Urinary proteomics as a novel tool for biomarker discovery in kidney diseases

Journal of Zhejiang University: Science B

Volumn 11, Issue 4, 2010, Pages 227-237

  Wu, Jing ^a   Chen, Yi Ding ^a   Gu, Wei ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

Biomarker; Clinical proteomics; Kidney diseases; Urinary proteomics

Indexed keywords

BIOLOGICAL MARKER;

CAPILLARY ELECTROPHORESIS; CENTRIFUGATION; DATA MINING; DIABETIC NEPHROPATHY; EARLY DIAGNOSIS; FANCONI RENOTUBULAR SYNDROME; HUMAN; IMMUNOGLOBULIN A NEPHROPATHY; INTERMETHOD COMPARISON; KIDNEY ALLOGRAFT REJECTION; KIDNEY DISEASE; KIDNEY INJURY; LABORATORY DIAGNOSIS; LIQUID CHROMATOGRAPHY; LUPUS ERYTHEMATOSUS NEPHRITIS; MASS SPECTROMETRY; NON INVASIVE PROCEDURE; PRECIPITATION; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEOMICS; REVIEW; SENSITIVITY AND SPECIFICITY; STORAGE TEMPERATURE; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS; URINALYSIS;

BIOLOGICAL MARKERS; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, CAPILLARY; FANCONI ANEMIA; FEMALE; GLOMERULONEPHRITIS, IGA; HUMANS; KIDNEY; KIDNEY DISEASES; LUPUS NEPHRITIS; MALE; MASS SPECTROMETRY; PROTEIN ARRAY ANALYSIS; PROTEOMICS; URINE;

EID: 77951096890     PISSN: 16731581     EISSN: 18621783     Source Type: Journal    
DOI: 10.1631/jzus.B0900327     Document Type: Review

References (52)

