Integrated analysis of the immunological and genetic status in and across cancer types: impact of mutational signatures beyond tumor mutational burden

References

• Ribas A, Wolchok JD. Cancer immunotherapy using checkpoint blockade. Science. 2018;359(6382);1350–1355. doi:10.1126/science.aar4060.
   PubMed Web of Science ®Google Scholar
• Pardoll DM. The blockade of immune checkpoints in cancer immunotherapy. Nat Rev Cancer. 2012;12(4);252–264. doi:10.1038/nrc3239.
   PubMed Web of Science ®Google Scholar
• Vanpouille-Box C, Lhuillier C, Bezu L, Aranda F, Yamazaki T, Kepp O, Fucikova J, Spisek R, Demaria S, Formenti SC, et al. Trial watch: immune checkpoint blockers for cancer therapy. Oncoimmunology. 2017;6(11):e1373237. doi:10.1080/2162402X.2017.1373237.
   PubMed Web of Science ®Google Scholar
• McDermott D, Lebbe C, Hodi FS, Maio M, Weber JS, Wolchok JD, Thompson JA, Balch CM. Durable benefit and the potential for long-term survival with immunotherapy in advanced melanoma. Cancer Treat Rev. 2014;40(9);1056–1064. doi:10.1016/j.ctrv.2014.06.012.
   PubMed Web of Science ®Google Scholar
• Kroemer G, Galluzzi L. Combinatorial immunotherapy with checkpoint blockers solves the problem of metastatic melanoma-An exclamation sign with a question mark. Oncoimmunology. 2015;4(7);e1058037. doi:10.1080/2162402X.2015.1008371.
   PubMed Web of Science ®Google Scholar
• Hellmann MD, Ciuleanu TE, Pluzanski A, Lee JS, Otterson GA, Audigier-Valette C, Minenza E, Linardou H, Burgers S, Salman P, et al. Nivolumab plus ipilimumab in lung cancer with a high tumor mutational burden. N Engl J Med. 2018. doi:10.1056/NEJMoa1801946.
   Web of Science ®Google Scholar
• Gandhi L, Rodriguez-Abreu D, Gadgeel S, Esteban E, Felip E, de Angelis F, Domine M, Clingan P, Hochmair MJ, Powell SF, et al. Pembrolizumab plus chemotherapy in metastatic non-small-cell lung cancer. N Engl J Med. 2018. doi:10.1056/NEJMoa1801005.
   Web of Science ®Google Scholar
• Nishino M, Ramaiya NH, Hatabu H, Hodi FS. Monitoring immune-checkpoint blockade: response evaluation and biomarker development. Nat Rev Clin Oncol. 2017;14(11);655–668. doi:10.1038/nrclinonc.2017.88.
   PubMed Web of Science ®Google Scholar
• Rimm DL, Han G, Taube JM, Yi ES, Bridge JA, Flieder DB, Homer R, West WW, Wu H, Roden AC, et al. A prospective, multi-institutional, pathologist-based assessment of 4 immunohistochemistry assays for PD-L1 Expression in non-small cell lung cancer. JAMA Oncol. 2017;3(8):1051–1058. doi:10.1001/jamaoncol.2017.0013.
   PubMed Web of Science ®Google Scholar
• Rosenberg JE, Hoffman-Censits J, Powles T, van der Heijden MS, Balar AV, Necchi A, Dawson N, O’Donnell PH, Balmanoukian A, Loriot Y, et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet. 2016;387(10031):1909–1920. doi:10.1016/S0140-6736(16)00561-4.
   PubMed Web of Science ®Google Scholar
• Chen DS, Mellman I. Elements of cancer immunity and the cancer-immune set point. Nature. 2017;541(7637);321–330. doi:10.1038/nature21349.
   PubMed Web of Science ®Google Scholar
• Scheerens H, Malong A, Bassett K, Boyd Z, Gupta V, Harris J, Mesick C, Simnett S, Stevens H, Gilbert H, et al. Current status of companion and complementary diagnostics: strategic considerations for development and launch. Clin Transl Sci. 2017;10(2):84–92. doi:10.1111/cts.12455.
   PubMed Web of Science ®Google Scholar
• Zaretsky JM, Garcia-Diaz A, Shin DS, Escuin-Ordinas H, Hugo W, Hu-Lieskovan S, Torrejon DY, Abril-Rodriguez G, Sandoval S, Barthly L, et al. Mutations associated with acquired resistance to PD-1 blockade in melanoma. N Engl J Med. 2016;375(9):819–829. doi:10.1056/NEJMoa1604958.
   PubMed Web of Science ®Google Scholar
• Kato S, Kurzrock R. Genomics of immunotherapy-associated hyperprogressors-response. Clin Cancer Res. 2017;23(20);6376. doi:10.1158/1078-0432.CCR-17-1990.
