Genomic and proteomic profiling of lung cancers: Lung cancer classification in the age of targeted therapy

Journal of Clinical Oncology

Volumn 23, Issue 14, 2005, Pages 3219-3226

  Meyerson, Matthew ^a   Carbone, David ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

CANCER CLASSIFICATION; CARCINOGENESIS; DNA FINGERPRINTING; GENE EXPRESSION PROFILING; GENE MUTATION; GENE TARGETING; GENOMICS; HISTOPATHOLOGY; HUMAN; LUNG ADENOCARCINOMA; LUNG CANCER; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; OUTCOME ASSESSMENT; PRIORITY JOURNAL; PROGNOSIS; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN TARGETING; PROTEOMICS; REVIEW; SURVIVAL; TUMOR DIFFERENTIATION; TWO DIMENSIONAL GEL ELECTROPHORESIS; GENE EXPRESSION REGULATION; GENETICS; LUNG TUMOR; PATHOLOGY;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; LUNG NEOPLASMS; PROTEOMICS;

EID: 19844380235     PISSN: 0732183X     EISSN: None     Source Type: Journal    
DOI: 10.1200/JCO.2005.15.511     Document Type: Review

References (69)

1. Jemal A, Murray T, Ward E, et al: Cancer statistics, 2005. CA Cancer J Clin 55:10-30, 2005
2. Chen G, Gharib TG, Huang CC, et al: Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics 1:304-313, 2002
3. Anderson L, Seilhamer J: A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18:533-537, 1997
4. Wilkins MR, Sanchez JC, Williams KL, et al: Current challenges and future applications for protein maps and post-translational vector maps in proteome projects. Electrophoresis 17:830-838, 1996
5. Pandey A, Mann M: Proteomics to study genes and genomes. Nature 405:837-846, 2000
6. Banks RE, Dunn MJ, Hochstrasser DF, et al: Proteomics: New perspectives, new biomedical opportunities. Lancet 356:1749-1756, 2000
7. Wright GL Jr: Two-dimensional acrylamide gel electrophoresis of cancer-patient serum proteins. Ann Clin Lab Sci 4:281-293, 1974
8. Chen G, Gharib TG, Huang CC, et al: Proteomic analysis of lung adenocarcinoma: Identification of a highly expressed set of proteins in tumors. Clin Cancer Res 8:2298-2305, 2002
9. Hanash S, Brichory F, Beer D: A proteomic approach to the identification of lung cancer markers. Dis Markers 17:295-300, 2001
10. Oh JM, Brichory F, Puravs E, et al: A database of protein expression in lung cancer. Proteomics 1:1303-1319, 2001
11. Brichory F, Beer D, Le Naour F, et al: Proteomics-based identification of protein gene product 9.5 as a tumor antigen that induces a humoral immune response in lung cancer. Cancer Res 61:7908-7912, 2001
12. Bergman AC, Benjamin T, Alaiya A, et al: Identification of gel-separated tumor marker proteins by mass spectrometry. Electrophoresis 21:679-686, 2000
13. Hirano T, Franzen B, Uryu K, et al: Detection of polypeptides associated with the histopathological differentiation of primary lung carcinoma. Br J Cancer 72:840-848, 1995
14. Hirano T, Fujioka K, Franzen B, et al: Relationship between TA01 and TA02 polypeptides associated with lung adenocarcinoma and histocytological features. Br J Cancer 75:978-985, 1997
15. Schmid HR, Schmitter D, Blum P, et al: Lung tumor cells: A multivariate approach to cell classification using two-dimensional protein pattern. Electrophoresis 16:1961-1968, 1995
16. Okuzawa K, Franzen B, Lindholm J, et al: Characterization of gene expression in clinical lung cancer materials by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 15:382-390, 1994
17. Gharib TG, Chen G, Wang H, et al: Proteomic analysis of cytokeratin isoforms uncovers association with survival in lung adenocarcinoma. Neoplasia 4:440-448, 2002
18. Oh P, Li Y, Yu J, et al: Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature 429:629-635, 2004
19. Liotta LA, Espina V, Mehta AI, et al: Protein microarrays: Meeting analytical challenges for clinical applications. Cancer Cell 3:317-325, 2003
20. Wulfkuhle JD, Aquino JA, Calvert VS, et al: Signal pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays. Proteomics 3:2085-2090, 2003
21. Huang J, Zhu H, Haggarty SJ, et al: Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A 101:16594-16599, 2004
22. Bonaldi T, Imhof A, Regula JT: A combination of different mass spectroscopic techniques for the analysis of dynamic changes of histone modifications. Proteomics 4:1382-1396, 2004
23. Metodiev MV, Timanova A, Stone DE: Differential phosphoproteome profiling by affinity capture and tandem matrix-assisted laser desorption/ionization mass spectrometry. Proteomics 4:1433-1438, 2004
24. Manza LL, Codreanu SG, Stamer SL, et al: Global shifts in protein sumoylation in response to electrophile and oxidative stress. Chem Res Toxicol 17:1706-1715, 2004
25. Badghisi H, Liebler DC: Sequence mapping of epoxide adducts in human hemoglobin with LC-tandem MS and the SALSA algorithm. Chem Res Toxicol 15:799-805, 2002
26. Link AJ, Eng J, Schieltz DM, et al: Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17:676-682, 1999
27. Stoeckli M, Chaurand P, Hallahan DE, et al: Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues. Nat Med 7:493-496, 2001
28. Chaurand P, Fouchecourt S, DaGue BB, et al: Profiling and imaging proteins in the mouse epididymis by imaging mass spectrometry. Proteomics 3:2221-2239, 2003
