Genomic alterations in lung adenocarcinoma

The Lancet Oncology

Volumn 16, Issue 7, 2015, Pages e342-e351

  Devarakonda, Siddhartha ^a   Morgensztern, Daniel ^a,b   Govindan, Ramaswamy ^a,b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFATINIB; B RAF KINASE; CERITINIB; CRIZOTINIB; DABRAFENIB; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; K RAS PROTEIN; NERATINIB; SCATTER FACTOR RECEPTOR; ANAPLASTIC LYMPHOMA KINASE; ANTINEOPLASTIC AGENT; BRAF PROTEIN, HUMAN; PROTEIN TYROSINE KINASE; RAS PROTEIN;

AMINO ACID SUBSTITUTION; CANCER CLASSIFICATION; CANCER GENETICS; CANCER PROGNOSIS; CANCER RESISTANCE; CLINICAL TRIAL (TOPIC); CLONAL EVOLUTION; COPY NUMBER VARIATION; DRUG EFFICACY; DRUG RESPONSE; DRUG SENSITIVITY; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE FUSION; GENE MUTATION; GENE REARRANGEMENT; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HUMAN; LUNG ADENOCARCINOMA; LUNG CARCINOGENESIS; MALIGNANT TRANSFORMATION; MUTATION RATE; NEXT GENERATION SEQUENCING; NON SMALL CELL LUNG CANCER; ONCOGENE; ONCOGENE K RAS; PHASE 2 CLINICAL TRIAL (TOPIC); PRIORITY JOURNAL; REVIEW; RNA SPLICING; SIGNAL TRANSDUCTION; SOMATIC MUTATION; TRANSCRIPTOMICS; ADENOCARCINOMA; CANCER STAGING; FEMALE; FORECASTING; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; LUNG NEOPLASMS; MALE; MOLECULARLY TARGETED THERAPY; PATHOLOGY; PERSONALIZED MEDICINE; PROCEDURES; TUMOR INVASION;

ADENOCARCINOMA; ANTINEOPLASTIC AGENTS; FEMALE; FORECASTING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; INDIVIDUALIZED MEDICINE; LUNG NEOPLASMS; MALE; MOLECULAR TARGETED THERAPY; NEOPLASM INVASIVENESS; NEOPLASM STAGING; PROTO-ONCOGENE PROTEINS B-RAF; RAS PROTEINS; RECEPTOR PROTEIN-TYROSINE KINASES; RECEPTOR, EPIDERMAL GROWTH FACTOR;

EID: 84937413847     PISSN: 14702045     EISSN: 14745488     Source Type: Journal    
DOI: 10.1016/S1470-2045(15)00077-7     Document Type: Review

References (98)

