Analytical constraints for the analysis of human cell line secretomes by shotgun proteomics

Journal of Proteomics

Volumn 75, Issue 3, 2012, Pages 1043-1054

  Malard, Véronique ^a   Chardan, Laetitia ^a   Roussi, Stamatiki ^a   Darolles, Carine ^a   Sage, Nicole ^a   Gaillard, Jean Charles ^a   Armengaud, Jean ^a  

^a DIF   (France)

Author keywords

LC MS MS; Lung; Secretome; Toxicoproteomics

Indexed keywords

CELL PROTEIN; COBALT; COBALT CHLORIDE; GLUCOSE; POLOXAMER; PROTEOME; SECRETOME; UNCLASSIFIED DRUG;

ANALYTICAL PARAMETERS; ARTICLE; BRONCHUS MUCOSA; CELL CULTURE; CELL METABOLISM; CELL PROLIFERATION; CELL VIABILITY; COMPARATIVE STUDY; CONTROLLED STUDY; CULTURE MEDIUM; CYTOTOXICITY; EPITHELIUM CELL; HUMAN; HUMAN CELL; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

ANTIMUTAGENIC AGENTS; BRONCHI; CELL LINE; COBALT; CULTURE MEDIA, CONDITIONED; EPITHELIAL CELLS; HUMANS; MASS SPECTROMETRY; PROTEOME; PROTEOMICS; RESPIRATORY MUCOSA;

EID: 84355166446     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.10.025     Document Type: Article

References (53)

