Elevated pressure improves the extraction and identification of proteins recovered from formalin- fixed, paraffin-embedded tissue surrogates

PLoS ONE

Volumn 5, Issue 12, 2010, Pages

  Fowler, Carol B ^a,b   Chesnick, Ingrid E ^a   Moore, Cedric D ^a   O'Leary, Timothy J ^b   Mason, Jeffrey T ^a  

^a ARMED FORCES INSTITUTE OF PATHOLOGY   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOVINE SERUM ALBUMIN; CARBONATE DEHYDRATASE; FORMALDEHYDE; LYSOZYME; MYOGLOBIN; PARAFFIN; PEPTIDE; PROTEIN; RIBONUCLEASE A; CROSS LINKING REAGENT; EGG WHITE; FIXATIVE;

AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; EMBEDDING; EXTRACTION; FORMALIN FIXED PARAFFIN EMBEDDED TISSUE SURROGATE; HEAT; HISTOCHEMISTRY; HISTOLOGY; HYDRATION; HYDROLYSIS; HYDROSTATIC PRESSURE; LIGHT SCATTERING; LIVER; MASS SPECTROMETRY; MOUSE; NONHUMAN; PEPTIDE ANALYSIS; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN FOLDING; PROTEOMICS; TISSUE FIXATION; ANIMAL; CHEMISTRY; CHICKEN; METABOLISM; METHODOLOGY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BOVINAE; EQUIDAE;

ANIMALS; CHICKENS; CROSS-LINKING REAGENTS; EGG WHITE; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FIXATIVES; FORMALDEHYDE; LIVER; MASS SPECTROMETRY; MICE; MURAMIDASE; PARAFFIN; PARAFFIN EMBEDDING; PROTEINS; TISSUE FIXATION;

EID: 78650087646     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014253     Document Type: Article

References (43)

