Proteomic Profiling of Urinary Proteins in Renal Cancer by Surface Enhanced Laser Desorption Ionization and Neural-Network Analysis: Identification of Key Issues Affecting Potential Clinical Utility

Cancer Research

Volumn 63, Issue 20, 2003, Pages 6971-6983

  Rogers, Mark A ^a   Clarke, Paul ^a   Noble, Jason ^b   Munro, Nicholas P ^a   Paul, Alan ^a   Selby, Peter J ^a   Banks, Rosamonde E ^a  

^a ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; TUMOR MARKER;

ADULT; AGED; ARTICLE; ARTIFICIAL NEURAL NETWORK; CANCER SCREENING; CONTROLLED STUDY; DIAGNOSTIC VALUE; FEMALE; HUMAN; KIDNEY CARCINOMA; MAJOR CLINICAL STUDY; MALE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN URINE LEVEL; PROTEOMICS; SURFACE ENHANCED LASER DESORPTION IONIZATION MASS SPECTROMETRY;

ADULT; AGED; AGED, 80 AND OVER; CARCINOMA, RENAL CELL; FEMALE; HUMANS; KIDNEY NEOPLASMS; MALE; MASS SPECTROMETRY; MIDDLE AGED; NEOPLASM PROTEINS; NEURAL NETWORKS (COMPUTER); PROTEIN ARRAY ANALYSIS; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 0142250869     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (51)

