Comparative proteomic assessment of matrisome enrichment methodologies

Biochemical Journal

Volumn 473, Issue 21, 2016, Pages 3979-3995

  Krasny, Lukas ^a   Paul, Angela ^a   Wai, Patty ^a   Howard, Beatrice A ^a   Natrajan, Rachael C ^a   Huang, Paul H ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DODECYL SULFATE SODIUM; TRYPSIN; SCLEROPROTEIN;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; EXTRACELLULAR MATRIX; EXTRACTION; FEMALE; HEART; INTERMETHOD COMPARISON; LIVER; LUNG; MAMMARY GLAND; MATRISOME; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; ANIMAL; HUMAN; LIQUID CHROMATOGRAPHY; METABOLISM; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROCEDURES; TANDEM MASS SPECTROMETRY;

ANIMALS; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, POLYACRYLAMIDE GEL; EXTRACELLULAR MATRIX; EXTRACELLULAR MATRIX PROTEINS; HUMANS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 85009350945     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BCJ20160686     Document Type: Article

References (46)

1. Mouw, J.K., Ou, G. and Weaver, V.M. (2014) Extracellular matrix assembly: A multiscale deconstruction. Nat. Rev. Mol. Cell Biol. 15, 771-785 doi:10.1038/nrm3902.
2. Pickup, M.W., Mouw, J.K. and Weaver, V.M. (2014) The extracellular matrix modulates the hallmarks of cancer. EMBO Rep. 15, 1243-1253 doi:10.15252/embr.201439246.
3. Payne, L.S. and Huang, P.H. (2013) The pathobiology of collagens in glioma. Mol. Cancer Res. 11, 1129-1140 doi:10.1158/1541-7786.MCR-13-0236.
4. Lu, P., Weaver, V.M. and Werb, Z. (2012) The extracellular matrix: A dynamic niche in cancer progression. J. Cell Biol. 196, 395-406 doi:10.1083/jcb.201102147.
5. Bateman, J.F., Boot-Handford, R.P. and Lamandé, S.R. (2009) Genetic diseases of connective tissues: cellular and extracellular effects of ECM mutations. Nat. Rev. Genet. 10, 173-183 doi:10.1038/nrg2520.
6. Wallace, K., Burt, A.D. and Wright, M.C. (2008) Liver fibrosis. Biochem. J. 411, 1-18 doi:10.1042/BJ20071570.
7. Roach, H.I., Aigner, T., Soder, S., Haag, J. and Welkerling, H. (2007) Pathobiology of osteoarthritis: pathomechanisms and potential therapeutic targets. Curr. Drug Targets 8, 271-282 doi:10.2174/138945007779940160.
8. Chistiakov, D.A., Sobenin, I.A. and Orekhov, A.N. (2013) Vascular extracellular matrix in atherosclerosis. Cardiol. Rev. 21, 270-288 doi:10.1097/CRD.0b013e31828c5ced.
9. Naba, A., Clauser, K.R., Hoersch, S., Liu, H., Carr, S.A. and Hynes, R.O. (2012) The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol. Cell. Proteomics 11, M111014647 doi:10.1074/mcp.M111.014647.
10. Naba, A., Clauser, K.R., Ding, H., Whittaker, C.A., Carr, S.A. and Hynes, R.O. (2016) The extracellular matrix: Tools and insights for the 'omics' era. Matrix Biol. 49, 10-24 doi:10.1016/j.matbio.2015.06.003.
11. Byron, A., Humphries, J.D. and Humphries, M.J. (2013) Defining the extracellular matrix using proteomics. Int. J. Exp. Pathol. 94, 75-92 doi:10.1111/iep.12011.
12. Xu, H., Xu, B., Yang, Q., Li, X., Ma, X., Xia, Q. et al. (2014) Comparison of decellularization protocols for preparing a decellularized porcine annulus fibrosus scaffold. PLoS ONE 9, e86723 doi:10.1371/journal.pone.0086723.
13. Hill, R.C., Calle, E.A., Dzieciatkowska, M., Niklason, L.E. and Hansen, K.C. (2015) Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering. Mol. Cell. Proteomics 14, 961-973 doi:10.1074/mcp.M114.045260.
