2-D Difference In-Gel Electrophoresis (2-D DIGE) and Urinary Proteomics

Renal and Urinary Proteomics: Methods and Protocols

Volumn , Issue , 2009, Pages 253-269

  Ramachandrarao, Satish P ^a   Shaw, Michael A ^b   Sharma, Kumar ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

2 D DIGE; CyDye labeling; Human urine; Microglobulin; Urinary proteomics

Indexed keywords

EID: 84861455434     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527628612.ch20     Document Type: Chapter

References (63)

1. James, P. (1997). Of genomes and proteomes. Biochem Biophys Res Commun,, 231, 1-6.
2. Saiki, R.K., Scharf, S., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A., and Arnheim, N. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science,, 230, 1350-1354.
3. Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F. et al. (1991). Complementary DNA sequencing:expressed sequence tags and human genome project. Science,, 252, 1651-1656.
4. Scherer, J.R., Kheterpal, I., Radhakrishnan, A., Ja, W.W., and Mathies, R.A. (1999). Ultra-high throughput rotary capillary array electrophoresis scanner for fluorescent DNA sequencing and analysis. Electrophoresis,, 20, 1508-1517.
5. O'Farrell, P.H. (1975). High resolution two-dimensional electrophoresis of proteins. J Biol Chem,, 250, 4007-4021.
6. Scheele, G.A. (1975). Two-dimensional gel analysis of soluble proteins. Characterization of guinea pig exocrine pancreatic proteins. J Biol Chem,, 250, 5375-5385.
7. Bjellqvist, B., Ek, K., Righetti, P.G., Gianazza, E., Gorg, A., Westermeier, R., and Postel, W. (1982). Isoelectric focusing in immobilized pH gradients:principle, methodology and some applications. J Biochem Biophys Methods,, 6, 317-339.
8. Unlu, M., Morgan, M.E., and Minden, J.S. (1997). Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis,, 18, 2071-2077.
9. Pieper, R., Gatlin, C.L., McGrath, A.M., Makusky, A.J., Mondal, M., Seonarain, M., Field, E., Schatz, C.R., Estock, M.A., Ahmed, N., Anderson, N.G., and Steiner, S. (2004). 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,, 4, 1159-1174.
10. Smith, G., Barratt, D., Rowlinson, R., Nickson, J., and Tonge, R. (2005). Development of a high-throughput method for preparing human urine for two-dimensional electrophoresis. Proteomics,, 5, 2315-2318.
11. Saito, M., Kimoto, M., Araki, T., Shimada, Y., Fujii, R., Oofusa, K., Hide, M., Usui, T., and Yoshizato, K. (2005). Proteome analysis of gelatin-bound urinary proteins from patients with bladder cancers. Eur Urol,, 48, 865-871.
12. Corthals, G.L., Wasinger, V.C., Hochstrasser, D.F., and Sanchez, J.C. (2000). The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis,, 21, 1104-1115.
13. Kalluri, R. (2006). Proteinuria with and without renal glomerular podocyte effacement. J Am Soc Nephrol,, 17, 2383-2389.
14. Marshall, T. and Williams, K.M. (1998). Clinical analysis of human urinary proteins using high resolution electrophoretic methods. Electrophoresis,, 19, 1752-1770.
15. Waller, K.V., Ward, K.M., Mahan, J.D., and Wismatt, D.K. (1989). Current concepts in proteinuria. Clin Chem,, 35, 755-765.
16. Delanghe, J. (1997). Use of specific urinary proteins as diagnostic markers for renal disease. Acta Clin Belg,, 52, 148-153.
17. Shihabi, Z.K., Konen, J.C., and O'Connor, M.L. (1991). Albuminuria vs urinary total protein for detecting chronic renal disorders. Clin Chem,, 37, 621-624.
18. Watts, N.B. (1991). Albuminuria and diabetic nephropathy: an evolving story. Clin Chem,, 37, 2027-2028.
19. Yudkin, J.S., Forrest, R.D., and Jackson, C.A. (1988). Microalbuminuria as predictor of vascular disease in non-diabetic subjects. Islington Diabetes Survey. Lancet,, 2, 530-533.
