A prototype antibody microarray platform to monitor changes in protein tyrosine phosphorylation

Molecular and Cellular Proteomics

Volumn 3, Issue 11, 2004, Pages 1102-1118

  Gembitsky, Dmitry S ^a   Lawlor, Kevin ^a   Jacovina, Andrew ^a   Yaneva, Mariana ^a   Tempst, Paul ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BCR ABL PROTEIN; EPIDERMAL GROWTH FACTOR; EPIDERMAL GROWTH FACTOR RECEPTOR; FLUORESCENT DYE; IMATINIB; MONOCLONAL ANTIBODY; PHOSPHOAMINO ACID; PHOSPHOTYROSINE; PROTEIN; PROTEOME; REAGENT; TISSUE EXTRACT;

ARTICLE; ASSAY; AUTOMATION; BODY FLUID; CELL TYPE; CLINICAL PROTOCOL; CONTROLLED STUDY; DEVELOPMENT; DEVICE; EUKARYOTE; GROWTH; HELA CELL; HUMAN; HUMAN CELL; INCUBATION TIME; MALIGNANT TRANSFORMATION; MASS SPECTROMETRY; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN PHOSPHORYLATION; SAMPLE; SIGNAL TRANSDUCTION; TISSUE TYPES; TUMOR CLASSIFICATION;

ANIMALS; ANTIBODIES, MONOCLONAL; CELLS, CULTURED; EPIDERMAL GROWTH FACTOR; FLUORESCENT DYES; HELA CELLS; HUMANS; MASS SPECTROMETRY; PHOSPHORYLATION; PHOSPHOTYROSINE; PIPERAZINES; PROTEIN ARRAY ANALYSIS; PROTEIN-TYROSINE KINASES; PROTEOME; PYRIMIDINES; SIGNAL TRANSDUCTION;

EUKARYOTA;

EID: 10944225411     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M400075-MCP200     Document Type: Article

References (66)

