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Journal of Zhejiang University SCIENCE B 2006 Vol.7 No.6 P.411-420

http://doi.org/10.1631/jzus.2006.B0411


Proteomic technology for biomarker profiling in cancer: an update


Author(s):  ALAOUI-JAMALI Moulay A., XU Ying-jie

Affiliation(s):  Lady Davis Institute for Medical Research and Segal Comprehensive Cancer Center of the Sir Mortimer B. Davis Jewish General Hospital, Department of Oncology and Medicine, McGill University, Montreal, Que. H3T 1E2, Canada

Corresponding email(s):   moulay.alaoui-jamali@mcgill.ca

Key Words:  Cancer, Biomarkers, Proteomics


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ALAOUI-JAMALI Moulay A., XU Ying-jie. Proteomic technology for biomarker profiling in cancer: an update[J]. Journal of Zhejiang University Science B, 2006, 7(6): 411-420.

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A1 - ALAOUI-JAMALI Moulay A.
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DOI - 10.1631/jzus.2006.B0411


Abstract: 
The progress in the understanding of cancer progression and early detection has been slow and frustrating due to the complex multifactorial nature and heterogeneity of the cancer syndrome. To date, no effective treatment is available for advanced cancers, which remain a major cause of morbidity and mortality. Clearly, there is urgent need to unravel novel biomarkers for early detection. Most of the functional information of the cancer-associated genes resides in the proteome. The later is an exceptionally complex biological system involving several proteins that function through posttranslational modifications and dynamic intermolecular collisions with partners. These protein complexes can be regulated by signals emanating from cancer cells, their surrounding tissue microenvironment, and/or from the host. Some proteins are secreted and/or cleaved into the extracellular milieu and may represent valuable serum biomarkers for diagnosis purpose. It is estimated that the cancer proteome may include over 1.5 million proteins as a result of posttranslational processing and modifications. Such complexity clearly highlights the need for ultra-high resolution proteomic technology for robust quantitative protein measurements and data acquisition. This review is to update the current research efforts in high-resolution proteomic technology for discovery and monitoring cancer biomarkers.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1] Aebersold, R., Goodlett, D.R., 2001. Mass spectrometry in proteomics. Chem. Rev., 101(2):269-295.

[2] Aebersold, R., Mann, M., 2003. Mass spectrometry-based proteomics. Nature, 422(6928):198-207.

[3] Anderson, N.L., Anderson, N.G., 2002. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics, 1(11):845-867.

[4] Bachelot, T., Ray-Coquard, I., Menetrier-Caux, C., Rastkha, M., Duc, A., Blay, J.Y., 2003. Prognostic value of serum levels of interleukin 6 and of serum and plasma levels of vascular endothelial growth factor in hormone-refractory metastatic breast cancer patients. Br. J. Cancer, 88(11):1721-1726.

[5] Balmain, A., Gray, J., Ponder, B., 2003. The genetics and genomics of cancer. Nature Genet., 33(Suppl. 3):238-244.

[6] Bast, R.C.Jr, Badgwell, D., Lu, Z., Marquez, R., Rosen, D., Liu, J., Baggerly, K.A., Atkinson, E.N., Skates, S., Zhang, Z., et al., 2005. New tumor markers: CA125 and beyond. Int. J. Gynecol. Cancer, 15(Suppl. 3):274-281.

[7] Bayer, E.M., Bottrill, A.R., Walshaw, J., Vigouroux, M., Naldrett, M.J., Thomas, C.L., Maule, A.J., 2006. Arabidopsis cell wall proteome defined using multidimensional protein identification technology. Proteomics, 6(1):301-311.

[8] Bichsel, V.E., Liotta, L.A., Petricoin, E.F., 2001. Cancer proteomics: from biomarker discovery to signal pathway profiling. Cancer J., 7:69-78.

[9] Blagoev, B., Ong, S.E., Kratchmarova, I., Mann, M., 2004. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol., 22(9):1139-1145.

[10] Boguski, M.S., McIntosh, M.W., 2003. Biomedical informatics for proteomics. Nature, 422(6928):233-237.

[11] Braun, S., Pantel, K., Muller, P., Janni, W., Hepp, F., Kentenich, C.R., Gastroph, S., Wischnik, A., Dimpfl, T., Kindermann, G., et al., 2000. Cytokeratin-positive cells in the bone marrow and survival of patients with stage I, II, or III breast cancer. N. Engl. J. Med., 342(8):525-533.

[12] Cagney, G., Emili, A. 2002. De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging. Nat. Biotechnol., 20(2):163-170.

[13] Celis, J.E., Gromov, P., 2003. Proteomics in translational cancer research: toward an integrated approach. Cancer Cell, 3(1):9-15.

