Genomic and transcriptional alterations in lung adenocarcinoma in relation to smoking history

Clinical Cancer Research

Volumn 20, Issue 18, 2014, Pages 4912-4924

  Karlsson, Anna ^a,b   Ringnér, Markus ^a,b   Lauss, Martin ^a   Botling, Johan ^c   Micke, Patrick ^c   Planck, Maria ^a,b   Staaf, Johan ^a,b  

^a LUND UNIVERSITY   (Sweden)

^b LUND UNIVERSITY   (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ADENOCARCINOMA; ADVERSE EFFECTS; DNA MICROARRAY; FEMALE; GENE DOSAGE; GENETIC TRANSCRIPTION; GENETICS; GENOMICS; HUMAN; LUNG NEOPLASMS; MALE; SMOKING;

ADENOCARCINOMA; FEMALE; GENE DOSAGE; GENOMICS; HUMANS; LUNG NEOPLASMS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SMOKING; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84907445431     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-14-0246     Document Type: Article

References (50)

1. Jemal A, Bray F, CenterMM,Ferlay J, Ward E, FormanD. Global cancer statistics. CA Cancer J Clin 2011;61:69-90.
2. Alavanja MC. Biologic damage resulting from exposure to tobacco smoke and from radon: implication for preventive interventions. Oncogene 2002;21:7365-75.
3. Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012;150:1121-34.
4. Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012;150:1107-20.
5. Sun S, Schiller JH, Gazdar AF. Lung cancer in never smokers-A different disease. Nat Rev Cancer 2007;7:778-90.
6. Suda K, Tomizawa K, Yatabe Y, Mitsudomi T. Lung cancers unrelated to smoking: characterized by single oncogene addiction? Int J Clin Oncol 2011;16:294-305.
7. Dogan S, Shen R, Ang DC, Johnson ML, D'Angelo SP, Paik PK, et al. Molecular epidemiology of EGFR and KRAS mutations in 3,026 lung adenocarcinomas: higher susceptibility of women to smoking-related KRAS-mutant cancers. Clin Cancer Res 2012;18:6169-77.
8. Sun Y, Ren Y, Fang Z, Li C, Fang R, Gao B, et al. Lung adenocarcinoma from East Asian never-smokers is a disease largely defined by targetable oncogenic mutant kinases. J Clin Oncol 2010;28:4616-20.
9. Job B, Bernheim A, Beau-Faller M, Camilleri-Broet S, Girard P, Hofman P, et al. Genomic aberrations in lung adenocarcinoma in never smokers. PLoS ONE 2010;5:e15145.
10. Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007;450:893-8.
11. Broet P, Dalmasso C, Tan EH, Alifano M, Zhang S,WuJ, et al. Genomic profiles specific to patient ethnicity in lung adenocarcinoma. Clin Cancer Res 2011;17:3542-50.
12. Thu KL, Vucic EA, Chari R, Zhang W, Lockwood WW, English JC, et al. Lung adenocarcinoma of never smokers and smokers harbor differential regions of genetic alteration and exhibit different levels of genomic instability. PLoS ONE 2012;7:e33003.
13. Fouret R, Laffaire J, Hofman P, Beau-Faller M, Mazieres J, Validire P, et al. A comparative and integrative approach identifies ATPase family, AAA domain containing 2 as a likely driver of cell proliferation in lung adenocarcinoma. Clin Cancer Res 2012;18:5606-16.
14. Huang YT, Lin X, Liu Y, Chirieac LR, McGovern R, Wain J, et al. Cigarette smoking increases copy number alterations in nonsmall-cell lung cancer. Proc Natl Acad Sci U S A 2011;108:16345-50.
15. Massion PP, Zou Y, Chen H, Jiang A, Coulson P, Amos CI, et al. Smoking-related genomic signatures in non-small cell lung cancer.Am J Respir Crit Care Med 2008;178:1164-72.
16. Spira A, Beane J, Shah V, Liu G, Schembri F, Yang X, et al. Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A 2004;101:10143-8.
17. Staaf J, Jonsson G, Jonsson M, Karlsson A, Isaksson S, Salomonsson A, et al. Relation between smoking history and gene expression profiles in lung adenocarcinomas. BMC Med Genomics 2012;5:22.
18. Landi MT, Dracheva T, Rotunno M, Figueroa JD, Liu H, Dasgupta A, et al. Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS ONE 2008;3: e1651.
19. Woodruff PG, Koth LL, Yang YH, RodriguezMW,Favoreto S, Dolganov GM, et al. A distinctive alveolar macrophage activation state induced by cigarette smoking. Am J Respir Crit Care Med 2005;172:1383-92.
20. Bosse Y, Postma DS, Sin DD, Lamontagne M, Couture C, Gaudreault N, et al. Molecular signature of smoking in human lung tissues. Cancer Res 2012;72:3753-63.
21. Boelens MC, van den Berg A, Fehrmann RS, Geerlings M, de JongWK, te Meerman GJ, et al. Current smoking-specific gene expression signature in normal bronchial epithelium is enhanced in squamous cell lung cancer. J Pathol 2009;218:182-91.
22. Powell CA, Spira A, Derti A, DeLisi C, Liu G, Borczuk A, et al. Gene expression in lung adenocarcinomas of smokers and nonsmokers.Am J Respir Cell Mol Biol 2003;29:157-62.
