Skip to main content

Genetic Alterations and Checkpoint Expression: Mechanisms and Models for Drug Discovery

  • Chapter
  • First Online:
Book cover Regulation of Cancer Immune Checkpoints

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1248))

Abstract

In this chapter, we will sketch a story that begins with the breakdown of chromosome homeostasis and genomic stability. Genomic alterations may render tumor cells eternal life at the expense of immunogenicity. Although antitumor immunity can be primed through neoantigens or inflammatory signals, tumor cells have evolved countermeasures to evade immune surveillance and strike back by modulating immune checkpoint related pathways. At present, monoclonal antibody drugs targeting checkpoints like PD-1 and CTLA-4 have significantly prolonged the survival of a variety of cancer patients, and thus have marked a great achievement in the history of antitumor therapy. Nevertheless, this is not the end of the story. As the relationship between genomic alteration and checkpoint expression is being delineated though the advances of preclinical animal models and emerging technologies, novel checkpoint targets are on the way to be discovered.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abdelhamed S, Ogura K, Yokoyama S, Saiki I, Hayakawa Y (2016) AKT-STAT3 Pathway as a Downstream Target of EGFR Signaling to Regulate PD-L1 Expression on NSCLC cells. J Cancer 7(12):1579–1586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Abel EL, Angel JM, Kiguchi K, DiGiovanni J (2009) Multi-stage chemical carcinogenesis in mouse skin: fundamentals and applications. Nat Protoc 4(9):1350–1362

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anderson K, Lutz C, van Delft FW, Bateman CM, Guo Y, Colman SM et al (2011) Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature 469(7330):356–361

    Article  CAS  PubMed  Google Scholar 

  • Angell TE, Lechner MG, Jang JK, LoPresti JS, Epstein AL (2014) MHC class I loss is a frequent mechanism of immune escape in papillary thyroid cancer that is reversed by interferon and selumetinib treatment in vitro. Clin Cancer Res: Off J Am Assoc Cancer Res 20(23):6034–6044

    Article  CAS  Google Scholar 

  • Ansell SM, Lesokhin AM, Borrello I, Halwani A, Scott EC, Gutierrez M et al (2015) PD-1 blockade with nivolumab in relapsed or refractory Hodgkin’s lymphoma. N Engl J Med 372(4):311–319

    Article  CAS  PubMed  Google Scholar 

  • Auslander N, Zhang G, Lee JS, Frederick DT, Miao B, Moll T et al (2018) Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. Nat Med 24(10):1545–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Badens C, Joly P, Agouti I, Thuret I, Gonnet K, Fattoum S et al (2011) Variants in genetic modifiers of beta-thalassemia can help to predict the major or intermedia type of the disease. Haematologica 96(11):1712–1714

    Article  PubMed  PubMed Central  Google Scholar 

  • Baert T, Vankerckhoven A, Riva M, Van Hoylandt A, Thirion G, Holger G et al (2019) Myeloid derived suppressor cells: key drivers of immunosuppression in ovarian cancer. Front Immunol 10:1273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baracco EE, Pietrocola F, Buque A, Bloy N, Senovilla L, Zitvogel L et al (2016) Inhibition of formyl peptide receptor 1 reduces the efficacy of anticancer chemotherapy against carcinogen-induced breast cancer. Oncoimmunology 5(6):e1139275

    Google Scholar 

  • Barrett MT, Lenkiewicz E, Malasi S, Basu A, Yearley JH, Annamalai L et al (2018) The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers. Breast Cancer Res 20(1):71

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z et al (2016) Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet 48(4):407–416

    Article  CAS  PubMed  Google Scholar 

  • Casey SC, Tong L, Li Y, Do R, Walz S, Fitzgerald KN et al (2016) MYC regulates the antitumor immune response through CD47 and PD-L1. Science 352(6282):227–231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cassetta L, Fragkogianni S, Sims AH, Swierczak A, Forrester LM, Zhang H et al (2019) Human tumor-associated macrophage and monocyte transcriptional landscapes reveal cancer-specific reprogramming, biomarkers, and therapeutic targets. Cancer Cell 35(4):588–602.e10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chan TA, Wolchok JD, Snyder A (2015) Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 373(20):1984

