A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer

Journal of the Pancreas

Volumn 14, Issue 4, 2013, Pages 405-414

  Paulo, Joao A ^a   Kadiyala, Vivek ^a   Brizard, Scott ^a   Banks, Peter A ^a   Steen, Hanno ^a   Conwell, Darwin L ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Autoimmune diseases; Biological markers; Chronic; Pancreas; Pancreatic neoplasms; Pancreatitis

Indexed keywords

FORMALDEHYDE; PARAFFIN;

ARTICLE; AUTOIMMUNE PANCREATITIS; CHRONIC PANCREATITIS; COMPARATIVE STUDY; CONTROLLED STUDY; FORMALIN FIXED PARAFFIN EMBEDDED PANCREATIC TISSUE; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; LIQUID CHROMATOGRAPHY; PANCREAS; PANCREAS CANCER; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; TANDEM MASS SPECTROMETRY; TISSUE PRESERVATION; TISSUE SECTION;

AUTOIMMUNE DISEASES; CHROMATOGRAPHY, LIQUID; COHORT STUDIES; FORMALDEHYDE; HUMANS; IMMUNOHISTOCHEMISTRY; PANCREATIC NEOPLASMS; PANCREATITIS; PANCREATITIS, CHRONIC; PARAFFIN EMBEDDING; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY; TISSUE FIXATION;

EID: 84880070896     PISSN: 15908577     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (59)