1. Siegel RL, Miller KD, Jemal A Cancer statistics, 2015. CA Cancer J Clin 2015, 65:5-29.
2. Travis WD Pathology of lung cancer. Clin Chest Med 2011, 32:669-692.
3. Zhou C, Wu YL, Chen G, et al. Erlotinib versus chemotherapy as first-line treatment for patients with advanced EGFR mutation-positive non-small-cell lung cancer (OPTIMAL, CTONG-0802): a multicentre, open-label, randomised, phase 3 study. Lancet Oncol 2011, 12:735-742.
4. Maemondo M, Inoue A, Kobayashi K, et al. Gefitinib or chemotherapy for non-small-cell lung cancer with mutated EGFR. N Engl J Med 2010, 362:2380-2388. the North-East Japan Study Group.
5. Paez JG, Jänne PA, Lee JC, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 2004, 304:1497-1500.
6. Kwak EL, Bang YJ, Camidge DR, et al. Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N Engl J Med 2010, 363:1693-1703.
7. Ledford H Big science: The cancer genome challenge. Nature 2010, 464:972-974.
8. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012, 489:519-525. Cancer Genome Atlas Research Network.
9. Govindan R, Ding L, Griffith M, et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012, 150:1121-1134.
10. Imielinski M, Berger AH, Hammerman PS, et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012, 150:1107-1120.
11. Network CGAR Comprehensive molecular profiling of lung adenocarcinoma. Nature 2014, 511:543-550. the Cancer Genome Atlas Research Network.
12. Zack TI, Schumacher SE, Carter SL, et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013, 45:1134-1140.
13. Beroukhim R, Mermel CH, Porter D, et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010, 463:899-905.
14. Weir BA, Woo MS, Getz G, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007, 450:893-898.
15. Li Y, Tergaonkar V Noncanonical functions of telomerase: implications in telomerase-targeted cancer therapies. Cancer Res 2014, 74:1639-1644.
16. Hanahan D, Weinberg RA The hallmarks of cancer. Cell 2000, 100:57-70.
17. Cerami E, Gao J, Dogrusoz U, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012, 2:401-404.
18. Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013, 6:pl1.
19. Yamaguchi T, Hosono Y, Yanagisawa K, Takahashi T NKX2-1/TTF-1: an enigmatic oncogene that functions as a double-edged sword for cancer cell survival and progression. Cancer Cell 2013, 23:718-723.
20. Yuan B, Li C, Kimura S, Engelhardt RT, Smith BR, Minoo P Inhibition of distal lung morphogenesis in Nkx2.1(-/-) embryos. Dev Dyn 2000, 217:180-190.
21. Morrisey EE, Hogan BL Preparing for the first breath: genetic and cellular mechanisms in lung development. Dev Cell 2010, 18:8-23.
22. Rudin CM, Durinck S, Stawiski EW, et al. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet 2012, 44:1111-1116.
23. Bass AJ, Watanabe H, Mermel CH, et al. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet 2009, 41:1238-1242.
24. Meyer N, Penn LZ Reflecting on 25 years with MYC. Nat Rev Cancer 2008, 8:976-990.
25. Patel JH, Loboda AP, Showe MK, Showe LC, McMahon SB Analysis of genomic targets reveals complex functions of MYC. Nat Rev Cancer 2004, 4:562-568.
26. A genomics-based classification of human lung tumors. Sci Transl Med 2013, 5:209ra153. Clinical Lung Cancer Genome Project (CLCGP) Network Genomic Medicine (NGM).
27. Hurlin PJ, Huang J The MAX-interacting transcription factor network. Semin Cancer Biol 2006, 16:265-274.
28. de Bruin EC, McGranahan N, Mitter R, et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 2014, 346:251-256.
29. Zhang J, Fujimoto J, Zhang J, et al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science 2014, 346:256-259.
30. Pleasance ED, Stephens PJ, O'Meara S, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 2010, 463:184-190.
31. Hammerman PS, Hayes DN, Wilkerson MD, et al. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012, 489:519-525. the Cancer Genome Atlas Research Network.
32. Kandoth C, McLellan MD, Vandin F, et al. Mutational landscape and significance across 12 major cancer types. Nature 2013, 502:333-339.
33. Hodis E, Watson IR, Kryukov GV, et al. A landscape of driver mutations in melanoma. Cell 2012, 150:251-263.
34. Lawrence MS, Stojanov P, Polak P, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013, 499:214-218.
35. Peifer M, Fernández-Cuesta L, Sos ML, et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet 2012, 44:1104-1110.
36. Subramanian J, Govindan R Lung cancer in never smokers: a review. J Clin Oncol 2007, 25:561-570.
37. Wennerberg K, Rossman KL, Der CJ The Ras superfamily at a glance. J Cell Sci 2005, 118:843-846.
