Lung cancer proteomics, clinical and technological considerations

Journal of Proteomics

Volumn 73, Issue 10, 2010, Pages 1851-1863

  Lehtiö, Janne ^a   De Petris, Luigi ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

2DE; Biomarker; Lung cancer; Mass spectrometry; NSCLC; Proteomics; Quantitative proteomics; SCLC

Indexed keywords

BEVACIZUMAB; BIOLOGICAL MARKER; BORTEZOMIB; CISPLATIN; ERLOTINIB; GEFITINIB; GEMCITABINE; TUMOR MARKER;

CANCER DIAGNOSIS; CANCER GROWTH; CANCER SURVIVAL; HUMAN; LUNG CANCER; NONHUMAN; PRIORITY JOURNAL; PROGNOSIS; PROTEIN ANALYSIS; PROTEOMICS; REVIEW; TREATMENT RESPONSE;

HUMANS; LUNG NEOPLASMS; NEOPLASM STAGING; PROGNOSIS; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 77956414890     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2010.05.015     Document Type: Review

References (74)

1. Jemal A., Siegel R., Ward E., Hao Y., Xu J., Thun M.J. Cancer statistics, 2009. CA Cancer J Clin 2009, 59:225-249.
2. Groome P.A., Bolejack V., Crowley J.J., Kennedy C., Krasnik M., Sobin L.H., et al. The IASLC Lung Cancer Staging Project: validation of the proposals for revision of the T, N, and M descriptors and consequent stage groupings in the forthcoming (seventh) edition of the TNM classification of malignant tumours. J Thorac Oncol 2007, 2:694-705.
3. Cox J., Mann M. Is proteomics the new genomics?. Cell 2007, 130:395-398.
4. Mueller L.N., Brusniak M.Y., Mani D.R., Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 2008, 7:51-61.
5. Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
6. Cargile B.J., Sevinsky J.R., Essader A.S., Stephenson J.L., Bundy J.L. Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics. J Biomol Tech 2005, 16:181-189.
7. Pernemalm M., Lewensohn R., Lehtio J. Affinity prefractionation for MS-based plasma proteomics. Proteomics 2009, 9:1420-1427.
8. de Godoy L.M., Olsen J.V., Cox J., Nielsen M.L., Hubner N.C., Frohlich F., et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455:1251-1254.
9. Berglund L., Bjorling E., Oksvold P., Fagerberg L., Asplund A., Szigyarto C.A., et al. A genecentric human protein atlas for expression profiles based on antibodies. Mol Cell Proteomics 2008, 7:2019-2027.
10. Uhlen M., Bjorling E., Agaton C., Szigyarto C.A., Amini B., Andersen E., et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 2005, 4:1920-1932.
11. Wingren C., Borrebaeck C.A. Antibody microarray analysis of directly labelled complex proteomes. Curr Opin Biotechnol 2008, 19:55-61.
12. Groseclose M.R., Massion P.P., Chaurand P., Caprioli R.M. High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics 2008, 8:3715-3724.
13. Cohen A.A., Geva-Zatorsky N., Eden E., Frenkel-Morgenstern M., Issaeva I., Sigal A., et al. Dynamic proteomics of individual cancer cells in response to a drug. Science 2008, 322:1511-1516.
14. Pernemalm M., De Petris L., Eriksson H., Branden E., Koyi H., Kanter L., et al. Use of narrow-range peptide IEF to improve detection of lung adenocarcinoma markers in plasma and pleural effusion. Proteomics 2009, 9:3414-3424.
15. De Petris L., Pernemalm M., Elmberger G., Bergman P., Orre L., Lewensohn R., et al. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants. Proteome Sci. 2010, 8:9.
16. Coate L.E., John T., Tsao M.S., Shepherd F.A. Molecular predictive and prognostic markers in non-small-cell lung cancer. Lancet Oncol 2009, 10:1001-1010.
17. Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127:635-648.
18. Mok T.S., Wu Y.L., Thongprasert S., Yang C.H., Chu D.T., Saijo N., et al. Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma. N Engl J Med 2009, 361:947-957.
19. Rosell R., Moran T., Queralt C., Porta R., Cardenal F., Camps C., et al. Screening for epidermal growth factor receptor mutations in lung cancer. N Engl J Med 2009, 361:958-967.
