Clinical impact of high-throughput gene expression studies in lung cancer

Journal of Thoracic Oncology

Volumn 4, Issue 1, 2009, Pages 109-118

  Beane, Jennifer ^a,b,c   Spira, Avrum ^a,b   Lenburg, Marc E ^a,b  

^a Boston University   (United States)

^b BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c BOSTON MEDICAL CENTER   (United States)

Author keywords

Gene expression; Lung cancer; Microarrays

Indexed keywords

2 MORPHOLINO 8 PHENYLCHROMONE; 7 ETHYL 10 HYDROXYCAMPTOTHECIN; ANTINEOPLASTIC AGENT; CARBOPLATIN; CISPLATIN; DNA; DOCETAXEL; ETOPOSIDE; FLUOROURACIL; GEMCITABINE; K RAS PROTEIN; MICRORNA; NAVELBINE; PACLITAXEL; PEMETREXED; PROTEIN P53; RNA; TUMOR MARKER;

BRONCHOSCOPY; CANCER ADJUVANT THERAPY; CANCER CELL CULTURE; CANCER CHEMOTHERAPY; CANCER DIAGNOSIS; CANCER GENETICS; CANCER INVASION; CANCER MORTALITY; CANCER RELAPSE; CANCER RISK; CANCER SURVIVAL; CAUSE OF DEATH; CHEMOSENSITIVITY; CLINICAL TRIAL; DNA MICROARRAY; EARLY DIAGNOSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; LUNG ADENOCARCINOMA; LUNG ALVEOLUS CELL CARCINOMA; LUNG CANCER; LUNG NON SMALL CELL CANCER; LUNG SMALL CELL CANCER; LYMPH NODE METASTASIS; METASTASIS; MICROMETASTASIS; PHARMACOGENOMICS; PRIORITY JOURNAL; PROGNOSIS; REVIEW; RNA ANALYSIS; TREATMENT RESPONSE; GENETICS; LUNG TUMOR;

GENE EXPRESSION PROFILING; HUMANS; LUNG NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 61549143718     PISSN: 15560864     EISSN: 15561380     Source Type: Journal    
DOI: 10.1097/JTO.0b013e31819151f8     Document Type: Review

References (88)

