A smoking-associated 7-gene signature for lung cancer diagnosis and prognosis

International Journal of Oncology

Volumn 41, Issue 4, 2012, Pages 1387-1396

  Wan, Ying Wooi ^a   Raese, Rebecca A ^a   Fortney, James E ^a   Xiao, Changchang ^a   Luo, Dajie ^a   Cavendish, John ^a   Gibson, Laura F ^a   Castranova, Vincent ^a,b   Qian, Yong ^a,b   Guo, Nancy Lan ^a  

^a WEST VIRGINIA UNIVERSITY   (United States)

^b NATIONAL INSTITUTE FOR OCCUPATIONAL SAFETY AND HEALTH   (United States)

Author keywords

Coexpression networks; Gene signature; Lung cancer diagnosis and prognosis; Signaling pathway; Smoking

Indexed keywords

4 (METHYLNITROSAMINO) 1 (3 PYRIDYL) 1 BUTANONE; BIOLOGICAL MARKER; PROTEIN P53;

ABC TRANSPORTER A4 GENE; AGED; ARTICLE; ATP BINDING CASSETTE A3 GENE; CANCER DIAGNOSIS; CANCER GROWTH; CANCER PROGNOSIS; CANCER SURVIVAL; CARCINOGENESIS; CARTILAGE ACIDIC PROTEIN 1 GENE; CONTROLLED STUDY; CYTOCHROME P450 3A4 GENE; DATA BASE; EPITHELIUM CELL; FEMALE; G PROTEIN COUPLED RECEPTOR C5C GENE; GENE; GENE EXPRESSION; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; LACTOTRANSFERRIN GENE; LUNG ADENOCARCINOMA; LUNG ALVEOLUS EPITHELIUM; LUNG CANCER; MAJOR CLINICAL STUDY; MALE; PHOSPHATIDYLINOSITOL GLYCAN ANCHOR BIOSYNTHESIS N GENE; PRIORITY JOURNAL; PROTEIN EXPRESSION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEMA3C GENE; SMOKING; WESTERN BLOTTING;

AGED; CELL TRANSFORMATION, NEOPLASTIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; NEOPLASM STAGING; NITROSAMINES; PROGNOSIS; RECEPTOR, EPIDERMAL GROWTH FACTOR; RETINOBLASTOMA PROTEIN; SIGNAL TRANSDUCTION; SMOKING; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84866501738     PISSN: 10196439     EISSN: 17912423     Source Type: Journal    
DOI: 10.3892/ijo.2012.1556     Document Type: Article

References (38)