1. NIH, Opportunities and Challenges in Digestive Diseases Research: Recommendations of the National Commission on Digestive Diseases, U.S. Department of Health and Human Services, National Institutes of Health, NIH publ. no. 08-6514 (2009) 159-167.
2. I. Nishimori, A. Tamakoshi, M. Otsuki, Prevalence of autoimmune pancreatitis in Japan from a nationwide survey in 2002, J Gastroenterol, 42 Suppl 18 (2007) 6-8.
3. R.K. Pearson, D.S. Longnecker, S.T. Chari, T.C. Smyrk, K. Okazaki, L. Frulloni, G. Cavallini, Controversies in clinical pancreatology: autoimmune pancreatitis: does it exist?, Pancreas, 27 (2003) 1-13.
4. I. Nishimori, A. Tamakoshi, S. Kawa, S. Tanaka, K. Takeuchi, T. Kamisawa, H. Saisho, K. Hirano, K. Okamura, N. Yanagawa, M. Otsuki, Influence of steroid therapy on the course of diabetes mellitus in patients with autoimmune pancreatitis: findings from a nationwide survey in Japan, Pancreas, 32 (2006) 244-248.
5. D.L. Finkelberg, D. Sahani, V. Deshpande, W.R. Brugge, Autoimmune pancreatitis, The New England journal of medicine, 355 (2006) 2670-2676.
6. R. Pannala, S.T. Chari, Autoimmune pancreatitis, Curr Opin Gastroenterol, 24 (2008) 591-596.
7. R. Law, M. Bronner, D. Vogt, T. Stevens, Autoimmune pancreatitis: a mimic of pancreatic cancer, Cleveland Clinic journal of medicine, 76 (2009) 607-615.
8. J.A. Paulo, L.S. Lee, P.A. Banks, H. Steen, D.L. Conwell, Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry, Pancreas, 41 (2012) 175-185.
9. S.R. Shi, R.J. Cote, C.R. Taylor, Antigen retrieval techniques: current perspectives, J Histochem Cytochem, 49 (2001) 931-937.
10. H. Steen, M. Mann, The ABC's (and XYZ's) of peptide sequencing, Nature reviews, 5 (2004) 699-711.
11. B.A. Reimel, S. Pan, D.H. May, S.A. Shaffer, D.R. Goodlett, M.W. McIntosh, L.M. Yerian, M.P. Bronner, R. Chen, T.A. Brentnall, Proteomics on Fixed Tissue Specimens-A Review, Curr Proteomics, 6 (2009) 63-69.
12. B.M. Balgley, T. Guo, K. Zhao, X. Fang, F.A. Tavassoli, C.S. Lee, Evaluation of archival time on shotgun proteomics of formalinfixed and paraffin-embedded tissues, Journal of proteome research, 8 (2009) 917-925.
13. X. Jiang, S. Feng, R. Tian, M. Ye, H. Zou, Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues, Journal of proteome research, 6 (2007) 1038-1047.
14. D.E. Palmer-Toy, B. Krastins, D.A. Sarracino, J.B. Nadol, Jr., S.N. Merchant, Efficient method for the proteomic analysis of fixed and embedded tissues, Journal of proteome research, 4 (2005) 2404-2411.
15. H. Xu, L. Yang, W. Wang, S.R. Shi, C. Liu, Y. Liu, X. Fang, C.R. Taylor, C.S. Lee, B.M. Balgley, Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues, Journal of proteome research, 7 (2008) 1098-1108.
16. D. Kessner, M. Chambers, R. Burke, D. Agus, P. Mallick, ProteoWizard: open source software for rapid proteomics tools development, Bioinformatics, 24 (2008) 2534-2536.
17. I.V. Shilov, S.L. Seymour, A.A. Patel, A. Loboda, W.H. Tang, S.P. Keating, C.L. Hunter, L.M. Nuwaysir, D.A. Schaeffer, The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra, Mol Cell Proteomics, 6 (2007) 1638-1655.
18. M.Q. Dong, J.D. Venable, N. Au, T. Xu, S.K. Park, D. Cociorva, J.R. Johnson, A. Dillin, J.R. Yates, 3rd, Quantitative mass spectrometry identifies insulin signaling targets in C. elegans, Science, 317 (2007) 660-663.
19. H. Liu, R.G. Sadygov, J.R. Yates, 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics, Anal Chem, 76 (2004) 4193-4201.
20. W. Cheung, M.M. Darfler, H. Alvarez, B.L. Hood, T.P. Conrads, N. Habbe, D.B. Krizman, J. Mollenhauer, G. Feldmann, A. Maitra, Application of a global proteomic approach to archival precursor lesions: deleted in malignant brain tumors 1 and tissue transglutaminase 2 are upregulated in pancreatic cancer precursors, Pancreatology: official journal of the International Association of Pancreatology, 8 (2008) 608-616.