1. Hunter, T. (1998) The Croonian Lecture 1997. The phosphorylation of proteins on tyrosine: Its role in cell growth and disease. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 353, 583-605
2. Schlessinger, J. (2000) Cell signaling by receptor tyrosine kinases. Cell 103, 211-225
3. Pawson, T., and Nash, P. (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300, 445-452
4. Daley, G. Q., and Ben-Neriah, Y. (1991) Implicating the bcr/abl gene in the pathogenesis of Philadelphia chromosome-positive human leukemia. Adv. Cancer Res. 57, 151-184
5. Kolibaba, K. S., and Bruker, B. J. (1997) Protein tyrosine kinases and cancer. Biochim. Biophys. Acta 133, F217-F248
6. Blume-Jensen, P., and Hunter, T. (2001) Oncogenic kinase signaling. Nature 411, 355-365
7. Deininger, M., W., Goldman, J. M., and Melo, J. V. (2000) The molecular biology of chronic myeloid leukemia. Blood 96, 3343-3356
8. Schindler, T., Bornmann, W., Pellicena, P., Miller, W. T., Clarkson, B., and Kuriyan, J. (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289, 1938-1942
9. Kurzrock, R., Kantarjian, H. M., Bruker, B. J., and Talpaz, M. (2003) Philadelphia chromosome-positive leukemias: from basic mechanisms to molecular therapeutics. Ann. Intern. Med. 138, 819-830
10. Mendelsohn, J., and Baselga, J. (2003) Status of epidermal growth factor receptor antagonists in the biology and treatment of cancer. J. Clin. Oncol. 21, 2787-2799
11. Blagosklonny, M. V. (2004) Gefitinib (Iressa) in oncogene-active cancers and therapy for common cancers. Cancer Biol. Ther. 3, [epub ahead of print]
12. Hunter, T., and Sefton, B. (1980) Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc. Natl. Acad. Sci. U. S. A. 77, 1311-1315
13. Baldwin, M. A. (2004) Protein identification by mass spectrometry: Issues to be considered. Mol. Cell. Proteomics 3, 1-9
14. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R., Mann, M., and Lodish, H. F. (2000) Analysis of receptor signaling pathways by mass spectrometry: Identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc. Natl. Acad. Sci. U. S. A. 97, 179-184
15. Pandey, A., Fernandez, M. M., Steen, H., Blagoev, B., Nielsen, M. N., Roche, S., Mann, M., and Lodish, H. F. (2000) Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. J. Biol. Chem. 275, 38633-38639
16. Mann, M., Ong, S. E., Gronborg, M., Steen, H., Jensen, O. N., and Pandey, A. (2002) Analysis of protein phosphorylation using mass spectrometry: Deciphering the phosphoproteome. Trends Biotechnol. 20, 261-268
17. Mann, M., and Jensen, O. N. (2003) Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21, 255-261
18. Machida, K., Mayer, B. J., and Nollau, P. (2003) Profiling the global tyrosine phosphorylation state. Mol. Cell. Proteomics 2, 215-233
19. Salomon, A. R., Ficarro, S. B., Brill, L. M., Brinker, A., Phung, Q. T., Ericson, C., Sauer, K., Brock, A., Horn, D. M., Shultz, P. G., and Peters, E. C. (2003) Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 100, 443-448
20. Grønborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S., Ohara, O., Mann, M., Jensen, O. N., and Pandey, A, (2002) A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phosphor-specific antibodies. Mol. Cell. Proteomics 1.7, 517-527
21. Steen, H., Fernandez, M., Ghaffari, S., Pandey, A., and Mann, M. (2003) Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Mol. Cell. Proteomics 2, 138-145
22. Zhou, H., Watts, J. D., and Aebersold, R. (2001) A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19, 375-378
23. Oda, Y., Nagasu, T., and Chait, B. T. (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19, 379-382
24. Posewitz, M. C., and Tempst, P. (1999) Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal. Chem. 71, 2883-2892
25. Brill, L. M., Salomon, A. R., Ficarro, S. B., Mukherji, M., Stettler-Gill, M., and Peters, E. C. (2004) Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. Anal. Chem. 76, 2763-2772
26. Liotta, L. A., Espina, V., Mehta, A. I., Calvert, V., Rosenblatt, K., Geho, D., Munson, P. J., Young, L., Wulfkuhle, J., and Petricoin, E. F. (2003) Protein microarrays: Meeting analytical challenges for clinical applications. Cancer Cell 3, 317-325
27. Haab, B. B., Dunham, M. J., and Brown, P. O. (2001) Protein microarrays for highly parallel detection and quantification of specific proteins and antibodies in complex solutions. Genome Biol. 2, research0004.1-0004.13