1. Christiani DC: Genetic susceptibility to lung cancer. J Clin Oncol 24: 1651-1652, 2006.
2. Spira A, Beane JE, Shah V, et al: Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med 13: 361-366, 2007.
3. Massion PP, Zou Y, Chen H, et al: Smoking-related genomic signatures in non-small cell lung cancer. Am J Respir Crit Care Med 178: 1164-1172, 2008.
4. Woenckhaus M, Klein-Hitpass L, Grepmeier U, et al: Smoking and cancer-related gene expression in bronchial epithelium and non-small-cell lung cancers. J Pathol 210: 192-204, 2006.
5. Guo NL, Tosun K and Horn K: Impact and interactions between smoking and traditional prognostic factors in lung cancer progression. Lung Cancer 66: 386-392, 2009.
6. Beer DG, Kardia SL, Huang CC, et al: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8: 816-824, 2002.
7. General Thoracic Surgery. Lippincott Williams & Wilkins, Philadelphia, PA, 2009.
8. Hung RJ, McKay JD, Gaborieau V, et al: A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature 452: 633-637, 2008.
9. Mani KM, Lefebvre C, Wang K, et al: A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 4: 169, 2008.
10. Cui Q, Ma Y, Jaramillo M, et al: A map of human cancer signaling. Mol Syst Biol 3: 152, 2007.
11. Guo NL, Wan YW, Bose S, et al: A novel network model identified a 13-gene lung cancer prognostic signature. Int J Comput Biol Drug Des 4: 19-39, 2011.
12. Wan YW, Beer DG and Guo NL: Signaling pathway-based identification of extensive prognostic gene signatures for lung adenocarcinoma. Lung Cancer 76: 98-105, 2012.
13. Schuller HM: Mechanisms of smoking-related lung and pancreatic adenocarcinoma development. Nat Rev Cancer 2: 455-463, 2002.
14. Hecht SS: Tobacco smoke carcinogens and lung cancer. J Natl Cancer Inst 91: 1194-1210, 1999.
15. Shedden K, Taylor JM, Enkemann SA, et al: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 14: 822-827, 2008.
16. Raponi M, Zhang Y, Yu J, et al: Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res 66: 7466-7472, 2006.
17. Bild AH, Yao G, Chang JT, et al: Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439: 353-357, 2006.
18. Li C: Automating dChip: toward reproducible sharing of micro-array data analysis. BMC Bioinformatics 9: 231, 2008.
19. Hildebrand DK, Laing JD and Rosenthal H: Prediction Analysis of Cross Classifications. John Wiley & Sons, New York, NY, 1977.
20. Guo NL and Wan YW: Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artif Intell Med: Feb 10, 2012 (Epub ahead of print).
21. Maglott D, Ostell J, Pruitt KD and Tatusova T: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 35: D26-D31, 2007.
22. Ogata H, Goto S, Sato K, et al: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27: 29-34, 1999.
23. Jensen LJ, Kuhn M, Stark M, et al: STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37: D412-D416, 2009.
24. Subramanian A, Tamayo P, Mootha VK, et al: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550, 2005.
25. Ucar D, Neuhaus I, Ross-MacDonald P, et al: Construction of a reference gene association network from multiple profiling data: application to data analysis. Bioinformatics 23: 2716-2724, 2007.
26. Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25: 402-408, 2001.
27. Witten IH and Frank E: Data Mining: Practical Machine Learning Tools and Techniques. 2nd edition. Morgan Kaufmann, San Francisco, CA, 2005.
28. Lonardo F, Dragnev KH, Freemantle SJ, et al: Evidence for the epidermal growth factor receptor as a target for lung cancer prevention. Clin Cancer Res 8: 54-60, 2002.
29. Cloutier JF, Drouin R, Weinfeld M, O'Connor TR and Castonguay A: Characterization and mapping of DNA damage induced by reactive metabolites of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) at nucleotide resolution in human genomic DNA. J Mol Biol 313: 539-557, 2001.
30. Ho YS, Chen CH, Wang YJ, et al: Tobacco-specific carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) induces cell proliferation in normal human bronchial epithelial cells through NFkappaB activation and cyclin D1 up-regulation. Toxicol Appl Pharmacol 205: 133-148, 2005.
31. Sachs K, Perez O, Pe'er D, Lauffenburger DA and Nolan GP: Causal protein-signaling networks derived from multiparameter single-cell data. Science 308: 523-529, 2005.
32. Choi JK, Yu U, Yoo OJ and Kim S: Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355, 2005.
33. Travis WD, Travis LB and Devesa SS: Lung cancer. Cancer 75: 191-202, 1995.
34. Ernster VL: The epidemiology of lung cancer in women. Ann Epidemiol 4: 102-110, 1994.
35. Levi F, Franceschi S, La Vecchia C, Randimbison L and Te VC: Lung carcinoma trends by histologic type in Vaud and Neuchatel, Switzerland, 1974-1994. Cancer 79: 906-914, 1997.
36. Thun MJ, Lally CA, Flannery JT, et al: Cigarette smoking and changes in the histopathology of lung cancer. J Natl Cancer Inst 89: 1580-1586, 1997.
37. Hoffmann D, Rivenson A and Hecht SS: The biological significance of tobacco-specific N-nitrosamines: smoking and adenocarcinoma of the lung. Crit Rev Toxicol 26: 199-211, 1996.
38. Ren JH, He WS, Yan GL, et al: EGFR mutations in nonsmall-cell lung cancer among smokers and non-smokers: a meta-analysis. Environ Mol Mutagen 53: 78-82, 2012.