Selective enrichment of newly synthesized proteins for quantitative secretome analysis

Nature Biotechnology

Volumn 30, Issue 10, 2012, Pages 984-990

  Eichelbaum, Katrin ^a   Winter, Markus ^a   Diaz, Mauricio Berriel ^b   Herzig, Stephan ^b   Krijgsveld, Jeroen ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIOUS; CELL LINES; CHEMOKINES; CLICK CHEMISTRY; CYTOKINES; GROWTH FACTOR; LIPOPOLYSACCHARIDES; LOW-ABUNDANCE PROTEINS; PRIMARY CELLS; PROTEIN SECRETION; SECRETED PROTEIN; SECRETOME; SELECTIVE ENRICHMENT; SERUM STARVATION; STABLE-ISOTOPE LABELING; TECHNICAL LIMITATIONS;

AMINO ACIDS; BODY FLUIDS; CELL CULTURE; ISOTOPES; PROTEINS;

BIOSYNTHESIS;

CHEMOKINE; CYTOKINE; GROWTH FACTOR; HORMONE; LIPOPOLYSACCHARIDE; PROTEIN;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL ADHESION; CELL CULTURE; CELL MIGRATION; CLICK CHEMISTRY; CONTROLLED STUDY; ISOTOPE LABELING; MACROPHAGE; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECRETION; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS;

CELL LINE; CLICK CHEMISTRY; CULTURE MEDIA; CULTURE MEDIA, SERUM-FREE; HEPATOCYTES; HUMANS; ISOTOPE LABELING; KINETICS; LIPOPOLYSACCHARIDES; MACROPHAGE ACTIVATION; PROTEIN BIOSYNTHESIS; PROTEIN INTERACTION MAPS; PROTEINS;

EID: 84867362036     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2356     Document Type: Article

References (44)