1. F.E. Ahmed 2009 Utility of mass spectrometry for proteome analysis: Part II. Ion-activation methods, statistics, bioinformatics and annotation Expert Rev. Proteomics 6 2 171 197 10.1586/epr.09.4 1:CAS:528:DC%2BD1MXkvFKhsro%3D 19385944
2. E. Bellei E. Rossi L. Lucchi S. Uggeri A. Albertazzi A. Tomasi A. Iannone 2008 Proteomic analysis of early urinary biomarkers of renal changes in type 2 diabetic patients Proteomics Clin. Appl. 2 4 478 491 10.1002/prca.200780109 1:CAS:528:DC%2BD1cXlt1Wltrg%3D (Pubitemid 351566257)
3. R.J. Caiazzo Jr. A.J. Maher M.P. Drummond C.I. Lander O.W. Tassinari B.P. Nelson B.C.S. Liu 2009 Protein microarrays as an application for disease biomarkers Proteomics Clin. Appl. 3 2 138 147 10.1002/prca.200800149 1:CAS:528:DC%2BD1MXislWiurc%3D
4. P.R. Cutillas A.G. Norden R. Cramer A.L. Burlingame R.J. Unwin 2003 Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome Clin. Sci. (Lond) 104 5 483 490 10.1042/CS20020342 1:CAS:528:DC%2BD3sXjtFKlsLc%3D (Pubitemid 36628143)
5. M. Dakna Z. He W.C. Yu H. Mischak W. Kolch 2009 Technical, bioinformatical and statistical aspects of liquid chromatography-mass spectrometry (LC-MS) and capillary electrophoresis-mass spectrometry (CE-MS) based clinical proteomics: a critical assessment J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 877 13 1250 1258 10.1016/j.jchromb.2008.10.048 1:CAS:528:DC%2BD1MXksVCrsrs%3D 19010091
6. J. Drube E. Schiffer H. Mischak M.J. Kemper T. Neuhaus L. Pape R. Lichtinghagen J.H. Ehrich 2009 Urinary proteome pattern in children with renal Fanconi syndrome Nephrol. Dial. Transplant. 24 7 2161 2169 10.1093/ndt/gfp063 1:CAS:528:DC%2BD1MXnslKjsL4%3D 19225019
7. X. Feng X. Liu Q. Luo B.F. Liu 2008 Mass spectrometry in systems biology: an overview Mass Spectrom. Rev. 27 6 635 660 10.1002/mas.20182 18636545
8. G.M. Fiedler S. Baumann A. Leichtle A. Oltmann J. Kase J. Thiery U. Ceglarek 2007 Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Clin. Chem. 53 3 421 428 10.1373/clinchem.2006.077834 1:CAS:528:DC%2BD2sXis1Wnsrg%3D 17272489 (Pubitemid 46447938)
9. E. Finkel 2006 Cloudy or clear? Best forecast for urine cultures CAP Today 20 11 86 90
10. E.T. Fung S.R. Weinberger E. Gavin F. Zhang 2005 Bioinformatics approaches in clinical proteomics Expert Rev. Proteomics 2 6 847 862 10.1586/14789450.2.6.847 1:CAS:528:DC%2BD28Xit1aitg%3D%3D 16307515 (Pubitemid 41748281)
11. W. Gu L.X. Zou P.F. Shan Y.D. Chen 2008 Analysis of urinary proteomic patterns for diabetic nephropathy by ProteinChip Proteomics Clin. Appl. 2 5 744 750 10.1002/prca.200780083 1:CAS:528:DC%2BD1cXms1emtbg%3D (Pubitemid 351772029)
12. M. Haubitz S. Wittke E.M. Weissinger M. Walden H.D. Rupprecht J. Floege H. Haller H. Mischak 2005 Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy Kidney Int. 67 6 2313 2320 10.1111/j.1523-1755. 2005.00335.x 1:CAS:528:DC%2BD2MXlsFyjtbc%3D 15882273 (Pubitemid 41623391)
13. J. Ho M. Lucy O. Krokhin K. Hayglass E. Pascoe G. Darroch D. Rush P. Nickerson C. Rigatto M. Reslerova 2009 Mass spectrometry-based proteomic analysis of urine in acute kidney injury following cardiopulmonary bypass: a nested case-control study Am. J. Kidney Dis. 53 4 584 595 10.1053/j.ajkd.2008. 10.037 1:CAS:528:DC%2BD1MXnslKrsb4%3D 19070948
