Development and validation of a novel protein extraction methodology for quantitation of protein expression in formalin-fixed paraffin-embedded tissues using western blotting

Journal of Pathology

Volumn 217, Issue 4, 2009, Pages 497-506

  Nirmalan, Niroshini J ^a   Harnden, Patricia ^a   Selby, Peter J ^a   Banks, Rosamonde E ^a,b  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Biomarker discovery; Formalin fixed paraffin embedded (FFPE) tissue; Heat induced antigen retrieval (HIAR); Proteomics; Renal cell carcinoma; Tissue biomarkers; Western blotting

Indexed keywords

ACTIN; BUFFER; FORMALDEHYDE; MEMBRANE PROTEIN; PARAFFIN; BIOLOGICAL MARKER; MONOCLONAL ANTIBODY; PROTEIN;

ANTIGEN RETRIEVAL; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DENSITOMETRY; EXTRACTION; FROZEN SECTION; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; KIDNEY CARCINOMA; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; VALIDATION STUDY; WESTERN BLOTTING; CHEMISTRY; ISOLATION AND PURIFICATION; KIDNEY TUMOR; MASS SPECTROMETRY; METHODOLOGY; PROTEOMICS; REPRODUCIBILITY; TISSUE FIXATION;

ACTINS; ANTIBODIES, MONOCLONAL; BIOLOGICAL MARKERS; BLOTTING, WESTERN; CARCINOMA, RENAL CELL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; KIDNEY NEOPLASMS; MASS SPECTROMETRY; MEMBRANE PROTEINS; PARAFFIN EMBEDDING; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; TISSUE FIXATION;

EID: 62849124399     PISSN: 00223417     EISSN: 10969896     Source Type: Journal    
DOI: 10.1002/path.2504     Document Type: Article

References (41)

