Is the time ripe for kidney tissue proteomics?

Proteomics - Clinical Applications

Volumn 5, Issue 5-6, 2011, Pages 215-221

  Charonis, Aristidis ^a   Luider, Theo ^b   Baumann, Marc ^c   Schanstra, Joost P ^d,e  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^b ERASMUS MEDICAL CENTER   (Netherlands)

^c UNIVERSITY OF HELSINKI   (Finland)

^d INSERM   (France)

^e UNIVERSITÉ PAUL SABATIER   (France)

Author keywords

Formalin fixed paraffin embedded biopsies; Kidney; Laser capture microdissection; MS imaging

Indexed keywords

PROTEOME;

ARTICLE; CELL TYPE; EPITHELIUM CELL; HUMAN; KIDNEY CORTEX; KIDNEY DISEASE; KIDNEY PARENCHYMA; LASER CAPTURE MICRODISSECTION; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROGNOSIS; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN URINE LEVEL; PROTEOMICS;

ANIMALS; HUMANS; KIDNEY; KIDNEY DISEASES; PROTEOME; PROTEOMICS;

EID: 79957597615     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201000111     Document Type: Article

References (33)

1. Decramer, S., Gonzalez de Peredo, A., Breuil, B., Mischak, H. et al., Urine in clinical proteomics. Mol. Cell. Proteomics 2008, 7, 1850-1862.
2. Mischak, H., Delles, C., Klein, J., Schanstra, J. P., Urinary proteomics based on capillary electrophoresis-coupled mass spectrometry in kidney disease: discovery and validation of biomarkers, and clinical application. Adv. Chronic Kidney Dis. 17, 493-506.
3. Mischak, H., Allmaier, G., Apweiler, R., Attwood, T. et al., Recommendations for biomarker identification and qualification in clinical proteomics. Sci. Transl. Med. 2010, 2, 46ps42.
4. Chevalier, R. L., Obstructive nephropathy: towards biomarker discovery and gene therapy. Nat. Clin. Pract. Nephrol. 2006, 2, 157-168.
5. Fioretto, P., Mauer, M., Histopathology of diabetic nephropathy. Semin. Nephrol. 2007, 27, 195-207.
6. Chatziantoniou, C., Boffa, J. J., Tharaux, P. L., Flamant, M. et al., Progression and regression in renal vascular and glomerular fibrosis. Int. J. Exp. Pathol. 2004, 85, 1-11.
7. Stockand, J. D., Sansom, S. C., Regulation of filtration rate by glomerular mesangial cells in health and diabetic renal disease. Am. J. Kidney Dis. 1997, 29, 971-981.
8. Zeisberg, M., Duffield, J. S., Resolved: EMT produces fibroblasts in the kidney. J. Am. Soc. Nephrol. 2010, 21, 1247-1253.
9. Mathieson, P. W., Update on the podocyte. Curr. Opin. Nephrol. Hypertens. 2009, 18, 206-211.
10. Arthur, J. M., Thongboonkerd, V., Scherzer, J. A., Cai, J. et al., Differential expression of proteins in renal cortex and medulla: a proteomic approach. Kidney Int. 2002, 62, 1314-1321.
11. Magni, F., Sarto, C., Valsecchi, C., Casellato, S. et al., Expanding the proteome two-dimensional gel electrophoresis reference map of human renal cortex by peptide mass fingerprinting. Proteomics 2005, 5, 816-825.
12. Zhao, Y., Denner, L., Haidacher, S. J., LeJeune, W. S., Tilton, R. G., Comprehensive analysis of the mouse renal cortex using two-dimensional HPLC - tandem mass spectrometry. Proteome Sci. 2008, 6, 15.
13. Adachi, J., Kumar, C., Zhang, Y., Olsen, J. V., Mann, M., The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 2006, 7, R80.
14. Pisitkun, T., Shen, R. F., Knepper, M. A., Identification and proteomic profiling of exosomes in human urine. Proc. Natl. Acad. Sci. USA 2004, 101, 13368-13373.
15. Thongboonkerd, V., Malasit, P., Renal and urinary proteomics: current applications and challenges. Proteomics 2005, 5, 1033-1042.