14. E.J. Hoorn T. Pistkun R. Zietse P. Gross J. Frokiaer N.S. Wang P.A. Gonzales R.A. Star M.A. Knepper 2005 Prospects for urinary proteomics: exosomes as a source of urinary biomarkers Nephrology (Carlton) 10 3 283 290 10.1111/j.1440-1797.2005.00387.x 1:CAS:528:DC%2BD2MXmsVGms7g%3D (Pubitemid 40910376)
15. F. Huang J. Clifton X. Yang T. Rosenquist D. Hixson S. Kovac D. Josic 2009 SELDI-TOF as a method for biomarker discovery in the urine of aristolochicacid-treated mice Electrophoresis 30 7 1168 1174 10.1002/elps.200800548 1:CAS:528:DC%2BD1MXlsVWht78%3D 19294690
16. H. Jiang G. Guan R. Zhang G. Liu J. Cheng X. Hou Y. Cui 2009 Identification of urinary soluble E-cadherin as a novel biomarker for diabetic nephropathy Diabetes Metab. Res. Rev. 25 3 232 241 10.1002/dmrr.940 1:CAS:528:DC%2BD1MXkvVWkt7o%3D 19177462
17. H. Jiang G. Guan R. Zhang G. Liu H. Liu X. Hou J. Cheng 2009 Increased urinary excretion of orosomucoid is a risk predictor of diabetic nephropathy Nephrology (Carlton) 14 3 332 337 10.1111/j.1440-1797.2008.01053.x 1:CAS:528:DC%2BD1MXmt1Gmtbo%3D
18. I.S. Klasen L.J. Reichert C.M. de Kat Angelino J.F. Wetzels 1999 Quantitative determination of low and high molecular weight proteins in human urine: influence of temperature and storage time Clin. Chem. 45 3 430 432 1:CAS:528:DyaK1MXhvVWis78%3D 10053054
19. A. Lapolla R. Seraglia L. Molin K. Williams C. Cosma R. Reitano A. Sechi E. Ragazzie P. Traldi 2009 Low molecular weight proteins in urines from healthy subjects as well as diabetic, nephropathic and diabeticnephropathic patients: a MALDI study J. Mass Spectrom. 44 3 419 425 10.1002/jms.1520 1:CAS:528: DC%2BD1MXktVSqtrc%3D 19165811
20. R.S. Lee F. Monigatti A.C. Briscoe Z. Waldon M.R. Freeman H. Steen 2008 Optimizing sample handling for urinary proteomics J. Proteome Res. 7 9 4022 4030 10.1021/pr800301h 1:CAS:528:DC%2BD1cXptVGju7k%3D 18662026
21. E. Lifshitz L. Kramer 2000 Outpatient urine culture: dose collection technique matter? Arch. Intern. Med. 160 16 2537 3540 10.1001/archinte.160.16. 2537 1:STN:280:DC%2BD3cvmtF2jtQ%3D%3D 10979067
22. J. Liu C.F. Chen C.W. Tsao C.C. Chang C.C. Chu D.L. Devoe 2009 Polymer microchips jntegrating solidphase extraction and high-performance liquid chromatography using reversed-phase polymethacrylate monoliths Anal. Chem. 81 7 2545 2554 10.1021/ac802359e 1:CAS:528:DC%2BD1MXivVeitbo%3D 19267447
23. J.L. López 2007 Two-dimensional electrophoresis in proteome expression analysis J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 849 1-2 190 202 17188947
24. H. Mischak B.A. Julian J. Novak 2007 High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine Proteomics Clin. Appl. 1 8 792 804 10.1002/prca.200700043 1:CAS:528:DC%2BD2sXpvFGgsL0%3D 20107618
25. H. Mischak J.J. Coon J. Novak E.M. Weissinger J.P. Schanstra A.F. Dominiczak 2009 Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments Mass Spectrom. Rev. 28 5 703 724 10.1002/mas.20205 1:CAS:528:DC%2BD1MXhtFaisbzM 18973238
26. K. Mosley F.W. Tam R.J. Edwards J. Crozier C.D. Pusey L. Lightstone 2006 Urinary proteomic profiles distinguish between active and inactive lupus nephritis Rheumatology (Oxford) 45 12 1497 1504 10.1093/rheumatology/kel351 1:CAS:528:DC%2BD28Xht1Kns7rO (Pubitemid 44817055)
27. M. Najam-ul-Haq M. Rainer L. Trojer I. Feuerstein R.M. Vallant C.W. Huck R. Bakry G.K. Bonn 2007 Alternative profiling platform based on MELDI and its applicability in clinical proteomics Expert Rev. Proteomics 4 4 447 452 10.1586/14789450.4.4.447 1:CAS:528:DC%2BD2sXptFyrtb8%3D 17705703 (Pubitemid 47347593)