[14] Celis, J.E., Celis, P., Palsdottir, H., Ostergaard, M., Gromov, P., Primdahl, H., Orntoft, T.F., Wolf, H., Celis, A., Gromova, I., 2002. Proteomic strategies to reveal tumor heterogeneity among urothelial papillomas. Mol. Cell Proteomics, 1(4):269-279.

[15] Chakravarti, D.N., Gallagher, S., Chakravarti, B., 2004. Difference gel electrophoresis: application in quantitative proteomics research. Current Proteomics, 1(4):261-271.

[16] Chen, E.I., Hewel, J., Felding-Habermann, B., Yates, J.R.3rd, 2006. Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol. Cell Proteomics., 5(1):53-56.

[17] Clarke, C.H., Buckley, J.A., Fung, E.T., 2005. SELDI-TOF-MS proteomics of breast cancer. Clin. Chem. Lab. Med., 43(12):1314-1320.

[18] Conrads, T.P., Hood, B.L., Petricoin III, E.F., Liotta, L.A., Veenstra, T.D., 2005. Cancer proteomics: many technologies, one goal. Expert Rev. Proteomics, 2(5):693-703.

[19] Corder, E.H., Guess, H.A., Hulka, B.S., Friedman, G.D., Sadler, M., Vollmer, R.T., Lobaugh, B., Drezner, M.K., Vogelman, J.H., Orentreich, N., 1993. Vitamin D and prostate cancer: a prediagnostic study with stored sera. Cancer Epidemiol., Biomarkers & Prev., 2:467-472.

[20] Durr, E., Yu, J., Krasinska, K.M., Carver, L.A., Yates, J.R., Testa, J.E., Oh, P., Schnitzer, J.E., 2004. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat. Biotechnol., 22(8):985-992.

[21] Ebanks, R.O., Goguen, M., McKinnon, S., Pinto, D.M., Ross, N.W., 2005. Identification of the major outer membrane proteins of Aeromonas salmonicida. Dis. Aquat. Organ., 68(1):29-38.

[22] Ebanks, R.O., Chisholm, K., McKinnon, S., Whiteway, M., Pinto, D.M., 2006. Proteomic analysis of Candida albicans yeast and hyphal cell wall and associated proteins. Proteomics, 6(7):2147-2156.

[23] Guzzetta, A.W., Chien, A.S., 2005. A double-vented tetraphasic continuous column approach to MuDPIT analysis on long capillary columns demonstrates superior proteomic coverage. J. Proteome Res., 4(6):2412-2419.

[24] Hammond, M.E., Taube, S.E., 2002. Issues and barriers to development of clinically useful tumor markers: a development pathway proposal. Semin. Oncol., 29(3):213-221.

[25] Hanash, S., 2001. 2-D or not 2-D: is there a future for 2-D gels in proteomics? Insights from the York proteomics meeting. Proteomics, 1:635-637.

[26] Hanash, S., 2003. Disease proteomics. Nature, 422(6928):226-232.

[27] Henderson, N.A., Steele, R.J., 2005. SELDI-TOF proteomic analysis and cancer detection. Surgeon, 3(6):383-390.

[28] Hoheisel, J.D., 2006. Microarray technology: beyond transcript profiling and genotype analysis. Nat. Rev. Genet., 7(3):200-210.

[29] Jessani, N., Niessen, S., Wei, B.Q., Nicolau, M., Humphrey, M., Ji, Y., Han, W., Noh, D.Y., Yates, J.R.3rd, Jeffrey, S.S., et al., 2005. A streamlined platform for high-content functional proteomics of primary human specimens. Nat. Methods, 2(9):691-697.

[30] Kachman, M.T., Wang, H., Schwartz, D.R., Cho, K.R., Lubman, D.M., 2002. A 2-D liquid separations/mass mapping method for interlysate comparison of ovarian cancers. Anal. Chem., 74(8):1779-1791.

[31] Kaji, H., Saito, H., Yamauchi, Y., Shinkawa, T., Taoka, M., Hirabayashi, J., Kasai, K., Takahashi, N., Isobe, T., 2003. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat. Biotechnol., 21(6):667-672.

[32] Khodavirdi, A.C., Song, Z., Yang, S., Zhong, C., Wang, S., Wu, H., Pritchard, C., Nelson, P.S., Roy-Burman, P., 2006. Increased expression of osteopontin contributes to the progression of prostate cancer. Cancer Res., 66(2):883-888.

[33] Knezevic, V., Leethanakul, C., Bichsel, V.E., Worth, J.M., Prabhu, V.V., Gutkind, J.S., Liotta, L.A., Munson, P.J., Petricoin III, E.F., Krizman, D.B., 2001. Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics, 1(10):1271-1278.

[34] Kozak, K.R., Su, F., Whitelegge, J.P., Faull, K., Reddy, S., Farias-Eisner, R., 2005. Characterization of serum biomarkers for detection of early stage ovarian cancer. Proteomics, 5(17):4589-4596.