1. Srinivas, P. R., Kramer, B. S., and Srivastava, S. Trends in biomarker research for cancer detection. Lancet Oncol., 2: 698-704, 2001.
2. Vogelzang, N. J., and Stadler, W. M. Kidney cancer. Lancet, 352: 1691-1696, 1998.
3. Pantuck, A. J., Zisman, A., and Belldegrun, A. S. The changing natural history of renal cell carcinoma. J. Urol., 166: 1611-1623, 2001.
4. Glaspy, J. A. Therapeutic options in the management of renal cell carcinoma. Semin. Oncol., 29: 41-46, 2002.
5. Zhou, M., and Rubin, M. A. Molecular markers for renal cell carcinoma: impact on diagnosis and treatment. Semin. Urol. Oncol., 19: 80-87, 2001.
6. Anderson, N. G., Anderson, N. L., and Tollaksen, S. L. Proteins of human urine. I. Concentration and analysis by two-dimensional electrophoresis. Clin. Chem., 25: 1199-1210, 1979.
7. Edwards, J. J., Tollaksen, S. L., and Anderson, N. G. Proteins of human urine. III. Identification and two-dimensional electrophoretic map positions of some major urinary proteins. Clin. Chem., 28: 941-948, 1982.
8. Marshall, T., Williams, K. M., and Vesterberg, O. Unconcentrated human urinary proteins analysed by high resolution two-dimensional electrophoresis with narrow pH gradients: preliminary findings after occupational exposure to cadmium. Electrophoresis, 6: 47-52, 1985.
9. Büeler, M. R., Wiederkehr, F., and Vonderschmitt, D. J. Electrophoretic, chromatographic and immunological studies of human urinary proteins. Electrophoresis, 16: 124-134, 1995.
10. Grover, P. K., and Resnick, M. I. Two-dimensional analysis of proteins in unprocessed human urine using double stain. J. Urol., 150: 1069-1072, 1993.
11. Spahr, C. S., Davis, M. T., McGinley, M. D., Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Courchesne, P. L., Chen, K., Wahl, R. C., Yu, W., Luethy, R., and Patterson, S. D. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics, 1: 93-107, 2001.
12. Pang, J. X., Ginanni, N., Dongre, A. R., Hefta, S. A., and Opiteck, G. J. Biomarker discovery in urine by proteomics. J. Proteome. Res., 1: 161-169, 2002.
13. Edwards, J. J., Anderson, N. G., Tollaksen, S. L., von Eschenbach, A. C., and Guevara, J., Jr. Proteins of human urine. II. Identification by two-dimensional electrophoresis of a new candidate marker for prostatic cancer. Clin. Chem., 28: 160-163, 1982.
14. Ostergaard, M., Wolf, H., Orntoft, T. F., and Celis, J. E. Psoriasin (S100A7): a putative urinary marker for the follow-up of patients with bladder squamous cell carcinomas. Electrophoresis, 20: 349-354, 1999.
15. Rasmussen, H. H., Orntoft, T. F., Wolf, H., and Celis, J. E. Towards a comprehensive database of proteins from the urine of patients with bladder cancer. J. Urol., 155: 2113-2119, 1996.
16. Stemnan, U. H. Tumor-associated trypsin inhibitor. Clin. Chem., 48: 1206-1209, 2002.
17. Konety, B. R., and Getzenberg, R. H. Urine based markers of urological malignancy. J. Urol., 165: 600-611, 2001.
18. Ross, J. S., and Cohen, M. B. Biomarkers for the detection of bladder cancer. Adv. Anat. Pathol., 8: 37-45, 2001.
19. Huang, S., Rhee, E., Patel, H., Park, E., and Kaswick, J. Urinary NMP22 and renal cell carcinoma. Urology, 55: 227-230, 2000.
20. Ozer, G., Altinel, M., Kocak, B., Yazicioglu, A., and Gonenc, F. Value of urinary NMP-22 in patients with renal cell carcinoma. Urology, 60: 593-597, 2002.
21. Rodriguez-Cuartero, A., Barcelona-Martin, F., and Perez-Blanco, F. J. Urinary β-glucuronidase in renal cell carcinoma. Clin. Nephrology, 53: 288-290, 2000.
22. Merchant, M., and Weinberger, S. R. Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis, 21: 1164-1177, 2000.
23. von Eggeling, F., Junker, K., Fiedle, W., Wollscheid, V., Durst, M., Claussen, U., and Ernst, G. Mass spectrometry meets chip technology: a new proteomic tool in cancer research? Electrophoresis, 22: 2898-2902, 2001.
24. Paweletz, C. P., Gillespie, J. W., Ornstein, D. K., Simone, N. L., Brown, M. R., Cole, K. A., Wang, Q-H., Huang, J., Hu, N., Yip, T-T., Rich, W. E., Kohn, E. C., Linchan, W. M., Weber, T., Taylor, P., Emmert-Buck, M. R., Liotta, L. A., and Petricoin, E. F. Rapid protein display profiling of cancer progression directly from human tissue using a protein biochip. Drug Dev. Res., 49: 34-42, 2000.
25. Wellmann, A., Wollscheid, V., Lu, H., Ma, Z. L., Albers, P., Schutze, K., Rohde, V., Behrens, P., Dreschers, S., Ko, Y., and Wernert, N. Analysis of microdissected prostate tissue with ProteinChip arrays - a way to new insights into carcinogenesis and to diagnostic tools. Int. J. Mol. Med., 9: 341-347, 2002.
26. Cazares, L. H., Adam, B. L., Ward, M. D., Nasim, S., Schellhammer, P. F., Semmes, O. J., and Wright, G. L., Jr. Normal, benign, preneoplastic, and malignant prostate cells have distinct protein expression profiles resolved by surface enhanced laser desorption/ionization mass spectrometry. Clin. Cancer Res., 8: 2541-2552, 2002.
27. Wright Jr., G. L., Cazares, L. H., Leung, S-M., Nasim, S., Adam, B. L., Yip, T-T., Schellhammer, P. F., Gong, L., and Vlathou, A. Proteinchip surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis., 2: 264-276, 1999.
28. Xiao, Z., Adam, B. L., Cazares, L. H., Clements, M. A., Davis, J. W., Schellhammer, P. F., Dalmasso, E. A., and Wright, G. L., Jr. Quantitation of serum prostate-specific membrane antigen by a novel protein biochip immunoassay discriminates benign from malignant prostate disease. Cancer Res., 61: 6029-6033, 2001.