1. Dowling P., Clynes M. Conditioned media from cell lines: a complementary model to clinical specimens for the discovery of disease-specific biomarkers. Proteomics 2011, 11:794-804.
2. Caccia D., Zanetti Domingues L., Micciche F., De Bortoli M., Carniti C., Mondellini P., et al. Secretome compartment is a valuable source of biomarkers for cancer-relevant pathways. J Proteome Res 2011, 10:4196-4207.
3. Chenau J., Michelland S., de Fraipont F., Josserand V., Coll J.L., Favrot M.C., et al. The cell line secretome, a suitable tool for investigating proteins released in vivo by tumors: application to the study of p53-modulated proteins secreted in lung cancer cells. J Proteome Res 2009, 8:4579-4591.
4. Lawlor K., Nazarian A., Lacomis L., Tempst P., Villanueva J. Pathway-based biomarker search by high-throughput proteomics profiling of secretomes. J Proteome Res 2009, 8:1489-1503.
5. Makridakis M., Vlahou A. Secretome proteomics for discovery of cancer biomarkers. J Proteomics 2010, 73:2291-2305.
6. Paulitschke V., Kunstfeld R., Mohr T., Slany A., Micksche M., Drach J., et al. Entering a new era of rational biomarker discovery for early detection of melanoma metastases: secretome analysis of associated stroma cells. J Proteome Res 2009, 8:2501-2510.
7. Pavlou M.P., Diamandis E.P. The cancer cell secretome: a good source for discovering biomarkers?. J Proteomics 2010, 73:1896-1906.
8. Ahrens C.H., Brunner E., Qeli E., Basler K., Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol 2010, 11:789-801.
9. Picotti P., Bodenmiller B., Mueller L.N., Domon B., Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 2009, 138:795-806.
10. Selevsek N., Matondo M., Sanchez Carbayo M., Aebersold R., Domon B. Systematic quantification of peptides/proteins in urine using selected reaction monitoring. Proteomics 2011, 11:1135-1147.
11. Christie-Oleza J.A., Armengaud J. In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study. Mar Drugs 2010, 8:2223-2239.
12. Clair G., Roussi S., Armengaud J., Duport C. Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions. Mol Cell Proteomics 2010, 9:1486-1498.
13. Peterson R., Grinyer J., Nevalainen H. Secretome of the coprophilous fungus Doratomyces stemonitis C8, isolated from Koala feces. Appl Environ Microbiol 2011, 77:3793-3801.
14. Chevallet M., Diemer H., Van Dorssealer A., Villiers C., Rabilloud T. Toward a better analysis of secreted proteins: the example of the myeloid cells secretome. Proteomics 2007, 7:1757-1770.
15. Gundacker N.C., Haudek V.J., Wimmer H., Slany A., Griss J., Bochkov V., et al. Cytoplasmic proteome and secretome profiles of differently stimulated human dendritic cells. J Proteome Res 2009, 8:2799-2811.
16. Skalnikova H., Motlik J., Gadher S.J., Kovarova H. Mapping of the secretome of primary isolates of mammalian cells, stem cells and derived cell lines. Proteomics 2011, 11:691-708.
17. Burghoff S., Schrader J. Secretome of human endothelial cells under shear stress. J Proteome Res 2011, 10:1160-1169.
18. Dowell J.A., Johnson J.A., Li L. Identification of astrocyte secreted proteins with a combination of shotgun proteomics and bioinformatics. J Proteome Res 2009, 8:4135-4143.
19. Ali M., Lillehoj E.P., Park Y., Kyo Y., Kim K.C. Analysis of the proteome of human airway epithelial secretions. Proteome Sci 2011, 9:4.
20. Srirajaskanthan R., Caplin M.E., Waugh M.G., Watkins J., Meyer T., Hsuan J.J., et al. Identification of Mac-2-binding protein as a putative marker of neuroendocrine tumors from the analysis of cell line secretomes. Mol Cell Proteomics 2010, 9:656-666.
21. Wu C.C., Hsu C.W., Chen C.D., Yu C.J., Chang K.P., Tai D.I., et al. Candidate serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines and the human protein atlas. Mol Cell Proteomics 2010, 9:1100-1117.
22. Villiers C., Chevallet M., Diemer H., Couderc R., Freitas H., Van Dorsselaer A., et al. From secretome analysis to immunology: chitosan induces major alterations in the activation of dendritic cells via a TLR4-dependent mechanism. Mol Cell Proteomics 2009, 8:1252-1264.
23. Planque C., Kulasingam V., Smith C.R., Reckamp K., Goodglick L., Diamandis E.P. Identification of five candidate lung cancer biomarkers by proteomics analysis of conditioned media of four lung cancer cell lines. Mol Cell Proteomics 2009, 8:2746-2758.
24. Chenau J., Michelland S., Seve M. Secretome: definitions and biomedical interest. Rev Med Interne 2008, 29:606-608.
25. Cooper S. Reappraisal of serum starvation, the restriction point, G0, and G1 phase arrest points. FASEB J 2003, 17:333-340.
26. Shin J.S., Hong S.W., Lee S.L., Kim T.H., Park I.C., An S.K., et al. Serum starvation induces G1 arrest through suppression of Skp2-CDK2 and CDK4 in SK-OV-3 cells. Int J Oncol 2008, 32:435-439.
27. Hasan N.M., Adams G.E., Joiner M.C. Effect of serum starvation on expression and phosphorylation of PKC-alpha and p53 in V79 cells: implications for cell death. Int J Cancer 1999, 80:400-405.