1. Hirsch FR, Merrick DT, Franklin WA. Role of biomarkers for early detection of lung cancer and chemoprevention. Eur Respir J 2002;19: 1151-1158.
2. Jett JR. Limitations of screening for lung cancer with low-dose spiral computed tomography. Clin Cancer Res 2005;11:4988s-4992s.
3. MacRedmond R, McVey G, Lee M, et al. Screening for lung cancer using low dose CT scanning: results of 2 year follow up. Thorax 2006;61:54-56.
4. Paik S, Shak S, Tang G, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004; 351:2817-2826.
5. Van de Vijver, He YD, van't Veer LJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347: 1999-2009.
6. Ma XJ, Wang Z, Ryan PD, et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004;5:607-616.
7. Marchionni L, Wilson RF, Wolff AC, et al. Systematic Review: Gene Expression Profiling Assays in Early-Stage Breast Cancer. Ann Intern Med 2008;148:358-369.
8. Sweet-Cordero A, Mukherjee S, Subramanian A, et al. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 2005;37:48-55.
9. Borczuk AC, Gorenstein L, Walter KL, et al. Non-small-cell lung cancer molecular signatures recapitulate lung developmental pathways. Am J Pathol 2003;163:1949-1960.
10. Bild AH, Yao G, Chang JT, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006;439:353- 357.
11. Fan JB, Chee MS, Gunderson KL. Highly parallel genomic assays. Nat Rev Genet 2006;7:632-644.
12. Thomas RK, Weir B, Meyerson M. Genomic approaches to lung cancer. Clin Cancer Res 2006;12:4384s-4391s.
13. Granville CA, Dennis PA. An overview of lung cancer genomics and proteomics. Am J Respir Cell Mol Biol 2005;32:169-176.
14. Risch A, Plass C. Lung cancer epigenetics and genetics. Int J Cancer 2008;123:1-7.
15. Emmert-Buck MR, Bonner RF, Smith PD, et al. Laser capture micro-dissection. Science 1996;274:998-1001.
16. Schena M, Shalon D, Davis RW, et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995;270:467-470.
17. Lockhart DJ, Dong H, Byrne MC, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996;14:1675-1680.
18. Velculescu VE, Zhang L, Vogelstein B, et al. Serial analysis of gene expression. Science 1995;270:484-487.
19. Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-628.
20. Cloonan N, Forrest AR, Kolle G, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 2008;5:613-619.
21. Morin RD, O'Connor MD, Griffith M, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 2008;18:610-621.
22. Shields PG. Molecular epidemiology of lung cancer. Ann Oncol 1999;10 Suppl 5:S7-S11.
23. Jett JR, Midthun DE. Screening for lung cancer: current status and future directions: Thomas A. Neff lecture. Chest 2004;125:(5 Suppl) 158S-162S.
24. Bach PB, Jett JR, Pastorino U, et al. Computed tomography screening and lung cancer outcomes. JAMA 2007;297:953-961.
25. Spira A, Beane J, Shah V, et al. Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A 2004; 101:10143-10148.
26. Beane J, Sebastiani P, Liu G, et al. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol 2007;8:R201.
27. Lonergan KM, Chari R, Deleeuw RJ, et al. Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression. Am J Respir Cell Mol Biol 2006;35:651-661.
28. Chari R, Lonergan KM, Ng RT, et al. Effect of active smoking on the human bronchial epithelium transcriptome. BMC Genomics 2007;8:297.
29. Hackett NR, Heguy A, Harvey BG, et al. Variability of antioxidant-related gene expression in the airway epithelium of cigarette smokers. Am J Respir Cell Mol Biol 2003;29:331-343.
30. Carolan BJ, Heguy A, Harvey BG, et al. Up-regulation of expression of the ubiquitin carboxyl-terminal hydrolase L1 gene in human airway epithelium of cigarette smokers. Cancer Res 2006;66:10729-10740.
31. Harvey BG, Heguy A, Leopold PL, et al. Modification of gene expression of the small airway epithelium in response to cigarette smoking. J Mol Med 2007;85:39-53.
32. Lampe JW, Stepaniants SB, Mao M, et al. Signatures of environmental exposures using peripheral leukocyte gene expression: tobacco smoke. Cancer Epidemiol Biomarkers Prev 2004;13:445-453.
33. Van Leeuwen DM, van AE, Gottschalk RW, et al. Cigarette smoke-induced differential gene expression in blood cells from monozygotic twin pairs. Carcinogenesis 2007;28:691-697.