20. Sharma, K., Ziyadeh, F.N., Alzahabi, B., McGowan, T.A., Kapoor, S., Kurnik, B.R., Kurnik, P.B., and Weisberg, L.S. (1997). Increased renal production of transforming growth factor-beta1 in patients with type II diabetes. Diabetes,, 46, 854-859.
21. Sun, W., Li, F., Wu, S., Wang, X., Zheng, D., Wang, J., and Gao, Y. (2005). Human urine proteome analysis by three separation approaches. Proteomics,, 5, 4994-5001.
22. Centers for Disease Control and Prevention (CDC) (2004) State-specific trends in chronic kidney failure-United States, 1990-2001. MMWR Morb Mortal Wkly Rep, 53, 918-920.
23. Ewens, K.G., George, R.A., Sharma, K., Ziyadeh, F.N., and Spielman, R.S. (2005). Assessment of 115 candidate genes for diabetic nephropathy by transmission/disequilibrium test. Diabetes,, 54, 3305-3318.
24. American Society of Health-System Pharmacists (2003) ASHP therapeutic position statement on strict glycemic control in patients with diabetes. Am J Health Syst Pharm 60, 2357-2362.
25. Benjamin, S.M., Valdez, R., Geiss, L.S., Rolka, D.B., and Narayan, K.M. (2003). Estimated number of adults with prediabetes in the US in 2000:opportunities for prevention. Diabetes Care,, 26, 645-649.
26. Breyer, M.D. (2007). Diabetic nephropathy: introduction. Semin Nephrol,, 27, 129.
27. Greenwald, A. (2006). Current nutritional treatments of obesity. Adv Psychosom Med,, 27, 24-41.
28. Babazono, T., Takahashi, C., and Iwamoto, Y. (2004). Definition of microalbuminuria in first-morning and random spot urine in diabetic patients. Diabetes Care,, 27, 1838-1839.
29. RPAH Biochemistry Department (2002) Trace and Toxic Elements-Urine Collection Procedures, http://www.cs.nsw.gov.au/csls/handbook/FactSheetView.asp?Number=41.
30. Mushnick, R., (2006) 24-hour Urine Protein, http://www.nlm.nih.gov/medlineplus/ency/article/003622.htm.
31. Bottini, P.V., Ribeiro Alves, M.A., and Garlipp, C.R. (2002) Electrophoretic pattern of concentrated urine: comparison between 24-hour collection and random samples. Am J Kidney Dis, 39, E2.
32. Molitch, M.E., DeFronzo, R.A., Franz, M.J., Keane, W.F., Mogensen, C.E., and Parving, H.H. (2003) Diabetic nephropathy. Diabetes Care, 26 (Suppl 1), S94-S98.
33. Schneider, R. (2004) Urologic procedures, in Clinical Procedures in Emergency Medicine, 4th edn (eds J.R. Roberts and J.R. Hedges), W.B. Saunders, Philadelphia, pp. 1086-1098.
34. Koraitim, M.M. (1999). Pelvic fracture urethral injuries: the unresolved controversy. J Urol,, 161, 1433-1441.
35. Cancio, L.C., Sabanegh, E.S. Jr, and Thompson, I.M. (1993). Managing the Foley catheter. Am Fam Physician,, 48, 829-836.
36. Saint, S. and Lipsky, B.A. (1999) Preventing catheter-related bacteriuria:should we? Can we? How? Arch Intern Med, 159, 800-808.
37. Daneshmand, S., Youssefzadeh, D., and Skinner, E.C. (2002). Review of techniques to remove a Foley catheter when the balloon does not deflate. Urology,, 59, 127-129.
38. Canes, D. (2006) Male urethral catheterization. N Engl J Med, 355, 1178-1179, author reply 1179.
39. Elley, K. and Semple, M. (1999) Collecting a mid-stream specimen of urine. Nurs Times, 95 (Suppl 1-2).
40. Thongboonkerd, V., McLeish, K.R., Arthur, J.M., and Klein, J.B. (2002). Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int,, 62, 1461-1469.
41. Sharma, K., Lee, S., Han, S., Lee, S., Francos, B., McCue, P., Wassell, R., Shaw, M.A., and RamachandraRao, S.P. (2005). Two-dimensional fluorescence difference gel electrophoresis analysis of the urine proteome in human diabetic nephropathy. Proteomics,, 5, 2648-2655.
42. Thongboonkerd, V., Chutipongtanate, S., and Kanlaya, R. (2006). Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. J Proteome Res,, 5, 183-191.
43. Barritault, D., Expert-Bezancon, A., Guerin, M.F., and Hayes, D. (1976). The use of acetone precipitation in the isolation of ribosomal proteins. Eur J Biochem,, 63, 131-135.
