Emerging studies of the urinary proteome: The end of the beginning?

Current Opinion in Nephrology and Hypertension

Volumn 14, Issue 6, 2005, Pages 579-585

  O'Riordan, Edmond ^a   Goligorsky, Michael S ^a  

^a NEW YORK MEDICAL COLLEGE   (United States)

Author keywords

Electrophoresis; Mass spectroscopy; Renal disease; Renal tumors; Transplant rejection

Indexed keywords

BETA 2 MICROGLOBULIN; BETA2 GLYCOPROTEIN 1; BIOCHEMICAL MARKER; CALRETICULIN; CATECHOL METHYLTRANSFERASE; GAMMA SYNUCLEIN; HEMOPEXIN; MEGALIN; OSTEOCALCIN; POLYPEPTIDE; PROTEOME; RETINOL BINDING PROTEIN; VITAMIN D BINDING PROTEIN;

AMINO ACID ANALYSIS; BIOINFORMATICS; BLADDER CANCER; CAPILLARY ELECTROPHORESIS; DIAGNOSTIC ACCURACY; DISEASE MARKER; GEL ELECTROPHORESIS; GENE EXPRESSION; GLOMERULOSCLEROSIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; IMMUNOGLOBULIN A NEPHROPATHY; KIDNEY CANCER; KIDNEY DISEASE; KIDNEY GRAFT REJECTION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MEMBRANOUS GLOMERULONEPHRITIS; NON INSULIN DEPENDENT DIABETES MELLITUS; PATHOPHYSIOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN URINE LEVEL; PROTEINURIA; PROTEOMICS; RETINOPATHY; REVIEW; SENSITIVITY AND SPECIFICITY; SEPARATION TECHNIQUE; TWO DIMENSIONAL GEL ELECTROPHORESIS; ULTRACENTRIFUGATION; URINARY EXCRETION; UROLITHIASIS;

EID: 27444444283     PISSN: 10624821     EISSN: None     Source Type: Journal    
DOI: 10.1097/01.mnh.0000168425.60729.36     Document Type: Review

References (43)