   PubMed Web of Science ®Google Scholar
• Jenkins RW, Barbie DA, Flaherty KT. Mechanisms of resistance to immune checkpoint inhibitors. Br J Cancer. 2018;118(1);9–16. doi:10.1038/bjc.2017.434.
   PubMed Web of Science ®Google Scholar
• Budczies J, Bockmayr M, Klauschen F, Endris V, Frohling S, Schirmacher P, Denkert C, Stenzinger A. Mutation patterns in genes encoding interferon signaling and antigen presentation: A pan-cancer survey with implications for the use of immune checkpoint inhibitors. Genes Chromosomes Cancer. 2017;56(8);651–659. doi:10.1002/gcc.22468.
   PubMed Web of Science ®Google Scholar
• Schumacher TN, Schreiber RD. Neoantigens in cancer immunotherapy. Science. 2015;348(6230);69–74. doi:10.1126/science.aaa4971.
   PubMed Web of Science ®Google Scholar
• Bloy N, Garcia P, Laumont CM, Pitt JM, Sistigu A, Stoll G, Yamazaki T, Bonneil E, Buque A, Humeau J, et al. Immunogenic stress and death of cancer cells: contribution of antigenicity vs adjuvanticity to immunosurveillance. Immunol Rev. 2017;280(1):165–174. doi:10.1111/imr.12582.
   PubMed Web of Science ®Google Scholar
• Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W, Yuan J, Wong P, Ho TS, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348(6230):124–128. doi:10.1126/science.aaa1348.
   PubMed Web of Science ®Google Scholar
• Teo MY, Seier K, Ostrovnaya I, Regazzi AM, Kania BE, Moran MM, Cipolla CK, Bluth MJ, Chaim J, Al-Ahmadie H, et al. Alterations in DNA damage response and repair genes as potential marker of clinical benefit from PD-1/PD-L1 Blockade in advanced urothelial cancers. J Clin Oncol. 2018;36(17):1685–1694. doi:10.1200/JCO.2017.75.7740.
   Web of Science ®Google Scholar
• Carbone DP, Reck M, Paz-Ares L, Creelan B, Horn L, Steins M, Felip E, van Den Heuvel MM, Ciuleanu TE, Badin F, et al. First-line nivolumab in stage IV or recurrent non-small-cell lung cancer. N Engl J Med. 2017;376(25):2415–2426. doi:10.1056/NEJMoa1613493.
   PubMed Web of Science ®Google Scholar
• Chabanon RM, Pedrero M, Lefebvre C, Marabelle A, Soria JC, Postel-Vinay S. Mutational landscape and sensitivity to immune checkpoint blockers. Clin Cancer Res. 2016;22(17);4309–4321. doi:10.1158/1078-0432.CCR-16-0903.
   PubMed Web of Science ®Google Scholar
• Le DT, Durham JN, Smith KN, Wang H, Bartlett BR, Aulakh LK, Lu S, Kemberling H, Wilt C, Luber BS, et al. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science. 2017;357(6349):409–413. doi:10.1126/science.aan6733.
   PubMed Web of Science ®Google Scholar
• Spranger S. Mechanisms of tumor escape in the context of the T-cell-inflamed and the non-T-cell-inflamed tumor microenvironment. Int Immunol. 2016;28(8);383–391. doi:10.1093/intimm/dxw014.
   PubMed Web of Science ®Google Scholar
• Galon J, Fox BA, Bifulco CB, Masucci G, Rau T, Botti G, Marincola FM, Ciliberto G, Pages F, Ascierto PA, et al. Immunoscore and Immunoprofiling in cancer: an update from the melanoma and immunotherapy bridge 2015. J Transl Med. 2016;14:273. doi:10.1186/s12967-016-0867-z.
   PubMed Web of Science ®Google Scholar
• Mlecnik B, Van Den Eynde M, Bindea G, Church SE, Vasaturo A, Fredriksen T, Lafontaine L, Haicheur N, Marliot F, Debetancourt D, et al. Comprehensive intrametastatic immune quantification and major impact of immunoscore on survival. J Natl Cancer Inst. 2018;110(1). doi:10.1093/jnci/djx216.
   PubMedGoogle 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
• Davoli T, Uno H, Wooten EC, Elledge SJ. Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science. 2017;355(6322). doi:10.1126/science.aaf8399.
   PubMed Web of Science ®Google Scholar
• Iglesia MD, Parker JS, Hoadley KA, Serody JS, Perou CM, Vincent BG. Genomic analysis of immune cell infiltrates across 11 tumor types. J Natl Cancer Inst. 2016;108(11). doi:10.1093/jnci/djw144.
   PubMedGoogle 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. e814 doi:10.1016/j.immuni.2018.03.023.
   PubMed Web of Science ®Google Scholar
• Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Borresen-Dale AL, et al. Signatures of mutational processes in human cancer. Nature. 2013;500(7463):415–421. doi:10.1038/nature12477.
