Mapping molecular networks using proteomics: A vision for patient-tailored combination therapy

Journal of Clinical Oncology

Volumn 23, Issue 15, 2005, Pages 3614-3621

  Petricoin III, Emanuel F ^a   Bichsel, Verena E ^b   Calvert, Valerie S ^b   Espina, Virginia ^b   Winters, Mary ^b   Young, Lynn ^b   Belluco, Claudio ^b   Trock, Bruce J ^b   Lippman, Marc ^b   Fishman, David A ^b   Sgroi, Dennis C ^b   Munson, Peter J ^b   Esserman, Laura J ^b   Liotta, Lance A ^b  

^a GEORGE MASON UNIVERSITY   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

GEFITINIB; TUMOR PROTEIN; ANTINEOPLASTIC AGENT;

CANCER; CANCER PATIENT; CANCER THERAPY; CLINICAL RESEARCH; DRUG EFFICACY; DRUG RESPONSE; DRUG TARGETING; GENOMICS; HUMAN; LUNG CANCER; MOLECULAR THERAPY; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MICROARRAY; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; REVIEW; TUMOR CELL; COMPARATIVE STUDY; FEMALE; FORECASTING; GENE EXPRESSION PROFILING; GENE THERAPY; GENETICS; IMMUNOTHERAPY; MALE; METHODOLOGY; MOLECULAR BIOLOGY; MORTALITY; MULTIMODALITY CANCER THERAPY; NEOPLASM; ONCOLOGY; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; STANDARD;

ANTINEOPLASTIC COMBINED CHEMOTHERAPY PROTOCOLS; COMBINED MODALITY THERAPY; FEMALE; FORECASTING; GENE EXPRESSION PROFILING; GENE THERAPY; HUMANS; IMMUNOTHERAPY; MALE; MEDICAL ONCOLOGY; MOLECULAR BIOLOGY; NEOPLASM PROTEINS; NEOPLASMS; PROTEIN ARRAY ANALYSIS; PROTEOMICS; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION;

EID: 20644464974     PISSN: 0732183X     EISSN: None     Source Type: Journal    
DOI: 10.1200/JCO.2005.02.509     Document Type: Review

References (59)