29. Reyzer ML, Hsieh Y, Ng K, et al: Direct analysis of drug candidates in tissue by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom 38:1081-1092, 2003
30. Reyzer ML, Caldwell RL, Dugger TC, et al: Early changes in protein expression detected by mass spectrometry predict tumor response to molecular therapeutics. Cancer Res 64:9093-9100, 2004
31. Shyr Y, Kim K: Weighted flexible compound covariate method for classifying microarray data, in Berrar D (ed): A Practical Approach to Microarray Data Analysis. New York, Kluwer Academic, 2003
32. Petricoin EF 3rd, Ornstein DK, Paweletz CP, et al: Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 94:1576-1578, 2002
33. Ardekani AM, Liotta LA, Petricoin EF 3rd: Clinical potential of proteomics in the diagnosis of ovarian cancer. Expert Rev Mol Diagn 2:312-320, 2002
34. Adam BL, Qu Y, Davis JW, et al: Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 62:3609-3614, 2002
35. Li J, Zhang Z, Rosenzweig J, et al: Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 48:1296-1304, 2002
36. Petricoin EF, Ardekani AM, Hitt BA, et al: Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359:572-577, 2002
37. Poon TC, Yip TT, Chan AT, et al: Comprehensive proteomic profiling identifies serum proteomic signatures for detection of hepatocellular carcinoma and its subtypes. Clin Chem 49:752-760, 2003
38. Yanagisawa K, Shyr Y, Xu BJ, et al: Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 362:433-439, 2003
39. Shen Y, Jacobs JM, Camp DG 2nd, et al: Ultra-high-efficiency strong cation exchange LC/ RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal Chem 76:1134-1144, 2004
40. Chee M, Yang R, Hubbell E, et al: Accessing genetic information with high-density DNA arrays. Science 274:610-614, 1996
41. Schena M, Shalon D, Davis RW, et al: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470, 1995
42. Dobbin KK, Beer DG, Meyerson M, et al: Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clin Cancer Res 11:565-572, 2005
43. 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 5:81, 2004
44. 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 10:2922-2927, 2004
45. Alizadeh AA, Eisen MB, Davis RE, et al: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503-511, 2000
46. Golub TR, Slonim DK, Tamayo P, et al: Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286:531-537, 1999
47. 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 98:13790-13795, 2001
48. Beer DG, Kardia SL, Huang CC, et al: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8:816-824, 2002
49. Garber ME, Troyanskaya OG, Schluens K, et al: Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A 98:13784-13789, 2001
50. Borczuk AC, Gorenstein L, Walter KL, et al: Non-small-cell lung cancer molecular signatures recapitulate lung developmental pathways. Am J Pathol 163:1949-1960, 2003
51. Heighway J, Knapp T, Boyce L, et al: Expression profiling of primary non-small cell lung cancer for target identification. Oncogene 21:7749-7763, 2002
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 127:1332-1342, 2004
53. 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 363:775-781, 2004
54. Powell CA, Spira A, Derti A, et al: Gene expression in lung adenocarcinomas of smokers and nonsmokers. Am J Respir Cell Mol Biol 29:157-162, 2003
55. 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 62:3971-3979, 2002
56. Tomida S, Koshikawa K, Yatabe Y, et al: Gene expression-based, individualized outcome prediction for surgically treated lung cancer patients. Oncogene 23:5360-5370, 2004
57. 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 99:12357-12362, 2002
58. Wikman H, Kettunen E, Seppanen JK, et al: Identification of differentially expressed genes in pulmonary adenocarcinoma by using cDNA array. Oncogene 21:5804-5813, 2002
59. 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 9:4695-4704, 2003
60. Zembutsu H, Ohnishi Y, Daigo Y, et al: Gene-expression profiles of human tumor xenografts in nude mice treated orally with the EGFR tyrosine kinase inhibitor ZD1839. Int J Oncol 23:29-39, 2003
61. Fujii T, Dracheva T, Player A, et al: A preliminary transcriptome map of non-small cell lung cancer. Cancer Res 62:3340-3346, 2002
62. Nacht M, Dracheva T, Gao Y, et al: Molecular characteristics of non-small cell lung cancer. Proc Natl Acad Sci U S A 98:15203-15208, 2001
63. Difilippantonio S, Chen Y, Pietas A, et al: Gene expression profiles in human non-small and small-cell lung cancers. Eur J Cancer 39:1936-1947, 2003
64. Ramaswamy S, Ross KN, Lander ES, et al: A molecular signature of metastasis in primary solid tumors. Nat Genet 33:49-54, 2003
65. Sweet-Cordero A, Mukherjee S, Subramanian A, et al: An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 37:48-55, 2005
66. Mariani TJ, Reed JJ, Shapiro SD: Expression profiling of the developing mouse lung: Insights into the establishment of the extracellular matrix. Am J Respir Cell Mol Biol 26:541-548, 2002
67. 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 350:2129-2139, 2004
68. Paez JG, Janne PA, Lee JC, et al: EGFR mutations in lung cancer: Correlation with clinical response to gefitinib therapy. Science 304:1497-1500, 2004
69. Pao W, Miller V, Zakowski M, et al: EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A 101:13306-13311, 2004