44. Wessel, D. and Flugge, U.I. (1984). A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem,, 138, 141-143.
45. Carmel, R. (1974). A rapid ammonium sulfate precipitation technic for separating serum vitamin B12-binding proteins. Method and applications. Am J Clin Pathol,, 62, 367-372.
46. Doskeland, S.O. and Ogreid, D. (1988). Ammonium sulfate precipitation assay for the study of cyclic nucleotide binding to proteins. Methods Enzymol,, 159, 147-150.
47. Verhoeven, G., Heyns, W., and De Moor, P. (1975). Ammonium sulfate precipitation as a tool for the study of androgen receptor proteins in rat prostate and mouse kidney. Steroids,, 26, 149-167.
48. Lakatos, A. and Jobst, K. (1992). The precipitation of histone-proteins with trichloroacetic acid. Clin Chim Acta,, 205, 153-154.
49. Wright, A.P., Bruns, M., and Hartley, B.S. (1989). Extraction and rapid inactivation of proteins from Saccharomyces cerevisiae by trichloroacetic acid precipitation. Yeast,, 5, 51-53.
50. Yeang, H.Y., Yusof, F., and Abdullah, L. (1995). Precipitation of Hevea brasiliensis latex proteins with trichloroacetic acid and phosphotungstic acid in preparation for the Lowry protein assay. Anal Biochem,, 226, 35-43.
51. Righetti, P.G., Boschetti, E., Lomas, L., and Citterio, A. (2006). Protein equalizer technology: the quest for a ''democratic proteome''. Proteomics,, 6, 3980-3992.
52. Fountoulakis, M., Juranville, J.F., Jiang, L., Avila, D., Roder, D., Jakob, P., Berndt, P., Evers, S., and Langen, H. (2004). Depletion of the high-abundance plasma proteins. Amino Acids,, 27, 249-259.
53. Greenough, C., Jenkins, R.E., Kitteringham, N.R., Pirmohamed, M., Park, B.K., and Pennington, S.R. (2004). A method for the rapid depletion of albumin and immunoglobulin from human plasma. Proteomics,, 4, 3107-3111.
54. Hinerfeld, D., Innamorati, D., Pirro, J., and Tam, S.W. (2004). Serum/Plasma depletion with chicken immunoglobulin Y antibodies for proteomic analysis from multiple Mammalian species. J Biomol Tech,, 15, 184-190.
55. Echan, L.A., Tang, H.Y., Ali-Khan, N., Lee, K., and Speicher, D.W. (2005). Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics,, 5, 3292-3303.
56. Gong, Y., Li, X., Yang, B., Ying, W., Li, D., Zhang, Y., Dai, S., Cai, Y., Wang, J., He, F., and Qian, X. (2006). Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J Proteome Res,, 5, 1379-1387.
57. Yan, J.X., Devenish, A.T., Wait, R., Stone, T., Lewis, S., and Fowler, S. (2002). Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics,, 2, 1682-1698.
58. Gharbi, S., Gaffney, P., Yang, A., Zvelebil, M.J., Cramer, R., Waterfield, M.D., and Timms, J.F. (2002). Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol Cell Proteomics,, 1, 91-98.
59. Yokota, H., Hiramoto, M., Okada, H., Kanno, Y., Yuri, M., Morita, S., Naitou, M., Ichikawa, A., Katoh, M., and Suzuki, H. (2007). Absence of increased alpha1-microglobulin in IgA nephropathy proteinuria. Mol Cell Proteomics,, 6, 738-744.
60. Rao, P.V., Lu, X., Standley, M., Pattee, P., Neelima, G., Girisesh, G., Dakshinamurthy, K.V., Roberts, C.T. Jr, and Nagalla, S.R. (2007). Proteomic identification of urinary biomarkers of diabetic nephropathy. Diabetes Care,, 30, 629-637.
61. Holly, M.K., Dear, J.W., Hu, X., Schechter, A.N., Gladwin, M.T., Hewitt, S.M., Yuen, P.S., and Star, R.A. (2006). Biomarker and drug-target discovery using proteomics in a new rat model of sepsis-induced acute renal failure. Kidney Int,, 70, 496-506.
62. Nedelkov, D. and Nelson, R.W. (2001). Analysis of human urine protein biomarkers via biomolecular interaction analysis mass spectrometry. Am J Kidney Dis,, 38, 481-487.
63. Hampel, D.J., Sansome, C., Sha, M., Brodsky, S., Lawson, W.E., and Goligorsky, M.S. (2001). Toward proteomics in uroscopy: urinary protein profiles after radiocontrast medium administration. J Am Soc Nephrol,, 12, 1026-1035.