38. Pylayeva-Gupta Y, Grabocka E, Bar-Sagi D RAS oncogenes: weaving a tumorigenic web. Nat Rev Cancer 2011, 11:761-774.
39. Ihle NT, Byers LA, Kim ES, et al. Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome. J Natl Cancer Inst 2012, 104:228-239.
40. Garassino MC, Marabese M, Rusconi P, et al. Different types of K-Ras mutations could affect drug sensitivity and tumour behaviour in non-small-cell lung cancer. Ann Oncol 2011, 22:235-237.
41. Castellano E, Sheridan C, Thin MZ, et al. Requirement for interaction of PI3-kinase p110α with RAS in lung tumor maintenance. Cancer Cell 2013, 24:617-630.
42. Kim HS, Mendiratta S, Kim J, et al. Systematic identification of molecular subtype-selective vulnerabilities in non-small-cell lung cancer. Cell 2013, 155:552-566.
43. Ostrem JM, Peters U, Sos ML, Wells JA, Shokat KM K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature 2013, 503:548-551.
44. Sharma SV, Bell DW, Settleman J, Haber DA Epidermal growth factor receptor mutations in lung cancer. Nat Rev Cancer 2007, 7:169-181.
45. Rosell R, Moran T, Queralt C, et al. Screening for epidermal growth factor receptor mutations in lung cancer. N Engl J Med 2009, 361:958-967. the Spanish Lung Cancer Group.
46. Ohashi K, Maruvka YE, Michor F, Pao W Epidermal growth factor receptor tyrosine kinase inhibitor-resistant disease. J Clin Oncol 2013, 31:1070-1080.
47. Yasuda H, Kobayashi S, Costa DB EGFR exon 20 insertion mutations in non-small-cell lung cancer: preclinical data and clinical implications. Lancet Oncol 2012, 13:e23-e31.
48. Camidge DR, Pao W, Sequist LV Acquired resistance to TKIs in solid tumours: learning from lung cancer. Nat Rev Clin Oncol 2014, 11:473-481.
49. Sequist LV, Soria JC, Goldman JW, et al. Rociletinib in EGFR-mutated non-small-cell lung cancer. N Engl J Med 2015, 372:1700-1709.
50. Jänne PA, Yang JC, Kim DW, et al. AZD9291 in EGFR inhibitor-resistant non-small-cell lung cancer. N Engl J Med 2015, 372:1689-1699.
51. Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med 2011, 364:2507-2516. the BRIM-3 Study Group.
52. Marchetti A, Felicioni L, Malatesta S, et al. Clinical features and outcome of patients with non-small-cell lung cancer harboring BRAF mutations. J Clin Oncol 2011, 29:3574-3579.
53. Paz-Ares LG, Biesma B, Heigener D, et al. Phase III, randomized, double-blind, placebo-controlled trial of gemcitabine/cisplatin alone or with sorafenib for the first-line treatment of advanced, nonsquamous non-small-cell lung cancer. J Clin Oncol 2012, 30:3084-3092. the NSCLC [non-small-cell lung cancer] Research Experience Utilizing Sorafenib (NExUS) Investigators Study Group.
54. Planchard D, Mazieres J, Riely GJ, et al. Interim results of phase II study BRF113928 of dabrafenib in BRAF V600E mutation-positive non-small cell lung cancer (NSCLC) patients. ASCO Meeting Abstracts. J Clin Oncol 2013, 31:8009. (abstr).
55. Seo JS, Ju YS, Lee WC, et al. The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res 2012, 22:2109-2119.
56. Camidge DR, Ou SHI, Shapiro G, et al. Efficacy and safety of crizotinib in patients with advanced c-MET-amplified non-small cell lung cancer (NSCLC). J Clin Oncol 2014, 32(suppl 5s):8001. (abstr).
57. Ou SH, Kwak EL, Siwak-Tapp C, et al. Activity of crizotinib (PF02341066), a dual mesenchymal-epithelial transition (MET) and anaplastic lymphoma kinase (ALK) inhibitor, in a non-small cell lung cancer patient with de novo MET amplification. J Thorac Oncol 2011, 6:942-946.
58. Pao W, Girard N New driver mutations in non-small-cell lung cancer. Lancet Oncol 2011, 12:175-180.
59. Mazières J, Peters S, Lepage B, et al. Lung cancer that harbors an HER2 mutation: epidemiologic characteristics and therapeutic perspectives. J Clin Oncol 2013, 31:1997-2003.
60. Arcila ME, Chaft JE, Nafa K, et al. Prevalence, clinicopathologic associations, and molecular spectrum of ERBB2 (HER2) tyrosine kinase mutations in lung adenocarcinomas. Clin Cancer Res 2012, 18:4910-4918.
61. Stephens P, Hunter C, Bignell G, et al. Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature 2004, 431:525-526.
62. De Grève J, Teugels E, Geers C, et al. Clinical activity of afatinib (BIBW 2992) in patients with lung adenocarcinoma with mutations in the kinase domain of HER2/neu. Lung Cancer 2012, 76:123-127.
63. Shimamura T, Ji H, Minami Y, et al. Non-small-cell lung cancer and Ba/F3 transformed cells harboring the ERBB2 G776insV_G/C mutation are sensitive to the dual-specific epidermal growth factor receptor and ERBB2 inhibitor HKI-272. Cancer Res 2006, 66:6487-6491.
64. Li D, Ambrogio L, Shimamura T, et al. BIBW2992, an irreversible EGFR/HER2 inhibitor highly effective in preclinical lung cancer models. Oncogene 2008, 27:4702-4711.
