Body fluid proteomics: Prospects for biomarker discovery

Proteomics - Clinical Applications

Volumn 1, Issue 9, 2007, Pages 1004-1015

  Ahn, Sung Min ^a,b   Simpson, Richard J ^a  

^a WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^b Gachon University College of Medicine   (South Korea)

Author keywords

Alzheimer's disease; Biomarker; Body fluid

Indexed keywords

ALBUMIN; AMYLOID BETA PROTEIN; ANTINEOPLASTIC HORMONE AGONISTS AND ANTAGONISTS; CARCINOEMBRYONIC ANTIGEN; PEPTIDE DERIVATIVE; PROTEIN DERIVATIVE; PROTEOME; TUMOR MARKER;

ALZHEIMER DISEASE; ANTIGEN DETECTION; BIOMEDICINE; BLOOD ANALYSIS; BODY FLUID; BREAST CANCER; CANCER STAGING; CEREBROSPINAL FLUID; CEREBROSPINAL FLUID ANALYSIS; CLINICAL CHEMISTRY; CLINICAL PROTEOMICS; CORRELATION ANALYSIS; DILUTION; DISEASE MARKER; EARLY DIAGNOSIS; GASTROINTESTINAL DISEASE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; PEPTIDOMICS; PRIORITY JOURNAL; PROGNOSIS; PROTEIN BINDING; PROTEIN BLOOD LEVEL; PROTEIN DEPLETION; PROTEIN DETERMINATION; PROTEOMICS; REVIEW; SENSITIVITY AND SPECIFICITY; URINALYSIS;

EID: 38349097360     PISSN: 18628346     EISSN: None     Source Type: Journal    
DOI: 10.1002/prca.200700217     Document Type: Review

References (107)

