Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry

Journal of Histochemistry and Cytochemistry

Volumn 57, Issue 9, 2009, Pages 849-860

  Scicchitano, Marshall S ^a   Dalmas, Deidre A ^a   Boyce, Rogely W ^a   Thomas, Heath C ^a   Frazier, Kendall S ^a  

^a GLAXOSMITHKLINE   (United States)

Author keywords

FFPE; Mass spectrometry; Western blot

Indexed keywords

ATORVASTATIN; FORMALDEHYDE; PARAFFIN; BIOLOGICAL MARKER; FIXATIVE; HEPTANOIC ACID DERIVATIVE; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; PROTEOME; PYRROLE DERIVATIVE;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CROSS LINKING; EMBEDDING; LASER CAPTURE MICRODISSECTION; LIQUID CHROMATOGRAPHY; LIVER; MALE; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; RAT; TEMPERATURE; TISSUE FIXATION; WESTERN BLOTTING; ANIMAL; CELL NUCLEUS; CYTOPLASM; INTRACELLULAR MEMBRANE; METABOLISM; SPRAGUE DAWLEY RAT; TANDEM MASS SPECTROMETRY;

RATTUS;

ANIMALS; BIOLOGICAL MARKERS; CELL NUCLEUS; CHROMATOGRAPHY, LIQUID; CYTOPLASM; FIXATIVES; FORMALDEHYDE; HEPTANOIC ACIDS; HYDROXYMETHYLGLUTARYL-COA REDUCTASE INHIBITORS; INTRACELLULAR MEMBRANES; LIVER; MALE; PARAFFIN EMBEDDING; PROTEOME; PYRROLES; RATS; RATS, SPRAGUE-DAWLEY; TANDEM MASS SPECTROMETRY;

EID: 70249095601     PISSN: 00221554     EISSN: None     Source Type: Journal    
DOI: 10.1369/jhc.2009.953497     Document Type: Article

References (40)

1. Abersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198-207
2. Aoki Y, Toyama A, Shimada T, Sugita T, Aoki C, Umino Y, Suzuki A, et al. (2007) A novel method for analyzing formalin-fixed paraffin embedded (FFPE) tissue sections by mass spectrometry imaging. Proc Jpn Acad 83:205-214
3. Bagnato C, Thumar J, Mayya V, Hwang S, Zebroski H, Claffey KP, Haudenschild C, et al. (2007) Proteomic analysis of human coronary atherosclerotic plaque: a feasibility study of direct tissue proteomics by liquid-chromatography and tandem mass spectrometry. Mol Cell Proteomics 6:1088-1102
4. Balgley BM, Guo T, Zhao K, Fang X, Tavassol FA, Lee CS (2009) Evaluation of archival time on shotgun proteomics of formalinfixed and paraffin-embedded tissues. J Proteome Res 8:912-925
5. Balgley BM,WangW, DeVoe DL, Lee CS (2007) Mass spectrometrybased tissue proteomics for cancer biomarker discovery. Personalized Medicine 4:45-58
6. Becker KF, Schott C, Hipp S, Metzger V, Porschewski P, Beck R, Nahrig RB, et al. (2007) Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis. J Pathol 211:370-378
7. Belief V, Boissiere F, Bibeau F, Desmetz C, Berthe ML, Rochaix P, Maudelonde T, et al. (2008) Proteomic analysis of RCL2 paraffinembedded tissues. J Cell Mol Med 12:2027-2036
8. Chang C, Chen SH, Ho SH, Yang CY, Wang HD, Tsai ML (2007) Proteomic analysis of proteins from bronchoalveolar lavage fluid reveals the action mechanism of ultra fine carbon black-induced lung injury in mice. Proteomics 7:4388-4397
9. Chaurand P, Latham JC, Lane KB, Mobley JA, Polosukhin VV,Wirth PS, Nanney LB, et al. (2008) Imaging mass spectrometry of intact proteins from alcohol-preserved tissue specimens: bypassing formalin fixation. J Proteome Res 7:3543-3555
10. Crockett DK, Lin Z, Vaughn CP, Lim MS, Elenitoba-Johnson KSJ (2005) Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab Invest 85:1405-1415
11. Fowler CB, Cunningham RE, O'Leary TJ, Mason JT (2007) 'Tissue surrogates' as a model for archival formalin-fixed paraffinembedded tissues. Lab Invest 87:836-846
12. Fox CH, Johnson FB, Whiting J, Roller PP (1985) Formaldehyde fixation. J Histochem Cytochem 33:845-853
13. Gu Y, Wu SL, Meyer JL, Hancock WS, Burg LJ, Linder J, Hanlon DW, et al. (2007) Proteomic analysis of high-grade dysplastic cervical cells obtained from ThinPrep slides using laser capture microdissection and mass spectrometry. J Proteome Res 6: 4256-4268
14. Guo T, Wang W, Rudnick PA, Song T, Li J, Zhuang Z, Weil RJ, et al. (2007) Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem 55:763-772
15. Hood BL, Darfler MM, Guiel TG, Furusato B, Lucas DA, Ringeisen BR, Sesterhenn IA (2005) Proteomic analysis of formalin-fixed prostate cancer tissue sections: quality evaluation by mass spectrometry. Mol Cell Proteomics 4:1741-1753
16. Hwang SI, Thumar J, Lundgren DH, Rezaul K, Mayya V, Wu L, Wright ME, et al. (2007) Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers for formalin-fixed paraffin-embedded archival tissues. Oncogene 26:65-76
17. Igel M, Sudhop T, von Bergmann K (2002) Pharmacology of 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors (statins), including rosuvastatin and pitavastatin. J Clin Pharmacol 42:835-845
18. Ikeda K, Monden T, Kanoh T, Tsujie M, Izawa H, Haba A, Ohnishi T, et al. (1998) Extraction and analysis of diagnostically useful proteins from formalin-fixed paraffin-embedded tissue sections. J Histochem Cytochem 46:397-403
19. Jain MR, Liu T, Darfler M, Fitzhugh V, Rinaggio J, Li H (2008) Quantitative proteomic analysis of formalin fixed paraffin embedded oral HPV lesions from HIV patients. Open Proteomics J 1:40-45
20. Lahm HW, Langen H (2001) Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis 21: 2105-2114
21. Lemaire R, Desmons A, Tabet JC, Day R, Salzet M, Fournier I (2007) Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections. J Proteome Res 6:1295-1305
22. Leme A, Bellato C, Bedi G, Del Bel Cury A, Koo H, Cury J (2008) Effects of sucrose on the extracellular matrix of plaque-like biofilm formed in vivo, studied by proteomic analysis. Caries Res 42:435-443
23. Licklider LJ, Thoreeen CC, Peng J, Gygi SP (2002) Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column. Anal Chem 74:3076-3083
24. Liu H, Sadygov R, Yates JR (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76:4193-4201
25. Liu T, Qian W, Mottaz H, Gritsenko M, Norbeck A, Moore R, Purvine S, et al. (2006) Evaluation of multiprotein immunoaffininty subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol Cell Proteomics 5:2167-2174
26. Martinet W, Abbeloos V, Van-Acker N, De Meyer GRY, Herman AG, Kockx M (2004) Western blot analysis of a limited number of cells: a valuable adjunct to proteome analysis of paraffin waxembedded, alcohol-fixed tissue after laser capture microdissection. J Pathol 202:382-388
27. Nirmalan NJ, Harnden P, Selby PJ, Banks RE (2009) Development and validation of a novel protein extraction methodology for quantitation of protein expression in formalin-fixed paraffin-embedded tissues using western blotting. J Pathol 217:497-506
28. Palmer-Toy DE, Krastins B, Sarracino DA, Nadol JB, Merchant SN (2005) Efficient method for the proteomic analysis of fixed and embedded tissues. J Proteome Res 4:2404-2411
29. Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837-846
30. Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, Braisted JC, Krizman DB, et al. (2008) Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression. Clin Cancer Res 14:1002-1014
31. Prieto DA, Hood BL, Darfler MM, Guiel TG, Lucas DA, Conrads TP, Veenstra TD, et al. (2005) Liquid Tissue: proteomic profiling of formalin-fixed tissues. Biotechniques 38(suppl):32-35
32. Seigneurin-Berny D, Verdel A, Curtet S, Lemercier C, Garin J, Rousseaux S, Khochbin S (2001) Identification of componenets of the murine histone deactylase 6 complex: link between acetylation and ubiquitination signaling pathways. Mol Cell Biochem 21:8035-8044
33. Suneja S, Mo Z, Potashner S (2006) Phospho-CREB and other phospho-proteins: improved recovery from brain tissue. J Neurosci Methods 150:238-241
34. Shi SR, Gu J, Turrens J (2000) Antigen Retrieval Techniques: Immunohistochemistry and Molecular Morphology. Natick, MA, Eaton Publishing, 17-40
35. Shi SR, Liu C, Balgley BM, LeeC, Taylor CR (2006) Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J Histochem Cytochem 54:739-743
36. Stauber J, Lemaire R, Franck J, Bonnel D, Croix D, Day R,Wisztorski M, et al. (2008) MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting. J Proteome Res 7:969-978
37. Steiner S, Gatlin C, Lennon J, McGrath A, Aponte A, Makusky A, Rohrs M, et al. (2000) Proteomics to display lovastatin-induced protein and pathway regulation in rat liver. Electrophoresis 21: 2129-2137
38. Steiner S, Gatlin C, Lennon J, McGrath A, Seonarain M, Makusky A, Aponte A, et al. (2001) Cholesterol biosynthesis regulation and protein changes in rat liver following treatment with fluvastatin. Toxicol Lett 120:369-377
39. Vasilescu J, Guo X, Kast J (2004) Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics 4:3845-3854
40. Xu H, Yang L, Wang W, Shi SR, Liu C, Liu Y, Fang X, et al. (2008) Antigen retrival for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J Proteome Res 7:1098-1108