Network-based approach identified cell cycle genes as predictor of overall survival in lung adenocarcinoma patients

Lung Cancer

Volumn 80, Issue 1, 2013, Pages 91-98

  Li, Yafei ^a,b   Tang, Hui ^e   Sun, Zhifu ^b   Bungum, Aaron O ^b   Edell, Eric S ^b   Lingle, Wilma L ^b   Stoddard, Shawn M ^b   Zhang, Mingrui ^c   Jen, Jin ^b   Yang, Ping ^b   Wang, Liang ^b,d  

^a THIRD MILITARY MEDICAL UNIVERSITY   (China)

^b MAYO CLINIC   (United States)

^c WINONA STATE UNIVERSITY   (United States)

^d MEDICAL COLLEGE OF WISCONSIN   (United States)

^e ABBVIE INC   (United States)

Author keywords

Cell cycle; Gene expression profiling; Lung cancer; Survival; Systems biology

Indexed keywords

ADULT; AGED; ARTICLE; CANCER GENETICS; CELL CYCLE; DEATH; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HIGH RISK PATIENT; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; MALE; MELK GENE; OVERALL SURVIVAL; PRIORITY JOURNAL; PROGNOSIS; RISK ASSESSMENT; SYSTEMS BIOLOGY; TPX2 GENE; TUMOR GENE; UBE2C GENE; VALIDATION STUDY;

ADENOCARCINOMA; AGED; AGED, 80 AND OVER; CELL CYCLE PROTEINS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; LUNG NEOPLASMS; MALE; MICROTUBULE-ASSOCIATED PROTEINS; MIDDLE AGED; MODELS, GENETIC; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PREDICTIVE VALUE OF TESTS; PROGNOSIS; PROTEIN-SERINE-THREONINE KINASES; SURVIVAL ANALYSIS; TIME FACTORS; UBIQUITIN-CONJUGATING ENZYMES;

EID: 84875252574     PISSN: 01695002     EISSN: 18728332     Source Type: Journal    
DOI: 10.1016/j.lungcan.2012.12.022     Document Type: Article

References (25)

1. Borczuk A.C., Toonkel R.L., Powell C.A. Genomics of lung cancer. Proc Am Thorac Soc 2009, 6:152-158.
2. Garber M.E., Troyanskaya O.G., Schluens K., Petersen S., Thaesler Z., Pacyna-Gengelbach M., et al. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A 2001, 98:13784-13789.
3. Bhattacharjee A., Richards W.G., Staunton J., Li C., Monti S., Vasa P., et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A 2001, 98:13790-13795.
4. Beer D.G., Kardia S.L., Huang C.C., Giordano T.J., Levin A.M., Misek D.E., et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002, 8:816-824.
5. Shedden K., Taylor J.M., Enkemann S.A., Tsao M.S., Yeatman T.J., Gerald W.L., et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008, 14:822-827.
6. Horvath S., Zhang B., Carlson M., Lu K.V., Zhu S., Felciano R.M., et al. Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A 2006, 103:17402-17407.
7. Zhang B., Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005, 4. Article17.
8. Fuller T.F., Ghazalpour A., Aten J.E., Drake T.A., Lusis A.J., Horvath S. Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm Genome 2007, 18:463-472.
9. Ghazalpour A., Doss S., Zhang B., Wang S., Plaisier C., Castellanos R., et al. Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet 2006, 2:e130.
10. Miller J.A., Oldham M.C., Geschwind D.H. A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci 2008, 28:1410-1420.
11. Yang X., Deignan J.L., Qi H., Zhu J., Qian S., Zhong J., et al. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet 2009, 41:415-423.
12. Yang P., Bamlet W.R., Sun Z., Ebbert J.O., Aubry M.C., Krowka M.J., et al. Alpha1-antitrypsin and neutrophil elastase imbalance and lung cancer risk. Chest 2005, 128:445-452.
13. Yang P., Sun Z., Krowka M.J., Aubry M.C., Bamlet W.R., Wampfler J.A., et al. Alpha1-antitrypsin deficiency carriers, tobacco smoke, chronic obstructive pulmonary disease, and lung cancer risk. Arch Intern Med 2008, 168:1097-1103.
14. Yang P., Wentzlaff K.A., Katzmann J.A., Marks R.S., Allen M.S., Lesnick T.G., et al. Alpha1-antitrypsin deficiency allele carriers among lung cancer patients. Cancer Epidemiol Biomarkers Prev 1999, 8:461-465.
15. Ballman K.V., Grill D.E., Oberg A.L., Therneau T.M. Faster cyclic loess: normalizing RNA arrays via linear models. Bioinformatics 2004, 20:2778-2786.
16. Langfelder P., Zhang B., Horvath S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 2008, 24:719-720.
17. Nikolsky Y., Ekins S., Nikolskaya T., Bugrim A. A novel method for generation of signature networks as biomarkers from complex high throughput data. Toxicol Lett 2005, 158:20-29.
18. Kadara H., Lacroix L., Behrens C., Solis L., Gu X., Lee J.J., et al. Identification of gene signatures and molecular markers for human lung cancer prognosis using an in vitro lung carcinogenesis system. Cancer Prev Res (Phila) 2008, 2:702-711.
19. Marie S.K., Okamoto O.K., Uno M., Hasegawa A.P., Oba-Shinjo S.M., Cohen T., et al. Maternal embryonic leucine zipper kinase transcript abundance correlates with malignancy grade in human astrocytomas. Int J Cancer 2008, 122:807-815.
20. Nakano I., Masterman-Smith M., Saigusa K., Paucar A.A., Horvath S., Shoemaker L., et al. Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells. J Neurosci Res 2008, 86:48-60.
21. Pickard M.R., Green A.R., Ellis I.O., Caldas C., Hedge V.L., Mourtada-Maarabouni M., et al. Dysregulated expression of Fau and MELK is associated with poor prognosis in breast cancer. Breast Cancer Res 2009, 11:R60.
22. Landi M.T., Dracheva T., Rotunno M., Figueroa J.D., 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.
23. Miura K., Bowman E.D., Simon R., Peng A.C., Robles A.I., Jones R.T., et al. Laser capture microdissection and microarray expression analysis of lung adenocarcinoma reveals tobacco smoking- and prognosis-related molecular profiles. Cancer Res 2002, 62:3244-3250.
24. Powell C.A., 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, 29:157-162.
25. Subramanian J., Govindan R. Lung cancer in never smokers: a review. J Clin Oncol 2007, 25:561-570.