1. Weinberg, R. A., The Biology of Cancer, Garland Science, New York 2007.
2. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C. et al., Science 1999, 286, 531-537.
3. Lu, J., Getz, G., Miska, E. A., Alvarez-Saavedra, E. et al., Nature 2005, 435, 834-838.
4. Ahn, S., Simpson, R., in: Thongbookerd, V. (Ed.), Proteomics of Human Body Fluids: Principles, Methods, and Applications, Humana Press, Totowa 2007, pp. 3-30.
5. Lilley, K. S., Friedman, D. B., Expert Rev. Proteomics 2004, 1, 401-409.
6. Unlu, M., Morgan, M. E., Minden, J. S., Electrophoresis 1997, 18, 2071-2077.
7. Marengo, E., Robotti, E., Antonucci, F., Cecconi, D. et al., Proteomics 2005, 5, 654-666.
8. Knowles, M. R., Cervino, S., Skynner, H. A., Hunt, S. P. et al., Proteomics 2003, 3, 1162-1171.
9. Lilley, K. S., Friedman, D. B., Expert Rev. Proteomics 2004, 1, 401-409.
10. Gundry, R. L., Fu, Q., Jelinek, C. A., Van Eyk, J. E., Cotter, R. J., Proteomics Clin. Appl. 2007, 1, 73-88.
11. Ong, S. E., Mann, M., Nat. Chem. Biol. 2005, 1, 252-262.
12. Washburn, M. P., Wolters, D., Yates, J. R., 3rd, Nat. Biotechnol. 2001, 19, 242-247.
13. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Mol. Cell. Proteomics 2002, 1, 376-386.
14. Beynon, R. J., Pratt, J. M., Mol. Cell. Proteomics 2005, 4, 857-872.
15. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Mol. Cell. Proteomics 2004, 3, 1154-1169.
16. Wu, W. W., Wang, G., Baek, S. J., Shen, R. F., J. Proteome Res. 2006, 5, 651-658.
17. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G. et al., Mol. Cell. Proteomics 2005, 4, 1487-1502.
18. Liu, H., Sadygov, R. G., Yates, J. R., 3rd, Anal. Chem. 2004, 76, 4193-4201.
19. Kapp, E. A., Schutz, F., Connolly, L. M., Chakel, J. A. et al., Proteomics 2005, 5, 3475-3490.
20. Julka, S., Regnier, F., J. Proteome Res. 2004, 3, 350-363.
21. Hu, S., Loo, J. A., Wong, D. T., Proteomics 2006, 6, 6326-6353.
22. Thongbookerd, V., Proteomics of Human body Fluids: Principles, Methods, and Applications, Humana Press, Totowa 2007.
23. Guyton, A. C., Hall, J. E., Textbook of Medical Physiology, W. B. Saunders, Philadelphia 2000, pp. 264-294.
24. Liotta, L. A., Ferrari, M., Petricoin, E., Nature 2003, 425, 905.
25. Jongeneel, C. V., Delorenzi, M., Iseli, C., Zhou, D. et al., Genome Res. 2005, 15, 1007-1014.
26. Grimmond, S. M., Miranda, K. C., Yuan, Z., Davis, M. J. et al., Genome Res. 2003, 13, 1350-1359.
27. Clark, H. F., Gurney, A. L., Abaya, E., Baker, K. et al., Genome Res. 2003, 13, 2265-2270.
28. Harter, C., Reinhard, C., Subcell. Biochem. 2000, 34, 1-38.
29. Bendtsen, J. D., Jensen, L. J., Blom, N., Von Heijne, G., Bronak, S., Protein Eng. Des. Sel. 2004, 17, 349-356.
30. Moritz, R. L., Ji, H., Schutz, F., Connolly, L. M. et al., Anal. Chem. 2004, 76, 4811-4824.
31. Bernard, O. K., Kapp, E. A., Simpson, R. J., J. Proteome Res. 2007, 6, 987-995.
32. Zhang, H., Li, X. J., Martin, D. B., Aebersold, R., Nat. Biotechnol. 2003, 21, 660-666.
33. Kaji, H., Saito, H., Yamauchi, Y, Shinkawa, T. et al., Nat. Biotechnol. 2003, 21, 667-672.
34. Moritz, R. L., Clippingdale, A. B., Kapp, E. A., Eddes, J. S. et al., Proteomics 2005, 5, 3402-3413.
35. Pieper, R., Su, Q., Gatlin, C. L., Huang, S. T. et al., Proteomics 2003, 3, 422-432.