28. M.T. Nguyen G.F. Ross C.L. Dent P. Devarajan 2005 Early prediction of acute renal injury using urinary proteomics Am. J. Nephrol. 25 4 318 326 10.1159/000086476 1:CAS:528:DC%2BD2MXnvFygu7c%3D 15961952 (Pubitemid 41160990)
29. M.T. Nguyen C.L. Dent G.F. Ross N. Harris P.B. Manning M.M. Mitsnefes P. Devarajan 2008 Urinary aprotinin as a predictor of acute kidney injury after cardiac surgery in children receiving aprotinin therapy Pediatr. Nephrol. 23 8 1317 1326 10.1007/s00467-008-0827-9 18506488
30. P.H. O'Farrell 1975 High resolution two-dimensional electrophoresis of proteins J. Biol. Chem. 250 10 4007 4021 236308
31. E. O'Riordan T.N. Orlova V.N. Podust P.N. Chander S. Yanagi M. Nakazato R. Hu K. Butt V. Delaney M.S. Goligorsky 2007 Characterization of urinary peptide biomarkers of acute rejection in renal allografts Am. J. Transplant. 7 4 930 940 10.1111/j.1600-6143.2007.01733.x 17331118 (Pubitemid 46481208)
32. E. Orvisky S.K. Drake B.M. Martin M. Abdel-Hamid H.W. Ressom R.S. Varghese Y. An D. Saha G.L. Hortin C.A. Loffredo, et al. 2006 Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with hepatocellular carcinoma Proteomics 6 9 2895 2902 10.1002/pmic.200500443 1:CAS:528:DC%2BD28XltF2itb4%3D 16586431
33. M. Palmblad A. Tiss R. Cramer 2009 Mass spectrometry in clinical proteomics-from the present to the future Proteomics Clin. Appl. 3 1 6 17 10.1002/prca.200800090 1:CAS:528:DC%2BD1MXhsFWqtL8%3D
34. D. Penque 2009 Two-dimensional gel electrophoresis and mass spectrometry for biomarker discovery Proteomics Clin. Appl. 3 2 155 172 10.1002/prca. 200800025 1:CAS:528:DC%2BD1MXislWiu78%3D
35. L.F. Quintana A. Solé-Gonzalez S.G. Kalko E. Bañon-Maneus M. Solé F. Diekmann A. Gutierrez-Dalmau J. Abian J.M. Campistol 2009 Urine proteomics to detect biomarkers for chronic allograft dysfunction J. Am. Soc. Nephrol. 20 2 428 435 10.1681/ASN.2007101137 1:CAS:528:DC%2BD1MXjtFCrtb8%3D 19056874
36. M.T. Rocchetti M. Centra M. Papale G. Bortone C. Palermo D. Centonze E. Ranieri S.D. Paolo L. Gesualdo 2008 Urine protein profile of IgA nephropathy patients may predict the response to ACE-inhibitor therapy Proteomics 8 1 206 216 10.1002/pmic.200700492 1:CAS:528:DC%2BD1cXht1yrtb8%3D 18095357
37. M. Saito M. Kimoto T. Araki Y. Shimada R. Fujii K. Oofusa M. Hide T. Usui K. Yoshizato 2005 Proteome analysis of gelatin-bound urinary proteins from patients with bladder cancers Eur. Urol. 48 5 865 871 10.1016/j.eururo.2005.04. 028 1:CAS:528:DC%2BD2MXht1CnsrfO 15964125 (Pubitemid 41495397)
38. S. Schaub J. Wilkins T. Weiler K. Sangster D. Rush P. Nickerson 2004 Urine protein profiling with surfaceenhanced laser-desorption/ionization time-of-flight mass spectrometry Kidney Int. 65 1 323 332 10.1111/j.1523-1755. 2004.00352.x 1:CAS:528:DC%2BD2cXmt1Whsw%3D%3D 14675066 (Pubitemid 38037520)
39. S. Schaub J.A. Wilkins M. Antonovici O. Krokhin T. Weiler D. Rush P. Nickerson 2005 Proteomic-based identification of cleaved urinary β2-microglobulin as a potential marker of acute tubular injury in renal allograft Am. J. Transplant. 5 4Pt1 729 738 10.1111/j.1600-6143.2005.00766.x 1:CAS:528:DC%2BD2MXjtlaitr0%3D 15760396 (Pubitemid 40461282)
40. M. Suzuki K. Wiers E.B. Brooks K.D. Greis K. Haines M.S. Klein-Gitelman J. Olson K. Onel K.M. O'Neil E.D. Silverman, et al. 2009 Initial validation of a novel protein biomarker panel for active pediatric lupus nephritis Pediatr. Res. 65 5 530 536 10.1203/PDR.0b013e31819e4305 1:CAS:528:DC%2BD1MXktl2ju7c%3D 19218887