    Article  CAS  PubMed  Google Scholar 

  • Chatterjee S, Martinez-Lopez W, Grigorova M, Darroudi F, Obe G, Natarajan AT (1999) Comparison of AluI-induced frequencies of dicentrics and translocations in human lymphocytes by chromosome painting. Mutagenesis 14(3):283–286

    Article  CAS  PubMed  Google Scholar 

  • Chen N, Fang W, Zhan J, Hong S, Tang Y, Kang S et al (2015) Upregulation of PD-L1 by EGFR Activation Mediates the Immune Escape in EGFR-Driven NSCLC: Implication for Optional Immune Targeted Therapy for NSCLC Patients with EGFR Mutation. J Thorac Oncol 10(6):910–923

    Article  CAS  PubMed  Google Scholar 

  • Chen R, Zinzani PL, Fanale MA, Armand P, Johnson NA, Brice P et al (2017a) Phase II study of the efficacy and safety of pembrolizumab for relapsed/refractory classic hodgkin lymphoma. J Clin Oncol: Off J Am Soc Clin Oncology 35(19):2125–2132

    Article  CAS  Google Scholar 

  • Chen N, Fang W, Lin Z, Peng P, Wang J, Zhan J et al (2017b) KRAS mutation-induced upregulation of PD-L1 mediates immune escape in human lung adenocarcinoma. Cancer Immunol Immunother 66(9):1175–1187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coelho MA, de Carne Trecesson S, Rana S, Zecchin D, Moore C, Molina-Arcas M et al (2017) Oncogenic RAS signaling promotes tumor immunoresistance by stabilizing PD-L1 mRNA. Immunity 47(6):1083–1099 e6

    Google Scholar 

  • Concha-Benavente F, Srivastava RM, Trivedi S, Lei Y, Chandran U, Seethala RR et al (2016) Identification of the cell-intrinsic and -extrinsic pathways downstream of EGFR and IFNgamma that induce PD-L1 expression in head and neck cancer. Cancer Res 76(5):1031–1043

    Article  CAS  PubMed  Google Scholar 

  • Cristescu R, Mogg R, Ayers M, Albright A, Murphy E, Yearley J et al (2018) Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science (New York, NY) 362(6411)

    Google Scholar 

  • Curiel TJ, Coukos G, Zou L, Alvarez X, Cheng P, Mottram P et al (2004) Specific recruitment of regulatory T cells in ovarian carcinoma fosters immune privilege and predicts reduced survival. Nat Med 10(9):942–949

    Article  CAS  PubMed  Google Scholar 

  • Currie GL, Delaney A, Bennett MI, Dickenson AH, Egan KJ, Vesterinen HM et al (2013) Animal models of bone cancer pain: systematic review and meta-analyses. Pain 154(6):917–926

    Article  PubMed  Google Scholar 

  • Day CP, Merlino G, Van Dyke T (2015) Preclinical mouse cancer models: a maze of opportunities and challenges. Cell 163(1):39–53

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Robertis M, Massi E, Poeta ML, Carotti S, Morini S, Cecchetelli L et al (2011) The AOM/DSS murine model for the study of colon carcinogenesis: From pathways to diagnosis and therapy studies. J Carcinog 10:9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diouf B, Cheng Q, Krynetskaia NF, Yang W, Cheok M, Pei D et al (2011) Somatic deletions of genes regulating MSH2 protein stability cause DNA mismatch repair deficiency and drug resistance in human leukemia cells. Nat Med 17(10):1298–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Donawho CK, Pride MW, Kripke ML (2001) Persistence of immunogenic pulmonary metastases in the presence of protective anti-melanoma immunity. Can Res 61(1):215–221

    CAS  Google Scholar 

  • Dunn GP, Bruce AT, Ikeda H, Old LJ, Schreiber RD (2002) Cancer immunoediting: from immunosurveillance to tumor escape. Nat Immunol 3(11):991–998

    Article  CAS  PubMed  Google Scholar 

  • Engelman JA, Luo J, Cantley LC (2006) The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nat Rev Genet 7(8):606–619

