Seminars in Nephrology
Volume 27, Issue 6 , Pages 584-596 , November 2007

Proteomic Methods for Biomarker Discovery in Urine

  • Daniel W. Wilkey

      Affiliations

    • Kidney Disease Program, University of Louisville, Louisville, KY.
    • Clinical Proteomics Center, University of Louisville, Louisville, KY.
    • ,
  • Michael L. Merchant, PhD

      Affiliations

    • Kidney Disease Program, University of Louisville, Louisville, KY.
    • Clinical Proteomics Center, University of Louisville, Louisville, KY.
    • Corresponding Author InformationAddress reprint requests to Michael L. Merchant, Room 209, Donald Baxter Research Building, 570 S. Preston St, Louisville, KY 40202.

References 

  1. Kenyon GL, DeMarini DM, Fuchs E, et al. Defining the mandate of proteomics in the post-genomics era: workshop report. Mol Cell Proteomics. 2002;1:763–780
  2. Susztak K, Sharma K, Schiffer M, et al. Genomic strategies for diabetic nephropathy. J Am Soc Nephrol. 2003;14(Suppl):S271–S278
  3. Susztak K, Bottinger EP. Diabetic nephropathy: a frontier for personalized medicine. J Am Soc Nephrol. 2006;17:361–367
  4. Atkinson AJ, Colburn WA, DeGruttola VG, et al. Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin Pharmacol Ther. 2001;69:89–95
  5. Pisitkun T, Johnstone R, Knepper MA. Discovery of urinary biomarkers. Mol Cell Proteomics. 2006;5:1760–1771
  6. Hewitt SM, Dear J, Star RA. Discovery of protein biomarkers for renal diseases. J Am Soc Nephrol. 2004;15:1677–1689
  7. Varghese SA, Powell TB, Budisavljevic MN, et al. Urine biomarkers predict the cause of glomerular disease. J Am Soc Nephrol. 2007;18:913–922
  8. Prieto DA, Hood BL, Darfler MM, et al. Liquid tissue: proteomic profiling of formalin-fixed tissues. Biotechniques. 2005;(June Suppl):32–35
  9. Hood BL, Conrads TP, Veenstra TD. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics. 2006;6:4106–4114
  10. Hood BL, Conrads TP, Veenstra TD. Unravelling the proteome of formalin-fixed paraffin-embedded tissue. Brief Funct Genomic Proteomic. 2006;5:169–175
  11. Hood BL, Darfler MM, Guiel TG, et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics. 2005;4:1741–1753
  12. Ichimura T, Bonventre JV, Bailly V, et al. Kidney injury molecule-1 (KIM-1), a putative epithelial cell adhesion molecule containing a novel immunoglobulin domain, is up-regulated in renal cells after injury. J Biol Chem. 1998;273:4135–4142
  13. Supavekin S, Zhang W, Kucherlapati R, et al. Differential gene expression following early renal ischemia/reperfusion. Kidney Int. 2003;63:1714–1724
  14. Holly MK, Dear JW, Hu X, et al. Biomarker and drug target discovery using proteomics in a new rat model of sepsis-induced acute renal failure. Kidney Int. 2006;70:496–506
  15. Zhou H, Pisitkun T, Aponte A, et al. Exosomal Fetuin-A identified by proteomics: a novel urinary biomarker for detecting acute kidney injury. Kidney Int. 2006;70:1847–1857
  16. Elliot S, Goldsmith P, Knepper M, et al. Urinary excretion of aquaporin-2 in humans: a potential marker of collecting duct responsiveness to vasopressin. J Am Soc Nephrol. 1996;7:403–409
  17. Hoorn EJ, Pisitkun T, Zietse R, et al. Prospects for urinary proteomics: exosomes as a source of urinary biomarkers. Nephrology (Carlton). 2005;10:283–290
  18. Pisitkun T, Shen RF, Knepper MA. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci U S A. 204;101:13368-73.
  19. Oates JC, Varghese S, Bland AM, et al. Prediction of urinary protein markers in lupus nephritis. Kidney Int. 2005;68:2588–2592
  20. Chalmers MJ, Mackay CL, Hendrickson CL, et al. Combined top-down and bottom-up mass spectrometric approach to characterization of biomarkers for renal disease. Anal Chem. 2005;77:7163–7171
  21. Decramer S, Wittke S, Mischak H, et al. Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis. Nat Med. 2006;12:398–400
  22. Meier M, Kaiser T, Herrmann A, et al. Identification of urinary protein pattern in type 1 diabetic adolescents with early diabetic nephropathy by a novel combined proteome analysis. J Diabetes Complications. 2005;19:223–232
  23. Schiffer E, Mischak H, Novak J. High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics. 2006;6:5615–5627
  24. Wittke S, Haubitz M, Walden M, et al. Detection of acute tubulointerstitial rejection by proteomic analysis of urinary samples in renal transplant recipients. Am J Transplant. 2005;5:2479–2488
  25. Bellman R. Adaptive control processes: a guided tour. Princeton University Press; 1961;
  26. Norden AG, Rodriguez-Cutillas P, Unwin RJ. Clinical urinary peptidomics: learning to walk before we can run. Clin Chem. 2007;53:375–376