   PubMed Web of Science ®Google Scholar
• Alexandrov LB, Jones PH, Wedge DC, Sale JE, Campbell PJ, Nik-Zainal S, Stratton MR. Clock-like mutational processes in human somatic cells. Nat Genet. 2015;47(12);1402–1407. doi:10.1038/ng.3441.
   PubMed Web of Science ®Google Scholar
• Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A, Nakagawa H, Shibata T, et al. Mutational signatures associated with tobacco smoking in human cancer. Science. 2016;354(6312):618–622. doi:10.1126/science.aag0299.
   PubMed Web of Science ®Google Scholar
• Mroz EA, Rocco JW. MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma. Oral Oncol. 2013;49(3);211–215. doi:10.1016/j.oraloncology.2012.09.007.
   PubMed Web of Science ®Google Scholar
• Rocco JW. Mutant allele tumor heterogeneity (MATH) and head and neck squamous cell carcinoma. Head Neck Pathol. 2015;9(1);1–5. doi:10.1007/s12105-015-0617-1.
   PubMed Web of Science ®Google Scholar
• Campbell BB, Light N, Fabrizio D, Zatzman M, Fuligni F, de Borja R, Davidson S, Edwards M, Elvin JA, Hodel KP, et al. Comprehensive analysis of hypermutation in human cancer. Cell. 2017;171(5):1042–1056. e1010 doi:10.1016/j.cell.2017.09.048.
   PubMed Web of Science ®Google Scholar
• Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, Selves J, Laurent-Puig P, Sautes-Fridman C, Fridman WH, et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17(1):218. doi:10.1186/s13059-016-1070-5.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5);453–457. doi:10.1038/nmeth.3337.
   PubMed Web of Science ®Google Scholar
• Hellmann MD, Nathanson T, Rizvi H, Creelan BC, Sanchez-Vega F, Ahuja A, Ni A, Novik JB, Mangarin LMB, Abu-Akeel M, et al. Genomic features of response to combination immunotherapy in patients with advanced non-small-cell lung cancer. Cancer Cell. 2018;33(5):843–852. e844 doi:10.1016/j.ccell.2018.03.018.
   PubMed Web of Science ®Google Scholar
• Patel SP, Kurzrock R. PD-L1 Expression as a predictive biomarker in cancer immunotherapy. Mol Cancer Ther. 2015;14(4);847–856. doi:10.1158/1535-7163.MCT-14-0983.
   PubMed Web of Science ®Google Scholar
• Teixido C, Vilarino N, Reyes R, Reguart N. PD-L1 expression testing in non-small cell lung cancer. Ther Adv Med Oncol. 2018;10:1758835918763493. doi:10.1177/1758835918763493.
   Web of Science ®Google Scholar
• McGranahan N, Furness AJ, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, Jamal-Hanjani M, Wilson GA, Birkbak NJ, Hiley CT, et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016;351(6280):1463–1469. doi:10.1126/science.aaf1490.
   PubMed Web of Science ®Google Scholar
• Karn T, Jiang T, Hatzis C, Sanger N, El-Balat A, Rody A, Holtrich U, Becker S, Bianchini G, Pusztai L. Association between genomic metrics and immune infiltration in triple-negative breast cancer. JAMA Oncol. 2017;3(12);1707–1711. doi:10.1001/jamaoncol.2017.2140.
   PubMed Web of Science ®Google Scholar
• Venkatesan S, Rosenthal R, Kanu N, McGranahan N, Bartek J, Quezada SA, Hare J, Harris RS, Swanton C. Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution. Ann Oncol. 2018;29(3);563–572. doi:10.1093/annonc/mdy003.
   PubMed Web of Science ®Google Scholar
• Norman JM, Mashiba M, McNamara LA, Onafuwa-Nuga A, Chiari-Fort E, Shen W. Collins KL: The antiviral factor APOBEC3G enhances the recognition of HIV-infected primary T cells by natural killer cells. Nat Immunol. 2011;12(10);975–983. doi:10.1038/ni.2087.
   PubMed Web of Science ®Google Scholar
• Casartelli N, Guivel-Benhassine F, Bouziat R, Brandler S, Schwartz O Moris A. The antiviral factor APOBEC3G improves CTL recognition of cultured HIV-infected T cells. J Exp Med. 2010;207(1);39–49. doi:10.1084/jem.20091933.
   PubMed Web of Science ®Google Scholar
• Beck-Engeser GB, Winkelmann R, Wheeler ML, Shansab M, Yu P, Wunsche S, Walchhutter A, Metzner M, Vettermann C, Eilat D, et al. APOBEC3 enzymes restrict marginal zone B cells. Eur J Immunol. 2015;45(3):695–704. doi:10.1002/eji.201445218.
   PubMed Web of Science ®Google Scholar