1. Makridakis, M. & Vlahou, A. Secretome proteomics for discovery of cancer biomarkers. J. Proteomics 73, 2291-2305 (2010).
2. Colzani, M. et al. Metabolic labeling and protein linearization technology allow the study of proteins secreted by cultured cells in serum-containing media. J. Proteome Res. 8, 4779-4788 (2009).
3. Finoulst, I. et al. Identifcation of low abundant secreted proteins and peptides from primary culture supernatants of human T-cells. J. Proteomics 75, 23-33 (2011).
4. Dowling, P. & Clynes, M. Conditioned media from cell lines: a complementary model to clinical specimens for the discovery of disease-specifc biomarkers. Proteomics 11, 794-804 (2011).
5. Pirkmajer, S. & Chibalin, A.V. Serum starvation: caveat emptor. Am. J. Physiol. Cell Physiol. 301, C272-C279 (2011).
6. Cooper, S. Reappraisal of serum starvation, the restriction point, G0, and G1 phase arrest points. FASEB J. 17, 333-340 (2003). (Pubitemid 36292949)
7. Hasan, N.M., Adams, G.E. & Joiner, M.C. Effect of serum starvation on expression and phosphorylation of PKC-α and p53 in V79 cells: implications for cell death. Int. J. Cancer 80, 400-405 (1999). (Pubitemid 29019627)
8. Levin, V.A. et al. Different changes in protein and phosphoprotein levels result from serum starvation of high-grade glioma and adenocarcinoma cell lines. J. Proteome Res. 9, 179-191 (2010).
9. Schwanhäusser, B., Gossen, M., Dittmar, G. & Selbach, M. Global analysis of cellular protein translation by pulsed SILAC Proteomics 9, 205-209 (2009).
10. Selbach, M. et al. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58-63 (2008).
11. Dieterich, D.C., Link, A.J., Graumann, J., Tirrell, D.A. & Schuman, E.M. Selective identifcation of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc. Natl. Acad. Sci. USA 103, 9482-9487 (2006). (Pubitemid 43955851)
12. Kiick, K.L., Saxon, E., Tirrell, D.A. & Bertozzi, C.R. Incorporation of azides into recombinant proteins for chemoselective modifcation by the Staudinger ligation. Proc. Natl. Acad. Sci. USA 99, 19-24 (2002). (Pubitemid 34060308)
13. Sardana, G., Jung, K., Stephan, C. & Diamandis, E.P. Proteomic analysis of conditioned media from the PC3, LNCaP, and 22Rv1 prostate cancer cell lines: discovery and validation of candidate prostate cancer biomarkers. J. Proteome Res. 7, 3329-3338 (2008).
14. Caccia, D. et al. Secretome compartment is a valuable source of biomarkers for cancer-relevant pathways. J. Proteome Res. 10, 4196-4207 (2011).
15. Patarroyo, M., Tryggvason, K. & Virtanen, I. Laminin isoforms in tumor invasion, angiogenesis and metastasis. Semin. Cancer Biol. 12, 197-207 (2002). (Pubitemid 34833063)
16. Manderson, A.P., Kay, J.G., Hammond, L.A., Brown, D.L. & Stow, J.L. Subcompartments of the macrophage recycling endosome direct the differential secretion of IL-6 and TNFα. J. Cell Biol. 178, 57-69 (2007). (Pubitemid 47026402)
17. Anderson, N.L. & Anderson, N.G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1, 845-867 (2002).
18. Pan, C., Kumar, C., Bohl, S., Klingmueller, U. & Mann, M. Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specifc functions. Mol. Cell. Proteomics 8, 443-450 (2009).
19. Schwanhäusser, B. et al. Global quantifcation of mammalian gene expression control. Nature 473, 337-342 (2011).
20. Stow, J.L., Low, P.C., Offenhauser, C. & Sangermani, D. Cytokine secretion in macrophages and other cells: pathways and mediators. Immunobiology 214, 601-612 (2009).
21. Bailey, M.J. et al. Extracellular proteomes of M-CSF (CSF-1) and GM-CSF-dependent macrophages. Immunol. Cell Biol. 89, 283-293 (2011).
22. Burghoff, S. & Schrader, J. Secretome of human endothelial cells under shear stress. J. Proteome Res. 10, 1160-1169 (2011).
23. Lietzén, N. et al. Quantitative subcellular proteome and secretome profling of infuenza A virus-infected human primary macrophages. PLoS Pathog. 7, e1001340 (2011).
24. Zhu, X. et al. Dual ligand stimulation of RAW 264.7 cells uncovers feedback mechanisms that regulate TLR-mediated gene expression. J. Immunol. 177, 4299-4310 (2006). (Pubitemid 44469758)
25. Li, M.O., Wan, Y.Y., Sanjabi, S., Robertson, A.K. & Flavell, R.A. Transforming growth factor-β regulation of immune responses. Annu. Rev. Immunol. 24, 99-146 (2006).
26. Weis, N., Weigert, A., von Knethen, A. & Brune, B. Heme oxygenase-1 contributes to an alternative macrophage activation profle induced by apoptotic cell supernatants. Mol. Biol. Cell 20, 1280-1288 (2009).
27. Yan, X.Q., Brady, G. & Iscove, N.N. Platelet-derived growth factor (PDGF) activates primitive hematopoietic precursors (pre-CFCmulti) by up-regulating IL-1 in PDGF receptor-expressing macrophages. J. Immunol. 150, 2440-2448 (1993). (Pubitemid 23127490)
28. Jones, S.A. Directing transition from innate to acquired immunity: defning a role for IL-6. J. Immunol. 175, 3463-3468 (2005). (Pubitemid 41292002)
29. Brunner, E. et al. A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol. 25, 576-583 (2007). (Pubitemid 46834841)
30. Klingmüller, U. et al. Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways. Syst. Biol. (Stevenage) 153, 433-447 (2006). (Pubitemid 44712259)
31. Villén, J. & Gygi, S.P. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat. Protoc. 3, 1630-1638 (2008).
32. Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663-670 (2003). (Pubitemid 36176744)
33. Wiśniewski, J.R., Zougman, A. & Mann, M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res. 8, 5674-5678 (2009).
34. Cox, J. & Mann, M. MaxQuant enables high peptide identifcation rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantifcation. Nat Biotechnol. 26, 1367-1372 (2008).
35. Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805 (2011).
36. Jain, E. et al. Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 10, 136 (2009).
37. Petersen, T.N., Brunak, S., von Heijne, G. & Nielsen, H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8, 785-786 (2011).
38. Gentleman, R.C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
39. Smyth, G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article3 (2004).
40. Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
41. Nikolsky, Y., Ekins, S., Nikolskaya, T. & Bugrim, A. A novel method for generation of signature networks as biomarkers from complex high throughput data. Toxicol. Lett. 158, 20-29 (2005). (Pubitemid 40910724)
42. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003). (Pubitemid 37428274)
43. Mi, H. et al. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 38, D204-D210 (2010).
44. Thomas, P.D. et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classifcation. Nucleic Acids Res. 31, 334-341 (2003). (Pubitemid 36150398)