Integrated analyses of copy number variations and gene expression in lung adenocarcinoma

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Lu, Tzu Pin ^a   Lai, Liang Chuan ^a   Tsai, Mong Hsun ^a   Chen, Pei Chun ^b   Hsu, Chung Ping ^c   Lee, Jang Ming ^d   Hsiao, Chuhsing Kate ^a   Chuang, Eric Y ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b PROVIDENCE UNIVERSITY   (Taiwan)

^c TAICHUNG VETERANS GENERAL HOSPITAL   (Taiwan)

^d NATIONAL TAIWAN UNIVERSITY HOSPITAL   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN KINASE B;

ADULT; ARTICLE; CANCER SURVIVAL; CONTROLLED STUDY; COPY NUMBER VARIATION; CYTOSKELETON; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; LUNG CARCINOGENESIS; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PREDICTION; PROGNOSIS; REPRODUCIBILITY; SURVIVAL TIME; ADENOCARCINOMA; AGED; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; LUNG TUMOR; MIDDLE AGED;

ADENOCARCINOMA; AGED; DNA COPY NUMBER VARIATIONS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 80052836856     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024829     Document Type: Article

References (53)

1. Chen CJ, Wu HY, Chuang YC, Chang AS, Luh KT, et al. (1990) Epidemiologic characteristics and multiple risk factors of lung cancer in Taiwan. Anticancer Res 10: 971-976.
2. Jemal A, Siegel R, Ward E, Murray T, Xu J, et al. (2007) Cancer statistics, 2007. CA Cancer J Clin 57: 43-66.
3. Lau SK, Boutros PC, Pintilie M, Blackhall FH, Zhu CQ, et al. (2007) Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol 25: 5562-5569.
4. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, et al. (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 99: 12963-12968.
5. Hirsch FR, Varella-Garcia M, Cappuzzo F, (2009) Predictive value of EGFR and HER2 overexpression in advanced non-small-cell lung cancer. Oncogene 28 (Suppl 1): S32-37.
6. Chitale D, Gong Y, Taylor BS, Broderick S, Brennan C, et al. (2009) An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene 28: 2773-2783.
7. Kawano O, Sasaki H, Okuda K, Yukiue H, Yokoyama T, et al. (2007) PIK3CA gene amplification in Japanese non-small cell lung cancer. Lung Cancer 58: 159-160.
8. Go H, Jeon YK, Park HJ, Sung SW, Seo JW, et al. (2010) High MET gene copy number leads to shorter survival in patients with non-small cell lung cancer. J Thorac Oncol 5: 305-313.
9. Li AR, Chitale D, Riely GJ, Pao W, Miller VA, et al. (2008) EGFR mutations in lung adenocarcinomas: clinical testing experience and relationship to EGFR gene copy number and immunohistochemical expression. J Mol Diagn 10: 242-248.
10. Holland AJ, Cleveland DW, (2009) Boveri revisited: chromosomal instability, aneuploidy and tumorigenesis. Nat Rev Mol Cell Biol 10: 478-487.
11. Balsara BR, Testa JR, (2002) Chromosomal imbalances in human lung cancer. Oncogene 21: 6877-6883.
12. Dai Z, Zhu WG, Morrison CD, Brena RM, Smiraglia DJ, et al. (2003) A comprehensive search for DNA amplification in lung cancer identifies inhibitors of apoptosis cIAP1 and cIAP2 as candidate oncogenes. Hum Mol Genet 12: 791-801.
13. Berger AH, Niki M, Morotti A, Taylor BS, Socci ND, et al. (2010) Identification of DOK genes as lung tumor suppressors. Nat Genet 42: 216-223.
14. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
15. Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, et al. (2010) Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 26: i237-245.
16. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, et al. (2005) Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A 102: 13544-13549.
17. Weir BA, Woo MS, Getz G, Perner S, Ding L, et al. (2007) Characterizing the cancer genome in lung adenocarcinoma. Nature 450: 893-898.
18. Kwei KA, Kim YH, Girard L, Kao J, Pacyna-Gengelbach M, et al. (2008) Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer. Oncogene 27: 3635-3640.
19. Esandi MC, van Someren GD, Bout A, Mulder AH, van Bekkum DW, et al. (1998) IL-1/IL-3 gene therapy of non-small cell lung cancer (NSCLC) in rats using 'cracked' adenoproducer cells. Gene Ther 5: 778-788.
20. Kato T, Daigo Y, Hayama S, Ishikawa N, Yamabuki T, et al. (2005) A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis. Cancer Res 65: 5638-5646.
21. Schmitt E, Naveau M, Mechulam Y, (2010) Eukaryotic and archaeal translation initiation factor 2: a heterotrimeric tRNA carrier. FEBS Lett 584: 405-412.
22. Papadimitrakopoulou V, Adjei AA, (2006) The Akt/mTOR and mitogen-activated protein kinase pathways in lung cancer therapy. J Thorac Oncol 1: 749-751.
23. Takeuchi K, Ito F, (2010) EGF receptor in relation to tumor development: molecular basis of responsiveness of cancer cells to EGFR-targeting tyrosine kinase inhibitors. FEBS J 277: 316-326.
24. Bild AH, Yao G, Chang JT, Wang Q, Potti A, et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439: 353-357.