14. Johnson, T.D., Hill, R.C., Dzieciatkowska, M., Nigam, V., Behfar, A., Christman, K.L. et al. (2016) Quantification of decellularized human myocardial matrix: A comparison of six patients. Proteomics Clin. Appl. 10, 75-83 doi:10.1002/prca.201500048.
15. Barallobre-Barreiro, J., Didangelos, A., Schoendube, F.A., Drozdov, I., Yin, X., Fernandez-Caggiano, M. et al. (2012) Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury. Circulation 125, 789-802 doi:10.1161/CIRCULATIONAHA.111.056952.
16. Schiller, H.B., Fernandez, I.E., Burgstaller, G., Schaab, C., Scheltema, R.A., Schwarzmayr, T. et al. (2015) Time-And compartment-resolved proteome profiling of the extracellular niche in lung injury and repair. Mol. Syst. Biol. 11, 819 doi:10.15252/msb.20156123.
17. Naba, A., Clauser, K.R., Whittaker, C.A., Carr, S.A., Tanabe, K.K. and Hynes, R.O. (2014) Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver. BMC Cancer 14, 518 doi:10.1186/1471-2407-14-518.
18. Naba, A., Clauser, K.R., Lamar, J.M., Carr, S.A. and Hynes, R.O. (2014) Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters. eLife 3, e01308 doi:10.7554/eLife.01308.
19. O'Brien, J., Hansen, K., Barkan, D., Green, J. and Schedin, P. (2011) Non-steroidal anti-inflammatory drugs target the pro-Tumorigenic extracellular matrix of the postpartum mammary gland. Int. J. Dev. Biol. 55, 745-755 doi:10.1387/ijdb.113379jo.
20. Maller, O., Hansen, K.C., Lyons, T.R., Acerbi, I., Weaver, V.M., Prekeris, R. et al. (2013) Collagen architecture in pregnancy-induced protection from breast cancer. J. Cell Sci. 126, 4108-4110 doi:10.1242/jcs.121590.
21. Randles, M.J., Woolf, A.S., Huang, J.L., Byron, A., Humphries, J.D., Price, K.L. et al. (2015) Genetic background is a key determinant of glomerular extracellular matrix composition and organization. J. Am. Soc. Nephrol. 26, 3021-3034 doi:10.1681/ASN.2014040419.
22. Lennon, R., Byron, A., Humphries, J.D., Randles, M.J., Carisey, A., Murphy, S. et al. (2014) Global analysis reveals the complexity of the human glomerular extracellular matrix. J. Am. Soc. Nephrol. 25, 939-951 doi:10.1681/ASN.2013030233.
23. de Castro Bras, L.E., Ramirez, T.A., DeLeon-Pennell, K.Y., Chiao, Y.A., Ma, Y., Dai, Q. et al. (2013) Texas 3-step decellularization protocol: looking at the cardiac extracellular matrix. J. Proteomics 86, 43-52 doi:10.1016/j.jprot.2013.05.004.
24. Nesvizhskii, A.I., Keller, A., Kolker, E. and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658 doi:10.1021/ac0341261.
25. Gilbert, T.W., Sellaro, T.L. and Badylak, S.F. (2006) Decellularization of tissues and organs. Biomaterials 27, 3675-3683 doi:10.1016/j.biomaterials.2006.02.014.
26. Keane, T.J., Londono, R., Turner, N.J. and Badylak, S.F. (2012) Consequences of ineffective decellularization of biologic scaffolds on the host response. Biomaterials 33, 1771-1781 doi:10.1016/j.biomaterials.2011.10.054.
27. Curtis, M.W. and Russell, B. (2011) Micromechanical regulation in cardiac myocytes and fibroblasts: implications for tissue remodeling. Pflügers Arch. Eur. J. Phys. 462, 105-117 doi:10.1007/s00424-011-0931-8.
28. Kandalam, V., Basu, R., Abraham, T., Wang, X., Awad, A., Wang, W. et al. (2010) Early activation of matrix metalloproteinases underlies the exacerbated systolic and diastolic dysfunction in mice lacking TIMP3 following myocardial infarction. Am. J. Physiol. Heart Circ. Physiol. 299, H1012-H1023 doi:10.1152/ajpheart.00246.2010.
29. Baudino, T.A., Carver, W., Giles, W. and Borg, T.K. (2006) Cardiac fibroblasts: friend or foe? Am. J. Physiol. Heart Circ. Physiol. 291, H1015-H1026 doi:10.1152/ajpheart.00023.2006.