1. Jou YJ, Lin CD, Lai CH, Chen CH, Kao JY, et al. (2010) Proteomic identification of salivary transferrin as a biomarker for early detection of oral cancer. Anal Chim Acta 681: 41-48.
2. Valera VA, Li NTE, Walter BA, Roberts DD, Linehan WM, et al. (2010) Protein expression profiling in the spectrum of renal cell carcinomas. J Cancer 1: 184-196.
3. Buxbaum JL, Eloubeidi MA (2010) Molecular and clinical markers of pancreas cancer. JOP 11: 536-544.
4. Caudle WM, Bammler TK, Lin Y, Pan S, Zhang J (2010) Using 'omics' to define pathogenesis and biomarkers of Parkinson's disease. Expert Rev Neurother 10: 925-942.
5. Velic A, Macek B, Wagner CA (2010) Toward quantitative proteomics of organ substructures: implications for renal physiology. Semin Nephrol 30: 487- 499.
6. Machida K, Eschrich S, Li J, Bai Y, Koomen J, et al. (2010) Characterizing tyrosine phosphorylation signaling in lung cancer using SH2 profiling. PLoS ONE 5: e13470-.
7. Fleron M, Greffe Y, Musmeci D, Massart AC, Hennequiere V, et al. (2010) Novel post-digest isotope coded protein labeling method for phospho- and glycoproteome analysis. J Proteomics 73: 1986-2005.
8. Reymond MA, Schlegel W (2007) Proteomics in cancer. Adv Clin Chem 44: 103-142.
9. Metz B, Kersten GFA, Baart GJ, de Jong A, Meiring H, et al. (2006) Identification of formaldehyde-induced modifications in proteins: reactions with insulin. Bioconjug Chem 17: 815-822.
10. Metz B, Kersten GFA, Hoogerhout P, Brugghe HF, Timmermans HA, et al. (2004) Identification of formaldehyde-induced modifications in proteins: reactions with model peptides. J Biol Chem 279: 6235-6243.
11. Sompuram SR, Vani K, Messana E, Bogen SA (2004) A Molecular Mechanism of Formalin Fixation and Antigen Retrieval. Am J Clin Pathol 121: 190-199.
12. Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, 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.
13. Nishimura T, Nomura M, Tojo H, Hamasaki H, Fukuda T, et al. (2010) Proteomic analysis of laser-microdissected paraffin-embedded tissues: (2) MRM assay for stage-related proteins upon non-metastatic lung adenocarcinoma. J Proteomics 73: 1100-1110.
14. Kawamura T, Nomura M, Tojo H, Fujii K, Hamasaki H, et al. (2010) Proteomic analysis of laser-microdissected paraffin-embedded tissues: (1) Stagerelated protein candidates upon non-metastatic lung adenocarcinoma. J Proteomics 73: 1089-1099.
15. Prieto DA, Hood BL, Darfler MM, Guiel TG, Lucas DA, et al. (2005) Liquid Tissue: proteomic profiling of formalin-fixed tissues. Biotechniques 38(Suppl): 32-35.
16. Shi S-R, Liu C, Balgley BM, Lee C, Taylor CR (2006) Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J Histochem Cytochem 54: 739-743.
17. Addis MF, Tanca A, Pagnozzi D, Crobu S, Fanciulli G, et al. (2009) Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteomics 9: 3815-3823.
18. Balgley BM, Guo T, Zhao K, Fang X, Tavassoli FA, et al. (2009) Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. J Proteome Res 8: 917-925.
19. Ostasiewicz P, Zielinska DF, Mann M, Wisniewski JR (2010) Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J Proteome Res 9: 3688-3700.
20. Azimzadeh O, Barjaktarovic Z, Aubele M, Calzada-Wack J, Sarioglu H, et al. (2010) Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gelfree and gel-based proteomics. J Proteome Res.
21. Fowler CB, Cunningham RE, O'Leary TJ, Mason JT (2007) "Tissue surrogates" as a model for archival formalin-fixed paraffin-embedded tissues. Lab Invest 87: 836-846.
22. Fowler CB, O'Leary TJ, Mason JT (2008) Modeling formalin fixation and histological processing with bovine ribonuclease A: Effects of ethanol dehydration on reversal of formaldehyde-induced cross-links. Lab Invest 88: 785-791.
23. Fowler CB, Cunningham RE, Waybright TJ, Blonder J, Veenstra TD, et al. (2008) Elevated hydrostatic pressure promotes protein recovery from formalinfixed, paraffin-embedded tissue surrogates. Lab Invest 88: 185-195.
24. Bratthauer GL (2010) Processing of tissue specimens. Methods Mol Biol 588: 93-102.
25. Rait VK, O'Leary TJ, Mason JT (2004) Modeling formalin fixation and antigen retrieval with bovine pancreatic ribonuclease A: I-structural and functional alterations. Lab Invest 84: 292-299.
26. Rait VK, Xu L, O'Leary TJ, Mason JT (2004) Modeling formalin fixation and antigen retrieval with bovine pancreatic RNase A II. Interrelationship of crosslinking, immunoreactivity, and heat treatment. Lab Invest 84: 300-306.
27. Strader MB, Tabb DL, Hervey WJ, Pan C, Hurst GB (2006) Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Anal Chem 78: 125-134.
28. Xu H, Yang L, Wang W, Shi SR, Liu C, et al. (2008) Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J Proteome Res 7: 1098-1108.
29. Guo T, Wang W, Rudnick PA, Song T, Li J, et al. (2007) Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem 55: 763-772.
30. Wlodawer A, Bott R, Sjölin L (1982) The refined crystal structure of ribonuclease A at 2.0 Åresolution. J Biol Chem 257: 1325-1332.
31. Berthou J, Lifchitz A, Artymiuk P, Jolles P (1983) An X-ray study of the physiological-temperature form of hen egg-white lysozyme at 2 A resolution. Proc R Soc Lond B Biol Sci 217: 471-489.
32. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, et al. (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181: 662-666.
33. Liljas A, Kannan KK, Bergsten PC, Waara I, Fridborg K, et al. (1972) Crystal structure of human carbonic anhydrase C. Nat New Biol 235: 131-137.
34. He XM, Carter DC (1992) Atomic structure and chemistry of human serum albumin. Nature 358: 209-214.
35. Carter DC, Ho JX (1994) Structure of Serum Albumin. Adv Protein Chem 45: 153-203.
36. Poole S, West S, Walters C (1984) Protein-Protein Interactions: Their Importance in Foaming of Heterogeneous Protein Systems. J Sci Food Agric 35: 701-711.
37. Refaee M, Tezuka T, Akasaka K, Williamson MP (2003) Pressure-dependent changes in the solution structure of hen egg-white lysozyme. J Mol Biol 327: 857-865.
38. Frye KJ, Royer CA (1998) Probing the contribution of internal cavities to the volume change of protein unfolding under pressure. Protein Sci 7: 2217-2222.
39. Kobashigawa Y, Sakurai M, Nitta K (1999) Effect of hydrostatic pressure on unfolding of alpha-lactalbumin: volumetric equivalence of the molten globule and unfolded state. Protein Sci 8: 2765-2772.
40. St John RJ, Carpenter JF, Randolph TW (1999) High pressure fosters protein refolding from aggregates at high concentrations. Proc Natl Acad Sci U S A 96: 13029-13033.
41. Moreno F, Molina E, Olano A, López-Fandiño R (2003) High-Pressure Effects on Maillard Reaction between Glucose and Lysine. Journal of Agricultural and Food Chemistry 51: 394-400.
42. Kerschgens J, Egener-Kuhn T, Mermod N (2009) Protein-binding microarrays: probing disease markers at the interface of proteomics and genomics. Trends Mol Med 15: 352-358.
43. Voshol H, Ehrat M, Traenkle J, Bertrand E, van Oostrum J (2009) Antibodybased proteomics: analysis of signaling networks using reverse protein arrays. Eur J Biochem 276: 6871-6879.