Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction

Journal of Proteomics

Volumn 138, Issue , 2016, Pages 106-114

  Ortea, I ^a   Rodriguez Ariza A ^b   Chicano Galvez E ^a   Arenas Vacas, M S ^b   Jurado Gamez B ^b  

^a Maimonides Institute for Research in Biomedicine of Cordoba   (Spain)

^b HOSPITAL UNIVERSITARIO REINA SOFÍA   (Spain)

Author keywords

Adenocarcinoma; BALF; Data independent acquisition; Lung cancer; Proteomics; SWATH

Indexed keywords

ALPHA 2 MACROGLOBULIN; BIOLOGICAL MARKER; COMPLEMENT C1Q SUBUNIT C; COMPLEMENT COMPONENT C1Q; COMPLEMENT COMPONENT C4; COMPLEMENT COMPONENT C4B BINDING PROTEIN; COMPLEMENT COMPONENT C5; COMPLEMENT FACTOR H; CYCLIN DEPENDENT KINASE 5; FIBRINOGEN; FIBRINOGEN ALPHA CHAIN; FIBRINOGEN BETA CHAIN; FIBRINOGEN GAMMA CHAIN; GLUTATHIONE TRANSFERASE P1; HAPTOGLOBIN; PROTEIN P25; PROTEIN P35; TUMOR MARKER; UNCLASSIFIED DRUG; TUMOR PROTEIN;

ADULT; AGED; ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; BRONCHOALVEOLAR LAVAGE FLUID; CONTROLLED STUDY; DOWN REGULATION; ENZYME ACTIVATION; FEMALE; GENE TRANSLOCATION; HUMAN; HUMAN TISSUE; LIQUID CHROMATOGRAPHY; LUNG ADENOCARCINOMA; MALE; MASS SPECTROMETRY; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SENSITIVITY AND SPECIFICITY; SEQUENTIAL WINDOWED ACQUISITION OF ALL THEORETICAL FRAGMENT ION MASS SPECTROMETRY; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY; TISSUE LEVEL; UPREGULATION; ADENOCARCINOMA; CLINICAL TRIAL; LUNG LAVAGE; LUNG TUMOR; METABOLISM; MIDDLE AGED; PATHOLOGY;

ADENOCARCINOMA; AGED; BIOMARKERS, TUMOR; BRONCHOALVEOLAR LAVAGE; BRONCHOALVEOLAR LAVAGE FLUID; FEMALE; HUMANS; LUNG NEOPLASMS; MALE; MASS SPECTROMETRY; MIDDLE AGED; NEOPLASM PROTEINS;

EID: 84959184360     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2016.02.010     Document Type: Article

References (38)

