Proteomic analysis of laser-microdissected paraffin-embedded tissues: (1) Stage-related protein candidates upon non-metastatic lung adenocarcinoma

Journal of Proteomics

Volumn 73, Issue 6, 2010, Pages 1089-1099

  Kawamura, Takeshi ^a   Nomura, Masaharu ^b   Tojo, Hiromasa ^c   Fujii, Kiyonaga ^d   Hamasaki, Hiroko ^e   Mikami, Sayaka ^f   Bando, Yasuhiko ^f   Kato, Harubumi ^b   Nishimura, Toshihide ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b TOKYO MEDICAL UNIVERSITY   (Japan)

^c OSAKA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^d HOKKAIDO UNIVERSITY   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

^f Biosys Technologies Inc   (Japan)

Author keywords

Formalin fixed paraffin embedded tissue; Laser microdissection; Lung adenocarcinoma; Mass spectrometry; Spectral counting; Stage related biomarkers

Indexed keywords

ADULT; AGED; AMINO ACID SEQUENCE; ARTICLE; CANCER STAGING; CLINICAL ARTICLE; FEMALE; HUMAN; HUMAN TISSUE; LASER MICRODISSECTION; LIQUID CHROMATOGRAPHY; LUNG ADENOCARCINOMA; LYMPH NODE METASTASIS; MALE; METASTASIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; TANDEM MASS SPECTROMETRY; UNINDEXED SEQUENCE; ADENOCARCINOMA; BIOLOGY; CHEMISTRY; GENE EXPRESSION REGULATION; LASER; LUNG TUMOR; METABOLISM; MIDDLE AGED; PROCEDURES;

ADENOCARCINOMA; ADULT; AGED; CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LASERS; LUNG NEOPLASMS; LYMPHATIC METASTASIS; MALE; MIDDLE AGED; NEOPLASM METASTASIS; PARAFFIN; PROTEOME; PROTEOMICS; TANDEM MASS SPECTROMETRY;

PARAFFIN; PROTEOME;

EID: 77950518174     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2009.11.011     Document Type: Article

References (40)

