Toward deciphering proteomes of formalin‐fixed paraffin‐embedded ( FFPE ) tissues

Abstract

Formalin‐fixed paraffin‐embedded ( FFPE ) tissue specimens comprise a potentially valuable resource for both prospective and retrospective biomarker discovery. Unlocking the proteomic profile of clinicopathological FFPE tissues is a critically essential step for annotating clinical findings and predicting biomarkers for ultimate disease prognosis and therapeutic follow‐up.

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References 71

1. 1.

   Fox CH, Johnson FB, Whiting J, Roller PP. Formaldehyde fixation. J. Histochem. Cytochem. 1985;33:845-853.

   Not in our library10.1177/33.8.3894502

2. 2.

   Puchtler H, Meloan SN. On the chemistry of formaldehyde fixation and its effects on immunohistochemical reactions. Histochemistry. 1985;82:201-204.

   Not in our library10.1007/bf00501395

3. 3.

   Ahram M, Flaig MJ, Gillespie JW, Duray PH, et al. Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications. Proteomics. 2003;3:413-421.

   Not in our library10.1002/pmic.200390056

4. 4.

   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.

   Not in our library10.1039/b800098k

5. 5.

   Zhang H, Lin Q, Ponnusamy S, Kothandaraman N, et al. Differential recovery of membrane proteins after extraction by aqueous methanol and trifluoroethanol. Proteomics. 2007;7:1654-1663.

   Not in our library10.1002/pmic.200600579

6. 6.

   Ishibe N, Schully S, Freedman A, Ramsey SD. Use of oncotype DX in women with node-positive breast cancer. Plos Curr. 2011;21:PMC3145540.

   Not in our library10.1371/currents.rrn1249

7. 7.

   Flanagan MB, Dabbs DJ, Brufsky AM, Beriwal S, et al. Histopathologic variables predict oncotype DX recurrence score. Mod. Pathol. 2008;21:1255-1261.

   Not in our library10.1038/modpathol.2008.54

8. 8.

   Solassol J, Ramos J, Crapez E, Saifi M, et al. KRAS mutation detection in paired frozen and formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissues. Int. J. Mol. Sci. 2011;12:3191-3204.

   Not in our library10.3390/ijms12053191

9. 9.

   Chung JY, Lee SJ, Kris Y, Braunschweig T, et al. A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue. Proteomics Clin. Appl. 2008;2:1539-1547.

   Not in our library10.1002/prca.200800005

10. 10.

    Hood BL, Conrads TP, Veenstra TD. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics. 2006;6:4106-4114.

    Not in our library10.1002/pmic.200600016

11. 11.

    Crockett DK, Lin Z, Vaughn CP, Lim MS, et al. Identification of proteins from formalin-fixed paraffin-embedded cells by LCMSMS. Lab. Invest. 2005;85:1405-1415.

    Not in our library10.1038/labinvest.3700343

12. 12.

    Yamashita S. Heat-induced antigen retrieval: mechanisms and application to histochemistry. Prog. Histochem. Cytochem. 2007;41:141-200.

    Not in our library10.1016/j.proghi.2006.09.001

13. 13.

    Sprung RW, Brock JW, Tanksley JP, Li M, et al. Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell. Proteomics. 2009;8:1988-1998.

    Not in our library10.1074/mcp.m800518-mcp200

14. 14.

    Matsuda KM, Chung JY, Hewitt SM. Histo-proteomic profiling of formalin-fixed, paraffin-embedded tissue. Expert Rev. Proteomics. 2010;7:227-237.

    Not in our library10.1586/epr.09.106

15. 15.

    Xiao Z, Li G, Chen Y, Li M, et al. Quantitative proteomic analysis of formalin-fixed and paraffin-embedded nasopharyngeal carcinoma using iTRAQ labeling, two-dimensional liquid chromatography, and tandem mass spectrometry. J. Histochem. Cytochem. 2010;58:517-527.

    Not in our library10.1369/jhc.2010.955526

16. 16.

    Toews J, Rogalski JC, Clark TJ, Kast J. Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions. Anal. Chim. Acta. 2008;618:168-183.

    Not in our library10.1016/j.aca.2008.04.049

17. 17.

    Azimzadeh O, Barjaktarovic Z, Aubele M, Calzada-Wack J, et al. Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. J. Proteome. Res. 2010;9:4710-4720.

    Not in our library10.1021/pr1004168

18. 18.

    Wisniewski JR, Ostasiewicz P, Mann M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J. Proteome. Res. 2011;10:3040-3049.

    Not in our library10.1021/pr200019m

19. 19.

