Proteomic approaches to uncover MMP function

Matrix Biology

Volumn 44-46, Issue , 2015, Pages 232-238

  Schlage, Pascal ^a   auf dem Keller, Ulrich ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Degradomics; ITRAQ; Matrix metalloproteinases; Proteomics; TAILS

Indexed keywords

MATRIX METALLOPROTEINASE;

ENVIRONMENT; EXTRACELLULAR SPACE; HUMAN; IN VITRO STUDY; IN VIVO STUDY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; ANIMAL; ENZYME SPECIFICITY; METABOLISM; PROCEDURES;

ANIMALS; HUMANS; IN VITRO TECHNIQUES; MASS SPECTROMETRY; MATRIX METALLOPROTEINASES; PROTEOMICS; SUBSTRATE SPECIFICITY;

EID: 84930756398     PISSN: 0945053X     EISSN: 15691802     Source Type: Journal    
DOI: 10.1016/j.matbio.2015.01.003     Document Type: Review

References (55)

1. Bensimon A., Heck A.J., Aebersold R. Mass spectrometry-based proteomics and network biology. Annu Rev Biochem 2012, 81:379-405.
2. Olsen J.V., Mann M. Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics 2013, 12:3444-3452.
3. Turk B., Turk D.S.A., Turk V. Protease signalling: the cutting edge. EMBO J 2012, 31:1630-1643.
4. Overall C.M., Blobel C.P. In search of partners: linking extracellular proteases to substrates. Nat Rev Mol Cell Biol 2007, 8:245-257.
5. Morrison C.J., Butler G.S., Rodriguez D., Overall C.M. Matrix metalloproteinase proteomics: substrates, targets, and therapy. Curr Opin Cell Biol 2009, 21:645-653.
6. Rodriguez D., Morrison C.J., Overall C.M. Matrix metalloproteinases: what do they not do? New substrates and biological roles identified by murine models and proteomics. Biochim Biophys Acta 1803, 2010:39-54.
7. Dufour A., Overall C.M. Missing the target: matrix metalloproteinase antitargets in inflammation and cancer. Trends Pharmacol Sci 2013, 34:233-242.
8. Boulware K.T., Daugherty P.S. Protease specificity determination by using cellular libraries of peptide substrates (CLiPS). Proc Natl Acad Sci U S A 2006, 103:7583-7588.
9. Matthews D.J., Wells J.A. Substrate phage: selection of protease substrates by monovalent phage display. Science 1993, 260:1113-1117.
10. Turk B.E., Huang L.L., Piro E.T., Cantley L.C. Determination of protease cleavage site motifs using mixture-based oriented peptide libraries. Nat Biotechnol 2001, 19:661-667.
11. Schilling O., auf dem Keller U., Overall C.M. Protease specificity profiling by tandem mass spectrometry using proteome-derived peptide libraries. Methods Mol Biol 2011, 753:257-272.
12. Schilling O., Overall C.M. Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat Biotechnol 2008, 26:685-694.
13. Jakoby T., van den Berg B.H., Tholey A. Quantitative protease cleavage site profiling using tandem-mass-tag labeling and LC-MALDI-TOF/TOF MS/MS analysis. J Proteome Res 2012, 11:1812-1820.
14. Starr A.E., Bellac C.L., Dufour A., Goebeler V., Overall C.M. Biochemical characterization and N-terminomics analysis of leukolysin, the membrane-type 6 matrix metalloprotease (MMP25): chemokine and vimentin cleavages enhance cell migration and macrophage phagocytic activities. J Biol Chem 2012, 287:13382-13395.
15. Marino G., Huesgen P.F., Eckhard U., Overall C.M., Schroder W.P., Funk C. Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity. Biochem J 2014, 457:335-346.
16. Prudova A., auf dem Keller U., Butler G.S., Overall C.M. Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics. Mol Cell Proteomics 2010, 9:894-911.
17. auf dem Keller U., Prudova A., Gioia M., Butler G.S., Overall C.M. A statistics-based platform for quantitative N-terminome analysis and identification of protease cleavage products. Mol Cell Proteomics 2010, 9:912-927.