20. VanMeter A.J., Rodriguez A.S., Bowman E.D., Jen J., Harris C.C., Deng J., et al. Laser capture microdissection and protein microarray analysis of human non-small cell lung cancer: differential epidermal growth factor receptor (EGPR) phosphorylation events associated with mutated EGFR compared with wild type. Mol Cell Proteomics 2008, 7:1902-1924.
21. Guo A., Villen J., Kornhauser J., Lee K.A., Stokes M.P., Rikova K., et al. Signaling networks assembled by oncogenic EGFR and c-Met. Proc Natl Acad Sci U S A 2008, 105:692-697.
22. Tian T., Hao J., Xu A., Luo C., Liu C., Huang L., et al. Determination of metastasis-associated proteins in non-small cell lung cancer by comparative proteomic analysis. Cancer Sci 2007, 98:1265-1274.
23. Xu A., Hao J., Zhang Z., Tian T., Jiang S., Liu C., et al. 14-kDa phosphohistidine phosphatase and its role in human lung cancer cell migration and invasion. Lung Cancer 2010, 67:48-56.
24. Yao H., Zhang Z., Xiao Z., Chen Y., Li C., Zhang P., et al. Identification of metastasis associated proteins in human lung squamous carcinoma using two-dimensional difference gel electrophoresis and laser capture microdissection. Lung Cancer 2009, 65:41-48.
25. Li R., Wang H., Bekele B.N., Yin Z., Caraway N.P., Katz R.L., et al. Identification of putative oncogenes in lung adenocarcinoma by a comprehensive functional genomic approach. Oncogene 2006, 25:2628-2635.
26. Bortner J.D., Das A., Umstead T.M., Freeman W.M., Somiari R., Aliaga C., et al. Down-regulation of 14-3-3 isoforms and annexin A5 proteins in lung adenocarcinoma induced by the tobacco-specific nitrosamine NNK in the A/J mouse revealed by proteomic analysis. J Proteome Res 2009, 8:4050-4061.
27. Oh P., Li Y., Yu J., Durr E., Krasinska K.M., Carver L.A., et al. Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature 2004, 429:629-635.
28. Durr E., Yu J., Krasinska K.M., Carver L.A., Yates J.R., Testa J.E., et al. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol 2004, 22:985-992.
29. Eriksson H., Lengqvist J., Hedlund J., Uhlen K., Orre L.M., Bjellqvist B., et al. Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms. Proteomics 2008, 8:3008-3018.
30. Orre L.M., Pernemalm M., Lengqvist J., Lewensohn R., Lehtio J. Up-regulation, modification, and translocation of S100A6 induced by exposure to ionizing radiation revealed by proteomics profiling. Mol Cell Proteomics 2007, 6:2122-2131.
31. De Petris L., Orre L.M., Kanter L., Pernemalm M., Koyi H., Lewensohn R., et al. Tumor expression of S100A6 correlates with survival of patients with stage I non-small-cell lung cancer. Lung Cancer 2009, 63:410-417.
32. Stahl S., Fung E., Adams C., Lengqvist J., Mork B., Stenerlow B., et al. Proteomics and pathway analysis identifies JNK signaling as critical for high linear energy transfer radiation-induced apoptosis in non-small lung cancer cells. Mol Cell Proteomics 2009, 8:1117-1129.
33. Rahman S.M., Shyr Y., Yildiz P.B., Gonzalez A.L., Li H., Zhang X., et al. Proteomic patterns of preinvasive bronchial lesions. Am J Respir Crit Care Med 2005, 172:1556-1562.
34. Wu X., Xiao Z., Chen Z., Li C., Li J., Feng X., et al. Differential analysis of two-dimension gel electrophoresis profiles from the normal-metaplasia-dysplasia-carcinoma tissue of human bronchial epithelium. Pathol Int 2004, 54:765-773.
35. Yanagisawa K., Shyr Y., Xu B.J., Massion P.P., Larsen P.H., White B.C., et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 2003, 362:433-439.
36. Au J.S., Cho W.C., Yip T.T., Law S.C. Proteomic approach to biomarker discovery in cancer tissue from lung adenocarcinoma among nonsmoking Chinese women in Hong Kong. Cancer Investig 2008, 26:128-135.
37. Gamez-Pozo A., Sanchez-Navarro I., Nistal M., Calvo E., Madero R., Diaz E., et al. MALDI profiling of human lung cancer subtypes. PLoS One 2009, 4:e7731.