    Jiang X, Feng S, Tian R, Ye M, et al. Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. J. Proteome. Res. 2007;6:1038-1047.

    Not in our library10.1021/pr0605318

20. 20.

    Mason JT, O'Leary TJ. Effects of formaldehyde fixation on protein secondary structure: a calorimetric and infrared spectroscopic investigation. J. Histochem. Cytochem. 1991;39:225-229.

    Not in our library10.1177/39.2.1987266

21. 21.

    Ronci M, Bonanno E, Colantoni A, Pieroni L, et al. Protein unlocking procedures of formalin-fixed paraffin-embedded tissues: application to MALDITOF imaging MS investigations. Proteomics. 2008;8:3702-3714.

    Not in our library10.1002/pmic.200701143

22. 22.

    Sompuram SR, Vani K, Messana E, Bogen SA. A molecular mechanism of formalin fixation and antigen retrieval. Am. J. Clin. Pathol. 2004;121:190-199.

    Not in our library10.1309/brn7-ctx1-e84n-wwpl

23. 23.

    Addis MF, Tanca A, Pagnozzi D, Crobu S, et al. Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteomics. 2009;9:3815-3823.

    Not in our library10.1002/pmic.200800971

24. 24.

    Tian Y, Gurley K, Meany DL, Kemp CJ, et al. N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues. J. Proteome. Res. 2009;8:1657-1662.

    Not in our library10.1021/pr800952h

25. 25.

    Berg D, Hipp S, Malinowsky K, Bollner C, et al. Molecular profiling of signalling pathways in formalin-fixed and paraffin-embedded cancer tissues. Eur. J. Cancer. 2010;46:47-55.

    Not in our library10.1016/j.ejca.2009.10.016

26. 26.

    Ostasiewicz P, Zielinska DF, Mann M, Wisniewski JR. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome. Res. 2010;9:3688-3700.

    Not in our library10.1021/pr100234w

27. 27.

    Cohen P. The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. Eur. J. Biochem. 2001;268:5001-5010.

    Not in our library10.1046/j.0014-2956.2001.02473.x

28. 28.

    Kornfeld S. Diseases of abnormal protein glycosylation: an emerging area. J. Clin. Invest. 1998;101:1293-1295.

    Not in our library10.1172/jci3140

29. 29.

    Durand G, Seta N. Protein glycosylation and diseases: blood and urinary oligosaccharides as markers for diagnosis and therapeutic monitoring. Clin. Chem. 2000;46(6 Pt 1):795-805.

    Not in our library

30. 30.

    Fowler CB, Cunningham RE, O'Leary TJ, Mason JT. ‘Tissue surrogates’ as a model for archival formalin-fixed paraffin-embedded tissues. Lab. Invest. 2007;87:836-846.

    Not in our library10.1038/labinvest.3700596

31. 31.

    Fowler CB, Chesnick IE, Moore CD, O'Leary TJ, et al. Elevated pressure improves the extraction and identification of proteins recovered from formalin-fixed, paraffin-embedded tissue surrogates. PLoS One. 2010;5:e14253.

    Not in our library10.1371/journal.pone.0014253

32. 32.

    Yamashita S, Okada Y. Mechanisms of heat-induced antigen retrieval: analyses in vitro employing SDSPAGE and immunohistochemistry. J. Histochem. Cytochem. 2005;53:13-21.

    Not in our library10.1177/002215540505300103

33. 33.

    Tanca A, Pagnozzi D, Falchi G, Biosa G, et al. Impact of fixation time on GeLCMSMS proteomic profiling of formalin-fixed, paraffin-embedded tissues. J. Proteomics. 2011;74:1015-1021.

    Not in our library10.1016/j.jprot.2011.03.015

34. 34.

    Godfrey TE, Kim SH, Chavira M, Ruff DW, et al. Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5’ nuclease quantitative reverse transcription-polymerase chain reaction. J. Mol. Diagn. 2000;2:84-91.

    Not in our library10.1016/s1525-1578(10)60621-6

35. 35.

    Klopfleisch R, Weiss AT, Gruber AD. Excavation of a buried treasure-DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues. Histol. Histopathol. 2011;26:797-810.

    Not in our library10.14670/hh-26.797

36. 36.

    Dani C, Blanchard JM, Piechaczyk M, El Sabouty S, et al. Extreme instability of myc mRNA in normal and transformed human cells. Proc. Natl. Acad. Sci. U.S.A. 1984;81:7046-7050.

    Not in our library10.1073/pnas.81.22.7046

37. 37.