    Article  CAS  PubMed  Google Scholar 

  • Erichsen HC, Chanock SJ (2004) SNPs in cancer research and treatment. Br J Cancer 90(4):747–751

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fang JY, Richardson BC (2005) The MAPK signalling pathways and colorectal cancer. Lancet Oncol 6(5):322–327

    Article  CAS  PubMed  Google Scholar 

  • Fidler IJ, Hart IR (1982) Biological diversity in metastatic neoplasms: origins and implications. Science 217(4564):998–1003

    Article  CAS  PubMed  Google Scholar 

  • Fillon M (2018) Immune checkpoint inhibitors are superior to docetaxel as second-line therapy for patients with non-small cell lung carcinoma. CA: Cancer J Clin 68(3):178–179

    Google Scholar 

  • Gali-Muhtasib HU, Yamout SZ, Sidani MM (2000) Tannins protect against skin tumor promotion induced by ultraviolet-B radiation in hairless mice. Nutr Cancer 37(1):73–77

    Article  CAS  PubMed  Google Scholar 

  • George S, Miao D, Demetri GD, Adeegbe D, Rodig SJ, Shukla S et al (2017) Loss of PTEN Is associated with resistance to Anti-PD-1 checkpoint blockade therapy in metastatic uterine leiomyosarcoma. Immunity 46(2):197–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Girotti MR, Lopes F, Preece N, Niculescu-Duvaz D, Zambon A, Davies L et al (2015) Paradox-breaking RAF inhibitors that also target SRC are effective in drug-resistant BRAF mutant melanoma. Cancer Cell 27(1):85–96

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Green MR, Monti S, Rodig SJ, Juszczynski P, Currie T, O’Donnell E et al (2010) Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma. Blood 116(17):3268–3277

    Google Scholar 

  • Han BS, Ji S, Woo S, Lee JH, Sin JI (2019) Regulation of the translation activity of antigen-specific mRNA is responsible for antigen loss and tumor immune escape in a HER2-expressing tumor model. Sci Rep 9(1):2855

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70

    Article  CAS  PubMed  Google Scholar 

  • Hantschel O, Grebien F, Superti-Furga G (2012) The growing arsenal of ATP-competitive and allosteric inhibitors of BCR-ABL. Cancer Res 72(19):4890–4895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hause RJ, Pritchard CC, Shendure J, Salipante SJ (2018) Corrigendum: Classification and characterization of microsatellite instability across 18 cancer types. Nat Med 24(4):525

    Article  CAS  PubMed  Google Scholar 

  • Heinrich PC, Behrmann I, Haan S, Hermanns HM, Muller-Newen G, Schaper F (2003) Principles of interleukin (IL)-6-type cytokine signalling and its regulation. Biochem J 374(Pt 1):1–20

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM et al (2019) Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun 10(1):1388

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hochhaus A, La Rosee P, Muller MC, Ernst T, Cross NC (2011) Impact of BCR-ABL mutations on patients with chronic myeloid leukemia. Cell Cycle 10(2):250–260

    Article  CAS  PubMed  Google Scholar 

  • Iannello A, Thompson TW, Ardolino M, Lowe SW, Raulet DH (2013) p53-dependent chemokine production by senescent tumor cells supports NKG2D-dependent tumor elimination by natural killer cells. J Exp Med 210(10):2057–2069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iengar P (2012) An analysis of substitution, deletion and insertion mutations in cancer genes. Nucleic Acids Res 40(14):6401–6413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iwai Y, Ishida M, Tanaka Y, Okazaki T, Honjo T, Minato N (2002) Involvement of PD-L1 on tumor cells in the escape from host immune system and tumor immunotherapy by PD-L1 blockade. Proc Natl Acad Sci U S A. 99(19):12293–12297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iwai Y, Terawaki S, Honjo T (2005) PD-1 blockade inhibits hematogenous spread of poorly immunogenic tumor cells by enhanced recruitment of effector T cells. Int Immunol 17(2):133–144

    Article  CAS  PubMed  Google Scholar 

  • Jackson NM, Ceresa BP (2017) EGFR-mediated apoptosis via STAT3. Exp Cell Res 356(1):93–103

    CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson JI, Decker S, Zaharevitz D, Rubinstein LV, Venditti JM, Schepartz S et al (2001) Relationships between drug activity in NCI preclinical in vitro and in vivo models and early clinical trials. Br J Cancer 84(10):1424–1431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C et al (2013) Mutational landscape and significance across 12 major cancer types. Nature 502(7471):333–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khong HT, Restifo NP (2002) Natural selection of tumor variants in the generation of “tumor escape” phenotypes. Nat Immunol 3(11):999–1005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim HP, Cho GA, Han SW, Shin JY, Jeong EG, Song SH et al (2014) Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene 33(47):5434–5441

    Article  CAS  PubMed  Google Scholar 

  • Koyama S, Akbay EA, Li YY, Aref AR, Skoulidis F, Herter-Sprie GS et al (2016) STK11/LKB1 deficiency promotes neutrophil recruitment and proinflammatory cytokine production to suppress T-cell activity in the lung tumor microenvironment. Cancer Res 76(5):999–1008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuang DM, Zhao Q, Peng C, Xu J, Zhang JP, Wu C et al (2009) Activated monocytes in peritumoral stroma of hepatocellular carcinoma foster immune privilege and disease progression through PD-L1. J Exp Med 206(6):1327–1337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leach DR, Krummel MF, Allison JP (1996) Enhancement of antitumor immunity by CTLA-4 blockade. Science 271(5256):1734–1736

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Di Santo JP (2019) Modeling infectious diseases in mice with a “Humanized” immune system. Microbiol Spectr 7(2)

    Google Scholar 

  • Li H, Wang J, Ma X, Sklar J (2009) Gene fusions and RNA trans-splicing in normal and neoplastic human cells. Cell Cycle 8(2):218–222

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Chen Q, Zheng D, Yin L, Chionh YH, Wong LH et al (2013) Induction of functional human macrophages from bone marrow promonocytes by M-CSF in humanized mice. J Immunol 191(6):3192–3199

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Mention JJ, Court N, Masse-Ranson G, Toubert A, Spits H et al (2016) A novel Flt3-deficient HIS mouse model with selective enhancement of human DC development. Eur J Immunol 46(5):1291–1299

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Strick-Marchand H, Lim AI, Ren J, Masse-Ranson G, Dan L et al (2017) Regulatory T cells control toxicity in a humanized model of IL-2 therapy. Nat Commun 8(1):1762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • LoPiccolo J, Blumenthal GM, Bernstein WB, Dennis PA (2008) Targeting the PI3K/Akt/mTOR pathway: effective combinations and clinical considerations. Drug Resist Updat 11(1–2):32–50

    Article  CAS  PubMed  Google Scholar 

  • Malaney P, Nicosia SV, Dave V (2014) One mouse, one patient paradigm: new avatars of personalized cancer therapy. Cancer Lett 344(1):1–12

    Article  CAS  PubMed  Google Scholar 

  • Mansfield AS, Peikert T, Smadbeck JB, Udell JBM, Garcia-Rivera E, Elsbernd L et al (2019) Neoantigenic potential of complex chromosomal rearrangements in mesothelioma. J Thorac Oncol: Off Publ Int Assoc Study Lung Cancer 14(2):276–287

    Article  CAS  Google Scholar 

  • Manz MG (2007) Human-hemato-lymphoid-system mice: opportunities and challenges. Immunity 26(5):537–541

    Article  CAS  PubMed  Google Scholar 

  • Mardis ER (2017) Neoantigen discovery in human cancers. Cancer J 23(2):97–101

    Article  CAS  PubMed  Google Scholar 

  • Marigo I, Bosio E, Solito S, Mesa C, Fernandez A, Dolcetti L et al (2010) Tumor-induced tolerance and immune suppression depend on the C/EBPbeta transcription factor. Immunity 32(6):790–802

    Article  CAS  PubMed  Google Scholar 

  • Masse-Ranson G, Dusseaux M, Fiquet O, Darche S, Boussand M, Li Y et al (2019) Accelerated thymopoiesis and improved T-cell responses in HLA-A2/-DR2 transgenic BRGS-based human immune system mice. Eur J Immunol 49(6):954–965