29. Vlahou, A., Schellhammer, P. F., Mendrinos, S., Patel, K., Kondylis, F. I., Gong, L., Nasim, S., and Wright Jr., G. L. Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am. J. Pathol., 158: 1491-1502, 2001.
30. Rosty, C., Christa, L., Kuzdzal, S., Baldwin, W. M., Zahurak, M. L., Carnot, F., Chan, D. W., Canto, M., Lillemoc, K. D., Cameron, J. L., Yeo, C. J., Hruban, R. H., and Goggins, M. Identification of hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. Cancer Res., 62: 1868-1875, 2002.
31. Petricoin, E. F., III, Ornstein, D. K., Paweletz, C. P., Ardekani, A., Hackett, P. S., Hitt, B. A., Velassco, A., Trucco, C., Wiegand, L., Wood, K., Simone, C. B., Levine, P. J., Linchan, W. M., Emmert-Buck, M. R., Steinberg, S. M., Kohn, E. C., and Liotta, L. A. Serum proteomic patterns for detection of prostate cancer. J. Natl. Cancer Inst., 94: 1576-1578, 2002.
32. Adam, B. L., Qu, Y., Davis, J. W., Ward, M. D., Clements, M. A., Cazares, L. H., Semmes, O. J., Schellhammer, P. F., Yasui, Y., Feng, Z., and Wright Jr., G. L. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res., 62: 3609-3614, 2002.
33. Li, J., Zhang, Z., Rosenzweig, J., Wang, Y. Y., and Chan, D. W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem., 48: 1296-1304, 2002.
34. Qu, Y., Adam, B-L., Yasui, Y., Ward, M. D., Cazares, L. H., Schellhammer, P. F., Feng, Z., Semmes, O. J., and Wright, G. L. Boosted decision free analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin. Chem., 48: 1835-1843, 2002.
35. Petricoin III, E. F., Ardekani, A. M., Hitt, B. A., Levine, P. J., Fusaro, V. A., Steinberg, S. M., Mills, G. B., Simone, C., Fishman, D. A., Kohn, E. C., and Liotta, L. A. Use of proteomic patterns in serum to identify ovarian cancer. Lancet, 359: 572-577, 2002.
36. Townsend, J. C., Sadler, W. A., and Shanks, G. M. The effect of storage pH on the precipitation of proteins in deep frozen urine samples. Ann. Clin. Biochem., 24(Pt I): 111-112, 1987.
37. Rumelhart, D. E., Hinton, G. E., and Williams, R. J. Learning internal representations by error propagation. In: D.E. Rumelhart and J. L. McClelland (eds.), Parallel Distributed Processing: Explorations in the Microstructure of Cognition, pp. 318-362. Cambridge, MA: MIT Press, 1986.
38. Hampel, D. J., Sansome, C., Sha, M., Brodsky, S., Lawson, W. E., and Goligorsky, M. S. Toward proteomics in uroscopy: urinary protein profiles after radiocontrast medium administration. J. Am. Soc. Nephrol., 12: 1026-1035, 2001.
39. Pati, S., Lee, Y., and Samaniego, F. Urinary proteins with pro-apoptotic and antitumor activity. Apoptosis, 5: 21-28, 2000.
40. Valore, E. V., Park, C. H., Quayle, A. J., Wiles, K. R., McCray, P. B., and Ganz, T. Human b-defensin-1: an antimicrobial peptide of urogenital tissues. J. Clin. Investig., 101: 1633-1642, 1998.
41. Zueht, H. D., Grabowsky, J., Schrader, M., Liepke, C., Jurgens, M., Schulz-Knappe, P., and Forssmann, W. G. Human β-defensin-1: a urinary peptide present in variant molecular forms and its putative functional implication. Eur. J. Med. Res., 3: 315-323, 1998.
42. Hiratsuka, T., Nakazato, M., Ihi, T., Minematsu, T., Chino, N., Nakanishi, T., Shimizu, A., Kangawa, K., and Matsukura, S. Structural analysis of human b-defensin-1 and its significance in urinary tract infection. Nephron, 85: 34-40, 1999.
43. Diamond, D. L., Kimball, J. R., Krisanaprakornkit, S., Ganz, T., and Dale, B. A. Detection of β-defensins secreted by human oral epithelial cells. J. Immunol. Methods, 256: 65-76, 2001.
44. Young, A. N., De Oliveira Salles, P. G., Lim, S. D., Cohen, C., Petros, J. A., Marshall, F. F., Neish, A. S., and Amin, M. B. β defensin-1, parvalbumin and vimentin: a panel of diagnostic immunohistochemical markers for renal tumors derived from gene expression profiling studies using cDNA microarrays. Am. J. Surg. Pathol., 27: 199-205, 2003.
45. Sullivan, P. M., Etzioni, R., Feng, Z., Potter, J. D., Thompson, M. L., Thornquist, M., Winget, M., and Yasui, Y. Phases of biomarker development for early detection of cancer. J. Natl. Cancer Inst., 93: 1054-1061, 2001.
46. Schultz, C. J., Dalton, R. N., Turner, C., Neil, H. A. W., and Dunger, D. B. Freezing method affects the concentration and variability of urine proteins and the interpretation of data on microalbuminuria. Diabetic Med., 17: 7-14, 2000.
47. Sargent, D., and Allegra, C. Issues in clinical trial design for tumor marker studies. Semin. Oncol., 29: 222-230, 2002.
48. Hammond, M. E., and Taube, S. E. Issues and barriers to development of clinically useful tumor markers: a development pathway proposal. Semin. Oncol., 29: 213-221, 2002.
49. Biomarkers Ad-hoc Group of the United Kingdom Coordinating Committee on Cancer Research. Biological markers: maintaining standards. Br. J. Cancer, 82: 1627-1628, 2000.
50. Hayes, D. F., Bast, R. C., Desch, C. E., Fritsche, H., Jr., Kemeny, N. E., Jessup, J. M., Locker, G. Y., Macdonald, J. S., Mennel, R. G., Norton, L., Ravdin, P., Taube, S., and Winn, R. J. Tumor marker utility grading system: a framework to evaluate clinical utility of tumor markers. J. Natl. Cancer Inst., 88: 1456-1466, 1996.
51. Verma, M., Wright, G. L., Jr., Hanash, S. M., Gopal-Srivastava, R., and Srivastava, S. Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers. Ann. N. Y. Acad. Sci., 945: 103-115, 2001.