Intertumor heterogeneity of non-small-cell lung carcinomas revealed by multiplexed mutation profiling and integrative genomics

International Journal of Cancer

Volumn 135, Issue 5, 2014, Pages 1092-1100

  Tan, Daniel S W ^a,b   Camilleri Broët, Sophie ^c,d   Tan, Eng Huat ^a   Alifano, Marco ^c,e   Lim, Wan Teck ^a   Bobbio, Antonio ^c,e   Zhang, Shenli ^f   Ng, Quan Sing ^a   Ang, Mei Kim ^a   Iyer, N Gopalakrishna ^a   Takano, Angela ^g   Lim, Kiat Hon ^h   Régnard, Jean François ^c,e   Tan, Patrick ^f,h   Broët, Philippe ^i,j,k  

^a DIVISION OF MEDICAL ONCOLOGY   (Singapore)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

^c UNIVERSITÉ PARIS DESCARTES   (France)

^d HÔPITAL EUROPÉEN GEORGES POMPIDOU   (France)

^e université Paris Cité   (France)

^f DUKE NUS MEDICAL SCHOOL   (Singapore)

^g SINGAPORE GENERAL HOSPITAL   (Singapore)

^h NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

ⁱ UNIVERSITÉ PARIS SACLAY   (France)

^j HÔPITAL PAUL BROUSSE   (France)

^k INSERM   (France)

more..

Author keywords

integrative genomics; multiplex mutation profiling; non small cell lung cancer; stratified medicine; tumor heterogeneity

Indexed keywords

ANAPLASTIC LYMPHOMA KINASE; B RAF KINASE; EPHRIN RECEPTOR A3; EPHRIN RECEPTOR A5; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; FIBROBLAST GROWTH FACTOR RECEPTOR 4; JANUS KINASE 2; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; NOTCH1 RECEPTOR; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE 3 KINASE; PROTEIN KINASE LKB1; PROTEIN P53; PROTEIN PATCHED 1; PROTEIN TYROSINE PHOSPHATASE SHP 2; SCATTER FACTOR RECEPTOR; TRANSCRIPTION FACTOR NRF2; VASCULOTROPIN RECEPTOR;

ADULT; AGED; AKT1 GENE; ALK GENE; ARTICLE; BRAF GENE; CANCER PROGNOSIS; CHROMOSOME 3Q; CONTROLLED STUDY; COPY NUMBER VARIATION; DDR2 GENE; EGFR GENE; EPHA3 GENE; EPHA5 GENE; FEMALE; FGFR4 GENE; GENE AMPLIFICATION; GENE INTERACTION; GENE MUTATION; GENETIC VARIABILITY; HUMAN; JAK2 GENE; LARGE CELL CARCINOMA; LUNG ADENOCARCINOMA; LUNG NON SMALL CELL CANCER; MAJOR CLINICAL STUDY; MALE; MASS SPECTROMETRY; MET GENE; MULTIPLEXED MUTATION PROFILING; MUTATIONAL ANALYSIS; NOTCH1 GENE; NRF2 GENE; NTRK1 GENE; NTRK2 GENE; NTRK3 GENE; ONCOGENE; ONCOGENE K RAS; ONCOGENE N RAS; PHYLOGENY; PIK3CA GENE; PRIORITY JOURNAL; PTCH1 GENE; PTEN GENE; PTPN11 GENE; PTPRD GENE; STK11 GENE; TP53 GENE;

INTEGRATIVE GENOMICS; MULTIPLEX MUTATION PROFILING; NON-SMALL-CELL LUNG CANCER; STRATIFIED MEDICINE; TUMOR HETEROGENEITY;

ADULT; AGED; AGED, 80 AND OVER; CARCINOMA, NON-SMALL-CELL LUNG; DNA COPY NUMBER VARIATIONS; FEMALE; GENOMICS; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; MUTATION; PHOSPHATIDYLINOSITOL 3-KINASES; PROGNOSIS; PROTEIN-SERINE-THREONINE KINASES; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS C-MET; RAS PROTEINS; RECEPTOR, EPIDERMAL GROWTH FACTOR; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84902549992     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.28750     Document Type: Article

References (39)

