Metabolic labeling and protein linearization technology allow the study of proteins secreted by cultured cells in serum-containing media

Journal of Proteome Research

Volumn 8, Issue 10, 2009, Pages 4779-4788

  Colzani, Mara ^a   Waridel, P ^a   Laurent, J ^b   Faes, E ^b   Ruegg C ^b,c   Quadroni, Manfredo ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

^c National Center of Competence in Research in Molecular Oncology   (Switzerland)

Author keywords

LC MS MS; Protein concentration linearization; Secretome analysis; Stable isotope labeling

Indexed keywords

AMINO ACID; CELL PROTEIN; HEXAPEPTIDE;

ARTICLE; BREAST CANCER; CANCER CELL CULTURE; CELL LABELING; CELL STRAIN MCF 7; CULTURE MEDIUM; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LINEARIZATION TECHNOLOGY; PROTEIN METABOLISM; PROTEIN SECRETION; PROTEOMICS;

ANIMALS; BLOOD PROTEINS; CATTLE; CELL LINE, TUMOR; CULTURE MEDIA, CONDITIONED; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; PEPTIDE FRAGMENTS; PEPTIDE MAPPING; PROTEINS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SERUM;

BOVINAE;

EID: 70349974392     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900476b     Document Type: Article

References (55)

1. Liotta, L. A.; Kohn, E. C. The microenvironment of the tumour-host interface. Nature 2001, 411 (6835), 375-379
2. Wulfkuhle, J. D.; Liotta, L. A.; Petricoin, E. F. Proteomic applications for the early detection of cancer. Nat. Rev. Cancer 2003, 3 (4), 267-275 (Pubitemid 37328862)
3. Petricoin, E. F.; Zoon, K. C.; Kohn, E. C.; Barrett, J. C.; Liotta, L. A. Clinical proteomics: translating benchside promise into bedside reality. Nat. Rev. Drug Discov. 2002, 1 (9), 683-695
4. Jacobs, J. M.; Adkins, J. N.; Qian, W. J.; Liu, T.; Shen, Y.; Camp, D. G., 2nd; Smith, R. D. Utilizing human blood plasma for proteomic biomarker discovery. J. Proteome Res. 2005, 4 (4), 1073-1085
5. Anderson, N. L.; Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1 (11), 845-867
6. Alaiya, A.; Al-Mohanna, M.; Linder, S. Clinical cancer proteomics: promises and pitfalls. J. Proteome Res. 2005, 4 (4), 1213-1222 (Pubitemid 41213336)
7. Liu, H.; Lin, D.; Yates, J. R. Multidimensional separations for protein/peptide analysis in the post-genomic era. Biotechniques 2002, 32 (4), 898. 900, 902 passim.
8. Adkins, J. N.; Varnum, S. M.; Auberry, K. J.; Moore, R. J.; Angell, N. H.; Smith, R. D.; Springer, D. L.; Pounds, J. G. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 2002, 1 (12), 947-955
9. Pieper, R.; Gatlin, C. L.; Makusky, A. J.; Russo, P. S.; Schatz, C. R.; Miller, S. S.; Su, Q.; McGrath, A. M.; Estock, M. A.; Parmar, P. P.; Zhao, M.; Huang, S. T.; Zhou, J.; Wang, F.; Esquer-Blasco, R.; Anderson, N. L.; Taylor, J.; Steiner, S. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 2003, 3 (7), 1345-1364 (Pubitemid 36929557)
10. Anderson, N. L.; Polanski, M.; Pieper, R.; Gatlin, T.; Tirumalai, R. S.; Conrads, T. P.; Veenstra, T. D.; Adkins, J. N.; Pounds, J. G.; Fagan, R.; Lobley, A. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomics 2004, 3 (4), 311-326
11. Lee, H. J.; Lee, E. Y.; Kwon, M. S.; Paik, Y. K. Biomarker discovery from the plasma proteome using multidimensional fractionation proteomics. Curr. Opin. Chem. Biol. 2006, 10 (1), 42-49 (Pubitemid 43202286)
12. Celis, J. E.; Gromov, P.; Cabezon, T.; Moreira, J. M.; Ambartsumian, N.; Sandelin, K.; Rank, F.; Gromova, I. Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment: a novel resource for biomarker and therapeutic target discovery. Mol. Cell. Proteomics 2004, 3 (4), 327-344
13. Shi, Y.; Elmets, C. A.; Smith, J. W.; Liu, Y. T.; Chen, Y. R.; Huang, C. P.; Zhu, W.; Ananthaswamy, H. N.; Gallo, R. L.; Huang, C. M. Quantitative proteomes and in vivo secretomes of progressive and regressive UV-induced fibrosarcoma tumor cells: mimicking tumor microenvironment using a dermis-based cell-trapped system linked to tissue chamber. Proteomics 2007, 7 (24), 4589-4600