25. Lee ES, Son DS, Kim SH, Lee J, Jo J, et al. (2008) Prediction of recurrence-free survival in postoperative non-small cell lung cancer patients by using an integrated model of clinical information and gene expression. Clin Cancer Res 14: 7397-7404.
26. Kuner R, Muley T, Meister M, Ruschhaupt M, Buness A, et al. (2009) Global gene expression analysis reveals specific patterns of cell junctions in non-small cell lung cancer subtypes. Lung Cancer 63: 32-38.
27. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
28. Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
29. Boelens MC, Gustafson AM, Postma DS, Kok K, van der Vries G, et al. (2010) A chronic obstructive pulmonary disease related signature in squamous cell lung cancer. Lung Cancer.
30. Boelens MC, Kok K, van der Vlies P, van der Vries G, Sietsma H, et al. (2009) Genomic aberrations in squamous cell lung carcinoma related to lymph node or distant metastasis. Lung Cancer 66: 372-378.
31. Miura I, Graziano SL, Cheng JQ, Doyle LA, Testa JR, (1992) Chromosome alterations in human small cell lung cancer: frequent involvement of 5q. Cancer Res 52: 1322-1328.
32. Hartel PH, Shackelford AL, Hartel JV, Wenger SL, (2008) Del(5q) is associated with clinical and histological parameters in small cell neuroendocrine lung carcinoma. Int J Surg Pathol 16: 419-423.
33. Yen CC, Liang SC, Jong YJ, Chen YJ, Lin CH, et al. (2007) Chromosomal aberrations of malignant pleural effusions of lung adenocarcinoma: different cytogenetic changes are correlated with genders and smoking habits. Lung Cancer 57: 292-301.
34. Shen H, Gao W, Wu YJ, Qiu HR, Shu YQ, (2009) Multicolor fluorescence in situ hybridization and comparative genomic hybridization reveal molecular events in lung adenocarcinomas and squamous cell lung carcinomas. Biomed Pharmacother 63: 396-403.
35. Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, et al. (2002) Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 62: 6240-6245.
36. Kikuchi N, Ishii Y, Morishima Y, Yageta Y, Haraguchi N, et al. (2010) Nrf2 protects against pulmonary fibrosis by regulating the lung oxidant level and Th1/Th2 balance. Respir Res 11: 31.
37. Zou W, Yang Y, Wu Y, Sun L, Chi Y, et al. (2010) Negative role of trihydrophobin 1 in breast cancer growth and migration. Cancer Sci 101: 2156-2162.
38. Cheng C, Kong X, Wang H, Gan H, Hao Y, et al. (2009) Trihydrophobin 1 Interacts with PAK1 and Regulates ERK/MAPK Activation and Cell Migration. J Biol Chem 284: 8786-8796.
39. Kotliarov Y, Kotliarova S, Charong N, Li A, Walling J, et al. (2009) Correlation analysis between single-nucleotide polymorphism and expression arrays in gliomas identifies potentially relevant target genes. Cancer Res 69: 1596-1603.
40. Woenckhaus M, Klein-Hitpass L, Grepmeier U, Merk J, Pfeifer M, et al. (2006) Smoking and cancer-related gene expression in bronchial epithelium and non-small-cell lung cancers. J Pathol 210: 192-204.
41. Lu TP, Tsai MH, Lee JM, Hsu CP, Chen PC, et al. (2010) Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Cancer Epidemiol Biomarkers Prev 19: 2590-2597.
42. Gazdar AF, Minna JD, (2008) Deregulated EGFR signaling during lung cancer progression: mutations, amplicons, and autocrine loops. Cancer Prev Res (Phila) 1: 156-160.
43. Dahabreh IJ, Linardou H, Siannis F, Kosmidis P, Bafaloukos D, et al. (2010) Somatic EGFR mutation and gene copy gain as predictive biomarkers for response to tyrosine kinase inhibitors in non-small cell lung cancer. Clin Cancer Res 16: 291-303.
44. Hutti JE, Shen RR, Abbott DW, Zhou AY, Sprott KM, et al. (2009) Phosphorylation of the tumor suppressor CYLD by the breast cancer oncogene IKKepsilon promotes cell transformation. Mol Cell 34: 461-472.
45. Su LJ, Chang CW, Wu YC, Chen KC, Lin CJ, et al. (2007) Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics 8: 140.
46. Xi L, Feber A, Gupta V, Wu M, Bergemann AD, et al. (2008) Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer. Nucleic Acids Res 36: 6535-6547.
47. Landi MT, Dracheva T, Rotunno M, Figueroa JD, Liu H, et al. (2008) Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS One 3: e1651.
48. Meloche S, Pouyssegur J, (2007) The ERK1/2 mitogen-activated protein kinase pathway as a master regulator of the G1- to S-phase transition. Oncogene 26: 3227-3239.
49. Caccavari F, Valdembri D, Sandri C, Bussolino F, Serini G, (2010) Integrin signaling and lung cancer. Cell Adh Migr 4: 124-129.
50. Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, et al. (2008) Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A 105: 16224-16229.
51. Raponi M, Zhang Y, Yu J, Chen G, Lee G, et al. (2006) Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res 66: 7466-7472.
52. Sturn A, Quackenbush J, Trajanoski Z, (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18: 207-208.
53. Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.