1. Jemal A, Bray F, Center MM, et al. Global cancer statistics. CA Cancer J Clin 2011; 61: 69-90.
2. Weir BA, Woo MS, Getz G, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007; 450: 893-8.
3. Mok TS, Wu Y-L, Thongprasert S, et al. Gefitinib or carboplatin- paclitaxel in pulmonary adenocarcinoma. N Engl J Med 2009; 361: 947-57.
4. Imielinski M, Berger AH, Hammerman PS, et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012; 150: 1107-20.
5. Camidge DR, Bang Y-J, Kwak EL, et al. Activity and safety of crizotinib in patients with ALK-positive non-small-cell lung cancer: updated results from a phase 1 study. Lancet Oncol 2012; 13: 1011-19.
6. Ding L, Getz G, Wheeler DA, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008; 455: 1069-75.
7. Pao W, Hutchinson KE,. Chipping away at the lung cancer genome. Nat Med 2012; 18: 349-51.
8. Li T, Kung H-J, Mack PC, et al. Genotyping and genomic profiling of non-small-cell lung cancer: implications for current and future therapies. J Clin Oncol 2013; 31: 1039-49.
9. Pal SK, Figlin RA, Reckamp K,. Targeted therapies for non-small cell lung cancer: an evolving landscape. Mol Cancer Ther 2010; 9: 1931-44.
10. Lindeman NI, Cagle PT, Beasley MB, et al. Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology. Arch Pathol Lab Med 2013; 137: 828-60.
11. Cardarella S, Ortiz TM, Joshi VA, et al. The introduction of systematic genomic testing for patients with non-small-cell lung cancer. J Thorac Oncol 2012; 7: 1767-74.
12. Sequist LV, Heist RS, Shaw AT, et al. Implementing multiplexed genotyping of non-small-cell lung cancers into routine clinical practice. Ann Oncol 2011; 22: 2616-24.
13. Su Z, Dias-Santagata D, Duke M, et al. A platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer. J Mol Diagn 2011; 13: 74-84.
14. Heideman DAM, Lurkin I, Doeleman M, et al. KRAS and BRAF mutation analysis in routine molecular diagnostics: comparison of three testing methods on formalin-fixed, paraffin-embedded tumor-derived DNA. J Mol Diagn 2012; 14: 247-55.
15. Thomas RK, Baker AC, Debiasi RM, et al. High-throughput oncogene mutation profiling in human cancer. Nat Genet 2007; 39: 347-51.
16. Yip PY, Yu B, Cooper WA, et al. Patterns of DNA mutations and ALK rearrangement in resected node negative lung adenocarcinoma. J Thorac Oncol 2013; 8: 408-14.
17. Torti D, Trusolino L,. Oncogene addiction as a foundational rationale for targeted anti-cancer therapy: promises and perils. EMBO Mol Med 2011; 3: 623-36.
18. Tan DS-W, Gerlinger M, Teh B-T, et al. Anti-cancer drug resistance: understanding the mechanisms through the use of integrative genomics and functional RNA interference. Eur J Cancer 2010; 46: 2166-77.
19. Broët P, Dalmasso C, Tan EH, et al. Genomic profiles specific to patient ethnicity in lung adenocarcinoma. Clin Cancer Res 2011; 17: 3542-50.
20. Broët P, Camilleri-Broët S, Zhang S, et al. Prediction of clinical outcome in multiple lung cancer cohorts by integrative genomics: implications for chemotherapy selection. Cancer Res 2009; 69: 1055-62.
21. Fujita PA, Rhead B, Zweig AS, et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2011; 39: D876-82.
22. Yee TW,. The VGAM package for categorical data analysis. J Stat Softw 2010; 32: 1-34.
23. Benjamini Y, Yekutieli D,. The control of the false discovery rate in multiple testing under dependency. Ann Stat 2001; 29: 1165-88.
24. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012; 491: 56-65.
25. Krishnaswamy S, Kanteti R, Duke-Cohan JS, et al. Ethnic differences and functional analysis of MET mutations in lung cancer. Clin Cancer Res 2009; 15: 5714-23.
26. Sequist LV, Waltman BA, Dias-Santagata D, et al. Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. Sci Transl Med 2011; 3: 75ra26.
27. Ludovini V, Bianconi F, Pistola L, et al. Phosphoinositide-3-kinase catalytic alpha and KRAS mutations are important predictors of resistance to therapy with epidermal growth factor receptor tyrosine kinase inhibitors in patients with advanced non-small cell lung cancer. J Thorac Oncol 2011; 6: 707-15.
28. Yu HA, Arcila ME, Rekhtman N, et al. Analysis of tumor specimens at the time of acquired resistance to EGFR-TKI therapy in 155 patients with EGFR-mutant lung cancers. Clin Cancer Res 2013; 19: 2240-7.
29. Benjamini Y, Yekutieli D,. Quantitative trait Loci analysis using the false discovery rate. Genetics 2005; 171: 783-90.
30. Yuan S, Yu S-L, Chen H-Y, et al. Clustered genomic alterations in chromosome 7p dictate outcomes and targeted treatment responses of lung adenocarcinoma with EGFR-activating mutations. J Clin Oncol 2011; 29: 3435-42.
31. 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: 228-39.
32. Kris MG, Johnson BE, Kwiatkowski DJ, et al. Identification of driver mutations in tumor specimens from 1,000 patients with lung adenocarcinoma: the NCI's lung cancer mutation consortium (LCMC). J Clin Oncol 2011; 29 (Suppl): CRA7506.
33. Ludovini V, Bianconi F, Pistola L, et al. Optimization of patient selection for EGFR-TKIs in advanced non-small cell lung cancer by combined analysis of KRAS, PIK3CA, MET, and non-sensitizing EGFR mutations. Cancer Chemother Pharmacol 2012; 69: 1289-99.
34. Janku F, Tsimberidou AM, Garrido-Laguna I, et al. PIK3CA mutations in patients with advanced cancers treated with PI3K/AKT/mTOR axis inhibitors. Mol Cancer Ther 2011; 10: 558-65.
35. Bendell JC, Rodon J, Burris HA, et al. Phase I, dose-escalation study of BKM120, an oral pan-Class I PI3K inhibitor, in patients with advanced solid tumors. J Clin Oncol 2012; 30: 282-90.
36. Weigelt B, Downward J,. Genomic determinants of PI3K pathway inhibitor response in cancer. Front Oncol 2012; 2: 1-16.
37. Wee S, Wiederschain D, Maira S-M, et al. PTEN-deficient cancers depend on PIK3CB. Proc Natl Acad Sci USA 2008; 105: 13057-62.
38. Shepherd FA, Domerg C, Hainaut P, et al. Pooled analysis of the prognostic and predictive effects of KRAS mutation status and KRAS mutation subtype in early-stage resected non-small-cell lung cancer in four trials of adjuvant chemotherapy. J Clin Oncol 2013; 31: 2173-81.
39. Tan D, Thomas G, Garrett M, et al. Biomarker-driven early clinical trials in oncology: a paradigm shift in drug development. Cancer J 2009; 15: 406-20.