[35] Lilley, K.S., Friedman, D.B., 2004. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Exp. Rev. Proteomics, 1(4):401-409.

[36] Liotta, L.A., Petricoin, E.F., 2006. Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. J. Clin. Invest., 116(1):26-30.

[37] Ludwig, J.A., Weinstein, J.N., 2005. Biomarkers in Cancer Staging, Prognosis and Treatment Selection. Nature Reviews Cancer, 5(11):845-856.

[38] Masselon, C., Pasa-Tolic, L., Tolic, N., Anderson, G.A., Bogdanov, B., Vilkov, A.N., Shen, Y., Zhao, R., Qian, W.J., Lipton, M.S., et al., 2005. Targeted comparative proteomics by liquid chromatography-tandem fourier ion cyclotron resonance mass spectrometry. Anal. Chem., 77(2):400-406.

[39] McCormack, A.L., Schieltz, D.M., Goode, B., Yang, S., Barnes, G., Drubin, D., Yates, J.R.3rd, 1997. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-Femtomole level. Anal. Chem., 69(4):767-776.

[40] Melanson, J.E., Chisholm, K.A., Pinto, D.M., 2006. Targeted comparative proteomics by liquid chromatography/matrix-assisted laser desorption/ionization triple-quadrupole mass spectrometry. Rapid Commun. Mass Spectrom., 20(5):904-910.

[41] Menard, C., Johann, D., Lowenthal, M., Muanza, T., Sproull, M., Ross, S., Gulley, J., Petricoin, E., Coleman, C.N., Whiteley, G., et al., 2006. Discovering clinical biomarkers of ionizing radiation exposure with serum proteomic analysis. Cancer Res., 66(3):1844-1850.

[42] Moshkovskii, S.A., Serebryakova, M.V., Kuteykin-Teplyakov, K.B., Tikhonova, O.V., Goufman, E.I., Zgoda, V.G., Taranets, I.N., Makarov, O.V., Archakov, A.I., 2005. Ovarian cancer marker of 11.7 kDa detected by proteomics is a serum amyloid A1. Proteomics, 5(14):3790-3797.

[43] Nemeth-Cawley, J.F., Tangarone, B.S., Rouse, J.C., 2003. “Top Down” characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. J. Proteome Res., 2(5):495-505.

[44] Nishizuka, S., Charboneau, L., Young, L., Major, S., Reinhold, W.C., Waltham, M., Kouros-Mehr, H., Bussey, K.J., Lee, J.K., Espina, V., et al., 2003. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl. Acad. Sci. (USA), 100:14229-14234.

[45] Ong, S.E., Mann, M., 2005. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol., 1(5):252-262.

[46] Orchekowski, R., Hamelinck, D., Li, L., Gliwa, E., vanBrocklin, M., Marrero, J.A., Vande, Woude, G.F., Feng, Z., Brand, R., Haab, B.B., 2005. Antibody microarray profiling reveals individual and combined serum proteins associated with pancreatic cancer. Cancer Res., 65(23):11193-11202.

[47] Ozier, O., Amin N., Ideker, T., 2003. Global architecture of genetic interactions on the protein network. Nat. Biotechnol., 21(5):490-491.

[48] Paweletz, C.P., Liotta, L.A., Petricoin, E.F., 2001. New technologies for biomarker analysis of prostate cancer progression: laser capture microdissection and tissue proteomics. Urology, 57(4):160-163.

[49] Pawlik, T.M., Hawke, D.H., Liu, Y., Krishnamurthy, S., Fritsche, H., Hunt, K.K., Kuerer, H.M., 2006. Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein. BMC Cancer, 6(1):68.

[50] Petricoin, E.F., Zoon, K.C., Kohn, E.C., Barrett, J.C., Liotta, L.A., 2002a. Clinical proteomics: translating benchside promise into bedside reality. Nature Rev. Drug Discov., 1(9):683-695.

[51] Petricoin III, E., Ardekani, A., Hitt, B., Levine, P., Fusaro, V., Steinberg, S., Mills, G., Simone, C., Fishman, D., Kohn, E., et al., 2002b. Use of proteomic patterns in serum to identify ovarian cancer. The Lancet, 359(9306):572-577.

[52] Petricoin, E.F., Ornstein, D.K., Liotta, L.A., 2004. Clinical proteomics: applications for prostate cancer biomarker discovery and detection. Urol. Oncol., 22(4):322-328.

[53] Phizicky, E., Bastiaens, P.I.H., Zhu, H., Snyder, M., Fields, S., 2003. Protein analysis on a proteomic scale. Nature, 422(6928):208-215.

[54] Pusztai, L., Gianni, L., 2004. Technology insight: emerging techniques to predict response to preoperative chemotherapy in breast cancer. Nat. Clin. Pract. Oncol., 1(1):44-50.