41. D. Theodorescu D. Fliser S. Wittke H. Mischak R. Krebs M. Walden M. Ross E. Eltze O. Bettendorf C. Wulfing A. Semjonow 2005 Pilot study of capillary electrophoresis coupled to mass spectrometry as a tool to define potential prostate cancer biomarkers in urine Electrophoresis 26 14 2797 2808 10.1002/elps.200400208 1:CAS:528:DC%2BD2MXotFamsrg%3D 15981297 (Pubitemid 41078989)
42. D. Theodorescu E. Schiffer H.W. Bauer F. Douwes F. Eichhorn R. Polley T. Schmidt W. Schöfer P. Zürbig D.M. Good, et al. 2008 Discovery and validation of urinary biomarkers for prostate cancer Proteomics Clin. Appl. 2 4 556 570 10.1002/prca.200780082 1:CAS:528:DC%2BD1cXlt1Wlt7w%3D 19759844 (Pubitemid 351566263)
43. V. Thongboonkerd 2007 Practical points in urinary proteomics J. Proteome Res. 6 10 3881 3890 10.1021/pr070328s 1:CAS:528:DC%2BD2sXpvFOit7o%3D 17824635 (Pubitemid 350032551)
44. J.F. Timms R. Cramer 2008 Difference gel electrophoresis Proteomics 8 23-24 4886 4897 10.1002/pmic.200800298 1:CAS:528:DC%2BD1MXlsFehug%3D%3D 19003860
45. P. Vestergaard R. Leverett 1958 Constancy of urinary creatinine excretion J. Lab. Clin. Med. 51 2 211 218 1:CAS:528:DyaG1cXjs1aktg%3D%3D 13514226
46. C. von Zur Muhlen E. Schiffer P. Zuerbig M. Kellmann M. Brasse N. Meert R.C. Vanholder A.F. Dominiczak Y.C. Chen H. Mischak, et al. 2009 Evaluation of urine proteome pattern analysis for its potential to reflect coronary artery atherosclerosis in symptomatic patients J. Proteome Res. 8 1 335 345 10.1021/pr800615t
47. E.M. Weissinger E. Schiffer B. Hertenstein J.L. Ferrara E. Holler M. Stadler H.J. Kolb A. Zander P. Zurbig M. Kellmann A. Ganser 2007 Proteomic patterns predict acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation Blood 109 12 5511 5519 10.1182/blood-2007-01-069757 1:CAS:528:DC%2BD2sXmslOrt7w%3D 17339419 (Pubitemid 46890577)
48. R. Wu L. Hu F. Wang M. Ye H. Zou 2008 Recent development of monolithic stationary phases with emphasis on microscale chromatographic separation J. Chromatogr. A 1184 1-2 369 392 10.1016/j.chroma.2007.09.022 1:CAS:528: DC%2BD1cXivVynsL4%3D 17923135 (Pubitemid 351296217)
49. P.G. Zerefos A. Vlahou 2008 Urine sample preparation and protein profiling by two-dimensional electrophoresis and matrix-assisted laser desorption ionization time of flight mass spectroscopy Methods Mol. Biol. 428 141 157 10.1007/978-1-59745-117-8-8 1:CAS:528:DC%2BD1cXislCqtLY%3D 18287772
50. X. Zhang M. Jin H. Wu T. Nadasdy G. Nadasdy N. Harris K. Green-Church H. Nagaraja D.J. Birmingham C.Y. Yu, et al. 2008 Biomarkers of lupus nephritis determined by serial urine proteomics Kidney Int. 74 6 799 807 10.1038/ki.2008.316 1:CAS:528:DC%2BD1cXhtVGgtbrF 18596723
51. H. Zhou P.S. Yuen T. Pisitkun P.A. Gonzales H. Yasuda J.W. Dear P. Gross M.A. Knepper R.A. Star 2006 Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery Kidney Int. 69 8 1471 1476 1:CAS:528:DC%2BD28XjsVWrs7k%3D 16501490
52. H. Zhou T. Pisitkun A. Aponte P.S. Yuen J.D. Hoffert H. Yasuda X. Hu L. Chawla R.F. Shen M.A. Knepper, et al. 2006 Exosomal Fetuin-A identified by proteomics: a novel urinary biomarker for detecting acute kidney injury Kidney Int. 70 10 1847 1857 10.1038/sj.ki.5001874 1:CAS:528:DC%2BD28XhtFKitrjP 17021608 (Pubitemid 44684818)