28. Moody, M. D., Van Arsdell, S. W., Murphy, K. P., Orencole, S. F., and Burns, C. (2001) Array-based ELISAs for high-throughput analysis of human cytokines. BioTechniques 31, 186-190
29. Delehanty, J. B., and Ligler, F. C. (2002) A microarray immunoassay for simultaneous detection of proteins and bacteria. Anal. Chem. 74, 5681-5687
30. Miller, J. C., Zhou, H., Kwekel, J., Cavallo, R., Burke, J., Butler, E. B., The, B. S., and Haab, B. B. (2003) Antibody microarray profiling of human prostate cancer serum: Antibody screening and identification of potential biomarkers. Proteomics 3, 56-63
31. Knezevic, V., Leethanakul, C., Bichsel, V. E., Worth, J. M., Prabhu, V. V., Gutkind, J. S., Liotta, L. A., Munson, P. J., Petricoin, E. F., and Krizman, D. B. (2001) Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics 1, 1271-1278
32. Sreekumar, A., Nyati, M. K., Varambally, S., Barrette, T. R., Ghosh, D., Lawrence, T. S., and Chinnaiyan, A. M. (2001) Profiling of cancer cells using protein microarrays: Discovery of novel radiation-regulated proteins. Cancer Res. 61, 7585-7593
33. Lueking, A., Possling, A., Huber, O., Beveridge, A., Horn, M., Eickhoff, H., Schuchardt, J., Lehrach, H., and Cahill, D. J. (2003) A nonredundant human protein chip for antibody screening and serum profiling. Mol. Cell. Proteomics 2, 1342-1349
34. Michaud, G. A., Salcius, M., Zhou, F., Bangham, R., Bonin, J., Guo, H., Snyder, M., Predki, P. F., and Schweitzer, B. I. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21, 1509-1512
35. Robinson, W. H., DiGennaro, C., Hueber, W., Haab, B. B., Kamachi, M., Dean E. J., Fournel, S., Fong, D., Genovese, M. C., de Vegvar, H. E., Skriner, K., Hirschberg, D. L., Morris, R. I., Muller, S., Pruijn, G. J., van Venrooij, W. J., Smolen, J. S., Brown, P. O., Steinman, L., and Utz, P. J. (2002) Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat. Med. 8, 295-301
36. Fall, B. I., Eberlein-Konig, B., Behrendt, H., Niessner, R., Ring, J., and Weller, M. G. (2003) Microarrays, for the screening of allergen-specific IgE in human serum. Anal. Chem. 75, 556-562
37. Paweletz, C. P., Charboneau, L., Bichsel, V., Simone, N. L., Chen, T., Gillespie, J. W., Emmert-Buck, M. R., Roth, M. J., Petricoin, E. F., and Liotta, L. A. (2001) Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, 1981-1089
38. Zhu, H., Bilgin, M., and Snyder, M. (2003) Proteomics. Annu. Rev. Biochem. 72, 783-812
39. Grubb, R. L., Calvert, V. S., Wulkuhle, J. D., Paweletz, C. P., Linehan, W. M., Phillips, J. L., Chuaqui, R., Valasco, A., Gillespie, J., Emmert-Buck, M., Liotta, L. A., and Petricoin, E. F. (2003) Signal pathway profiling of prostate cancer using reverse phase protein arrays. Proteomics 3, 2142-2146
40. Nielsen, U. B., Cardone, M. H., Sinskey, A. J., MacBeath, G., and Sorger, P. K. (2003) Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc. Natl. Acad. Sci. U. S. A. 100, 9330-9335
41. BCR-ABL . Leukemia Res. 24, 289-297
42. Frackelton, R. A., Posner, M., Kannan, B., and Mermelstein, F. (1991) Generation of monoclonal antibodies against phosphotyrosine and their use for affinity purification of phosphotyrosine-containing proteins. Methods Enzymol. 201, 79-92
43. Erjument-Bromage, H., Lui, M., Lacomis, L., Grewal, A., Annan, R. S., McNulty, D. E., Carr, S. A., and Tempst, P. (1998) Examination of micro-tip reversed-phase liquid chromatographic extraction of peptides pools for mass spectrometric analysis. J. Chromatogr. A 826, 167-181
44. Winkler, G. S., Lacomis, L., Philip, J., Erjument-Bromage, H., Svejstrup, J. Q., and Tempst, P. (2002) Isolation and mass spectrometry of transcription factor complexes. Methods 26, 260-269
45. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567
46. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K. (eds.) (2003) Current Protocols in Molecular Biology, Vol. 2, John Willey & Sons, Inc., Hoboken, NJ
47. Guschin, D., Yershov, G., Zaslavsky, A., Gemmell, A., Shik, V., Proudnikov, D., Arenkov, P., and Mirzabekov, A. (1997) Manual manufacturing of oligonucleotide, DNA and protein microchips. Anal. Biochem. 250, 203-211
48. Wisniewski, D., Strife, A., Swendeman, S., Erdjument-Bromage, H., Geromanos, S., Kavanaugh, W. M., Tempst, P., and Clarkson, B. (1999) A novel SH2-containing phosphatidylinositol 3,4,5-trisphosphate 5-phosphotase (SHIP2) is constitutively tyrosine phosphorylated and associated with src homologous and collagen gene (SHC) in chronic myelogenous leukemia progenitor cells. Blood 93, 2707-2720