1. Knepper MA. Proteomics and the kidney. J Am Soc Nephrol 2002; 13:1398-1408.
2. Arthur JM. Proteomics. Curr Opin Nephrol Hypertens 2003; 12:423-430.
3. Hewitt SM, Dear J, Star RA. Discovery of protein biomarkers for renal diseases. J Am Soc Nephrol 2004; 15:1677-1689. Roadmap for biomarker discovery in renal disease.
4. Osicka TM, Houlihan CA, Chan JG, et al. Albuminuria in patients with type 1 diabetes is directly linked to changes in the lysosome-mediated degradation of albumin during renal passage. Diabetes 2000; 49:1579-1584.
5. D'Amico G, Bazzi C. Pathophysiology of proteinuria. Kidney Int 2003; 63:809-825.
6. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003; 422:198-207.
7. Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 2004; 287:L1-L23.
8. Hachey DL, Chaurand P. Proteomics in reproductive medicine: the technology for separation and identification of proteins. J Reprod Immunol 2004; 63:61-73. Excellent up-to-date review of the current proteomic technologies and approaches for the non-specialist in proteomics.
9. Issaq HJ, Chan KC, Janini GM, et al. Multidimensional separation of peptides for effective proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 817:35-47. Thorough review of the crucial first step in sample analysis.
10. Fung EDD, Simonsen A, Weinberger S. The use of SELDI protein chip array technology in renal disease research. In: Goligorsky MS, editor. Renal disease: techniques and protocols. Totowa, NJ: Humana Press; 2003 pp. 295-314.
11. Anderson NG, Anderson NL, Tollaksen SL. Proteins of human urine. I. Concentration and analysis by two-dimensional electrophoresis. Clin Chem 1979; 25:1199-1210.
12. Edwards JJ, Tollaksen SL, Anderson NG. Proteins of human urine. III. Identification and two-dimensional electrophoretic map positions of some major urinary proteins. Clin Chem 1982; 28:941-948.
13. Marouga R, David S, Hawkins E. The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 2005; 382:669-678. A key development in abundance profiling.
14. Spahr CS, Davis MT, McGinley MD, et al. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 2001; 1:93-107.
15. Li J, Zhang Z, Rosenzweig J, et al. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002; 48:1296-1304.
16. Adam BL, Qu Y, Davis JW, et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 2002; 62:3609-3614.
17. Qu Y, Adam BL, Yasui Y, et al. Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin Chem 2002; 48:1835-1843.
18. Boguski MS, McIntosh MW. Biomedical informatics for proteomics. Nature 2003; 422:233-237.
19. Granger CB, Van Eyk JE, Mockrin SC, Anderson NL. National Heart, Lung, and Blood Institute Clinical Proteomics Working Group report. Circulation 2004; 109:1697-1703.
20. O'Riordan E, Orlova TN, Mei JJ, et al. Bioinformatic analysis of the urine proteome of acute allograft rejection. J Am Soc Nephrol 2004; 15:3240-3248. Practical description of approaches to the analysis of SELDI data.
21. Oh J, Pyo JH, Jo EH, et al. Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics 2004; 4:3485-3497. Excellent rigorous analysis of the urinary proteome.
22. Smith G, Barratt D, Rowlinson R, et al. Development of a high-throughput method for preparing human urine for two-dimensional electrophoresis. Proteomics 2005; 5:2315-2318. Simplified yet effective method of urinary proteomic analysis.
23. Pieper R, Gatlin CL, McGrath AM, et al. Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 2004; 4:1159-1 174. A thorough account of the normal urinary proteome that shows the continued value of 2-DE.
24. Lafitte D, Dussol B, Andersen S, et al. Optimized preparation of urine samples for two-dimensional electrophoresis and initial application to patient samples. Clin Biochem 2002; 35:581-589.
25. Thongboonkerd V, McLeish KR, Arthur JM, Klein JB. Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int 2002; 62:1461-1469.
26. Thongboonkerd V, Klein JB, Arthur JM. Proteomic identification of a large complement of rat urinary proteins. Nephron Exp Nephrol 2003; 95:e69-e78.
27. Celis JE, Ostergaard M, Rasmussen HH, et al. A comprehensive protein resource for the study of bladder cancer: http://biobase.dk/cgi-bin/celis. Electrophoresis 1999; 20:300-309.
28. Schaub S, Wilkins J, Weiler T, et al. Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 2004; 65:323-332. Useful technical note on common pitfalls and normal variability.
29. Pisitkun T, Shen RF, Knepper MA. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci USA 2004; 101:13368-13373. Novel thorough description of the proteome of a urinary subcompartment; the first of its kind.
30. Norden AG, Sharratt P, Cutillas PR, et al. Quantitative amino acid and proteomic analysis: very low excretion of polypeptides >750 Da in normal urine. Kidney Int 2004; 66:1994-2003. Focused description of the low-molecular-mass proteins in normal urine excluded by most techniques.
31. Thongboonkerd V, Klein JB, Pierce WM, et al. Sodium loading changes urinary protein excretion: a proteomic analysis. Am J Physiol Renal Physiol 2003; 284:F1155-F1163.
32. Weissinger EM, Wittke S, Kaiser T, et al. Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int 2004; 65:2426-2434. Novel approaches to the urinary diagnosis of kidney disease.
33. Mischak H, Kaiser T, Waiden M, et al. Proteomic analysis for the assessment of diabetic renal damage in humans. Clin Sci (Lond) 2004; 107:485-495. Premier description of the diabetic urinary proteome.
34. Haubitz M, Wittke S, Weissinger EM, et al. Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int 2005; 67:2313-2320. First description of the IgA nephropathy urinary proteome.
35. Hampel DJ, Sansome C, Sha M, et al. Toward proteomics in uroscopy: urinary protein profiles after radiocontrast medium administration. J Am Soc Nephrol 2001; 12:1026-1035.
36. Cutillas PR, Chalkley RJ, Hansen KC, et al. The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol 2004; 287:F353-F364.
37. Cadieux PA, Seiko DT, Watterson JD, et al. Surface-enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS): a new proteomic urinary test for patients with urolithiasis. J Clin Lab Anal 2004; 18:170-175.
38. Clarke W, Silverman BC, Zhang Z, et al. Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg 2003; 237:660-664; discussion 664-665.
39. Schaub S, Rush D, Wilkins J, et al. Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol 2004; 15:219-227. Good biomarker identified with a high-throughput technique; good reproducibility; it also has longitudinal data.
40. Schaub S, Wilkins JA, Antonovici M, et al. Proteomic-based identification of cleaved urinary beta2-microglobulin as a potential marker for acute tubular injury in renal allografts. Am J Transplant 2005; 5:729-738. The identification of a biomarker discovered by proteomic methods also develops a pathophysiologic basis for the biomarker.
41. Rogers M, Clarke P, Noble J, et al. Proteomic profiling of urinary proteins in renal cancer by SELDI and neural network analysis: identification of key issues affecting potential clinical utility. Cancer Res 2003; 63:6971-6983.
42. Iwaki H, Kageyama S, Isono T, et al. Diagnostic potential in bladder cancer of a panel of tumor markers (calreticulin, γ-synuclein, and catechol-o-methyltransferase) identified by proteomic analysis. Cancer Sci 2004; 95:955-961. Based on previous proteomic analyses, the authors confirm the diagnostic validity of the selected biomarkers of bladder cancer.
43. Ivaska K, Hellman J, Likojarvi J, et al. Identification of novel proteolytic forms of osteocalcin in human urine. Biochem Biophys Res Commun 2003; 306:973-980.