23. Miura K, Bowman ED, Simon R, Peng AC, Robles AI, Jones RT, et al. Laser capture microdissection and microarray expression analysis of lung adenocarcinoma reveals tobacco smoking-and prognosis-related molecular profiles. Cancer Res 2002;62:3244-50.
24. Hayes DN, Monti S, Parmigiani G, Gilks CB, Naoki K, Bhattacharjee A, et al. Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol 2006;24:5079-90.
25. Takeuchi T, Tomida S, Yatabe Y, Kosaka T, Osada H, Yanagisawa K, et al. Expression profile-defined classification of lung adenocarcinoma shows close relationship with underlying major genetic changes and clinicopathologic behaviors. J Clin Oncol 2006;24:1679-88.
26. Wilkerson MD, Yin X, Walter V, Zhao N, Cabanski CR, Hayward MC, et al. Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation. PLoS ONE 2012;7:e36530.
27. Okayama H, Kohno T, Ishii Y, Shimada Y, Shiraishi K, Iwakawa R, et al. Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res 2012;72: 100-11.
28. Shibata T, Hanada S, Kokubu A, Matsuno Y, Asamura H, Ohta T, et al. Gene expression profiling of epidermal growth factor receptor/KRAS pathway activation in lung adenocarcinoma. Cancer Sci 2007;98: 985-91.
29. Planck M, Edlund K, Botling J, Micke P, Isaksson S, Staaf J. Genomic and transcriptional alterations in lung adenocarcinoma in relation to EGFR and KRAS mutation status. PLoS ONE 2013;8:e78614.
30. Staaf J, Isaksson S, Karlsson A, Jonsson M, Johansson L, Jonsson P, et al. Landscape of somatic allelic imbalances and copy number alterations in human lung carcinoma. Int J Cancer 2012;1:2020-31.
31. Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008; 14:822-7.
32. Chitale D, Gong Y, Taylor BS, Broderick S, Brennan C, Somwar R, et al. An integrated genomic analysis of lung cancer reveals loss ofDUSP4 in EGFR-mutant tumors. Oncogene 2009;28:2773-83.
33. Der SD, Sykes J, Pintilie M, Zhu CQ, Strumpf D, Liu N, et al. Validation of a histology-independent prognostic gene signature for early-stage, non-small-cell lung cancer including stage IA patients. J Thorac Oncol 2014;9:59-64.
34. Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, et al. Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. Bioinformatics 2013;29:2892-9.
35. Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics 2010;26:1572-3.
36. Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 2006;38:1043-8.
37. Cheung WK, Zhao M, Liu Z, Stevens LE, Cao PD, Fang JE, et al. Control of alveolar differentiation by the lineage transcription factors GATA6 and HOPX inhibits lung adenocarcinoma metastasis. Cancer Cell 2013;23:725-38.
38. Lauss M, Visne I, Kriegner A, Ringner M, Jonsson G, Hoglund M. Monitoring of technical variation in quantitative high-throughput datasets. Cancer Inform 2013;12:193-201.
39. Woenckhaus M, Klein-Hitpass L, Grepmeier U, Merk J, Pfeifer M, Wild P, et al. Smoking and cancer-related gene expression in bronchial epithelium and non-small-cell lung cancers. J Pathol 2006;210: 192-204.
40. Yatabe Y. EGFR mutations and the terminal respiratory unit. Cancer Metastasis Rev 2010;29:23-36.
41. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature 2013;500:415-21.
42. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013;499:214-8.
43. An SJ, Chen ZH, Su J, Zhang XC, Zhong WZ, Yang JJ, et al. Identification of enriched driver gene alterations in subgroups of non-small cell lung cancer patients based on histology and smoking status. PLoS ONE 2012;7:e40109.
44. Shibata T, Uryu S, Kokubu A, Hosoda F, Ohki M, Sakiyama T, et al. Genetic classification of lung adenocarcinoma based on array-based comparative genomic hybridization analysis: its association with clinicopathologic features. Clin Cancer Res 2005;11:6177-85.
45. Fong Y, Lin YS, Liou CP, Li CF, Tzeng CC. Chromosomal imbalances in lung adenocarcinomas with or without mutations in the epidermal growth factor receptor gene. Respirology 2010;15:700-5.
46. Beane J, Sebastiani P, Liu G, Brody JS, Lenburg ME, Spira A. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol 2007;8:R201.
47. Subramanian J, Govindan R. Lung cancer in never smokers: a review. J Clin Oncol 2007;25:561-70.
48. Kadara H, Kabbout M, Wistuba II. Pulmonary adenocarcinoma: a renewed entity in 2011. Respirology 2011;17:50-65.
49. Planck M, Isaksson S, Veerla S, Staaf J. Identification of transcriptional subgroups in EGFR-mutated and EGFR/KRAS-wild type lung adenocarcinoma reveals gene signatures associated with patient outcome. Clin Cancer Res 2013;19:5116-26.
50. Tang H, Xiao G, Behrens C, Schiller J, Allen J, Chow CW, et al. A 12-gene set predicts survival benefits from adjuvant chemotherapy in non-small-cell lung cancer patients. Clin Cancer Res 2013;19: 1577-86.