16. Umar, A., Luider, T. M., Foekens, J. A., Pasa-Tolic, L., NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells. Proteomics 2007, 7, 323-329.
17. Umar, A., Kang, H., Timmermans, A. M., Look, M. P. et al., Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer. Mol. Cell. Proteomics 2009, 8, 1278-1294.
18. Umar, A., Dalebout, J. C., Timmermans, A. M., Foekens, J. A., Luider, T. M., Method optimisation for peptide profiling of microdissected breast carcinoma tissue by matrix-assisted laser desorption/ionisation-time of flight and matrix-assisted laser desorption/ionisation-time of flight/time of flight-mass spectrometry. Proteomics 2005, 5, 2680-2688.
19. Mustafa, D. A., Burgers, P. C., Dekker, L. J., Charif, H. et al., Identification of glioma neovascularization-related proteins by using MALDI-FTMS and nano-LC fractionation to microdissected tumor vessels. Mol. Cell. Proteomics 2007, 6, 1147-1157.
20. Yoshida, Y., Miyazaki, K., Kamiie, J., Sato, M. 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, 1083-1096.
21. Sitek, B., Potthoff, S., Schulenborg, T., Stegbauer, J. et al., Novel approaches to analyse glomerular proteins from smallest scale murine and human samples using DIGE saturation labelling. Proteomics 2006, 6, 4337-4345.
22. Miyamoto, M., Yoshida, Y., Taguchi, I., Nagasaka, Y. et al., In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J. Proteome Res. 2007, 6, 3680-3690.
23. Pisitkun, T., Bieniek, J., Tchapyjnikov, D., Wang, G. et al., High-throughput identification of IMCD proteins using LC-MS/MS. Physiol. Genomics 2006, 25, 263-276.
24. Curthoys, N. P., Taylor, L., Hoffert, J. D., Knepper, M. A., Proteomic analysis of the adaptive response of rat renal proximal tubules to metabolic acidosis. Am. J. Physiol. Renal. Physiol. 2007, 292, F140-147.
25. Hoffert, J. D., Wang, G., Pisitkun, T., Shen, R. F., Knepper, M. A., An automated platform for analysis of phosphoproteomic datasets: application to kidney collecting duct phosphoproteins. J. Proteome Res. 2007, 6, 3501-3508.
26. Sethi, S., Gamez, J. D., Vrana, J. A., Theis, J. D. et al., Glomeruli of dense deposit disease contain components of the alternative and terminal complement pathway. Kidney Int. 2009, 75, 952-960.
27. Xu, B. J., Combining laser capture microdissection and proteomics: Methodologies and clinical applications. Proteomics Clin. Appl. 2010, 4, 116-123.
28. Lasagni, L., Romagnani, P., Glomerular epithelial stem cells: the good, the bad, and the ugly. J. Am. Soc. Nephrol. 2010, 21, 1612-1619.
29. DeSouza, L. V., Krakovska, O., Darfler, M. M., Krizman, D. B. et al., mTRAQ-based quantification of potential endometrial carcinoma biomarkers from archived formalin-fixed paraffin-embedded tissues. Proteomics 2010, 10, 3108-3116.
30. Xu, B. J., Shyr, Y., Liang, X., Ma, L. J. et al., Proteomic patterns and prediction of glomerulosclerosis and its mechanisms. J. Am. Soc. Nephrol. 2005, 16, 2967-2975.
31. Mouledous, L., Hunt, S., Harcourt, R., Harry, J. L. et al., Proteomic analysis of immunostained, laser-capture microdissected brain samples. Electrophoresis 2003, 24, 296-302.
32. Fend, F., Emmert-Buck, M. R., Chuaqui, R., Cole, K. et al., Immuno-LCM: laser capture microdissection of immunostained frozen sections for mRNA analysis. Am. J. Pathol. 1999, 154, 61-66.
33. Guo, T., Wang, W., Rudnick, P. A., Song, T. et al., Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J. Histochem. Cytochem. 2007, 55, 763-772.