28. Levin V.A., Panchabhai S.C., Shen L., Kornblau S.M., Qiu Y., Baggerly K.A. Different changes in protein and phosphoprotein levels result from serum starvation of high-grade glioma and adenocarcinoma cell lines. J Proteome Res 2010, 9:179-191.
29. Dupierris V., Masselon C., Court M., Kieffer-Jaquinod S., Bruley C. A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa. Bioinformatics 2009, 25:1980-1981.
30. Carvalho P.C., Fischer J.S., Chen E.I., Yates J.R., Barbosa V.C. PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 2008, 9:316.
31. Kulasingam V., Diamandis E.P. Strategies for discovering novel cancer biomarkers through utilization of emerging technologies. Nat Clin Pract Oncol 2008, 5:588-599.
32. Kall L., Krogh A., Sonnhammer E.L. A combined transmembrane topology and signal peptide prediction method. J Mol Biol 2004, 338:1027-1036.
33. Palomares L.A., Gonzalez M., Ramirez O.T. Evidence of Pluronic F-68 direct interaction with insect cells: impact on shear protection, recombinant protein, and baculovirus production*. Enzyme Microb Technol 2000, 26:324-331.
34. Xiao T., Ying W., Li L., Hu Z., Ma Y., Jiao L., et al. An approach to studying lung cancer-related proteins in human blood. Mol Cell Proteomics 2005, 4:1480-1486.
35. Zwickl H., Traxler E., Staettner S., Parzefall W., Grasl-Kraupp B., Karner J., et al. A novel technique to specifically analyze the secretome of cells and tissues. Electrophoresis 2005, 26:2779-2785.
36. Prise K.M., O'Sullivan J.M. Radiation-induced bystander signalling in cancer therapy. Nat Rev Cancer 2009, 9:351-360.
37. Fuentes-Mattei E., Rivera E., Gioda A., Sanchez-Rivera D., Roman-Velazquez F.R., Jimenez-Velez B.D. Use of human bronchial epithelial cells (BEAS-2B) to study immunological markers resulting from exposure to PM(2.5) organic extract from Puerto Rico. Toxicol Appl Pharmacol 2010, 243:381-389.
38. Park E.J., Park K. Induction of pro-inflammatory signals by 1-nitropyrene in cultured BEAS-2B cells. Toxicol Lett 2009, 184:126-133.
39. Veranth J.M., Reilly C.A., Veranth M.M., Moss T.A., Langelier C.R., Lanza D.L., et al. Inflammatory cytokines and cell death in BEAS-2B lung cells treated with soil dust, lipopolysaccharide, and surface-modified particles. Toxicol Sci 2004, 82:88-96.
40. Shen J., Behrens C., Wistuba I.I., Feng L., Lee J.J., Hong W.K., et al. Identification and validation of differences in protein levels in normal, premalignant, and malignant lung cells and tissues using high-throughput Western Array and immunohistochemistry. Cancer Res 2006, 66:11194-11206.
41. Reddel R.R., Ke Y., Gerwin B.I., McMenamin M.G., Lechner J.F., Su R.T., et al. Transformation of human bronchial epithelial cells by infection with SV40 or adenovirus-12 SV40 hybrid virus, or transfection via strontium phosphate coprecipitation with a plasmid containing SV40 early region genes. Cancer Res 1988, 48:1904-1909.
42. Bradshaw A.D., Puolakkainen P., Dasgupta J., Davidson J.M., Wight T.N. Helene Sage E. SPARC-null mice display abnormalities in the dermis characterized by decreased collagen fibril diameter and reduced tensile strength. J Invest Dermatol 2003, 120:949-955.
43. ATSDR AfTSaDR- toxicological profile for cobalt 2004, Agency for Toxic Substances and Disease Registry - U.S. Department of Health and Human Services. http://www.atsdr.cdc.gov/toxprofiles/tp33.pdf.
44. Ménager G.L., Goyffon, Bresson, Ansoborlo, Malard Cobalt Chap29. Toxicologie nucléaire environnementale et humaine 2009, Lavoisier.
45. De Boeck M., Kirsch-Volders M., Lison D. Cobalt and antimony: genotoxicity and carcinogenicity. Mutat Res 2003, 533:135-152.
46. Lison D., De Boeck M., Verougstraete V., Kirsch-Volders M. Update on the genotoxicity and carcinogenicity of cobalt compounds. Occup Environ Med 2001, 58:619-625.
47. Salnikow K., Su W., Blagosklonny M.V., Costa M. Carcinogenic metals induce hypoxia-inducible factor-stimulated transcription by reactive oxygen species-independent mechanism. Cancer Res 2000, 60:3375-3378.
48. Pulido M.D., Parrish A.R. Metal-induced apoptosis: mechanisms. Mutat Res 2003, 533:227-241.
49. Bruick R.K. Oxygen sensing in the hypoxic response pathway: regulation of the hypoxia-inducible transcription factor. Genes Dev 2003, 17:2614-2623.
50. Chlorinated drinking-water; chlorination by-products; some other halogenated compounds; cobalt and cobalt compounds. IARC Monogr Eval Carcinog Risks Hum 1991, 1-544. International Agency for Research on Cancer (IARC) Working Group, Lyon.
51. Varsano S., Frolkis I., Shapiro H., Ophir D. Human nasal epithelium adsorbs complement C3-related fragments and expresses cell membrane complement regulatory proteins. Laryngoscope 1996, 106:599-604.
52. Goto Y., Ogawa K., Hattori A., Tsujimoto M. Secretion of endoplasmic reticulum aminopeptidase 1 is involved in the activation of macrophages induced by lipopolysaccharide and interferon-{gamma}. J Biol Chem 2011, 286:21906-21914.
53. Maxwell P., Salnikow K. HIF-1: an oxygen and metal responsive transcription factor. Cancer Biol Ther 2004, 3:29-35.