1. Mountain C.F. Revisions in the international system for staging lung cancer. Chest 111 (1997) 1710-1717
2. Asamura H., Goya T., Koshiishi Y., Sohara Y., Eguchi K., Mori M., et al. A Japanese Lung Cancer Registry study: prognosis of 13,010 resected lung cancers. J Thorac Oncol 3 (2008) 46-52
3. Herbst R.S., John V., Heymach J.V., and Lippman S.M. Lung Cancer. N Engl J Med 359 (2008) 367-380
4. Pazdur R., Wagman L.D., Camphausen K.A., and Hoskins W. Cancer management: a multidisciplinary approach. 11th Edition (2008) 114
5. Shi S.R., Cote R.J., and Taylor C.R. Antigen retrieval immunohistochemistry: past, present, and future. J Histochem Cytochem 45 (1997) 327-343
6. Tourtellotte W.W., Verity A.N., Schmid P., Martinez S., and Shapshak P. Covalent binding of formalin fixed paraffin embedded brain tissue sections to glass slides suitable for in situ hybridization. J Virol Methods 15 (1987) 87-99
7. Zhao J., Wu R., Au A., Marquez A., Yu Y., and Shi Z. Determination of HER2 gene amplification by chromogenic in situ hybridization (CISH) in archival breast carcinoma. Mod Pathol 15 (2002) 657-665
8. Prieto D.A., Hood B.L., Darfler M.M., Guiel T.G., Lucas D.A., Conrads T.P., et al. Liquid Tissue™: proteomic profiling of formalin-fixed tissues. BioTechniques 38 (2005) S32-S35
9. Hood B.L., Darfer M.M., Furusato B., Lucas D.A., Ringeisen B.R., Sesterhenn I.A., et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics 4 (2005) 1741-1753
10. Hood B.L., Conrads T.P., and Veenstra T.D. Unravelling the proteome of formalin-fixed paraffin-embedded tissue. Brief Funct Genomic Proteomic 5 (2006) 169-175
11. 3THood B.L., Conrads T.P., and Veenstra T.D. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: Unlocking the proteome within. Proteomics 6 (2006) 4106-4114
12. Mueller L.N., Brusniak M.Y., Mani D.R., and Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 7 (2008) 51-61
13. Ronci M., Bonanno E., Colantoni A., Pieroni L., Di Ilio C., Spagnoli L.G., et al. Protein unlocking procedures of formalin-fixed paraffin-embedded tissues: application to MALDI-TOF imaging MS investigations. Proteomics 8 (2008) 3702-3714
14. Overton W.R., Catalano E., and McCoy Jr. J.P. Method to make paraffin-embedded breast and lymph tissue mimic fresh tissue in DNA analysis. Cytometry 26 (1996) 166-171
15. Xie H., and Griffin T.J. Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics. J Proteome Res 5 (2006) 1003-1009
16. Fujii K., Nakano T., Kanazawa M., Akimoto S., Hirano T., Kato H., et al. Clinical-scale high-throughput human plasma proteome analysis: lung adenocarcinoma. Proteomics 5 (2005) 1150-1159
17. Fujii K., Nakano T., Hike H., Usui F., Bando Y., Tojo H., et al. Fully automated online multi-dimensional protein profiling system for complex mixtures. J Chromatogr A 1057 (2004) 107-113
18. Perkins D.N., Pappin D.J., Creasy D.M., and Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20 (1999) 3551-3567
19. Elias J.E., Haas W., Faherty B.K., and Gygi S.P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2 (2005) 667-675
20. Patwardhan A.J., Strittmatter E.F., Camp II D.G., Smith R.D., and Palavicini M.G. Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data. J Proteome Res 4 (2005) 1952-1960
21. Orosch M., Swamy S., Hubbard T., and Choudhary J. Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold. Mol Cell Proteomics 7 (2008) 962-970
22. Craig R., and Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20 (2004) 1466-1467
23. Craig R., and Beavis R.C. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom 17 (2003) 2310-2316
24. Chen S.S., Deutsch E.W., Yi E.C., Li X.-j., Goodlett D.R., and Aebersold R. Improving mass and liquid chromatography based identification of proteins using Bayesian scoring. J Proteome Res 4 (2005) 2174-2184
25. Old W.M., Meyer-Arendt K., Aveline-Wolf L., Pierce K.G., Mendoza A., Sevinsky J.R., et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4 (2005) 1487-1502
26. Zybailov B., Coleman M.K., Florens L., and Washburn M.P. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem 77 (2005) 6218-6224
27. Sokal R.R., and Rohlf F.J. Biometry: the principles and practice of statistics in biological research (1995), W.H. Freeman, New York 729-731
28. Kall L., Storey J.D., MacCoss M.J., and Noble W.S. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 7 (2008) 29-34
29. Wang G., Wu W.W., Zhang Z., Masilamani S., and Shen R.F. Decoy methods for assessing false positives and false discovery rates in shotgun proteomics. Anal Chem 81 (2009) 146-159
30. Ueno T., Elmberger G., Weaver T.E., Toi M., and Linder S. The aspartic protease napsin A suppresses tumor growth independent of its catalytic activity. Lab Invest 88 (2008) 256-263
31. Brasch F., Ochs M., Kahne T., Guttentag S., Schauer-Vukasinovic V., Derrick M., et al. Involvement of napsin A in the C- and N-terminal processing of surfactant protein B in type-II pneumocytes of the human lung. J Biol Chem 278 (2003) 49006-49014
32. Ueno T., Linder S., and Elmberger G. Aspartic proteinase napsin is a useful marker for diagnosis of primary lung adenocarcinoma. Br J Cancer 88 (2003) 1229-1233
33. Jagirdar J. Application of immunohistochemistry to the diagnosis of primary and metastatic carcinoma to the lung. Arch Pathol Lab Med 132 (2008) 384-396
34. Chuman Y., Bergman A., Ueno T., Saito S., Sakaguchi K., Alaiya A.A., et al. Napsin A, a member of the aspartic protease family, is abundantly expressed in normal lung and kidney tissue and is expressed in lung adenocarcinomas. FEBS Lett 462 (1999) 129-134
35. Dejmek A., Naucler P., Smedjeback A., Kato H., Maeda M., Yashima K., et al. Napsin A (TA02) is a useful alternative to thyroid transcription factor-1 (TTF-1) for the identification of pulmonary adenocarcinoma cells in pleural effusions. Diagn Cytopathol 35 (2007) 493-497
36. Hiratsuka S., Watanabe A., Aburatani H., and Maru Y. Tumour-mediated lung metastasis. Nat Cell Biol 8 (2006) 1369-1375
37. Rafii S., and Lyden D. S100 chemokines mediate bookmarking of premetastatic niches. Nat Cell Biol 8 (2006) 1321-1323
38. Hiratsuka S., Watanabe A., Sakurai Y., Akashi-Takamura S., Ishibashi S., Miyake K., Shibuya M., Akira S., Aburatani H., and Maru Y. The S100A8-serum amyloid A3-TLR4 paracrine cascade establishes a pre-metastatic phase. Nat Cell Biol 10 (2008) 1349-1355
39. Liu D., Rudland P.S., Sibson D.R., Platt-Higgins A., and Barraclough R. Human homologue of cement gland protein, a novel metastasis inducer associated with breast carcinomas. Cancer Res 65 (2005) 3796-3805
40. Nishimura T, Nomura M, Tojo M, Hamasaki H, Fukuda T, Fujii K, et al. Proteomic analysis of laser-microdissected paraffin-embedded tissues: (2) MRM assay for stage-related proteins upon non-metastatic lung adenocarcinoma. To be published as the following article in Journal of Proteomics, this volume. doi:10.1016/j.jprot.2009.11.011.