1. Cho WCS, Cheng CHK. Oncoproteomics: current trends and future perspectives. Exp Rev Proteom 2007;4:401-410.
2. Cho WCS. Contribution of oncoproteomics to cancer biomarker discovery. Mol Cancer 2007;6:60.
3. Wilson JF. The promise of disease proteomics: faster detec tion, diagnosis, and drug development. Ann Intern Med 2004;140:317-319.
4. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 2006;24:971-983.
5. Bodovitz S, Joos T. The proteomics bottleneck: strategies for preliminary validation of potential biomarkers and drug targets. Trends Biotechnol 2004;22:4-7.
6. Becker KF, Schott C, Hipp S, Metzger V, Porschewski P, Beck R, et al. Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis. J Pathol 2007;211:370-378.
7. Hood BL, Conrads TP, Veenstra TD. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics 2006;6:4106-4114.
8. Ahram M, Flaig MJ, Gillespie JW, Duray PH, Linehan WM, Ornstein DK, et al. Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications. Proteomics 2003;3:413-421.
9. Shi SR, Liu C, Balgley BM, Lee C, Taylor CR. Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J Histochem Cytochem 2006;54:739-743.
10. Hood BL, Darfler MM, Guiel TG, Furusato B, Lucas DA, Ringeisen BR, et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteom 2005;4:1741-1753.
11. Guo T, Wang WJ, Rudnick PA, Song T, Li J, Zhuang ZP, et al. Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem 2007;55:763-772.
12. Crockett DK, Lin ZS, Vaughn CP, Lim MS, Elenitoba-Johnson KS. Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab Invest 2005;85:1405-1415.
13. Bagnato C, Thumar J, Mayya V, Hwang SI, Zebroski H, Claf fey KP, et al. Proteomics analysis of human coronary atheroscle rotic plaque - a feasibility study of direct tissue proteomics by liquid chromatography and tandem mass spectrometry. Mol Cell Proteom 2007;6:1088-1102.
14. Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. Mol Biosyst 2008;4:712-720.
15. Shi SR, Key ME, Kalra KL. Antigen retrieval in formalinfixed, paraffin-embedded tissues: an enhancement method for immunohistochemical staining based on microwave oven heating of tissue sections. J Histochem Cytochem 1991;39:741-748.
16. Shi SR, Datar R, Liu C, Wu L, Zhang Z, Cote RJ, et al. DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat-induced retrieval in alkaline solution. Histochem Cell Biol 2004;122:211- 218.
17. Stanta G, Bonin S, Perin R. RNA extraction from formalin-fixed and paraffin-embedded tissues. Methods Mol Biol 1998;86:23-26.
18. Yamashita S. Heat-induced antigen retrieval: mechanisms and application to histochemistry. Progr Histochem Cytochem 2007;41:141-200.
19. Layfield R, Bailey K, Lowe J, Allibone R, Mayer RJ, Landon M. Extraction and protein sequencing of immunoglobulin light chain from formalin-fixed cerebrovascular amyloid deposits. J Pathol 1996;180:455-459.
20. Prieto DA, Hood BL, Darfler MM, Guiel TG, Lucas DA, Con rads TP, et al. Liquid tissue: proteomic profiling of formalin fixed tissues. Biotechniques 2005;38:532-535.
21. Guo T, Wang W, Rudnick PA, Song T, Li J, Zhuang Z, et al. Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem 2007;55:763-772.
22. Palmer-Toy DE, Krastins B, Sarracino DA, Nadol JB, Mer chant SN. Efficient method for the proteomic analysis of fixed and embedded tissues. J Proteome Res 2005;4:2404-2411.
23. Ikeda K, Monden T, Kanoh T, Tsujie M, Izawa H, Haba A, et al. Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J Histochem Cytochem 1998;46:397-404.
24. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970;227:680-685.
25. Hwang SI, Thumar J, Lundgren DH, Rezaul K, Mayya V, Wu L, et al. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffinembedded archival tissues. Oncogene 2007;26:65-76.
26. Thongboonkerd V. Proteomic analysis of renal diseases: unrav elling the pathophysiology and biomarker discovery. Expert Rev Proteomics 2005;2:349-366.
27. Banks RE, Craven RA, Harnden P, Madaan S, Joyce A, Selby PJ. Key clinical issues in renal cancer: a challenge for proteomics. World J Urol 2007;25:537-556.
28. Craven RA, Banks RE. Laser capture microdissection and pro teomics: possibilities and limitations. Proteomics 2001;1:1200-1204.
29. Craven RA, Hanrahan S, Totty N, Harnden P, Stanley AJ, Maher ER, et al. Proteomic identification of a role for the von Hippel-Lindau tumour suppressor in changes in the expression of mitochondrial proteins and septin 2 in renal cell carcinoma. Pro teomics 2006;6:3880-3893.
30. Craven RA, Stanley AJ, Hanrahan S, Dods J, Unwin R, Totty N, et al. Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma. Proteomics 2006;6:2853-2864.
31. Craven RA, Banks RE. Understanding and managing renal cell carcinoma: can proteomic studies contribute to clinical practice? Contrib Nephrol 2008;160:88-106.
32. Towbin H, Staehelin T, Gordon J. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci USA 1979;76:4350-4354.
33. +-based detection system for Western blotting: avoidance of streptavidin binding to endogenous biotin and biotin-containing proteins in kidney and other tissues. Proteomics 2003;3:558-561.
34. Pastwa E, Somiari SB, Czyz M, Somiari RI. Proteomics in human cancer research. Proteom Clin Appl 2007;1:4-17.
35. Becker KF, Schott C, Becker I, Hofler H. Guided protein extraction from formalin-fixed tissues for quantitative multiplex analysis avoids detrimental effects of histological stains. Proteom Clin Appl 2008;2:737-743.
36. Patel V, Hood BL, Molinolo A, Lee NH, Conrads TP, Braisted JC, et al. Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression. Clin Cancer Res 2008;14:1002-1014.
37. Broughton J, Swennen D, Wilkinson BM, Joyet P, Gaillardin C, Stirling CJ. Cloning of SEC61 homologues from Schizosaccha romyces pombe and Yarrowia lipolytica reveals the extent of func tional conservation within this core component of the ER translocation machinery. J Cell Sci 1997;110:2715-2727.
38. Metz B, Kersten GFA, Hoogerhout P, Brugghe HF, Timmer mans HAM, de Jong A, et al. Identification of formaldehydeinduced modifications in proteins: reactions with model peptides. J Biol Chem 2004;279: 6235-6243.
39. Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, et al. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteom Clin Appl 2007;1:148-156.
40. Qualman SJ, France M, Grizzle WE, LiVolsi VA, Moskaluk CA, Ramirez NC, et al. Establishing a tumour bank: banking, informatics and ethics. Br J Cancer 2004;90:1115-1119.
41. Shi SR, Liu C, Perez J, Taylor CR. Protein-embedding technique: a potential approach to standardization of immunohistochemistry for formalin-fixed paraffin-embedded tissue sections. J Histochem Cytochem 2005;53:1167-1170.