    Article  CAS  PubMed  Google Scholar 

  • Mathew M, Enzler T, Shu CA, Rizvi NA (2018) Combining chemotherapy with PD-1 blockade in NSCLC. Pharmacol Ther 186:130–137

    Article  CAS  PubMed  Google Scholar 

  • Mattarollo SR, Loi S, Duret H, Ma Y, Zitvogel L, Smyth MJ (2011) Pivotal role of innate and adaptive immunity in anthracycline chemotherapy of established tumors. Cancer Res 71(14):4809–4820

    Article  CAS  PubMed  Google Scholar 

  • Melkus MW, Estes JD, Padgett-Thomas A, Gatlin J, Denton PW, Othieno FA et al (2006) Humanized mice mount specific adaptive and innate immune responses to EBV and TSST-1. Nat Med 12(11):1316–1322

    Article  CAS  PubMed  Google Scholar 

  • Mestas J, Hughes CC (2004) Of mice and not men: differences between mouse and human immunology. J Immunol. 172(5):2731–2738

    Article  CAS  PubMed  Google Scholar 

  • Migden MR, Rischin D, Schmults CD, Guminski A, Hauschild A, Lewis KD et al (2018) PD-1 blockade with cemiplimab in advanced cutaneous squamous-cell carcinoma. N Engl J Med 379(4):341–351

    Article  CAS  PubMed  Google Scholar 

  • Mitelman F, Johansson B, Mertens F (2004) Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet 36(4):331–334

    Article  CAS  PubMed  Google Scholar 

  • Moncunill V, Gonzalez S, Bea S, Andrieux LO, Salaverria I, Royo C et al (2014) Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads. Nat Biotechnol 32(11):1106–1112

    Article  CAS  PubMed  Google Scholar 

  • Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J et al (2011) Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics 4:11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Natarajan AT, Boei JJ (2003) Formation of chromosome aberrations: insights from FISH. Mutat Res 544(2–3):299–304

    Article  CAS  PubMed  Google Scholar 

  • Nguyen KB, Cousens LP, Doughty LA, Pien GC, Durbin JE, Biron CA (2000) Interferon alpha/beta-mediated inhibition and promotion of interferon gamma: STAT1 resolves a paradox. Nat Immunol 1(1):70–76

    Article  CAS  PubMed  Google Scholar 

  • Niglio SA, Jia R, Ji J, Ruder S, Patel VG, Martini A et al (2019) Programmed death-1 or programmed death ligand-1 blockade in patients with platinum-resistant metastatic urothelial cancer: a systematic review and meta-analysis. Eur Urol

    Google Scholar 

  • Nonomura C, Otsuka M, Kondou R, Iizuka A, Miyata H, Ashizawa T et al (2019) Identification of a neoantigen epitope in a melanoma patient with good response to anti-PD-1 antibody therapy. Immunol Lett 208:52–59

    Article  CAS  PubMed  Google Scholar 

  • Okita R, Maeda A, Shimizu K, Nojima Y, Saisho S, Nakata M (2017) PD-L1 overexpression is partially regulated by EGFR/HER2 signaling and associated with poor prognosis in patients with non-small-cell lung cancer. Cancer Immunol Immunother 66(7):865–876

    Article  CAS  PubMed  Google Scholar 

  • Ota K, Azuma K, Kawahara A, Hattori S, Iwama E, Tanizaki J et al (2015) Induction of PD-L1 Expression by the EML4-ALK Oncoprotein and Downstream Signaling Pathways in Non-Small Cell Lung Cancer. Clin Cancer Res 21(17):4014–4021

    Article  CAS  PubMed  Google Scholar 

  • Parsa AT, Waldron JS, Panner A, Crane CA, Parney IF, Barry JJ et al (2007) Loss of tumor suppressor PTEN function increases B7-H1 expression and immunoresistance in glioma. Nat Med 13(1):84–88

