Biomarker discovery with SELDI-TOF MS in human urine associated with early renal injury: Evaluation with computational analytical tools

Nephrology Dialysis Transplantation

Volumn 22, Issue 10, 2007, Pages 2932-2943

  Vanhoutte, Kurt J A ^a   Laarakkers, Coby ^b   Marchiori, Elena ^c   Pickkers, Peter ^b   Wetzels, Jack F M ^b   Willems, Johannes L ^b   Van Den Heuvel, Lambert P ^b   Russel, Frans G M ^a   Masereeuw, Rosalinde ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

Biomarkers; Classification; Clinical proteomics; Mass spectrometry; Renal injury; Surface enhanced laser desorption ionization time of flight

Indexed keywords

BIOLOGICAL MARKER; CREATININE;

ANALYTICAL EQUIPMENT; ARTICLE; CONTROLLED STUDY; CORONARY ARTERY BYPASS GRAFT; CREATININE BLOOD LEVEL; HUMAN; INTENSIVE CARE UNIT; KIDNEY INJURY; MACHINE LEARNING; PRIORITY JOURNAL; SPECTROMETER; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; URINALYSIS; VOLUNTEER;

ACUTE-PHASE PROTEINS; ADULT; AGED; ALGORITHMS; ALPHA-GLOBULINS; BIOLOGICAL MARKERS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION REGULATION; HUMANS; KIDNEY DISEASES; LIPOCALINS; MALE; MIDDLE AGED; PRINCIPAL COMPONENT ANALYSIS; PROTEOMICS; PROTO-ONCOGENE PROTEINS; SOFTWARE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TIME FACTORS; URINALYSIS;

EID: 36048980620     PISSN: 09310509     EISSN: 14602385     Source Type: Journal    
DOI: 10.1093/ndt/gfm170     Document Type: Article

References (45)

