Proteomics and nephrology

Journal of Nephrology

Volumn 25, Issue 6, 2012, Pages 865-871

  Bonomini, Mario ^a   Sirolli, Vittorio ^a   Magni, Fulvio ^b   Urbani, Andrea ^c,d  

^a UNIVERSITY OF CHIETI   (Italy)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

^c IRCCS FONDAZIONE SANTA LUCIA   (Italy)

^d UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

Biomarker; Kidney; Mass spectrometry; Proteome; Urinary proteomics

Indexed keywords

ALPHA 1 MICROGLOBULIN; BETA 2 MICROGLOBULIN; KIDNEY INJURY MOLECULE 1; NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN; OROSOMUCOID;

ARTICLE; CHRONIC KIDNEY DISEASE; DISEASE ACTIVITY; DISEASE ASSOCIATION; DISEASE MARKER; HEMODIALYSIS; HUMAN; KIDNEY EXAMINATION; KIDNEY FUNCTION; KIDNEY INJURY; KIDNEY TRANSPLANTATION; MEDICAL RESEARCH; MOLECULAR PATHOLOGY; NEPHROLOGY; PERITONEAL DIALYSIS; PROTEOMICS;

ANIMALS; BIOLOGICAL MARKERS; BLOOD PROTEINS; HUMANS; KIDNEY DISEASES; KIDNEY TRANSPLANTATION; NEPHROLOGY; PERITONEAL DIALYSIS; PREDICTIVE VALUE OF TESTS; PROGNOSIS; PROTEINURIA; PROTEOMICS; RENAL DIALYSIS;

EID: 84870598809     PISSN: 11218428     EISSN: 17246059     Source Type: Journal    
DOI: 10.5301/jn.5000217     Document Type: Article

References (68)