1. Siegel R., Naishadham D., Jemal A. Cancer statistics, 2012. CA Cancer J. Clin. 2012, 62:10-29.
2. Meza R., Meernik C., Jeon J., Cote M.L. Lung cancer incidence trends by gender, race and histology in the United States, 1973-2010. PLoS One 2015, 10.
3. Kerr K.M. Pulmonary adenocarcinomas: classification and reporting. Histopathology 2009, 54:12-27.
4. Navani N., Nankivell M., Lawrence D.R., Lock S., Makker H., Baldwin D.R., et al. Lung cancer diagnosis and staging with endobronchial ultrasound-guided transbronchial needle aspiration compared with conventional approaches: an open-label, pragmatic, randomised controlled trial. Lancet Respir. Med. 2015, 3:282-289.
5. Port J., Harrison S. Electromagnetic navigational bronchoscopy. Semin. Interv. Radiol. 2013, 30:128-132.
6. Nguyen E.V., Gharib S.A., Schnapp L.M., Goodlett D.R. Shotgun MS proteomic analysis of bronchoalveolar lavage fluid in normal subjects. Proteomics Clin. Appl. 2014, 8:737-747.
7. Foster M.W., Thompson J.W., Que L.G., Yang I.V., Schwartz D.A., Moseley M.A., Marshall H.E. Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. J. Proteome Res. 2013, 12:2194-2205.
8. Noël-Georis I., Bernard A., Falmagne P., Wattiez R. Database of bronchoalveolar lavage fluid proteins. J. Chromatogr. B 2002, 771:221-236.
9. Wattiez R., Hermans C., Cruyt C., Bernard A., Falmagne P. Human bronchoalveolar lavage fluid protein two-dimensional database: study of interstitial lung diseases. Electrophoresis 2000, 21:2703-2712.
10. Foster M.W., Morrison L.D., Todd J.L., Snyder L.D., Thompson J.W., Soderblom E.J., et al. Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis. J. Proteome Res. 2015, 14:1238-1249.
11. Plymoth A., Lofdahl C.G., Ekberg-Jansson A., Dahlback M., Broberg P., Foster M., et al. Protein expression patterns associated with progression of chronic obstructive pulmonary disease in bronchoalveolar lavage of smokers. Clin. Chem. 2007, 53:636-644.
12. Silva E., Bourin S., Sabounchi-Schutt F., Laurin Y., Barker E., Newman L., et al. A quantitative proteomic analysis of soluble bronchoalveolar fluid proteins from patients with sarcoidosis and chronic beryllium disease. Sarcoidosis Vasc. Diffuse Lung. Dis. 2007, 24:24-32.
13. Okamoto T., Miyazaki Y., Shirahama R., Tamaoka M., Inase N. Proteome analysis of bronchoalveolar lavage fluid in chronic hypersensitivity pneumonitis. Allergol. Int. 2012, 61:83-92.
14. Pastor M.D., Nogal A., Molina-Pinelo S., Melendez R., Salinas A., Gonzalez de la Pena A., et al. Identification of proteomic signatures associated with lung cancer and COPD. J. Proteomics 2013, 89:227-237.
15. Oumeraci T., Schmidt B., Wolf T., Zapatka M., Pich A., Brors B., et al. Bronchoalveolar lavage fluid of lung cancer patients: mapping the uncharted waters using proteomics technology. Lung Cancer 2011, 72:136-138.
16. Uribarri M., Hormaeche I., Zalacain R., Lopez-Vivanco G., Martinez A., Nagore D., Ruiz-Arguello M.B. A new biomarker panel in bronchoalveolar lavage for an improved lung cancer diagnosis. J. Thorac. Oncol. 2014, 9:1504-1512.
17. Almatroodi S.A., McDonald C.F., Collins A.L., Darby I.A., Pouniotis D.S. Quantitative proteomics of bronchoalveolar lavage fluid in lung adenocarcinoma. Cancer Genomics Proteomics 2015, 12:39-48.
18. Venable J.D., Dong M.-Q., Wohlschlegel J., Dillin A., Yates J.R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 2004, 1:39-45.
19. Picotti P., Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9:555-566.
20. Gillet L.C., Navarro P., Tate S., Röst H., Selevsek N., Reiter L., et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 2012, 11.
21. Huang Q., Yang L., Luo J., Guo L., Wang Z., Yang X., et al. SWATH enables precise label-free quantification on proteome scale. Proteomics 2015, 15:1215-1223.
22. Selevsek N., Chang C.Y., Gillet L.C., Navarro P., Bernhardt O.M., Reiter L., et al. Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Mol. Cell. Proteomics 2015, 14:739-749.
23. Carvalho P.C., Han X., Xu T., Cociorva D., Carvalho M.G., Barbosa V.C., Yates J.R. XDIA: improving on the label-free data-independent analysis. Bioinformatics 2010, 26:847-848.
24. National Comprehensive Cancer Network website NCCN Guidelines Version 2 (Accessed date Nov 20, 2015). http://www.nccn.org/professionals/physician_gls/f_guidelines.asp#site.
25. Vowinckel J., Capuano F., Campbell K., Deery M.J., Lilley K.S., Ralser M. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics. F1000 Research 2 2014, 272.
26. Choi M., Chang C.Y., Clough T., Broudy D., Killeen T., MacLean B., Vitek O. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 2014, 30:2524-2526.
27. Chang C.Y., Picotti P., Hüttenhain R., Heinzelmann-Schwarz V., Jovanovic M., Aebersold R., Vitek O. Protein significance analysis in selected reaction monitoring (SRM) measurements. Mol. Cell. Proteomics 2012, 11. M111.014662.
28. Robin X., Turck N., Hainard A., Tiberti N., Lisacek F., Sanchez J.C., Müller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinf. 2001, 12:77.
29. Tarca A.L., Draghici S., Khatri P., Hassan S.S., Mittal P., Kim J.S., et al. A novel signaling pathway impact analysis. Bioinformatics 2009, 25:75-82.
30. Linden A. Measuring diagnostic and predictive accuracy in disease management: an introduction to receiver operating characteristic (ROC) analysis. J. Eval. Clin. Pract. 2006, 12:132-139.
31. Corrales L., Ajona D., Rafail S., Lasarte J.J., Riezu-Boj J.I., Lambris J.D., et al. Anaphylatoxin C5a creates a favorable microenvironment for lung cancer progression. J. Immunol. 2012, 189:4674-4683.
32. Ajona D., Pajares M.J., Corrales L., Perez-Gracia J.L., Agorreta J., Lozano M.D., et al. Investigation of complement activation product C4d as a diagnostic and prognostic biomarker for lung cancer. J. Natl. Cancer Inst. 2013, 105:1385-1393.
33. Abdullah M., Goldmann T. Pulmonary haptoglobin (pHp) is part of the surfactant system in the human lung. Diagn. Pathol. 2012, 7:158.
34. Yokohira M., Yamakawa K., Nakano Y., Numano T., Furukawa F., Kishi S., et al. Immunohistochemical characteristics of surfactant proteins a, B, C and d in inflammatory and tumorigenic lung lesions of f344 rats. J. Toxicol. Pathol. 2014, 27:175-182.
35. Abdullah M., Schultz H., Kähler D., Branscheid D., Dalhoff K., Zabel P., et al. Expression of the acute phase protein haptoglobin in human lung cancer and tumor-free lung tissues. Pathol. Res. Pract. 2009, 205:639-647.
36. Heo S.H., Lee S.J., Ryoo H.M., Park J.Y., Cho J.Y. Identification of putative serum glycoprotein biomarkers for human lung adenocarcinoma by multilectin affinity chromatography and LC-MS/MS. Proteomics 2007, 7:4292-4302.
37. Li Q.K., Shah P., Li Y., Aiyetan P.O., Chen J., Yung R., et al. Glycoproteomic analysis of bronchoalveolar lavage (BAL) fluid identifies tumor-associated glycoproteins from lung adenocarcinoma. J. Proteome Res. 2013, 12:3689-3696.
38. Sun K.H., Chang K.H., Clawson S., Ghosh S., Mirzaei H., Regnier F., Shah K. Glutathione-S-transferase P1 is a critical regulator of Cdk5 kinase activity. J. Neurochem. 2011, 118:902-914.