1. Johann DJ Jr, McGuigan MD, Patel AR et al. Clinical proteomics and biomarker discovery. Ann NY Acad Sci 2004; 1022: 295-305
2. Espina V, Mehta AI, Winters ME et al. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 2003; 3: 2091-2100
3. Bischoff R, Luider TM. Methodological advances in the discovery of protein and peptide disease markers. J Chromatogr B Analyt Technol Biomed Life Sci 2004; 803: 27-40
4. Thongboonkerd V, Malasit P. Renal and urinary proteomics: current applications and challenges. Proteomics 2005; 5: 1033-1042
5. Knepper MA. Proteomics and the kidney. J Am Soc Nephrol 2002; 13: 1398-1408
6. Thongboonkerd V. Proteomics in nephrology: current status and future directions. Am J Nephrol 2004; 24: 360-378
7. Thongboonkerd V. Proteomic analysis of renal diseases: unraveling the pathophysiology and biomarker discovery. Expert Rev Proteomics 2005; 2: 349-366
8. Hewitt SM, Dear J, Star RA. Discovery of protein biomarkers for renal diseases. J Am Soc Nephrol 2004; 15: 1677-1689
9. Fleck C, Sutter L, Appenroth D et al. Use of gene chip technology for the characterisation of the regulation of renal transport processes and of nephrotoxicity in rats. Exp Toxicol Pathol 2003; 54: 401-410
10. Luhe A, Hildebrand H, Bach U, Dingermann T, Ahr HJ. A new approach to studying ochratoxin A (OTA)-induced nephrotoxicity: expression profiling in vivo and in vitro employing cDNA microarrays. Toxicol Sci 2003; 73: 315-328
11. Rossi RM, Kist C, Wurster U, Kulpmann WR, Ehrich JH. Estimation of ifosfamide/cisplatinum-induced renal toxicity by urinary protein analysis. Pediatr Nephrol 1994; 8: 151-156
12. Branten AJ, du Buf-Vereijken PW, Klasen IS et al. Urinary excretion of beta2-microglobulin and IgG predict prognosis in idiopathic membranous nephropathy: a validation study. J Am Soc Nephrol 2005; 16: 169-174
13. Issaq HJ, Veenstra TD, Conrads TP, Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem Biophys Res Commun 2002; 292: 587-592
14. Clarke W, Chan DW. ProteinChips: the essential tools for proteomic biomarker discovery and future clinical diagnostics. Clin Chem Lab Med 2005; 43: 1279-1280
15. Mishra J, Dent C, Tarabishi R et al. Neutrophil gelatinase-associated lipocalin (NGAL) as a biomarker for acute renal injury after cardiac surgery. Lancet 2005; 365: 1231-1238
16. 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
17. O'riordan E, Goligorsky MS. Emerging studies of the urinary proteome: the end of the beginning? Curr Opin Nephrol Hypertens 2005; 14: 579-585
18. Espina V, Dettloff KA, Cowherd S, Petricoin EF, III, Liotta LA. Use of proteomic analysis to monitor responses to biological therapies. Expert Opin Biol Ther 2004; 4: 83-93
19. Eijkenboom JJ, van Eijk LT, Pickkers P, Peters WH, Wetzels JF, van der Hoeven HG. Small increases in the urinary excretion of glutathione S-transferase A1 and P1 after cardiac surgery are not associated with clinically relevant renal injury. Intensive Care Med 2005; 31: 664-667
20. 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
21. Klasen IS, Reichert LJ, de Kat Angelino CM, Wetzels JF. Quantitative determination of low and high molecular weight proteins in human urine: influence of temperature and storage time. Clin Chem 1999; 45: 430-432
22. Rogers MA, Clarke P, Noble J et al. 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 Res 2003; 63: 6971-6983
23. Schaub S, Wilkins J, Weiler T, Sangster K, Rush D, Nickerson P. Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 2004; 65: 323-332
24. West-Nielsen M, Hogdall EV, Marchiori E, Hogdall CK, Schou C, Heegaard NH. Sample handling for mass spectrometric proteomic investigations of human sera. Anal Chem 2005; 77: 5114-5123
25. Jackson JE. A User's Guide to Principal Components. John Wiley and Sons, New York: 1991; 1-592
26. Jolliffe IT. Principal Component Analysis. Springer-Verlag, New York: 2002; 1-478
27. Krzanowski WJ. Principles of Multivariate Analysis. Oxford University Press, Oxford: 1988; 1-608
28. Kira K, Rendell LA. A practical approach to feature selection. In: Sleeman D, Edwards P, eds. Proceedings of the Ninth international Workshop on Machine Learning (Aberdeen, Scotland, United Kingdom). Morgan Kaufmann Publishers, San Francisco: 1992; 249-256
29. Marchiori E, Heegaard NH, Jimenez C, West-Nielsen M. Feature Selection for Classification with Proteomic Data of Mixed Quality. Proc IEEE Symp Computat Intel Bioinf Computat Biol 2005; 385-391
30. Vapnik VN. The Nature of Statistical Learning Theory. John Wiley and Sons, Inc., New York: 1998; 1-314
31. Good PI. Permutation Tests: A Practical Guide to Resampling Methods for Testing Hypotheses Springer-Verlag, New York: 1994
32. Hilario M, Kalousis A, Pellegrini C, Muller M. Processing and classification of protein mass spectra. Mass Spectrom Rev 2006; 25: 409-449
33. Pavlidis P, Wapinski I, Noble WS. Support vector machine classification on the web. Bioinformatics 2004; 20: 586-587
34. Golland P, Liang F, Mukherjee S, Panchenko D. Permutation tests for classification. Learning Theory, Proceedings 2005; 3559: 501-515.
35. Simon R, Radmacher MD, Dobbin K, McShane LM. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003; 95: 14-18
36. Farhoud MH, Wessels HJ, Wevers RA, van Engelen BG, van den Heuvel LP, Smeitink JA. Serial isoelectric focusing as an effective and economic way to obtain maximal resolution and high-throughput in 2D-based comparative proteomics of scarce samples: proof-of-principle. J Proteome Res 2005; 4: 2364-2368
37. Tjalsma H, Pluk W, van den Heuvel LP, Peters WH, Roelofs R, Swinkels DW. Proteomic inventory of "anchorless" proteins on the colon adenocarcinoma cell surface. Biochim Biophys Acta 2006; 1764: 1607-1617
38. Vlahou A, Fountoulakis A. Proteomic approaches in the search for disease biomarkers. J Chrom B-Anal Technol Biomed Life Sci 2005; 814: 11-19
39. Nguyen MT, Ross GF, Dent CL, Devarajan P. Early prediction of acute renal injury using urinary proteomics. Am J Nephrol 2005; 25: 318-326
40. Clarke W, Silverman BC, Zhang Z, Chan DW, Klein AS, Molmenti EP. Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg 2003; 237: 660-664
41. Kemna E, Tjalsma H, Laarakkers C, Nemeth E, Willems H, Swinkels D. Novel urine hepcidin assay by mass spectrometry. Blood 2005; 106: 3268-3270
42. Tantipaiboonwong P, Sinchaikul S, Sriyam S, Phutrakul S, Chen ST. Different techniques for urinary protein analysis of normal and lung cancer patients. Proteomics 2005; 5: 1140-1149
43. Blaikley J, Sutton P, Walter M et al. Tubular proteinuria and enzymuria following open heart surgery. Intensive Care Med 2003; 29: 1364-1367
44. Hampel DJ, Sansome C, Sha M, Brodsky S, Lawson WE, Goligorsky MS. Toward proteomics in uroscopy: urinary protein profiles after radiocontrast medium administration. J Am Soc Nephrol 2001; 12: 1026-1035
45. Pisitkun T, Shen RF, Knepper MA. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci USA 2004; 10: 13368-13373