34. Spira A, Beane JE, Shah V, et al. Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med 2007;13:361-366.
35. Beane J, Sebastiani P, Whitfield TH, et al. A Prediction Model for Lung Cancer Diagnosis that Integrates Genomic and Clinical Features. Cancer Prevention Research 2008;1:65-76.
36. Lynch TJ, Bell DW, Sordella R, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 2004;350:2129-2139.
37. Garber ME, Troyanskaya OG, Schluens K, et al. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A 2001;98:13784-13789.
38. Bhattacharjee A, Richards WG, Staunton J, 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.
39. Hayes DN, Monti S, Parmigiani G, et al. Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol 2006;24:5079-5090.
40. Hibi K, Liu Q, Beaudry GA, et al. Serial analysis of gene expression in non-small cell lung cancer. Cancer Res 1998;58:5690-5694.
41. Nacht M, Dracheva T, Gao Y, et al. Molecular characteristics of non-small cell lung cancer. Proc Natl Acad Sci U S A 2001;98:15203-15208.
42. Yamagata N, Shyr Y, Yanagisawa K, et al. A training-testing approach to the molecular classification of resected non-small cell lung cancer. Clin Cancer Res 2003;9:4695-4704.
43. Kim B, Lee HJ, Choi HY, et al. Clinical validity of the lung cancer biomarkers identified by bioinformatics analysis of public expression data. Cancer Res 2007;67:7431-7438.
44. Sugita M, Geraci M, Gao B, et al. Combined use of oligonucleotide and tissue microarrays identifies cancer/testis antigens as biomarkers in lung carcinoma. Cancer Res 2002;62:3971-3979.
45. Talbot SG, Estilo C, Maghami E, et al. Gene expression profiling allows distinction between primary and metastatic squamous cell carcinomas in the lung. Cancer Res 2005;65:3063-3071.
46. Virtanen C, Ishikawa Y, Honjoh D, et al. Integrated classification of lung tumors and cell lines by expression profiling. Proc Natl Acad Sci U S A 2002;99:12357-12362.
47. Jones MH, Virtanen C, Honjoh D, et al. Two prognostically significant subtypes of high-grade lung neuroendocrine tumours independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles. Lancet 2004;363:775-781.
48. He P, Varticovski L, Bowman ED, et al. Identification of carboxypep-tidase E and gamma-glutamyl hydrolase as biomarkers for pulmonary neuroendocrine tumors by cDNA microarray. Hum Pathol 2004;35: 1196-1209.
49. Ramaswamy S, Ross KN, Lander ES, et al. A molecular signature of metastasis in primary solid tumors. Nat Genet 2003;33:49-54.
50. Kikuchi T, Daigo Y, Katagiri T, et al. Expression profiles of non-small cell lung cancers on cDNA microarrays: identification of genes for prediction of lymph-node metastasis and sensitivity to anti-cancer drugs. Oncogene 2003;22:2192-2205.
51. Inamura K, Shimoji T, Ninomiya H, et al. A metastatic signature in entire lung adenocarcinomas irrespective of morphological heterogeneity. Hum Pathol 2007;38:702-709.
52. Hoang CD, D'Cunha J, Tawfic SH, et al. Expression profiling of non-small cell lung carcinoma identifies metastatic genotypes based on lymph node tumor burden. J Thorac Cardiovasc Surg 2004;127:1332-1341.
53. Xi L, Lyons-Weiler J, Coello MC, et al. Prediction of lymph node metastasis by analysis of gene expression profiles in primary lung adenocarcinomas. Clin Cancer Res 2005;11:4128-4135.
54. Beer DG, Kardia SL, Huang CC, et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002;8:816-824.
55. Yanaihara N, Caplen N, Bowman E, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 2006;9: 189-198.
56. Hoffman PC, Mauer AM, Vokes EE. Lung cancer. Lancet 2000;355: 479-485.
57. Nesbitt JC, Putnam JB Jr, Walsh GL, et al. Survival in early-stage non-small cell lung cancer. Ann Thorac Surg 1995;60:466-472.
58. Booth CM, Shepherd FA. Adjuvant chemotherapy for resected non-small cell lung cancer. J Thorac Oncol 2006;1:180-187.
59. Miura K, Bowman ED, Simon R, 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.
60. Endoh H, Tomida S, Yatabe Y, et al. Prognostic model of pulmonary adenocarcinoma by expression profiling of eight genes as determined by quantitative real-time reverse transcriptase polymerase chain reaction. J Clin Oncol 2004;22:811-819.