38. Xiao X., Liu D., Tang Y., Guo F., Xia L., Liu J., et al. Development of proteomic patterns for detecting lung cancer. Dis Markers 2003, 19:33-39.
39. Yildiz P.B., Shyr Y., Rahman J.S., Wardwell N.R., Zimmerman L.J., Shakhtour B., et al. Diagnostic accuracy of MALDI mass spectrometric analysis of unfractionated serum in lung cancer. J Thorac Oncol 2007, 2:893-901.
40. Yang S.Y., Xiao X.Y., Zhang W.G., Zhang L.J., Zhang W., Zhou B., et al. Application of serum SELDI proteomic patterns in diagnosis of lung cancer. BMC Cancer 2005, 5:83.
41. Jacot W., Lhermitte L., Dossat N., Pujol J.L., Molinari N., Daures J.P., et al. Serum proteomic profiling of lung cancer in high-risk groups and determination of clinical outcomes. J Thorac Oncol 2008, 3:840-850.
42. Au J.S., Cho W.C., Yip T.T., Yip C., Zhu H., Leung W.W., et al. Deep proteome profiling of sera from never-smoked lung cancer patients. Biomed Pharmacother 2007, 61:570-577.
43. Han K.Q., Huang G., Gao C.F., Wang X.L., Ma B., Sun L.Q., et al. Identification of lung cancer patients by serum protein profiling using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. Am J Clin Oncol 2008, 31:133-139.
44. Howard B.A., Wang M.Z., Campa M.J., Corro C., Fitzgerald M.C., Patz E.F. Identification and validation of a potential lung cancer serum biomarker detected by matrix-assisted laser desorption/ionization-time of flight spectra analysis. Proteomics 2003, 3:1720-1724.
45. Fujii K., Nakano T., Kanazawa M., Akimoto S., Hirano T., Kato H., et al. Clinical-scale high-throughput human plasma proteome analysis: lung adenocarcinoma. Proteomics 2005, 5:1150-1159.
46. Pan J., Chen H.Q., Sun Y.H., Zhang J.H., Luo X.Y. Comparative proteomic analysis of non-small-cell lung cancer and normal controls using serum label-free quantitative shotgun technology. Lung 2008, 186:255-261.
47. Chen G., Gharib T.G., Huang C.C., Thomas D.G., Shedden K.A., Taylor J.M., et al. Proteomic analysis of lung adenocarcinoma: identification of a highly expressed set of proteins in tumors. Clin Cancer Res 2002, 8:2298-2305.
48. Chen G., Gharib T.G., Thomas D.G., Huang C.C., Misek D.E., Kuick R.D., et al. Proteomic analysis of eIF-5A in lung adenocarcinomas. Proteomics 2003, 3:496-504.
49. Chen G., Gharib T.G., Huang C.C., Taylor J.M., Misek D.E., Kardia S.L., et al. Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics 2002, 1:304-313.
50. Bonaldi T., Straub T., Cox J., Kumar C., Becker P.B., Mann M. Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Mol Cell 2008, 31:762-772.
51. Dowling P., O'Driscoll L., Meleady P., Henry M., Roy S., Ballot J., et al. 2-D difference gel electrophoresis of the lung squamous cell carcinoma versus normal sera demonstrates consistent alterations in the levels of ten specific proteins. Electrophoresis 2007, 28:4302-4310.
52. Okano T., Kondo T., Kakisaka T., Fujii K., Yamada M., Kato H., et al. Plasma proteomics of lung cancer by a linkage of multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis. Proteomics 2006, 6:3938-3948.
53. Patz E.F., Campa M.J., Gottlin E.B., Kusmartseva I., Guan X.R., Herndon J.E. Panel of serum biomarkers for the diagnosis of lung cancer. J Clin Oncol 2007, 25:5578-5583.
54. Soltermann A., Ossola R., Kilgus-Hawelski S., von Eckardstein A., Suter T., Aebersold R., et al. N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics. Cancer 2008, 114:124-133.
55. Tyan Y.C., Wu H.Y., Lai W.W., Su W.C., Liao P.C. Proteomic profiling of human pleural effusion using two-dimensional nano liquid chromatography tandem mass spectrometry. J Proteome Res 2005, 4:1274-1286.
56. Tyan Y.C., Wu H.Y., Su W.C., Chen P.W., Liao P.C. Proteomic analysis of human pleural effusion. Proteomics 2005, 5:1062-1074.