49. Mahabeleshwar, G., Das, R., and Kundu, G. C. (2004) Tyrosine kinase, p56lck-induced cell motility, and urokinase-type plasminogen activator secretion involve activation of epidermal growth factor receptor/extracellular signal regulated kinase pathways. J. Biol. Chem. 279, 9733-9742
50. Zhou, H., Bouwman, K., Schotanus, M., Verweij, C., Marrero, J. A., Dillon, D., Costa, J., Lizardi, P., and Haab, B. B. (2004) Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements. Genome Biol. 5, R28.1-R28.12
51. Traina, F., Carvalheira, J. B., Saad, M. J., Costa, F., and Saad, S. T. (2003) BCR-ABL binds to IRS-1 and IRS-1 phosphorylation is inhibited by imatinib in K562 cells. FEBS Lett. 535, 17-20
52. Parmar, S., Katsoulidis, E., Verma, A., Li, Y., Sassano, A., Lal, L., Majchrzak, B., Ravandi, F., Tallman, M. S., Fish, E. N., and Platanuias, L. C. (2004) Role of the p38 MAP kinase pathway in the generation of the effects of imatinib mesylate (STI571) in BCR-ABL expressing cells. J. Biol. Chem. 279, 25345-25352
53. Liu, S. K., and McGlade, C. J. (1998) Gads is a novel SH2 and SH3 domain-containing adaptor protein that binds to tyrosine-phosphorylated Shc. Oncogene 17, 3073-3082
54. Zhang, W., Trible, R. P., Zhu, M., Liu, S. K., McGlade, J. C., and Samelson, L. E. (2000) Association of Grab2, Gads, and phospholypase, C-γ1 with phosphorylated LAT tyrosine residues. J. Biol. Chem. 275, 23355-23361
55. Hsia, D. A., Mitra, S. K., Hauck, C. R., Streblow, D. N., Nelson, J. A., Ilic, D., Huang, S., Li, E., Nemerow, E. R., Leng, J., Spencer, K. S., Cheresh, D. A., and Schlaepfer, D. D. (2003) Differential regulation of cell motility and invasion by FAK. J. Cell Biol. 160, 753-767
56. Elledge, S. J., Richman, R., Hall, F. L., Williams, R. T., Lodgson, N., and Harper, J. W. (1992) CDK2 encodes a 33-kDa cyclin A-associated protein kinase and is expressed before CDC2 in the cell cycle. Proc. Natl. Acad. Sci. U. S. A. 89, 2907-2911
57. Jorissen, R. N., Walker, F., Pouliot, N., Garret, T. P., Ward, C. W., and Burgess, A. W. (2003) Epidermal growth factor receptor: Mechanisms of activation and signaling. Exp. Cell Res. 284, 31-53
58. Lock, P., Casagranda, F., and Dunn, A. R. (1999) Independent SH2-binding sites mediate interaction of Dok-related protein with RasGTPase-activating protein and Nck. J. Biol. Chem. 274, 22775-22784
59. Dang, A., Frost, J. A., and Cobb, M. H. (1998) The MEK-1 proline-rich insert is required for efficient activation of the mitogen-activated protein kinases ERK-1 and ERK-2 in mammalian cells. J. Biol. Chem. 273, 19909-19913
60. Pearson, G., Bumeister, R., Henry, D. O., Cobb, M. H., and White, M. A. (2000) Uncoupling Raf1 from MEK1/2 impairs only a subset of cellular responses to Raf activation. J. Biol. Chem. 275, 37303-37306
61. Holzberg, D., Knight, C. G., Dittrich-Breiholz, O., Schneider, H., Dorrie, A., Hoffmann, E., Resch, K., and Kracht, M. (2003) Disruption of the c-Jun-Jnk complex by a cell-permiable peptide containing the c-Jun domain induces apoptosis and affects a distinct set of interleukin-1-induced inflammatory genes. J. Biol. Chem. 278, 40213-40223
62. Nichols, G. L., Raines, M. A., Vera, J. C., Lacomis, L., Tempst, P., and Golde, D. W. (1994) Identification of CRKL as the constitutively phosphorylated 39-kD tyrosine phosphoprotein in chronic myelogenous leukemia cells. Blood 84, 2912-2918
63. Forbes, L. V., Moss, S. J., and Segal, A. W. (1999) Phosphorylation of p67 phox in the neutrophil occurs in the cytosol and is independent pf p47 phox. FEBS Lett. 449, 225-229
64. Yang, M., Zhang, H., Voyno-Yasenetskaya, T., and Ye, R. D. (2003) Requirement of Gβγ and c-Src in D2 dopamine receptor-mediated nuclear factor-kB activation. Mol. Pharmacol. 64, 447-455
65. Peters, D. J., McGrew, B. R., Perron, D. C., Liptak, L. M., and Laudano, A. P. (1990) In vivo phosphorylation and membrane association of the fyn proto-oncogene product in IM-9 human lymphoblasts. Oncogene 5, 1313-1319
66. Kremer, K. N., Humphreys, T. D., Kumar, A., Qian, N., and Hedin, K. E. (2003) Distinct role of ZAP-70 and Src homology 2 domain-containing leukocyte protein of 76 kDa in the prolonged activation of extracellular signal-regulated protein kinase by the stromal cell-derived factor-1α/CXCL12 chemokine. J. Immunol. 171, 360-367