65. Gómez-Seguí I, Makishima H, Jerez A, et al. Novel recurrent mutations in the RAS-like GTP-binding gene RIT1 in myeloid malignancies. Leukemia 2013, 27:1943-1946.
66. Berger AH, Imielinski M, Duke F, et al. Oncogenic RIT1 mutations in lung adenocarcinoma. Oncogene 2014, 33:4418-4423.
67. Lawrence MS, Stojanov P, Mermel CH, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014, 505:495-501.
68. Shaw AT, Kim DW, Mehra R, et al. Ceritinib in ALK-rearranged non-small-cell lung cancer. N Engl J Med 2014, 370:1189-1197.
69. Shaw AT, Kim DW, Nakagawa K, et al. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med 2013, 368:2385-2394.
70. Kris MG, Johnson BE, Berry LD, et al. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs. JAMA 2014, 311:1998-2006.
71. Shaw AT, Ou SH, Bang YJ, et al. Crizotinib in ROS1-rearranged non-small-cell lung cancer. N Engl J Med 2014, 371:1963-1971.
72. Gainor JF, Shaw AT Novel targets in non-small cell lung cancer: ROS1 and RET fusions. Oncologist 2013, 18:865-875.
73. Vaishnavi A, Capelletti M, Le AT, et al. Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer. Nat Med 2013, 19:1469-1472.
74. Zhang J, Manley JL Misregulation of pre-mRNA alternative splicing in cancer. Cancer Discov 2013, 3:1228-1237.
75. Liu J, Lee W, Jiang Z, et al. Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Res 2012, 22:2315-2327.
76. van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
77. Paik S, Shak S, Tang G, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004, 351:2817-2826.
78. Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
79. Dunleavy K, Roschewski M, Wilson WH Precision treatment of distinct molecular subtypes of diffuse large B-cell lymphoma: ascribing treatment based on the molecular phenotype. Clin Cancer Res 2014, 20:5182-5193.
80. Wilkerson MD, Yin X, Walter V, et al. Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation. PLoS One 2012, 7:e36530.
81. Hayes DN, Monti S, Parmigiani G, et al. Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol 2006, 24:5079-5090.
82. Parker JL, Lushina N, Bal PS, Petrella T, Dent R, Lopes G Impact of biomarkers on clinical trial risk in breast cancer. Breast Cancer Res Treat 2012, 136:179-185.
83. Senkus E, Kyriakides S, Penault-Llorca F, et al. Primary breast cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 2013, 24(suppl 6):vi7-v23. the ESMO Guidelines Working Group.
84. Dawson MA, Kouzarides T Cancer epigenetics: from mechanism to therapy. Cell 2012, 150:12-27.
85. Wong NC, Ng J, Hall NE, et al. Exploring the utility of human DNA methylation arrays for profiling mouse genomic DNA. Genomics 2013, 102:38-46.
86. Yates LR, Campbell PJ Evolution of the cancer genome. Nat Rev Genet 2012, 13:795-806.
87. Gerlinger M, Rowan AJ, Horswell S, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012, 366:883-892.
88. Ding L, Ley TJ, Larson DE, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 2012, 481:506-510.
89. DeNicola GM, Karreth FA, Humpton TJ, et al. Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis. Nature 2011, 475:106-109.
90. Shibata T, Ohta T, Tong KI, et al. Cancer related mutations in NRF2 impair its recognition by Keap1-Cul3 E3 ligase and promote malignancy. Proc Natl Acad Sci USA 2008, 105:13568-13573.
91. Singh A, Misra V, Thimmulappa RK, et al. Dysfunctional KEAP1-NRF2 interaction in non-small-cell lung cancer. PLoS Med 2006, 3:e420.
92. Hur W, Sun Z, Jiang T, et al. A small-molecule inducer of the antioxidant response element. Chem Biol 2010, 17:537-547.
93. Wang XJ, Sun Z, Villeneuve NF, et al. Nrf2 enhances resistance of cancer cells to chemotherapeutic drugs, the dark side of Nrf2. Carcinogenesis 2008, 29:1235-1243.
94. Wang XJ, Hayes JD, Henderson CJ, Wolf CR Identification of retinoic acid as an inhibitor of transcription factor Nrf2 through activation of retinoic acid receptor alpha. Proc Natl Acad Sci USA 2007, 104:19589-19594.
95. Ren D, Villeneuve NF, Jiang T, et al. Brusatol enhances the efficacy of chemotherapy by inhibiting the Nrf2-mediated defense mechanism. Proc Natl Acad Sci USA 2011, 108:1433-1438.
96. Delmore JE, Issa GC, Lemieux ME, et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 2011, 146:904-917.
97. Shimamura T, Chen Z, Soucheray M, et al. Efficacy of BET bromodomain inhibition in Kras-mutant non-small cell lung cancer. Clin Cancer Res 2013, 19:6183-6192.
98. Hagemann IS, Devarakonda S, Lockwood CM, et al. Clinical next-generation sequencing in patients with non-small cell lung cancer. Cancer 2015, 121:631-639.