    Article  CAS  PubMed  Google Scholar 

  • Przybytkowski E, Aguilar-Mahecha A, Nabavi S, Tonellato PJ, Basik M (2013) Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome. Methods Mol Biol 973:15–38

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qin F, Song Z, Babiceanu M, Song Y, Facemire L, Singh R et al (2015) Discovery of CTCF-sensitive Cis-spliced fusion RNAs between adjacent genes in human prostate cells. PLoS Genet 11(2):e1005001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quigley D, Silwal-Pandit L, Dannenfelser R, Langerod A, Vollan HK, Vaske C et al (2015) Lymphocyte invasion in IC10/Basal-like breast tumors is associated with wild-type TP53. Mol Cancer Res: MCR 13(3):493–501

    Article  CAS  PubMed  Google Scholar 

  • Rakhra K, Bachireddy P, Zabuawala T, Zeiser R, Xu L, Kopelman A et al (2010) CD4(+) T cells contribute to the remodeling of the microenvironment required for sustained tumor regression upon oncogene inactivation. Cancer Cell 18(5):485–498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Remon J, Esteller L, Taus A (2019) Nivolumab plus ipilimumab combination therapy for the first-line treatment NSCLC: evidence to date. Cancer Manag Res 11:4893–4904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Risch NJ (2000) Searching for genetic determinants in the new millennium. Nature 405(6788):847–856

    Article  CAS  PubMed  Google Scholar 

  • Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ et al (2015) Cancer immunology. mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science (New York, NY). 348(6230):124–128

    Google Scholar 

  • Rongvaux A, Willinger T, Martinek J, Strowig T, Gearty SV, Teichmann LL et al (2014) Development and function of human innate immune cells in a humanized mouse model. Nat Biotechnol 32(4):364–372

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sade-Feldman M, Kanterman J, Ish-Shalom E, Elnekave M, Horwitz E, Baniyash M (2013) Tumor necrosis factor-alpha blocks differentiation and enhances suppressive activity of immature myeloid cells during chronic inflammation. Immunity 38(3):541–554

    Article  CAS  PubMed  Google Scholar 

  • Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW et al (2018) Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell 175(4):998–1013.e20

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakamuro D, Elliott KJ, Wechsler-Reya R, Prendergast GC (1996) BIN1 is a novel MYC-interacting protein with features of a tumour suppressor. Nat Genet 14(1):69–77

    Article  CAS  PubMed  Google Scholar 

  • Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC et al (2018) Oncogenic signaling pathways in the cancer genome atlas. Cell 173(2):321–337 e10

    Google Scholar 

  • Schramek D, Leibbrandt A, Sigl V, Kenner L, Pospisilik JA, Lee HJ et al (2010) Osteoclast differentiation factor RANKL controls development of progestin-driven mammary cancer. Nature 468(7320):98–102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Seiwert TY, Zuo Z, Keck MK, Khattri A, Pedamallu CS, Stricker T et al (2015) Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas. Clin Cancer Res: Off J Am Assoc Cancer Res 21(3):632–641

    Article  CAS  Google Scholar 

  • Seiwert TY, Burtness B, Mehra R, Weiss J, Berger R, Eder JP et al (2016) Safety and clinical activity of pembrolizumab for treatment of recurrent or metastatic squamous cell carcinoma of the head and neck (KEYNOTE-012): an open-label, multicentre, phase 1b trial. Lancet Oncol 17(7):956–965

    Article  CAS  PubMed  Google Scholar 

  • Seront E, Pinto A, Bouzin C, Bertrand L, Machiels JP, Feron O (2013) PTEN deficiency is associated with reduced sensitivity to mTOR inhibitor in human bladder cancer through the unhampered feedback loop driving PI3K/Akt activation. Br J Cancer 109(6):1586–1592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shuai K (2000) Modulation of STAT signaling by STAT-interacting proteins. Oncogene 19(21):2638–2644

    Article  CAS  PubMed  Google Scholar 

  • Shultz LD, Saito Y, Najima Y, Tanaka S, Ochi T, Tomizawa M et al (2010) Generation of functional human T-cell subsets with HLA-restricted immune responses in HLA class I expressing NOD/SCID/IL2r gamma(null) humanized mice. Proc Natl Acad Sci U S A. 107(29):13022–13027