30. Chapman, D., Weber, K.T. and Eghbali, M. (1990) Regulation of fibrillar collagen types I and III and basement membrane type IV collagen gene expression in pressure overloaded rat myocardium. Circ. Res. 67, 787-794 doi:10.1161/01.RES.67.4.787.
31. Didangelos, A., Yin, X., Mandal, K., Baumert, M., Jahangiri, M. and Mayr, M. (2010) Proteomics characterization of extracellular space components in the human aorta. Mol. Cell. Proteomics 9, 2048-2062 doi:10.1074/mcp.M110.001693.
32. Didangelos, A., Yin, X., Mandal, K., Saje, A., Smith, A., Xu, Q. et al. (2011) Extracellular matrix composition and remodeling in human abdominal aortic aneurysms: A proteomics approach. Mol. Cell. Proteomics 10, M111 008128 doi:10.1074/mcp.M111.008128.
33. Wiseman, B.S. and Werb, Z. (2002) Stromal effects on mammary gland development and breast cancer. Science 296, 1046-1049 doi:10.1126/science.1067431.
34. O'Brien, J.H., Vanderlinden, L.A., Schedin, P.J. and Hansen, K.C. (2012) Rat mammary extracellular matrix composition and response to ibuprofen treatment during postpartum involution by differential GeLC-MS/MS analysis. J. Proteome Res. 11, 4894-4905 doi:10.1021/pr3003744.
35. Balestrini, J.L. and Niklason, L.E. (2015) Extracellular matrix as a driver for lung regeneration. Ann. Biomed. Eng. 43, 568-576 doi:10.1007/s10439-014-1167-5.
36. Han, S. and Mallampalli, R.K. (2015) The role of surfactant in lung disease and host defense against pulmonary infections. Ann. Am. Thorac. Soc. 12, 765-774 doi:10.1513/AnnalsATS.201411-507FR.
37. Bedossa, P. and Paradis, V. (2003) Liver extracellular matrix in health and disease. J. Pathol. 200, 504-515 doi:10.1002/path.1397.
38. Martinez-Hernandez, A. and Amenta, P.S. (1993) The hepatic extracellular matrix. I. Components and distribution in normal liver. Virchows Arch. A Pathol. Anat. Histopathol. 423, 1-11 doi:10.1007/BF01606425.
39. Martinez-Hernandez, A. (1985) The hepatic extracellular matrix. II. Electron immunohistochemical studies in rats with CCl4-induced cirrhosis. Lab. Invest. 53, 166-186 PMID:3894794.
40. Lange, V., Picotti, P., Domon, B. and Aebersold, R. (2008) Selected reaction monitoring for quantitative proteomics: A tutorial. Mol. Syst. Biol. 4, 222 doi:10.1038/msb.2008.61.
41. Kasimir, M.T., Rieder, E., Seebacher, G., Silberhumer, G., Wolner, E., Weigel, G. et al. (2003) Comparison of different decellularization procedures of porcine heart valves. Int. J. Artif. Organs 26, 421-427 PMID:12828309.
42. Cartmell, J.S. and Dunn, M.G. (2000) Effect of chemical treatments on tendon cellularity and mechanical properties. J. Biomed. Mater. Res. 49, 134-140 doi:10.1002/(SICI)1097-4636(200001)49:1<134::AID-JBM17>3.0.CO;2-D.
43. Yanagishita, M., Podyma-Inoue, K.A. and Yokoyama, M. (2009) Extraction and separation of proteoglycans. Glycoconj. J. 26, 953-959 doi:10.1007/s10719-008-9138-4.
44. Neuman, R.E. and Logan, M.A. (1950) The determination of collagen and elastin in tissues. J. Biol. Chem. 186, 549-556 PMID:14794650.
45. Harkness, M.L.R. and Harkness, R.D. (1956) The effect of pregnancy and lactation on the collagen content of the mammary gland of the rat. J. Physiol. 132, 476-481 doi:10.1113/jphysiol.1956.sp005540.
46. Barallobre-Barreiro, J., Oklu, R., Lynch, M., Fava, M., Baig, F., Yin, X. et al. (2016) Extracellular matrix remodelling in response to venous hypertension: proteomics of human varicose veins. Cardiovasc. Res. 110, 419-430 doi:10.1093/cvr/cvw075.