36. Brand, J., Haslberger, T., Zolg, W., Pestlin, G., Palme, S., Proteomics 2006, 6, 3236-3242.
37. Zolg, J. W., Langen, H., Mol. Cell. Proteomics 2004, 3, 345-354.
38. Bjorhall, K., Miliotis, T., Davidsson, P., Proteomics 2005, 5, 307-317.
39. Rabilloud, T., Proteomics 2002, 2, 3-10.
40. Fountoulakis, M., Juranville, J. F., Jiang, L., Avila, D. et al., Amino Acids 2004, 27, 249-259.
41. Sedlaczek, P., Frydecka, I., Gabrys, M., Van Dalen, A. et al., Cancer 2002, 95, 1886-1893.
42. Trape, J., Molina, R., Sant, F., Tumour Biol. 2004, 25, 276-281.
43. Celis, J. E., Gromov, P., Cabezon, T., Moreira, J. M. et al., Mol. Cell. Proteomics 2004, 3, 327-344.
44. Leak, L. V., Liotta, L. A., Krutzsch, H., Jones, M. et al., Proteomics 2004, 4, 753-765.
45. Painter, P. C., Cope, J. Y., Smith, J. L., in: Burtis, C. A., Ashwood, E. R. (Eds.), Fundamentals of Clinical Chemistry, W. B. Saunders Company, Philadelphia 2001.
46. van de Peppel, J., Kemmeren, P., van Bakel, H., Radonjic, M. et al., EMBO Rep. 2003, 4, 387-393.
47. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S. et al., Proc. Natl. Acad. Sci. USA 2005, 102, 15545-15550.
48. Peters, T., All About Albumin: Biochemistry, Genetics, and Medical Applications, Academic Press, San Diego 1996.
49. Klipp, E., Herwig, R., Kowald, A., Wierling, C., Lehrach, H., Systems Biology in Practice: Concepts, limplementation and Application, Wiley VCH, Weinheim 2005.
50. van der Great J., Stroobant, P., van der Heijden, R., Curr. Opin. Chem. Biol. 2004, 8, 559-565.
51. Davidov, E., Clish, C. B., Oresic, M., Meys, M. et al., Omics 2004, 8, 267-288.
52. Tirumalai, R. S., Chan, K. C., Prieto, D. A., Issaq, H. J. et al., Mol. Cell. Proteomics 2003, 2, 1096-1103.
53. Tiselius, A., Biochem. J. 1937, 31, 1464-1477.
54. O'Connell, T. X., Horita, T. J., Kasravi, B., Am. Fam. Physician 2005, 71, 105-112.
55. Bossuyt, X., Adv. Clin. Chem. 2006, 42, 43-80.
56. Righetti, P. G., Castagna, A., Antonioii, P., Boschetti, E., Electrophoresis 2005, 26, 297-319.
57. Mehta, A. I., Ross, S., Lowenthal, M. S., Fusaro, V. et al., Dis. Markers 2003, 19, 1-10.
58. Petricoin, E. E., Paweletz, C. P., Liotta, L. A., J. Mammary Gland Biol. Neoplasia 2002, 7, 433-440.
59. Wulfkuhle, J. D., Liotta, L. A., Petricoin, E. F., Nat. Rev. Cancer 2003, 3, 267-275.
60. Petricoin, E. F., Zoon, K. C., Kohn, E. C., Barrett, J. C., Liotta, L. A., Nat. Rev. Drug. Discov. 2002, 7, 683-695.
61. Diamandis, E. P., J. Proteome Res. 2006, 5, 2079-2082.
62. Lopez-Otin, C., Overall, C. M., Nat. Rev. Mol. Cell Biol. 2002, 3, 509-519.
63. Overall, C. M., Kleifeld, O., Nat. Rev. Cancer 2006, 6, 227-239.
64. Overall, C. M., Dean, R. A., Cancer Metastasis Rev. 2006, 25, 69-75.
65. Villanueva, J., Shaffer, D. R., Philip, J., Chaparro, C. A. et al., J. Clin. Invest. 2006, 116, 271-284.
66. Hulmes, J. D., Bethea, B., Ho, K., Huang, S. P. et al., Clin. Proteomics 2004, 1, 17-32.
67. Rai, A. J., Gelfand, C. A., Haywood, B. C., Warunek, D. J. et al., Proteomics 2005, 5, 3262-3277.
68. Mogielnicki, R. P., Waldmann, T. A., Strober, W., J. Clin. Invest. 1971, 50, 901-909.
69. Lowenthal, M. S., Mehta, A. I., Frogale, K., Bandle, R. W. et al., Clin. Chem. 2005, 51, 1933-1945.