    Balgley BM, Guo T, Zhao K, Fang X, et al. Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. J. Proteome. Res. 2009;8:917-925.

    Not in our library10.1021/pr800503u

38. 38.

    Ikeda K, Monden T, Kanoh T, Tsujie M, et al. Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J. Histochem. Cytochem. 1998;46:397-403.

    Not in our library10.1177/002215549804600314

39. 39.

    Ha GH, Lee SU, Kang DG, Ha NY, et al. Proteome analysis of human stomach tissue: separation of soluble proteins by two-dimensional polyacrylamide gel electrophoresis and identification by mass spectrometry. Electrophoresis. 2002;23:2513-2524.

    Not in our library10.1002/1522-2683(200208)23:15<2513::aid-elps2513>3.0.co;2-w

40. 40.

    Xie H, Bandhakavi S, Griffin TJ. Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae. Anal. Chem. 2005;77:3198-3207.

    Not in our library10.1021/ac0482256

41. 41.

    Shi SR, Liu C, Balgley BM, Lee C, et al. Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J. Histochem. Cytochem. 2006;54:739-743.

    Not in our library10.1369/jhc.5b6851.2006

42. 42.

    Palmer-Toy DE, Krastins B, Sarracino DA, Nadol JB, et al. Efficient method for the proteomic analysis of fixed and embedded tissues. J. Proteome. Res. 2005;4:2404-2411.

    Not in our library10.1021/pr050208p

43. 43.

    Xu H, Yang L, Wang W, Shi SR, et al. Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J. Proteome. Res. 2008;7:1098-1108.

    Not in our library10.1021/pr7006768

44. 44.

    Ferro M, Seigneurin-Berny D, Rolland N, Chapel A, et al. Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins. Electrophoresis. 2000;21:3517-3526.

    Not in our library10.1002/1522-2683(20001001)21:16<3517::aid-elps3517>3.0.co;2-h

45. 45.

    Chertov O, Biragyn A, Kwak LW, Simpson JT, et al. Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry. Proteomics. 2004;4:1195-1203.

    Not in our library10.1002/pmic.200300677

46. 46.

    Tian Y, Zhang H. Isolation of proteins by heat-induced extraction from formalin-fixed, paraffin-embedded tissue and preparation of tryptic peptides for mass spectrometric analysis. Curr. Protoc. Mol. Biol. 2010;26:11-17.

    Not in our library10.1002/0471142727.mb1026s90

47. 47.

    Wang H, Qian WJ, Mottaz HM, Clauss TR, et al. Development and evaluation of a micro- and nanoscale proteomic sample preparation method. J. Proteome. Res. 2005;4:2397-2403.

    Not in our library10.1021/pr050160f

48. 48.

    Buck M. Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins. Q. Rev. Biophys. 1998;31:297-355.

    Not in our library10.1017/s003358359800345x

49. 49.

    Rait VK, Xu L, O'Leary TJ, Mason JT. Modeling formalin fixation and antigen retrieval with bovine pancreatic RNase A II. Interrelationship of cross-linking, immunoreactivity, and heat treatment. Lab. Invest. 2004;84:300-306.

    Not in our library10.1038/labinvest.3700041

50. 50.

    Hwang SI, Thumar J, Lundgren DH, Rezaul K, et al. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene. 2007;26:65-76.

    Not in our library10.1038/sj.onc.1209755

51. 51.

    Bagnato C, Thumar J, Mayya V, Hwang SI, et al. Proteomics analysis of human coronary atherosclerotic plaque: a feasibility study of direct tissue proteomics by liquid chromatography and tandem mass spectrometry. Mol. Cell. Proteomics. 2007;6:1088-1102.

    Not in our library10.1074/mcp.m600259-mcp200

52. 52.

    Guo T, Wang W, Rudnick PA, Song T, et al. Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J. Histochem. Cytochem. 2007;55:763-772.

    Not in our library10.1369/jhc.7a7177.2007

53. 53.

    Scicchitano MS, Dalmas DA, Boyce RW, Thomas HC, et al. Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry. J. Histochem. Cytochem. 2009;57:849-860.

    Not in our library10.1369/jhc.2009.953497

54. 54.

    Nirmalan NJ, Harnden P, Selby PJ, Banks RE. 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. 2009;217:497-506.

    Not in our library10.1002/path.2504

55. 55.

    Grantzdorffer I, Yumlu S, Gioeva Z, Von wasielewski R, et al. Comparison of different tissue sampling methods for protein extraction from formalin-fixed and paraffin-embedded tissue specimens. Exp. Mol. Pathol. 2010;88:190-196.