18. Becker-Pauly C., Barre O., Schilling O., auf dem Keller U., Ohler A., Broder C., et al. Proteomic analyses reveal an acidic prime side specificity for the astacin metalloprotease family reflected by physiological substrates. Mol Cell Proteomics 2011, 10. [M111 009233].
19. auf dem Keller U., Schilling O. Proteomic techniques and activity-based probes for the system-wide study of proteolysis. Biochimie 2010, 92:1705-1714.
20. Deu E., Verdoes M., Bogyo M. New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol 2012, 19:9-16.
21. Saghatelian A., Jessani N., Joseph A., Humphrey M., Cravatt B.F. Activity-based probes for the proteomic profiling of metalloproteases. Proc Natl Acad Sci U S A 2004, 101:10000-10005.
22. Chan E.W.S., Chattopadhaya S., Panicker R.C., Huang X., Yao S.Q. Developing photoactive affinity probes for proteomic profiling: hydroxamate-based probes for metalloproteases. J Am Chem Soc 2004, 126:14435-14446.
23. Sieber S.A., Niessen S., Hoover H.S., Cravatt B.F. Proteomic profiling of metalloprotease activities with cocktails of active-site probes. Nat Chem Biol 2006, 2:274-281.
24. Fahlman R.P., Chen W., Overall C.M. Absolute proteomic quantification of the activity state of proteases and proteolytic cleavages using proteolytic signature peptides and isobaric tags. J Proteomics 2014, 100:79-91.
25. McQuibban G.A., Gong J.H., Tam E.M., McCulloch C.A., Clark-Lewis I., Overall C.M. Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3. Science 2000, 289:1202-1206.
26. Hwang I.K., Park S.M., Kim S.Y., Lee S.T. A proteomic approach to identify substrates of matrix metalloproteinase-14 in human plasma. Biochim Biophys Acta 2004, 1702:79-87.
27. Hemers E., Duval C., McCaig C., Handley M., Dockray G.J., Varro A. Insulin-like growth factor binding protein-5 is a target of matrix metalloproteinase-7: implications for epithelial-mesenchymal signaling. Cancer Res 2005, 65:7363-7369.
28. Chiao Y.A., Zamilpa R., Lopez E.F., Dai Q., Escobar G.P., Hakala K., et al. In vivo matrix metalloproteinase-7 substrates identified in the left ventricle post-myocardial infarction using proteomics. J Proteome Res 2010, 9:2649-2657.
29. Zamilpa R., Lopez E.F., Chiao Y.A., Dai Q., Escobar G.P., Hakala K., et al. Proteomic analysis identifies in vivo candidate matrix metalloproteinase-9 substrates in the left ventricle post-myocardial infarction. Proteomics 2010, 10:2214-2223.
30. Minden J.S. DIGE: past and future. Methods Mol Biol 2012, 854:3-8.
31. Greenlee K.J., Corry D.B., Engler D.A., Matsunami R.K., Tessier P., Cook R.G., et al. Proteomic identification of in vivo substrates for matrix metalloproteinases 2 and 9 reveals a mechanism for resolution of inflammation. J Immunol 2006, 177:7312-7321.
32. Yates J.R. The revolution and evolution of shotgun proteomics for large-scale proteome analysis. J Am Chem Soc 2013, 135:1629-1640.
33. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
34. Tam E.M., Morrison C.J., Wu Y.I., Stack M.S., Overall C.M. Membrane protease proteomics: Isotope-coded affinity tag MS identification of undescribed MT1-matrix metalloproteinase substrates. Proc Natl Acad Sci U S A 2004, 101:6917-6922.
35. Dean R.A., Butler G.S., Hamma-Kourbali Y., Delbe J., Brigstock D.R., Courty J., et al. Identification of candidate angiogenic inhibitors processed by matrix metalloproteinase 2 (MMP-2) in cell-based proteomic screens: disruption of vascular endothelial growth factor (VEGF)/heparin affin regulatory peptide (pleiotrophin) and VEGF/Connective tissue growth factor angiogenic inhibitory complexes by MMP-2 proteolysis. Mol Cell Biol 2007, 27:8454-8465.