  27. Zhou H, Yuen PS, Pisitkun T, et al. Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney Int. 2006;69:1471–1476
  28. Adachi J, Kumar C, Zhang Y, et al. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 2006;7:R80
  29. 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
  30. Fiedler GM, Baumann S, Leichtle A, et al. Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin Chem. 2007;53:421–428
  31. Merrick BA, Tomer KB. Toxicoproteomics: a parallel approach to identifying biomarkers. Environ Health Perspec. 2003;111:A578–A579
  32. Wittmann-Liebold B, Graack HR, Pohl T. Two-dimensional gel electrophoresis as tool for proteomics studies in combination with protein identification by mass spectrometry. Proteomics. 2006;6:4688–4703
  33. Lopez JL. Two-dimensional electrophoresis in proteome expression analysis. J Chromatogr B Analyt Technol Biomed Life Sci. 2007;849:190–202
  34. Smith RD. Future directions for electrospray ionization for biological analysis using mass spectrometry. Biotechniques. 2006;41:147–148
  35. Smith RD, Tang K, Shen Y. Ultra-sensitive and quantitative characterization of proteomes. Mol Biosyst. 2006;2:221–230
  36. Smith RD, Shen Y, Tang K. Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes. Acc Chem Res. 2004;37:269–278
  37. Powell DW, Merchant ML, Link AJ. Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry. Expert Rev Proteomics. 2006;3:63–74
  38. McDonald T, Sheng S, Stanley B, et al. Expanding the subproteome of the inner mitochondria using protein separation technologies: one- and two-dimensional liquid chromatography and two-dimensional gel electrophoresis. Mol Cell Proteomics. 2006;5:2392–2411
  39. Sheng S, Chen D, Van Eyk JE. Multidimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phase of the human serum proteome: optimization and protein database. Mol Cell Proteomics. 2006;5:26–34
  40. Lemley KV. An introduction to biomarkers: applications to chronic kidney disease. Pediatr Nephrol. 2007;DOI number 10.1007/s00467-007-0455-9
  41. Geurts P, Fillet M, de Seny D, et al. Proteomic mass spectra classification using decision tree based ensemble methods. Bioinformatics. 2005;21:3138–3145
  42. Silva JC, Denny R, Dorschel C, et al. Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol Cell Proteomics. 2006;5:589–607
  43. Silva JC, Gorenstein MV, Li GZ, et al. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics. 2006;5:144–156
  44. Silva JC, Denny R, Dorschel CA, et al. Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem. 2005;77:2187–2200
  45. Russo LM, Sandoval RM, McKee M, et al. The normal kidney filters nephrotic levels of albumin retrieved by proximal tubule cells: retrieval is disrupted in nephritic states. Kidney Int. 2007;71:504–513
  46. Thomas MC, Burns WC, Cooper ME. Tubular changes in early diabetic nephropathy. Adv Chronic Kidney Dis. 2005;12:177–186
  47. van Timmeren MM, Bakker SJ, Vaidya VS, et al. Tubular kidney injury molecule-1 in protein-overload nephropathy. Am J Physiol. 2006;291:F456–F464
  48. Theilig F, Kriz W, Jerichow T, et al. Abrogation of protein uptake through megalin-deficient proximal tubules does not safeguard against tubulointerstitial injury. J Am Soc Nephrol. 2007;18:1824–1834
  49. Yokota H, Hiramoto M, Okada H, et al. Absence of Increased α1-microglobulin in IgA nephropathy proteinuria. Mol Cell Proteomics. 2007;6:738–744
  50. Myers BD, Okarma TB, Friedman S, et al. Mechanisms of proteinuria in human glomerulonephritis. J Clin Invest. 1982;70:732–746
  51. Machii R, Sakatume M, Kubota R, et al. Examination of the molecular diversity of alpha1 antitrypsin in urine: deficit of an alpha1 globulin fraction on cellulose acetate membrane electrophoresis. J Clin Lab Anal. 2005;19:16–21
  52. Clarke W, Silverman BC, Zhang Z, et al. Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg. 2003;237:660–664
  53. Fliser D, Novak J, Thongboonkerd V, et al. Advances in urinary proteome analysis and biomarker discovery. J Am Soc Nephrol. 2007;18:1057–1071
  54. Wittke S, Fliser D, Haubitz M, et al. Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J Chromatogr A. 2003;1013:173–181
  55. Rossing K, Mischak H, Parving HH, et al. Impact of diabetic nephropathy and angiotensin II receptor blockade on urinary polypeptide patterns. Kidney Int. 2005;68:193–205

PII: S0270-9295(07)00123-4

doi: 10.1016/j.semnephrol.2007.09.001

Seminars in Nephrology
Volume 27, Issue 6 , Pages 584-596 , November 2007

Article Tools

* Image Usage & Resolution