1. Peng J, Gygi SP. Proteomics: the move to mixtures. J Mass Spectrom. 2001;36(10):1083-1091.
2. Janech MG, Raymond JR, Arthur JM. Proteomics in renal research. Am J Physiol Renal Physiol. 2007;292(2):F501-F512.
3. Mullen W, Delles C, Mischak H. Euro KUP COST action. Urinary proteomics in the assessment of chronic kidney disease. Curr Opin Nephrol Hypertens. 2011;20(6):654-661.
4. Bennett MR, Devarajan P. Proteomic analysis of acute kidney injury: biomarkers to mechanisms. Proteomics Clin Appl. 2011;5(1-2):67-77.
5. He JC, Chuang PY, Ma'ayan A, Iyengar R. Systems biology of kidney diseases. Kidney Int. 2012;81(1):22-39.
6. Kienzl-Wagner K, Pratschke J, Brandacher G. Proteomics: a blessing or a curse? Application of proteomics technology to transplant medicine. Transplantation. 2011;92(5):499-509.
7. Konvalinka A, Scholey JW, Diamandis EP. Searching for new biomarkers of renal diseases through proteomics. Clin Chem. 2012;58(2):353-365.
8. Moon PG, You S, Lee JE, Hwang D, Baek MC. Urinary exosomes and proteomics. Mass Spectrom Rev. 2011;30(6): 1185-1202.
9. Thongboonkerd V. Urinary proteomics: towards biomarker discovery, diagnostics and prognostics. Mol Biosyst. 2008;4(8):810-815.
10. Magni F, Sarto C, Valsecchi C, et al. Expanding the proteome two-dimensional gel electrophoresis reference map of human renal cortex by peptide mass fingerprinting. Proteomics. 2005;5(3):816-825.
11. Obelchuk LI, Tsomartova DA, Kovalyov LI, et al. Standardized and extended catalog of major proteins of the human kidney. Biochemistry (Mosc). 1997;62(2):191-199.
12. Velic A, Macek B, Wagner CA. Toward quantitative proteomics of organ substructures: implications for renal physiology. Semin Nephrol. 2010;30(5):487-499.
13. Hoffert JD, Chou CL, Knepper MA. Aquaporin-2 in the "-omics" era. J Biol Chem. 2009;284(22):14683-14687.
14. Hoorn EJ, Pisitkun T, Yu MJ, Knepper MA. Proteomic approaches for the study of cell signaling in the renal collecting duct. Contrib Nephrol. 2008;160:172-185.
15. Yoshida Y, Miyazaki K, Kamiie J, et al. Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database. Proteomics. 2005;5(4):1083-1096.
16. Human Kidney & Urine Proteome Project. Available at: www.hkupp.org. Accessed October 1, 2012.
17. Huang TH, Ka SM, Hsu YJ, et al. Rab 23 plays a role in the pathophysiology of mesangial cells: a proteomic analysis. Proteomics. 2011;11(3):380-394.
18. Schordan S, Schordan E, Endlich N, et al. Alterations of the podocyte proteome in response to high glucose concentrations. Proteomics. 2009;9(19):4519-4528.
19. Satoskar AA, Shapiro JP, Bott CN, et al. Characterization of glomerular diseases using proteomic analysis of laser capture microdissected glomeruli. Mod Pathol. 2012;25(5):709-721.
20. Sethi S, Vrana JA, Theis JD, et al. Laser microdissection and mass spectrometry-based proteomics aids the diagnosis and typing of renal amyloidosis. Kidney Int. 2012;82(2):226-234.
21. Nirmalan NJ, Hughes C, Peng J, et al. Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations. J Proteome Res. 2011;10(2):896-906.
22. Nakatani S, Wei M, Ishimura E, et al. Proteome analysis of laser microdissected glomeruli from formalin-fixed paraffin-embedded kidneys of autopsies of diabetic patients: nephronectin is associated with the development of diabetic glomerulosclerosis. Nephrol Dial Transplant. 2012;27(5):1889-1897.
23. Magistroni R, Cantù M, Ligabue G, et al. Interstitial fluid obtained from kidney biopsy as new source of renal biomarkers. J Nephrol. 2011;24(3):329-337.
24. Fliser D, Novak J, Thongboonkerd V, et al. Advances in urinary proteome analysis and biomarker discovery. J Am Soc Nephrol. 2007;18(4):1057-1071.
25. Mischak H, Schiffer E, Zuerbig P, Dakna M, Metzger J. Urinary proteome analysis using capillary electrophoresis coupled mass spectrometry: a powerful tool in clinical diagnosis, prognosis and therapy evaluation. J Med Biochem. 2009;28(4):223-234.
26. Santucci L, Candiano G, Bruschi M, et al. Combinatorial peptide ligand libraries for the analysis of low-expression proteins: validation for normal urine and definition of a first protein MAP. Proteomics. 2012;12(4-5):509-515.
27. Mischak H, Kolch W, Aivaliotis M, et al. Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics Clin Appl. 2010;4(4):464-478.
28. Pisitkun T, Shen RF, Knepper MA. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci USA. 2004;101(36):13368-13373.
29. Rossing K, Mischak H, Dakna M, et al. PREDICTIONS Network. Urinary proteomics in diabetes and CKD. J Am Soc Nephrol. 2008;19(7):1283-1290.
30. Soggiu A, Piras C, Bonizzi L, Hussein HA, Pisanu S, Roncada P. A discovery-phase urine proteomics investigation in type 1 diabetes. Acta Diabetol. 2012. [Epub ahead of print].
31. Snell-Bergeon JK, Maahs DM, Ogden LG, et al. Evaluation of urinary biomarkers for coronary artery disease, diabetes, and diabetic kidney disease. Diabetes Technol Ther. 2009;11(1): 1-9.
32. Alkhalaf A, Zürbig P, Bakker SJ, et al. PREDICTIONS Group. Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy. PLoS ONE. 2010;5(10):e13421.
33. Merchant ML, Perkins BA, Boratyn GM, et al. Urinary peptidome may predict renal function decline in type 1 diabetes and microalbuminuria. J Am Soc Nephrol. 2009;20(9):2065-2074.
34. Papale M, Di Paolo S, Magistroni R, et al. Urine proteome analysis may allow noninvasive differential diagnosis of diabetic nephropathy. Diabetes Care. 2010;33(11):2409-2415.
35. Good DM, Zürbig P, Argilés A, et al. Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol Cell Proteomics. 2010;9(11):2424-2437.
36. Mischak H, Rossing P. Proteomic biomarkers in diabetic nephropathy: reality or future promise? Nephrol Dial Transplant. 2010;25(9):2843-2845.