    Article  PubMed  PubMed Central  Google Scholar 

  • Simhadri VL, Hamasaki-Katagiri N, Lin BC, Hunt R, Jha S, Tseng SC et al (2017) Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B. J Med Genet 54(5):338–345

    Article  CAS  PubMed  Google Scholar 

  • Sivan A, Corrales L, Hubert N, Williams JB, Aquino-Michaels K, Earley ZM et al (2015) Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350(6264):1084–1089

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Skaro M, Nanda N, Gauthier C, Felsenstein M, Jiang Z, Qiu M et al (2019) Prevalence of germline mutations associated with cancer risk in patients with intraductal papillary mucinous neoplasms. Gastroenterology 156(6):1905–1913

    Article  CAS  PubMed  Google Scholar 

  • Slatkin M (2008) Linkage disequilibrium–understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9(6):477–485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song M, Chen D, Lu B, Wang C, Zhang J, Huang L et al (2013) PTEN loss increases PD-L1 protein expression and affects the correlation between PD-L1 expression and clinical parameters in colorectal cancer. PLoS ONE 8(6):e65821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spranger S, Bao R, Gajewski TF (2015) Melanoma-intrinsic beta-catenin signalling prevents anti-tumour immunity. Nature 523(7559):231–235

    Article  CAS  PubMed  Google Scholar 

  • Spranger S, Dai D, Horton B, Gajewski TF (2017) Tumor-residing Batf3 dendritic cells are required for effector T cell trafficking and adoptive T cell therapy. Cancer Cell 31(5):711–23.e4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steidl C, Lee T, Shah SP, Farinha P, Han G, Nayar T et al (2010) Tumor-associated macrophages and survival in classic Hodgkin’s lymphoma. N Engl J Med 362(10):875–885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steidl C, Shah SP, Woolcock BW, Rui L, Kawahara M, Farinha P et al (2011) MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature 471(7338):377–381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sullivan RJ, Hamid O, Gonzalez R, Infante JR, Patel MR, Hodi FS et al (2019) Atezolizumab plus cobimetinib and vemurafenib in BRAF-mutated melanoma patients. Nat Med 25(6):929–935

    Article  CAS  PubMed  Google Scholar 

  • Sumimoto H, Takano A, Teramoto K, Daigo Y (2016) RAS-Mitogen-Activated Protein Kinase Signal Is Required for Enhanced PD-L1 Expression in Human Lung Cancers. PLoS ONE 11(11):e0166626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Szabados B, van Dijk N, Tang YZ, van der Heijden MS, Wimalasingham A, Gomez de Liano A et al (2018) Response rate to chemotherapy after immune checkpoint inhibition in metastatic urothelial cancer. Eur Urol 73(2):149–152

    Google Scholar 

  • Taboada EN, Acedillo RR, Luebbert CC, Findlay WA, Nash JH (2005) A new approach for the analysis of bacterial microarray-based Comparative Genomic Hybridization: insights from an empirical study. BMC Genom 6:78

    Article  CAS  Google Scholar 

  • Tran E, Turcotte S, Gros A, Robbins PF, Lu YC, Dudley ME et al (2014) Cancer immunotherapy based on mutation-specific CD4 + T cells in a patient with epithelial cancer. Science (New York, NY). 344(6184):641–645

    Article  CAS  Google Scholar 

  • Tretiakova MS, Wang W, Wu Y, Tykodi SS, True L, Liu YJ (2019) Gene fusion analysis in renal cell carcinoma by fusionplex RNA sequencing and correlations of molecular findings with clinicopathological features. Genes Chromosom Cancer

    Google Scholar 

  • Tung N, Lin NU, Kidd J, Allen BA, Singh N, Wenstrup RJ et al (2016) Frequency of germline mutations in 25 cancer susceptibility genes in a sequential series of patients with breast cancer. J Clin Oncol: Off J Am Soc Clin Oncol 34(13):1460–1468

    Article  CAS  Google Scholar 

  • Turajlic S, Litchfield K, Xu H, Rosenthal R, McGranahan N, Reading JL et al (2017) Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis. Lancet Oncol 18(8):1009–1021

