cancer immunogram”, Science, 352, 658, 10.1126/science.aaf2834 Roemer, 2016, PD-L1 and PD-L2 genetic alterations define classical Hodgkin lymphoma and predict outcome, J Clin Oncol, 34, 2690, 10.1200/JCO.2016.66.4482 Inoue, 2016, Clinical significance of PD-L1 and PD-L2 copy number gains in non-small-cell lung cancer, Oncotarget, 7, 32113, 10.18632/oncotarget.8528