14. Xue, H.; Lu, B.; Lai, M. The cancer secretome: a reservoir of biomarkers. J. Transl. Med. 2008, 6, 52.
15. Simpson, J. C.; Mateos, A.; Pepperkok, R. Maturation of the mammalian secretome. Genome Biol. 2007, 8 (4), 211.
16. Kulasingam, V.; Diamandis, E. P. Tissue culture-based breast cancer biomarker discovery platform. Int. J. Cancer 2008, 123 (9), 2007-2012
17. 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 (11), 1757-1770 (Pubitemid 46910996)
18. Liang, X.; Huuskonen, J.; Hajivandi, M.; Manzanedo, R.; Predki, P.; Amshey, J. R.; Pope, R. M. Identification and quantification of proteins differentially secreted by a pair of normal and malignant breast-cancer cell lines. Proteomics 2009, 9 (1), 182-193
19. Kulasingam, V.; Diamandis, E. P. Proteomics analysis of conditioned media from three breast cancer cell lines: a mine for biomarkers and therapeutic targets. Mol. Cell. Proteomics 2007, 6 (11), 1997-2011.
20. Emanuelsson, O.; Brunak, S.; von Heijne, G.; Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2007, 2 (4), 953-971 (Pubitemid 46745592)
21. Mbeunkui, F.; Fodstad, O.; Pannell, L. K. Secretory protein enrichment and analysis: an optimized approach applied on cancer cell lines using 2D LC-MS/MS. J. Proteome Res. 2006, 5 (4), 899-906.
22. Chen, Y.; Zhang, Y.; Yin, Y.; Gao, G.; Li, S.; Jiang, Y.; Gu, X.; Luo, J. SPD - a web-based secreted protein database. Nucleic Acids Res. 2005, 33 (Database issue), D169-73. (Pubitemid 40207853)
23. Martin, D. B.; Gifford, D. R.; Wright, M. E.; Keller, A.; Yi, E.; Goodlett, D. R.; Aebersold, R.; Nelson, P. S. Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res. 2004, 64 (1), 347-355
24. Gronborg, M.; Kristiansen, T. Z.; Iwahori, A.; Chang, R.; Reddy, R.; Sato, N.; Molina, H.; Jensen, O. N.; Hruban, R. H.; Goggins, M. G.; Maitra, A.; Pandey, A. Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol. Cell. Proteomics 2006, 5 (1), 157-171 (Pubitemid 43169348)
25. Cooper, S. Reappraisal of serum starvation, the restriction point, G0, and G1 phase arrest points. FASEB J. 2003, 17 (3), 333-340 (Pubitemid 36292949)
26. Shin, J. S.; Hong, S. W.; Lee, S. L.; Kim, T. H.; Park, I. C.; An, S. K.; Lee, W. K.; Lim, J. S.; Kim, K. I.; Yang, Y.; Lee, S. S.; Jin, D. H.; Lee, M. S. Serum starvation induces G1 arrest through suppression of Skp2-CDK2 and CDK4 in SK-OV-3 cells. Int. J. Oncol. 2008, 32 (2), 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 (3), 400-405
28. Zander, L.; Bemark, M. Identification of genes deregulated during serum-free medium adaptation of a Burkitt's lymphoma cell line. Cell Prolif. 2008, 41 (1), 136-155
29. Thulasiraman, V.; Lin, S.; Gheorghiu, L.; Lathrop, J.; Lomas, L.; Hammond, D.; Boschetti, E. Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis 2005, 26 (18), 3561-3571 (Pubitemid 41410379)
30. Righetti, P. G.; Boschetti, E.; Lomas, L.; Citterio, A. Protein Equalizer Technology: the quest for a "democratic proteome. Proteomics 2006, 6 (14), 3980-3992
31. Ong, S. E.; Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1 (5), 252-262
32. Beynon, R. J.; Pratt, J. M. Metabolic labeling of proteins for proteomics. Mol. Cell. Proteomics 2005, 4 (7), 857-872
33. Panchaud, A.; Affolter, M.; Moreillon, P.; Kussmann, M. Experimental and computational approaches to quantitative proteomics: status quo and outlook. J. Proteomics 2008, 71 (1), 19-33.
34. Alvarez-Llamas, G.; Szalowska, E.; de Vries, M. P.; Weening, D.; Landman, K.; Hoek, A.; Wolffenbuttel, B. H.; Roelofsen, H.; Vonk, R. J. Characterization of the human visceral adipose tissue secretome. Mol. Cell. Proteomics 2007, 6 (4), 589-600. (Pubitemid 46630092)