21. B.L. Hood, M.M. Darfler, T.G. Guiel, B. Furusato, D.A. Lucas, B.R. Ringeisen, I.A. Sesterhenn, T.P. Conrads, T.D. Veenstra, D.B. Krizman, Proteomic analysis of formalin-fixed prostate cancer tissue, Mol Cell Proteomics, 4 (2005) 1741-1753.
22. P. Ostasiewicz, D.F. Zielinska, M. Mann, J.R. Wisniewski, 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).
23. T. Guo, W. Wang, P.A. Rudnick, T. Song, J. Li, Z. Zhuang, R.J. Weil, D.L. DeVoe, C.S. Lee, B.M. Balgley, Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens, J Histochem Cytochem, 55 (2007) 763-772.
24. S.R. Shi, C. Liu, B.M. Balgley, C. Lee, C.R. Taylor, Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry, J Histochem Cytochem, 54 (2006) 739-743.
25. L.F. Waanders, K. Chwalek, M. Monetti, C. Kumar, E. Lammert, M. Mann, Quantitative proteomic analysis of single pancreatic islets, Proceedings of the National Academy of Sciences of the United States of America, 106 (2009) 18902-18907.
26. D.K. Crockett, Z. Lin, C.P. Vaughn, M.S. Lim, K.S. Elenitoba-Johnson, Identification of proteins from formalin-fixed paraffinembedded cells by LC-MS/MS, Lab Invest, 85 (2005) 1405-1415.
27. G.M. Cavestro, L. Frulloni, T.M. Neri, P. Seghini, A. Nouvenne, A. Zanetti, P. Bovo, F. Di Mario, L. Okolicsanyi, G. Cavallini, Association of HLA-DRB1*0401 allele with chronic pancreatitis, Pancreas, 26 (2003) 388-391.
28. T.L. Freitag, C. Cham, H.H. Sung, G.F. Beilhack, I. Durinovic-Bello, S.D. Patel, R.T. Bronson, D. Schuppan, G. Sonderstrup, Human risk allele HLA-DRB1*0405 predisposes class II transgenic Ab0 NOD mice to autoimmune pancreatitis, Gastroenterology, 139 (2010) 281-291.
29. X. Li, R. Ni, J. Chen, Z. Liu, M. Xiao, F. Jiang, C. Lu, The presence of IGHG1 in human pancreatic carcinomas is associated with immune evasion mechanisms, Pancreas, 40 (2011) 753-761.
30. T. Yoshida, N. Shiraki, H. Baba, M. Goto, S. Fujiwara, K. Kume, S. Kume, Expression patterns of epiplakin1 in pancreas, pancreatic cancer and regenerating pancreas, Genes Cells, 13 (2008) 667-678.
31. E. Levi, D.S. Klimstra, A. Andea, O. Basturk, N.V. Adsay, MUC1 and MUC2 in pancreatic neoplasia, J Clin Pathol, 57 (2004) 456-462.
32. Z. Zhao, H. Liu, X. Wang, Z. Li, Separation and identification of HSP-associated protein complexes from pancreatic cancer cell lines using 2D CN/SDS-PAGE coupled with mass spectrometry, J Biomed Biotechnol, 2011 (2011) 193052.
33. C.H. Fox, F.B. Johnson, J. Whiting, P.P. Roller, Formaldehyde fixation, J Histochem Cytochem, 33 (1985) 845-853.
34. R.J. McKenna, Jr., W.V. Houck, New approaches to the minimally invasive treatment of lung cancer, Curr Opin Pulm Med, 11 (2005) 282-286.
35. K.F. Becker, C. Schott, S. Hipp, V. Metzger, P. Porschewski, R. Beck, J. Nährig, I. Becker, H. Höfler, Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis, The Journal of Pathology, 211 (2007) 370-378.
36. V. Thongboonkerd, Proteomics of human body fluids: principles, methods, and applications, Humana Press, Totowa, N.J., 2007.
37. S. Decramer, A. Gonzalez de Peredo, B. Breuil, H. Mischak, B. Monsarrat, J.L. Bascands, J.P. Schanstra, Urine in clinical proteomics, Mol Cell Proteomics, 7 (2008) 1850-1862.
38. D.M. Good, V. Thongboonkerd, J. Novak, J.L. Bascands, J.P. Schanstra, J.J. Coon, A. Dominiczak, H. Mischak, Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future, J Proteome Res, 6 (2007) 4549-4555.
39. Y.K. Paik, H. Kim, E.Y. Lee, M.S. Kwon, S.Y. Cho, Overview and introduction to clinical proteomics, Methods Mol Biol, 428 (2008) 1-31.
40. J. Barratt, P. Topham, Urine proteomics: the present and future of measuring urinary protein components in disease, Cmaj, 177 (2007) 361-368.
41. G.L. Hortin, D. Sviridov, Diagnostic potential for urinary proteomics, Pharmacogenomics, 8 (2007) 237-255.
42. H. Muller, H. Brenner, Urine markers as possible tools for prostate cancer screening: review of performance characteristics and practicality, Clinical chemistry, 52 (2006) 562-573.