37. Rossing K, Mischak H, Rossing P, Schanstra JP, Wiseman A, Maahs DM. The urinary proteome in diabetes and diabetes- associated complications: new ways to assess disease progression and evaluate therapy. Proteomics Clin Appl. 2008;2 (7-8):997-1007.
38. Zürbig P, Decramer S, Dakna M, et al. The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease. Proteomics. 2009;9(8): 2108-2117.
39. Devarajan P. Neutrophil gelatinase-associated lipocalin: a promising biomarker for human acute kidney injury. Biomark Med. 2010;4(2):265-280.
40. Vaidya VS, Waikar SS, Ferguson MA, et al. Urinary biomarkers for sensitive and specific detection of acute kidney injury in humans. Clin Transl Sci. 2008;1(3):200-208.
41. Devarajan P, Krawczeski CD, Nguyen MT, Kathman T, Wang Z, Parikh CR. Proteomic identification of early biomarkers of acute kidney injury after cardiac surgery in children. Am J Kidney Dis. 2010;56(4):632-642.
42. Andersen S, Mischak H, Zürbig P, Parving HH, Rossing P. Urinary proteome analysis enables assessment of renoprotective treatment in type 2 diabetic patients with microalbuminuria. BMC Nephrol. 2010;11(1):29.
43. Rocchetti MT, Centra M, Papale M, et al. Urine protein profile of IgA nephropathy patients may predict the response to ACE-inhibitor therapy. Proteomics. 2008;8(1):206-216.
44. Niwa T. Update of uremic toxin research by mass spectrometry. Mass Spectrom Rev. 2011;30(3):510-521.
45. Galli F. Protein damage and inflammation in uraemia and dialysis patients. Nephrol Dial Transplant. 2007;22(Suppl 5): v20-v36.
46. Miyata T, Oda O, Inagi R, et al. beta 2-Microglobulin modified with advanced glycation end products is a major component of hemodialysis-associated amyloidosis. J Clin Invest. 1993;92(3):1243-1252.
47. Pavone B, Bucci S, Sirolli V, et al. beta2-Microglobulin causes abnormal phosphatidylserine exposure in human red blood cells. Mol Biosyst. 2011;7(3):651-658.
48. Zwaal RF, Comfurius P, Bevers EM. Surface exposure of phosphatidylserine in pathological cells. Cell Mol Life Sci. 2005;62(9):971-988.
49. Pavone B, Sirolli V, Giardinelli A, et al. Plasma protein carbonylation in chronic uremia. J Nephrol. 2011;24(4):453-464.
50. Bonomini M, Pavone B, Sirolli V, et al. Proteomics characterization of protein adsorption onto hemodialysis membranes. J Proteome Res. 2006;5(10):2666-2674.
51. Aoike I. Clinical significance of protein adsorbable membranes: long-term clinical effects and analysis using a proteomic technique. Nephrol Dial Transplant. 2007;22(Suppl 5):v13-v19.
52. Pavone B, Sirolli V, Bucci S, et al. Adsorption and carbonylation of plasma proteins by dialyser membrane material: in vitro and in vivo proteomics investigations. Blood Transfus. 2010;8(Suppl. 3):113-119.
53. Mares J, Richtrova P, Hricinova A, et al. Proteomic profiling of blood-dialyzer interactome reveals involvement of lectin complement pathway in hemodialysis-induced inflammatory response. Proteomics Clin Appl. 2010;4(10-11):829-838.
54. Urbani A, Lupisella S, Sirolli V, et al. Proteomic analysis of protein adsorption capacity of different haemodialysis membranes. Mol Biosyst. 2012;8(4):1029-1039.
55. Ficheux A, Gayrard N, Szwarc I, et al. The use of SDS-PAGE scanning of spent dialysate to assess uraemic toxin removal by dialysis. Nephrol Dial Transplant. 2011;26(7):2281-2289.
56. Urbani A, Sirolli V, Lupisella S, et al. Proteomic investigations on the effect of different membrane materials on blood protein adsorption during hemodialysis. Blood Transfus. 2012;10 Suppl 2:s101-s112.
57. Hallbauer J, Kreusch S, Klemm A, Wolf G, Rhode H. Longterm serum proteomes are quite similar under high- and low-flux hemodialysis treatment. Proteomics Clin Appl. 2010;4(12):953-961.
58. Cuccurullo M, Evangelista C, Vilasi A, et al. Proteomic analysis of peritoneal fluid of patients treated by peritoneal dialysis: effect of glucose concentration. Nephrol Dial Transplant. 2011;26(6):1990-1999.
59. Sritippayawan S, Chiangjong W, Semangoen T, et al. Proteomic analysis of peritoneal dialysate fluid in patients with different types of peritoneal membranes. J Proteome Res. 2007;6(11):4356-4362.
60. Raaijmakers R, Pluk W, Schröder CH, et al. Proteomic profiling and identification in peritoneal fluid of children treated by peritoneal dialysis. Nephrol Dial Transplant. 2008;23(7):2402-2405.
61. Lin WT, Tsai CC, Chen CY, Lee WJ, Su CC, Wu YJ. Proteomic analysis of peritoneal dialysate fluid in patients with dialysisrelated peritonitis. Ren Fail. 2008;30(8):772-777.
62. Wang HY, Tian YF, Chien CC, et al. Differential proteomic characterization between normal peritoneal fluid and diabetic peritoneal dialysate. Nephrol Dial Transplant. 2010;25(6): 1955-1963.
63. Wang H-Y, Lin C-Y, Chien C-C, et al. Impact of uremic environment on peritoneum: a proteomic view. J Proteomics. 2012;75(7):2053-2063.
64. Sigdel TK, Kaushal A, Gritsenko M, et al. Shotgun proteomics identifies proteins specific for acute renal transplant rejection. Proteomics Clin Appl. 2010;4(1):32-47.
65. Ling XB, Sigdel TK, Lau K, et al. Integrative urinary peptidomics in renal transplantation identifies biomarkers for acute rejection. J Am Soc Nephrol. 2010;21(4):646-653.
66. Metzger J, Chatzikyrkou C, Broecker V, et al. Diagnosis of subclinical and clinical acute T-cell-mediated rejection in renal transplant patients by urinary proteome analysis. Proteomics Clin Appl. 2011;5(5-6):322-333.
67. Johnston O, Cassidy H, O'Connell S, et al. Identification of b2-microglobulin as a urinary biomarker for chronic allograft nephropathy using proteomic methods. Proteomics Clin Appl. 2011;5(7-8):422-431.
68. Thompson D, Develter W, Cairns DA, et al. A pilot study to investigate the potential of mass spectrometry profiling in the discovery of novel serum markers in chronic renal disease. Proteomics Clin Appl. 2011;5(9-10):523-531.