36. Butler G.S., Overall C.M. Proteomic validation of protease drug targets: pharmacoproteomics of matrix metalloproteinase inhibitor drugs using isotope-coded affinity tag labelling and tandem mass spectrometry. Curr Pharm Des 2007, 13:263-270.
37. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
38. Pierce A., Unwin R.D., Evans C.A., Griffiths S., Carney L., Zhang L., et al. Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases. Mol Cell Proteomics 2008, 7:853-863.
39. Dean R.A., Overall C.M. Proteomics discovery of metalloproteinase substrates in the cellular context by iTRAQ labeling reveals a diverse MMP-2 substrate degradome. Mol Cell Proteomics 2007, 6:611-623.
40. Liu H., Sadygov R.G., Yates J.R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76:4193-4201.
41. Vaisar T., Kassim S.Y., Gomez I.G., Green P.S., Hargarten S., Gough P.J., et al. MMP-9 sheds the beta2 integrin subunit (CD18) from macrophages. Mol Cell Proteomics 2009, 8:1044-1060.
42. Xu D., Suenaga N., Edelmann M.J., Fridman R., Muschel R.J., Kessler B.M. Novel MMP-9 substrates in cancer cells revealed by a label-free quantitative proteomics approach. Mol Cell Proteomics 2008, 7:2215-2228.
43. Mahrus S., Trinidad J.C., Barkan D.T., Sali A., Burlingame A.L., Wells J.A. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 2008, 134:866-876.
44. Timmer J.C., Enoksson M., Wildfang E., Zhu W., Igarashi Y., Denault J.B., et al. Profiling constitutive proteolytic events in vivo. Biochem J 2007, 407:41-48.
45. Kleifeld O., Doucet A., auf dem Keller U., Prudova A., Schilling O., Kainthan R.K., et al. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat Biotechnol 2010, 28:281-288.
46. Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 2003, 21:566-569.
47. Rogers L.D., Overall C.M. Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol Cell Proteomics 2013, 12:3532-3542.
48. Plasman K., Van Damme P., Gevaert K. Contemporary positional proteomics strategies to study protein processing. Curr Opin Chem Biol 2013, 17:66-72.
49. Kleifeld O., Doucet A., Prudova A., auf dem Keller U., Gioia M., Kizhakkedathu J.N., et al. Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates. Nat Protoc 2011, 6:1578-1611.
50. auf dem Keller U., Overall C.M. CLIPPER-an add-on to the trans-proteomic pipeline for the automated analysis of TAILS N-terminomics data. Biol Chem 2012, 393:1477-1483.
51. Marchant D.J., Bellac C.L., Moraes T.J., Wadsworth S.J., Dufour A., Butler G.S., et al. A new transcriptional role for matrix metalloproteinase-12 in antiviral immunity. Nat Med 2014, 20:493-502.
52. auf dem Keller U., Prudova A., Eckhard U., Fingleton B., Overall C.M. Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation. Sci Signal 2013, 6:rs2.
53. Bellac C.L., Dufour A., Krisinger M.J., Loonchanta A., Starr A.E., Auf dem Keller U., et al. Macrophage matrix metalloproteinase-12 dampens inflammation and neutrophil influx in arthritis. Cell Rep 2014, 9:618-632.
54. Sabino F., Hermes O., Egli F.E., Kockmann T., Schlage P., Croizat P., et al. In vivo assessment of protease dynamics in cutaneous wound healing by degradomics analysis of porcine wound exudates. Mol Cell Proteomics Feb 2015, 14(2):354-370.
55. Schlage P., Egli F.E., Nanni P., Wang L.W., Kizhakkedathu J.N., Apte S.S., et al. Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome. Mol Cell Proteomics 2014, 13:580-593.