1. Heinrich MC, Corless CL, Demetri GD, et al: Kinase mutations and imatinib response in patients with metastatic gastrointestinal stromal tumor. J Clin Oncol 21:4342-4349, 2003
2. Duensing A, Medeiros F, McConarty B, et al: Mechanisms of oncogenic KIT signal transduction in primary gastrointestinal stromal tumors (GISTs). Oncogene 23:3999-4006, 2004
3. Heinrich MC, Corless CL, Duensing A, et al: PDGFRA activating mutations in gastrointestinal stromal tumors. Science 299:708-710, 2003
4. Lim YP, Diong LS, Qi R, et al: Phosphoproteomic fingerprinting of epidermal growth factor signaling and anticancer drug action in human tumor cells. Mol Cancer Ther 2:1369-1377, 2003
5. Druker BJ, Sawyers CL, Kantarjian H, et al: Activity of a specific inhibitor of the BCR-ABL tyrosine kinase in the blast crisis of chronic myeloid leukemia and acute lymphoblastic leukemia with the Philadelphia chromosome. N Engl J Med 344:1038-1042, 2001
6. Davies H, Bignell GR, Cox C, et al: Mutations of the BRAF gene in human cancer. Nature 417:949-954, 2002
7. Samuels Y, Wang Z, Bardelli A, et al: High frequency of mutations of the PIK3CA gene in human cancers. Science 304:554, 2004
8. Bardelli A, Parsons DW, Silliman N, et al: Mutational analysis of the tyrosine kinome in colorectal cancers. Science 300:949, 2003
9. Giaccone G, Herbst RS, Manegold C, et al: Gefitinib in combination with gemcitabine and cisplatin in advanced non-small-cell lung cancer: A phase III trial-INTACT 1. J Clin Oncol 22:777-784, 2004
10. Slamon DJ, Leyland-Jones B, Shak S, et al: Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med 344:783-792, 2001
11. Wakeling AE, Guy SP, Woodburn JR, et al: ZD1839 (Iressa): An orally active inhibitor of epidermal growth factor signaling with potential for cancer therapy. Cancer Res 62:5749-5754, 2002
12. Arteaga CL: ErbB-targeted therapeutic approaches in human cancer. Exp Cell Res 284:122-130, 2003
13. Baselga J, Rischin D, Ranson M, et al: Phase I safety, pharmacokinetic, and pharmacodynamic trial of ZD1839, a selective oral epidermal growth factor receptor tyrosine kinase inhibitor, in patients with five selected solid tumor types. J Clin Oncol 20:4292-4302, 2002
14. Kris MG, Natale RB, Herbst RS, et al: Efficacy of gefitinib, an inhibitor of the epidermal growth factor receptor tyrosine kinase, in symptomatic patients with non-small cell lung cancer: A randomized trial. JAMA 290:2149-2158, 2003
15. Herbst RS, Giaccone G, Schiller JH, et al: Gefitinib in combination with paclitaxel and carboplatin in advanced non-small-cell lung cancer: A phase III trial-INTACT 2. J Clin Oncol 22:785-794, 2004
16. Pegram MD, Konecny G, Slamon DJ: The molecular and cellular biology of HER2/neu gene amplification/overexpression and the clinical development of Herceptin (trastuzumab) therapy for breast cancer. Cancer Treat Res 103:57-75, 2000
17. Li B, Chang CM, Yuan M, et al: Resistance to small molecule inhibitors of epidermal growth factor receptor in malignant gliomas. Cancer Res 63:7443-7450, 2003
18. 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
19. 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
20. Slonim DK: From patterns to pathways: Gene expression data analysis comes of age. Nat Genet 32:502-508, 2002
21. Ferrando AA, Neuberg DS, Staunton J, et al: Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 1:75-87, 2002
22. Ge H, Walhout AJ, Vidal M: Integrating 'omic' information: A bridge between genomics and systems biology. Trends Genet 19:551-560, 2003
23. Petricoin EF, Liotta LA: Molecular profiling of human cancer. Nat Rev Genet 1:48-56, 2000
24. Manning G, Whyte DB, Martinez R, et al: The protein kinase complement of the human genome. Science 298:1912-1934, 2002
25. Pawson T: Regulation and targets of receptor tyrosine kinases. Eur J Cancer 5:S3-S10, 2002 (suppl)
26. Spirin V, Mirny LA: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100:12123-12128, 2003
27. Liotta LA, Kohn EC: The microenvironment of the tumour-host interface. Nature 411:375-379, 2001
28. Nielsen UB, Cardone MH, Sinskey AJ, et al: Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc Natl Acad Sci U S A 100:9330-9335, 2003
29. Liotta LA, Espina V, Mehta AI, et al: Protein microarrays: Meeting analytical challenges for clinical applications. Cancer Cell 3:317-325, 2003
30. Grubb RL, Calvert VS, Wulkuhle JD, et al: Signal pathway profiling of prostate cancer using reverse phase protein arrays. Proteomics 3:2142-2146, 2003
31. 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
32. Paweletz CP, Charboneau L, Bichsel VE, et al: Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20:1981-1989, 2001
33. Nishizuka S, Chen ST, Gwadry FG, et al: Diagnostic markers that distinguish colon and ovarian adenocarcinomas: Identification by genomic, proteomic, and tissue array profiling. Cancer Res 63:5243-5250, 2003
34. Nishizuka S, Charboneau L, Young L, et al: Proteomic profiling of the NCI60 cancer cell lines using new high-density 'reverse-phase' lysate microarrays. Proc Natl Acad Sci U S A 100:14229-14234, 2003
35. Mills GB, Kohn E, Lu Y, et al: Linking molecular diagnostics to molecular therapeutics: Targeting the PI3K pathway in breast cancer. Semin Oncol 30:93-104, 2003
36. Ma XJ, Salunga R, Tuggle JT, et al: Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci U S A 100:5974-5979, 2003
37. Thor AD, Liu S, Edgerton S, et al: Activation (tyrosine phosphorylation) of ErbB-2 (HER-2/neu): A study of incidence and correlation with outcome in breast cancer. J Clin Oncol 18:3230-3239, 2000
38. Petricoin EF, Zoon KC, Kohn EC, et al: Clinical proteomics: Translating benchside promise into bedside reality. Nat Rev Drug Discov 1:683-695, 2002
39. Carter SL, Brechbuhler CM, Griffin M, et al: Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 20:2242-2250, 2004
40. Jenster G: A visualisation concept of dynamic signaling networks. Mol Cell Endocrinol 15:218:1-6, 2004
41. Toroczkai Z, Bassler KE: Network dynamics: Jamming is limited in scale-free systems. Nature 428:716, 2004
42. Kunin V, Pereira-Leal JB, Ouzounis CA: Functional evolution of the yeast protein interaction network. Mol Biol Evol 21:1171-1176, 2004
43. Bar-Yam Y, Epstein IR: Response of complex networks to stimuli. Proc Natl Acad Sci U S A 101:4341-4345, 2004
44. Yook SH, Oltvai ZN, Barabasi AL: Functional and topological characterization of protein interaction networks. Proteomics 4:928-942, 2004
45. Hasty J, McMillen D, Isaacs F, et al: Computational studies of gene regulatory networks: In numero molecular biology, Nat Rev Genet 2:268-279, 2001
46. Bray D: Molecular networks: The top-down view. Science 301:1864-1865, 2003
47. Jansen R, Yu H, Greenbaum D, et al: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-453, 2003
48. Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2, 2003
49. Arteaga CL: EGF receptor as a therapeutic target: Patient selection and mechanisms of resistance to receptor-targeted drugs. J Clin Oncol 21:2893-2915, 2003 (23 suppl)
50. Arteaga CL, Baselga J: Clinical trial design and end points for epidermal growth factor receptor-targeted therapies: Implications for drug development and practice. Clin Cancer Res 9:1579-1589, 2003
51. Shawver LK, Slamon D, Ullrich A: Smart drugs: Tyrosine kinase inhibitors in cancer therapy. Cancer Cell 1:117-123, 2002
52. Gschwind A, Fischer OM, Ullrich A: The discovery of receptor tyrosine kinases: Targets for cancer therapy. Nat Rev Cancer 4:361-370, 2004
53. 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
54. He T, Alving K, Feild B, et al: Quantitation of phosphopeptides using affinity chromatography and stable isotope labeling. J Am Soc Mass Spectrom 15:363-373, 2004
55. Barati MT, Powell DW, McLeish KR: Proteomic approach to identification of novel kinase substrates in mesangial cells. Contrib Nephrol 141:231-244, 2004
56. Ficarro SB, McCleland ML, Stukenberg PT, et al: Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20:301-305, 2002
57. Zhou H, Watts JD, Aebersold R: A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol 19:375-378, 2001
58. Stancato LF, Petricoin EF: Fingerprinting of signal transduction pathways using a combination of anti-phosphotyrosine immunoprecipitations and two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 22:2120-2124, 2001
59. Oda Y, Nagasu T, Chait BY: Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 19:379-382, 2001