43. N.P. Munro, D.A. Cairns, P. Clarke, M. Rogers, A.J. Stanley, J.H. Barrett, P. Harnden, D. Thompson, I. Eardley, R.E. Banks, M.A. Knowles, Urinary biomarker profiling in transitional cell carcinoma, International journal of cancer, 119 (2006) 2642-2650.
44. V. Thongboonkerd, Urinary proteomics: towards biomarker discovery, diagnostics and prognostics, Molecular bioSystems, 4 (2008) 810-815.
45. J.A. Paulo, L.S. Lee, B. Wu, K. Repas, P.A. Banks, H. Steen, D. Conwell, Cytokine protein microarray analysis of pancreatic fluid in tandem with the endoscopic pancreatic function test (ePFT), Pancreatology, Submitted (2010).
46. H. Tammen, Specimen collection and handling: standardization of blood sample collection, Methods Mol Biol, 428 (2008) 35-42.
47. L. Nonn, A. Vaishnav, L. Gallagher, P.H. Gann, mRNA and micro-RNA expression analysis in laser-capture microdissected prostate biopsies: valuable tool for risk assessment and prevention trials, Exp Mol Pathol, 88 (2010) 45-51.
48. N. Ikenaga, K. Ohuchida, K. Mizumoto, J. Yu, H. Fujita, K. Nakata, J. Ueda, N. Sato, E. Nagai, M. Tanaka, S100A4 mRNA is a diagnostic and prognostic marker in pancreatic carcinoma, J Gastrointest Surg, 13 (2009) 1852-1858.
49. A. Liu, M.T. Tetzlaff, P. Vanbelle, D. Elder, M. Feldman, J.W. Tobias, A.R. Sepulveda, X. Xu, MicroRNA expression profiling outperforms mRNA expression profiling in formalin-fixed paraffin-embedded tissues, Int J Clin Exp Pathol, 2 (2009) 519-527.
50. L.M. Gjerdrum, H.N. Abrahamsen, B. Villegas, B.S. Sorensen, H. Schmidt, S.J. Hamilton-Dutoit, The influence of immunohistochemistry on mRNA recovery from microdissected frozen and formalin-fixed, paraffin-embedded sections, Diagn Mol Pathol, 13 (2004) 224-233.
51. M. Ahram, M.J. Flaig, J.W. Gillespie, P.H. Duray, W.M. Linehan, D.K. Ornstein, S. Niu, Y. Zhao, E.F. Petricoin, 3rd, M.R. Emmert-Buck, Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications, Proteomics, 3 (2003) 413-421.
52. V.K. Rait, L. Xu, T.J. O'Leary, J.T. Mason, Modeling formalin fixation and antigen retrieval with bovine pancreatic RNase A II. Interrelationship of cross-linking, immunoreactivity, and heat treatment, Lab Invest, 84 (2004) 300-306.
53. V.K. Rait, T.J. O'Leary, J.T. Mason, Modeling formalin fixation and antigen retrieval with bovine pancreatic ribonuclease A: Istructural and functional alterations, Lab Invest, 84 (2004) 292-299.
54. M. Benchekroun, J. DeGraw, J. Gao, L. Sun, K. von Boguslawsky, A. Leminen, L.C. Andersson, M. Heiskala, Impact of fixative on recovery of mRNA from paraffin-embedded tissue, Diagn Mol Pathol, 13 (2004) 116-125.
55. R.L. Romero, A.C. Juston, J. Ballantyne, B.E. Henry, The applicability of formalin-fixed and formalin fixed paraffin embedded tissues in forensic DNA analysis, J Forensic Sci, 42 (1997) 708-714.
56. M.R. Emmert-Buck, R.F. Bonner, P.D. Smith, R.F. Chuaqui, Z. Zhuang, S.R. Goldstein, R.A. Weiss, L.A. Liotta, Laser capture microdissection, Science New York, N. Y, 274 (1996) 998-1001.
57. V. Patel, B.L. Hood, A.A. Molinolo, N.H. Lee, T.P. Conrads, J.C. Braisted, D.B. Krizman, T.D. Veenstra, J.S. Gutkind, Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression, Clin Cancer Res, 14 (2008) 1002-1014.
58. A. Michalski, E. Damoc, O. Lange, E. Denisov, D. Nolting, M. Muller, R. Viner, J. Schwartz, P. Remes, M. Belford, J.J. Dunyach, J. Cox, S. Horning, M. Mann, A. Makarov, Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes, Mol Cell Proteomics, 11 (2012) O111 013698.
59. A. Michalski, E. Damoc, J.P. Hauschild, O. Lange, A. Wieghaus, A. Makarov, N. Nagaraj, J. Cox, M. Mann, S. Horning, Mass spectrometry-based proteomics using Q Exactive, a highperformance benchtop quadrupole Orbitrap mass spectrometer, Mol Cell Proteomics, 10 (2011) M111 011015.