    Article  CAS  PubMed  Google Scholar 

  • van der Lee DI, Reijmers RM, Honders MW, Hagedoorn RS, de Jong RC, Kester MG et al (2019) Mutated nucleophosmin 1 as immunotherapy target in acute myeloid leukemia. J Clin Investig 129(2):774–785

    Article  PubMed  PubMed Central  Google Scholar 

  • Velusamy T, Palanisamy N, Kalyana-Sundaram S, Sahasrabuddhe AA, Maher CA, Robinson DR et al (2013) Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A. 110(8):3035–3040

    Article  PubMed  PubMed Central  Google Scholar 

  • Vesely MD, Kershaw MH, Schreiber RD, Smyth MJ (2011) Natural innate and adaptive immunity to cancer. Ann Rev Immunol 29:235–271

    Article  CAS  Google Scholar 

  • Vetizou M, Pitt JM, Daillere R, Lepage P, Waldschmitt N, Flament C et al (2015) Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 350(6264):1079–1084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J, Jia Y, Zhao S, Zhang X, Wang X, Han X et al (2017) BIN1 reverses PD-L1-mediated immune escape by inactivating the c-MYC and EGFR/MAPK signaling pathways in non-small cell lung cancer. Oncogene 36(45):6235–6243

    Article  CAS  PubMed  Google Scholar 

  • Watson IR, Takahashi K, Futreal PA, Chin L (2013) Emerging patterns of somatic mutations in cancer. Nat Rev Genet 14(10):703–718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang H, Zhong Y, Peng C, Chen JQ, Tian D (2010) Important role of indels in somatic mutations of human cancer genes. BMC Med Genet 11:128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang W, Lee KW, Srivastava RM, Kuo F, Krishna C, Chowell D et al (2019) Immunogenic neoantigens derived from gene fusions stimulate T cell responses. Nat Med 25(5):767–775

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoo HY, Kim P, Kim WS, Lee SH, Kim S, Kang SY et al (2016) Frequent CTLA4-CD28 gene fusion in diverse types of T-cell lymphoma. Haematologica 101(6):757–763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoshihara K, Wang Q, Torres-Garcia W, Zheng S, Vegesna R, Kim H et al (2015) The landscape and therapeutic relevance of cancer-associated transcript fusions. Oncogene 34(37):4845–4854

    Article  CAS  PubMed  Google Scholar 

  • Yoshizato T, Nannya Y, Atsuta Y, Shiozawa Y, Iijima-Yamashita Y, Yoshida K et al (2017) Genetic abnormalities in myelodysplasia and secondary acute myeloid leukemia: impact on outcome of stem cell transplantation. Blood 129(17):2347–2358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Younes A, Santoro A, Shipp M, Zinzani PL, Timmerman JM, Ansell S et al (2016) Nivolumab for classical Hodgkin’s lymphoma after failure of both autologous stem-cell transplantation and brentuximab vedotin: a multicentre, multicohort, single-arm phase 2 trial. Lancet Oncol. 17(9):1283–1294

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang W, Moore L, Ji P (2011) Mouse models for cancer research. Chin J Cancer. 30(3):149–152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Gong M, Yuan H, Park HG, Frierson HF, Li H (2012) Chimeric transcript generated by cis-splicing of adjacent genes regulates prostate cancer cell proliferation. Cancer Discov 2(7):598–607

    Article  CAS  PubMed  Google Scholar 

  • Zitvogel L, Pitt JM, Daillere R, Smyth MJ, Kroemer G (2016) Mouse models in oncoimmunology. Nat Rev Cancer 16(12):759–773

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yan Li .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Ding, S., Li, S., Zhang, S., Li, Y. (2020). Genetic Alterations and Checkpoint Expression: Mechanisms and Models for Drug Discovery. In: Xu, J. (eds) Regulation of Cancer Immune Checkpoints. Advances in Experimental Medicine and Biology, vol 1248. Springer, Singapore. https://doi.org/10.1007/978-981-15-3266-5_10

Download citation

Publish with us

Policies and ethics