61. Tomida S, Koshikawa K, Yatabe Y, et al. Gene expression-based, individualized outcome prediction for surgically treated lung cancer patients. Oncogene 2004;23:5360-5370.
62. charoenrat P, Rusch V, Talbot SG, et al. Casein kinase II alpha subunit and C1-inhibitor are independent predictors of outcome in patients with squamous cell carcinoma of the lung. Clin Cancer Res 2004;10:5792-5803.
63. Raponi M, Zhang Y, Yu J, et al. Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res 2006;66:7466-7472.
64. Seike M, Yanaihara N, Bowman ED, et al. Use of a cytokine gene expression signature in lung adenocarcinoma and the surrounding tissue as a prognostic classifier. J Natl Cancer Inst 2007;99:1257-1269.
65. Larsen JE, Pavey SJ, Passmore LH, et al. Gene expression signature predicts recurrence in lung adenocarcinoma. Clin Cancer Res 2007;13: 2946-2954.
66. Potti A, Mukherjee S, Petersen R, et al. A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 2006;355:570-580.
67. Sun Z, Yang P, Aubry MC, et al. Can gene expression profiling predict survival for patients with squamous cell carcinoma of the lung? Mol Cancer 2004;3:35.
68. Lu Y, Lemon W, Liu PY, et al. A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med 2006;3:e467.
69. Borczuk AC, Shah L, Pearson GD, et al. Molecular signatures in biopsy specimens of lung cancer. Am J Respir Crit Care Med 2004;170:167-174.
70. Chen HY, Yu SL, Chen CH, et al. A five-gene signature and clinical outcome in non-small-cell lung cancer. N Engl J Med 2007;356:11-20.
71. Chen JJ, Peck K, Hong TM, et al. Global analysis of gene expression in invasion by a lung cancer model. Cancer Res 2001;61:5223-5230.
72. Jiang H, Deng Y, Chen HS, et al. Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics 2004;5:81.
73. Parmigiani G, Garrett-Mayer ES, Anbazhagan R, et al. A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clin Cancer Res 2004;10:2922-2927.
74. Tamayo P, Scanfeld D, Ebert BL, et al. Metagene projection for cross-platform, cross-species characterization of global transcriptional states. Proc Natl Acad Sci U S A 2007;104:5959-5964.
75. Shedden K, Taylor JM, Enkemann SA, et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008;14:822-827.
76. Dobbin KK, Beer DG, Meyerson M, et al. Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microar-rays. Clin Cancer Res 2005;11:565-572.
77. Fan C, Oh DS, Wessels L, et al. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 2006;355:560-569.
78. Shi L, Reid LH, Jones WD, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006;24:1151-1161.
79. Johnson SM, Grosshans H, Shingara J, et al. RAS is regulated by the let-7 microRNA family. Cell 2005;120:635-647.
80. Takamizawa J, Konishi H, Yanagisawa K, et al. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 2004;64:3753-3756.
81. Yu SL, Chen HY, Chang GC, et al. MicroRNA signature predicts survival and relapse in lung cancer. Cancer Cell 2008;13:48-57.
82. Staunton JE, Slonim DK, Coller HA, et al. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A 2001;98:10787-10792.
83. Grever MR, Schepartz SA, Chabner BA. The National Cancer Institute: cancer drug discovery and development program. Semin Oncol 1992; 19:622-638.
84. Stinson SF, Alley MC, Kopp WC, et al. Morphological and immuno-cytochemical characteristics of human tumor cell lines for use in a disease-oriented anticancer drug screen. Anticancer Res 1992;12:1035-1053.
85. Potti A, Dressman HK, Bild A, et al. Genomic signatures to guide the use of chemotherapeutics. Nat Med 2006;12:1294-1300.
86. Hsu DS, Balakumaran BS, Acharya CR, et al. Pharmacogenomic strategies provide a rational approach to the treatment of cisplatin-resistant patients with advanced cancer. J Clin Oncol 2007;25:4350-4357.
87. Gyorffy B, Surowiak P, Kiesslich O, et al. Gene expression profiling of 30 cancer cell lines predicts resistance towards 11 anticancer drugs at clinically achieved concentrations. Int J Cancer 2006;118:1699- 1712.
88. Gemma A, Li C, Sugiyama Y, et al. Anticancer drug clustering in lung cancer based on gene expression profiles and sensitivity database. BMC Cancer 2006;6:174.