70. Weston, A. D., Hood, L., J. Proteome Res. 2004, 3, 179-196.
71. Golde, T. E., Dickson, D., Hutton, M., Curr. Alzheimer Res. 2006, 3, 421-430.
72. Irizarry, M. C., NeuroRx 2004, 1, 226-234.
73. Kojro, E., Gimpl, G., Lammich, S., Marz, W., Fahrenholz, F., Proc. Natl. Acad. Sci. USA 2001, 98, 5815-5820.
74. De Pietri Tonelli, D., Mihailovich, M., Di Cesare, A., Codazzi, F. et al., Nucleic Acids Res. 2004, 32, 1808-1817.
75. Behar, D., Wrigley, J, D., Nadin, A., Evin, G. et al., J. Biol. Chem. 2001, 276, 45394-45402.
76. Mattson, M. P., Physiol. Rev. 1997, 77, 1081-1132.
77. Turner, R. S., Semin. Neurol. 2006, 26, 499-506.
78. Zlokovic, B. V., J. Neurochem. 2004, 89, 807-811.
79. Bohrmann, B., Tjernberg, L., Kuner, P., Poli, S. et al., J. Biol. Chem. 1999, 274, 16990-15995.
80. Schenk, D. B., Yednock, T., Neurobiol. Aging 2002, 23, 677-679; discussion 683-674.
81. Nicholson, J. K., Mol. Syst. Biol. 2006, 2, 52.
82. Anderson, L., J. Physioi. 2005, 563, 23-60.
83. Diamandis, E. P., Mol. Cell. Proteomics 2004, 3, 367-378.
84. Etzioni, R., Urban, N., Ramsey, S., McIntosh, M. et al., Nat. Rev. Cancer 2003, 3, 243-252.
85. Hartwell, L., Mankoff, D., Paulovich, A., Ramsey, S., Swisher, E., Nat. Biotechnol. 2006, 24, 905-908.
86. Guyton, A. C., Hall, J. E., Textbook of Medical Physiology, W. B. Saunders, Philadelphia 2000, pp. 144-151.
87. Bossuyt, X., Bogaerts, A., Schiettekatte, G., Blanckaert, N., Clin. Chem. 1998, 44, 944-949.
88. Liotta, L. A., Petricoin, E. F., J. Clin. Invest. 2006, 116, 26-30.
89. Omenn, G. S., Exploring the Human Plasma Proteome, Wiley-VCH, Weinheim 2006.
90. Gronborg, M., Bunkenborg, J., Kristiansen, T. Z., Jensen, O. N. et al., J. Proteome Res. 2004, 3, 1042-1055.
91. Hortin, G. L., Sviridov, D., Pharmacogenomics 2007, 8, 237-255.
92. Dihazi, H., Muller, G. A., Expert Rev. Proteomics 2007, 4, 39-50.
93. Tyan, Y. C., Wu, H. Y., Lai, W. W., Su, W. C., Liao, P. C., J. Proteome Res. 2005, 4, 1274-1286.
94. Tyan, Y. C., Wu, H. Y., Su, W. C., Chen, R. W., Liao, P. C., Proteomics 2005, 5, 1062-1074.
95. Bard, M. P., Hegmans, J. P., Hemmes, A., Luider, T. M. et al., Am. J. Respir. Cell Mol. Biol. 2004, 31, 114-121.
96. Andre, F., Schartz, N. E., Movassagh, M., Flament, C. et al., Lancet 2002, 360, 295-305.
97. Pawlik, T. M., Hawke, D. H., Liu, Y., Krishnamurthy, S. et al., BMC Cancer 2006, 6, 68.
98. Pilch, B., Mann, M., Genome Biol. 2006, 7, R40.
99. Sinz, A., Bantscheff, M., Mikkat, S., Ringel, B. et al., Electrophoresis 2002, 23, 3445-3456.
100. Wattiez, R., Falmagne, P., J. Chromatogr. B Analyt Technol. Biomed. Life Sci. 2005, 815, 169-178.
101. de Souza, G. A., Godoy, L. M., Mann, M., Genome Biol. 2006, 7, R72.
102. Vitorino, R., Lobo, M. J., Ferrer-Correira, A. J., Dubin, J. R. et al., Proteomics 2004, 4, 1109-1115.
103. Pandey, M., Shukla, V. K., Eur. J. Cancer Prev. 2000, 9, 165-171.
104. Thadikkaran, L., Crettaz, D., Siegenthaler, M. A., Gallot, D. et al., Clin. Chim. Acta 2005, 360, 27-36.
105. Vuadens, F., Benay, C., Crettaz, D., Gallot, D. et al., Proteomics 2003, 3, 1521-1525.
106. Oleksiewicz, M. B., Scand. J. Gastroenterol. 2004, 39, 787-788.
107. Ludwig, J. A., Weinstein, J. N., Nat. Rev. Cancer 2005, 5, 845-856.