35. Roelofsen, H.; Dijkstra, M.; Weening, D.; de Vries, M. P.; Hoek, A.; Vonk, R. J., Comparison of isotope-labeled amino acid incorporation rates (CILAIR) provides a quantitative method to study tissue secretomes. Mol. Cell. Proteomics 2008, 8 (2), 316-324
36. Liu, H.; Sadygov, R. G.; Yates, J. R., 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76 (14), 4193-4201
37. Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 1996, 68 (5), 850-858 (Pubitemid 26101214)
38. Wilm, M.; Shevchenko, A.; Houthaeve, T.; Breit, S.; Schweigerer, L.; Fotsis, T.; Mann, M. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 1996, 379 (6564), 466-469 (Pubitemid 26039530)
39. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75 (17), 4646-4658 (Pubitemid 37082259)
40. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74 (20), 5383-5392 (Pubitemid 35215372)
41. Lange, V.; Picotti, P.; Domon, B.; Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4, 222.
42. Roux-Dalvai, F.; Gonzalez de Peredo, A.; Simo, C.; Guerrier, L.; Bouyssie, D.; Zanella, A.; Citterio, A.; Burlet-Schiltz, O.; Boschetti, E.; Righetti, P. G.; Monsarrat, B. Extensive analysis of the cytoplasmic proteome of human erythrocytes using the peptide ligand library technology and advanced mass spectrometry. Mol. Cell. Proteomics 2008, 7 (11), 2254-2269
43. Kuster, B.; Schirle, M.; Mallick, P.; Aebersold, R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell. Biol. 2005, 6 (7), 577-583 (Pubitemid 40943048)
44. Zwickl, H.; Traxler, E.; Staettner, S.; Parzefall, W.; Grasl-Kraupp, B.; Karner, J.; Schulte-Hermann, R.; Gerner, C. A novel technique to specifically analyze the secretome of cells and tissues. Electrophoresis 2005, 26 (14), 2779-2785 (Pubitemid 41078987)
45. Sihlbom, C.; Kanmert, I.; Bahr, H.; Davidsson, P. Evaluation of the combination of bead technology with SELDI-TOF-MS and 2-D DIGE for detection of plasma proteins. J. Proteome Res. 2008, 7 (9), 4191-4198
46. Ong, S. E.; Kratchmarova, I.; Mann, M. Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2003, 2 (2), 173-181 (Pubitemid 37099053)
47. Nagaraja, G. M.; Othman, M.; Fox, B. P.; Alsaber, R.; Pellegrino, C. M.; Zeng, Y.; Khanna, R.; Tamburini, P.; Swaroop, A.; Kandpal, R. P. Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: comprehensive profiles by representational difference analysis, microarrays and proteomics. Oncogene 2006, 25 (16), 2328-2338
48. Patwardhan, A. J.; Strittmatter, E. F.; Camp, D. G., 2nd; Smith, R. D.; Pallavicini, M. G. Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data. J. Proteome Res. 2005, 4 (6), 1952-1960
49. Mbeunkui, F.; Metge, B. J.; Shevde, L. A.; Pannell, L. K. Identification of differentially secreted biomarkers using LC-MS/MS in isogenic cell lines representing a progression of breast cancer. J. Proteome Res. 2007, 6 (8), 2993-3002.
50. Ghiselli, G.; Iozzo, R. V. Overexpression of bamacan/SMC3 causes transformation. J. Biol. Chem. 2000, 275 (27), 20235-20238
51. Kazerounian, S.; Yee, K. O.; Lawler, J. Thrombospondins in cancer. Cell. Mol. Life Sci. 2008, 65 (5), 700-712
52. Yang, J.; Everett, A. D. Hepatoma-derived growth factor binds DNA through the N-terminal PWWP domain. BMC Mol. Biol. 2007, 8, 101.
53. Everett, A. D.; Narron, J. V.; Stoops, T.; Nakamura, H.; Tucker, A. Hepatoma-derived growth factor is a pulmonary endothelial cell-expressed angiogenic factor. Am. J. Physiol. Lung Cell. Mol. Physiol. 2004, 286 (6), L1194-201. (Pubitemid 38656655)
54. Righetti, P. G.; Boschetti, E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass Spectrom. Rev. 2008, 27 (6), 596-608.
55. Kratchmarova, I.; Blagoev, B.; Haack-Sorensen, M.; Kassem, M.; Mann, M. Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science 2005, 308 (5727), 1472-1477 (Pubitemid 40791302)