    Not in our library10.1016/j.yexmp.2009.09.009

56. 56.

    Becker KF, Schott C, Hipp S, Metzger V, et al. Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis. J. Pathol. 2007;211:370-378.

    Not in our library10.1002/path.2107

57. 57.

    Paulo JA, Lee LS, Banks PA, Steen H, et al. Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. Pancreas. 2011;41:175-185.

    Not in our library10.1097/mpa.0b013e318227a6b7

58. 58.

    Nomura M, Fukuda T, Fujii K, Kawamura T, et al. Preferential expression of potential markers for cancer stem cells in large cell neuroendocrine carcinoma of the lung. An FFPE proteomic study. J. Clin. Bioinforma. 2011;3:23.

    Not in our library10.1186/2043-9113-1-23

59. 59.

    Berg D, Wolff C, Langer R, Schuster T, et al. Discovery of new molecular subtypes in oesophageal adenocarcinoma. PLoS One. 2011;6:e23985.

    Not in our library10.1371/journal.pone.0023985

60. 60.

    Naidoo K, Jones R, Dmitrovic B, Wijesuriya N, et al. Proteome of formalin-fixed paraffin-embedded pancreatic ductal adenocarcinoma and lymph node metastases. J. Pathol. 2011.

    Not in our library10.1002/path.3959

61. 61.

    Tanca A, Addis MF, Pagnozzi D, Cossu-Rocca P, et al. Proteomic analysis of formalin-fixed, paraffin-embedded lung neuroendocrine tumor samples from hospital archives. J. Proteomics. 2011;74:359-370.

    Not in our library10.1016/j.jprot.2010.12.001

62. 62.

    Casadonte R, Caprioli RM. Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry. Nat. Protoc. 2011;6:1695-1709.

    Not in our library10.1038/nprot.2011.388

63. 63.

    Wolff C, Schott C, Malinowsky K, Berg D, et al. Producing reverse phase protein microarrays from formalin-fixed tissues. Methods Mol. Biol. 2011;785:123-140.

    Not in our library10.1007/978-1-61779-286-1_9

64. 64.

    Byrum S, Avaritt NL, Mackintosh SG, Munkberg JM, et al. A quantitative proteomic analysis of FFPE melanoma. J. Cutan. Pathol. 2011;38:933-936.

    Not in our library10.1111/j.1600-0560.2011.01761.x

65. 65.

    Koomen JM, Smalley KS. Using quantitative proteomic analysis to understand genotype specific intrinsic drug resistance in melanoma. Oncotarget. 2011;2:329-335.

    Not in our library10.18632/oncotarget.263

66. 66.

    Gámez-Pozo A, Sánchez-Navarro I, Calvo E, Díaz E, et al. Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches. Mol. Biosyst. 2011;7:2368-2374.

    Not in our library10.1039/c1mb05113j

67. 67.

    Müller BM, Kronenwett R, Hennig G, Euting H, et al. Quantitative determination of estrogen receptor, progesterone receptor, and HER2 mRNA in formalin-fixed paraffin-embedded tissue: a new option for predictive biomarker assessment in breast cancer. Diagn. Mol. Pathol. 2011;20:1-10.

    Not in our library10.1097/pdm.0b013e3181e3630c

68. 68.

    Abramovitz M, Barwick BG, Willis S, Young B, et al. Molecular characterization of formalin-fixed paraffin-embedded (FFPE) breast tumor specimens using a custom 512-gene breast cancer bead array-based platform. Br. J. Cancer. 2011;105:1574-1581.

    Not in our library10.1038/bjc.2011.355

69. 69.

    Munding JB, Adai AT, Maghnouj A, Urbanik A, et al. Global microRNA expression profiling of microdissected tissues identifies miR-135b as a novel biomarker for pancreatic ductal adenocarcinoma. Int. J. Cancer.

    Not in our library10.1002/ijc.26466

70. 70.

    Bateman NW, Sun M, Bhargava R, Hood BL, et al. Differential proteomic analysis of late-stage and recurrent breast cancer from formalin-fixed paraffin-embedded tissues. J. Proteome. Res. 2011;10:1323-1332.

    Not in our library10.1021/pr101073s

71. 71.

    Berg D, Langer R, Tran K, Walch A, et al. Protein microarray-based comparison of HER2, estrogen receptor, and progesterone receptor status in core biopsies and surgical specimens from FFPE breast cancer tissues. Appl. Immunohistochem. Mol. Morphol. 2011;19:300-305.

    Not in our library10.1097/pai.0b013e3182054f9f

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