57. Chen G., Gharib T.G., Wang H., Huang C.C., Kuick R., Thomas D.G., et al. Protein profiles associated with survival in lung adenocarcinoma. Proc Natl Acad Sci U S A 2003, 100:13537-13542.
58. Liu Y.F., Xiao Z.Q., Li M.X., Li M.Y., Zhang P.F., Li C., et al. Quantitative proteome analysis reveals annexin A3 as a novel biomarker in lung adenocarcinoma. J Pathol 2009, 217:54-64.
59. Gharib T.G., Chen G., Wang H., Huang C.C., Prescott M.S., Shedden K., et al. Proteomic analysis of cytokeratin isoforms uncovers association with survival in lung adenocarcinoma. Neoplasia 2002, 4:440-448.
60. Cuezva J.M., Chen G., Alonso A.M., Isidoro A., Misek D.E., Hanash S.M., et al. The bioenergetic signature of lung adenocarcinomas is a molecular marker of cancer diagnosis and prognosis. Carcinogenesis 2004, 25:1157-1163.
61. Yanagisawa K., Tomida S., Shimada Y., Yatabe Y., Mitsudomi T., Takahashi T. A 25-signal proteomic signature and outcome for patients with resected non-small-cell lung cancer. J Natl Cancer Inst 2007, 99:858-867.
62. Campa M.J., Wang M.Z., Howard B., Fitzgerald M.C., Patz E.F. Protein expression profiling identifies macrophage migration inhibitory factor and cyclophilin a as potential molecular targets in non-small cell lung cancer. Cancer Res 2003, 63:1652-1656.
63. Howard B.A., Zheng Z., Campa M.J., Wang M.Z., Sharma A., Haura E., et al. Translating biomarkers into clinical practice: prognostic implications of cyclophilin A and macrophage migratory inhibitory factor identified from protein expression profiles in non-small cell lung cancer. Lung Cancer 2004, 46:313-323.
64. Xu B.J., Gonzalez A.L., Kikuchi T., Yanagisawa K., Massion B.P., Wu H., et al. MALDI-MS derived prognostic protein markers for resected non-small cell lung cancer. Proteomics Clin Appl 2008, 2:1508-1517.
65. Voortman J., Pham T.V., Knol J.C., Giaccone G., Jimenez C.R. Prediction of outcome of non-small cell lung cancer patients treated with chemotherapy and bortezomib by time-course MALDI-TOF-MS serum peptide profiling. Proteome Sci 2009, 7:34.
66. Taguchi F., Solomon B., Gregorc V., Roder H., Gray R., Kasahara K., et al. Mass spectrometry to classify non-small-cell lung cancer patients for clinical outcome after treatment with epidermal growth factor receptor tyrosine kinase inhibitors: a multicohort cross-institutional study. J Natl Cancer Inst 2007, 99:838-846.
67. Spurrier B., Honkanen P., Holway A., Kumamoto K., Terashima M., Takenoshita S., et al. Protein and lysate array technologies in cancer research. Biotechnol Adv 2008, 26:361-369.
68. Schwenk J.M., Igel U., Kato B.S., Nicholson G., Karpe F., Uhlen M., et al. Comparative protein profiling of serum and plasma using an antibody suspension bead array approach. Proteomics 2010, 10:532-540.
69. Picotti P., Rinner O., Stallmach R., Dautel F., Farrah T., Domon B., et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods 2009, 7:43-46.
70. Schiess R., Wollscheid B., Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol 2009, 3:33-44.
71. Addona T.A., Abbatiello S.E., Schilling B., Skates S.J., Mani D.R., Bunk D.M., et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009, 27:633-641.
72. Salmon S., Chen H., Chen S., Herbst R., Tsao A., Tran H., et al. Classification by mass spectrometry can accurately and reliably predict outcome in patients with non-small cell lung cancer treated with erlotinib-containing regimen. J Thorac Oncol 2009, 4:689-696.
73. Okano T., Kondo T., Fujii K., Nishimura T., Takano T., Ohe Y., et al. Proteomic signature corresponding to the response to gefitinib (Iressa, ZD1839), an epidermal growth factor receptor tyrosine kinase inhibitor in lung adenocarcinoma. Clin Cancer Res 2007, 13:799-805.
74. Maeda J., Hirano T., Ogiwara A., Akimoto S., Kawakami T., Fukui Y., et al. Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy. Br J Cancer 2008, 98:596-603.