[55] Ramus, C., de Peredo, A.G., Dahout, C., Gallagher, M., Garin, J., 2006. An optimized strategy for ICAT quantification of membrane proteins. Mol. Cell Proteomics., 5(1):68-78.

[56] Ricolleau, G., Charbonnel, C., Lode, L., Loussouarn, D., Joalland, M.P., Bogumil, R., Jourdain, S., Minvielle, S., Campone, M., Deporte-Fety, R., et al., 2006. Surface-enhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node-negative breast cancer tumors. Proteomics, 6(6):1963-1975.

[57] Righetti, P.G., Castagna, A., Herbert, B., Reymond, F., Rossier, J.S., 2003. Prefractionation techniques in proteome analysis. Proteomics, 3(8):1397-1407.

[58] Schrimpf, S.P., Meskenaite, V., Brunner, E., Rutishauser, D., Walther, P., Eng, J., Aebersold, R., Sonderegger, P., 2005. Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics, 5(10):2531-2541.

[59] Shadforth, I.P., Dunkley, T.P., Lilley, K.S., Bessant, C., 2005. i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics, 6(1):145.

[60] Shen, Y., Strittmatter, E.F., Zhang, R., Metz, T.O., Moore, R.J., Li, F., Udseth, H.R., Smith, R.D., Unger, K.K., Kumar, D., et al., 2005. Making broad proteome protein measurements in 1~5 min using high-speed RPLC separations and high-accuracy mass measurements. Anal. Chem., 77(23):7763-7773.

[61] Sidransky, D., 2002. Emerging molecular markers of cancer. Nature Rev. Cancer, 2(3):210-219.

[62] Staunton, J.E., Slonim, D.K., Coller, H.A., Tamayo, P., Angelo, M.J., Park, J., Scherf, U., Lee, J.K., Reinhold, W.O., Weinstein, J.N., Mesirov, J.P., et al., 2001. Chemosensitivity prediction by transcriptional profiling. Proc. Natl. Acad. Sci. (USA), 98:10787-10792.

[63] Tyers, M., Mann, M., 2003. From genomics to proteomics. Nature, 422(6928):193-197.

[64] van de Vijver, M.J., He, Y.D., van′t Veer, L.J., Dai. H., Hart, A.A., Voskuil, D.W., Schreiber, G.J., Peterse, J.L., Roberts, C., Marton, M.J., et al., 2002. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med., 347(25):1999-2009.

[65] van′t Veer, L.J., Dai, H., van de Vijver, M.J., He, Y.D., Hart, A.A., Mao, M., Peterse, H.L., van der Kooy, K., Marton, M.J., Witteveen, A.T., et al., 2002. Gene-expression profiling predicts clinical outcome of breast cancer. Nature, 415(6871):530-536.

[66] Wang, H., Clouthier, S.G., Galchev, V., Misek, D.E., Duffner, U., Min, C.K., Zhao, R., Tra, J., Omenn, G.S., Ferrara, J.L., et al., 2005. Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Molecular & Cellular Proteomics, 4(5):618-625.

[67] Washburn, M.P., Ulaszek, R.R., Yates, J.R.3rd, 2003. Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology. Anal. Chem., 75(19):5054-5061.

[68] Wolters, D.A., Washburn, M.P., Yates, J.R.III., 2001. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem., 73(23):5683-5690.

[69] Wu, C.C., MacCoss, M.J., Howell, K.E., Yates, J.R.3rd, 2003. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol., 21(5):532-538.

[70] Wu, W.W., Wang, G., Baek, S.J., Shen, R.F., 2006. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res., 5(3):651-658.

[71] Wulfkuhle, J.D., Liotta, L.A., Petricoin, E.F., 2003. Proteomic applications for the early detection of cancer. Nature Rev. Cancer, 3(4):267-275.

[72] Ye, B., Cramer, D.W., Skates, S.J., Gygi, S.P., Pratomo, V., Fu, L., Horick, N.K., Licklider, L.J., Schorge, J.O., Berkowitz, R.S., et al., 2003. Haptoglobin-alpha subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. Clin. Cancer Res., 9(8):2904-2911.

[73] Yu, K.H., Rustgi, A.K., Blair, I.A., 2005. Characterization of proteins in human pancreatic cancer serum using differential gel electrophoresis and tandem mass spectrometry. J. Proteome Res., 4(5):1742-1751.

[74] Zhang, Z., Bast, R.C.Jr., Yu, Y., Li, J., Sokoll, L.J., Rai, A.J., Rosenzweig, J.M., Cameron, B., Wang, Y.Y., Meng, X.Y., et al., 2004. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res., 64(16):5882-5890.

[75] Ziauddin, J., Sabatini, D.M., 2001. Microarrays of cells expressing defined cDNAs. Nature, 411(6833):107-110.

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