Proteomic analysis of altered extracellular matrix turnover in bleomycin-induced pulmonary fibrosis

Molecular and Cellular Proteomics

Volumn 13, Issue 7, 2014, Pages 1741-1752

  Decaris, Martin L ^a   Gatmaitan, Michelle ^a   FlorCruz, Simplicia ^a   Luo, Flora ^a   Li, Kelvin ^a   Holmes, William E ^a   Hellerstein, Marc K ^a,b   Turner, Scott M ^a   Emson, Claire L ^a  

^a KINEMED INC   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BLEOMYCIN; COLLAGEN; COLLAGEN TYPE 1; COLLAGEN TYPE 6; FIBRONECTIN; LAMININ; PERLECAN; PROTEIN GLUTAMINE GAMMA GLUTAMYLTRANSFERASE 2; SCLEROPROTEIN; DEUTERIUM OXIDE; PROTEOGLYCAN;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BASEMENT MEMBRANE; BLEOMYCIN-INDUCED PULMONARY FIBROSIS; COLLAGEN SYNTHESIS; CONTROLLED STUDY; CROSS LINKING; LIQUID CHROMATOGRAPHY; LUNG PARENCHYMA; MASS SPECTROMETRY; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN METABOLISM; PROTEIN SYNTHESIS; PROTEOMICS; TANDEM MASS SPECTROMETRY; ANIMAL; BIOSYNTHESIS; C57BL MOUSE; CHEMICALLY INDUCED; EXTRACELLULAR MATRIX; FIBER; GENE EXPRESSION PROFILING; ISOTOPE LABELING; LUNG FIBROSIS; MASS FRAGMENTOGRAPHY; METABOLISM; PATHOLOGY;

ANIMALS; BASEMENT MEMBRANE; BLEOMYCIN; COLLAGEN TYPE I; DEUTERIUM OXIDE; EXTRACELLULAR MATRIX; EXTRACELLULAR MATRIX PROTEINS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GENE EXPRESSION PROFILING; ISOTOPE LABELING; MICE; MICE, INBRED C57BL; MICROFIBRILS; PROTEOGLYCANS; PROTEOMICS; PULMONARY FIBROSIS;

EID: 84904136313     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.037267     Document Type: Article

References (44)

1. Cox, T. R., and Erler, J. T. (2011) Remodeling and homeostasis of the extracellular matrix: implications for fibrotic diseases and cancer. Dis. Model. Mech. 4, 165-178
2. Daley, W. P., Peters, S. B., and Larsen, M. (2008) Extracellular matrix dynamics in development and regenerative medicine. J. Cell Sci. 121, 255-264 (Pubitemid 351356696)
3. Kisseleva, T., and Brenner, D. A. (2008) Mechanisms of fibrogenesis. Exp. Biol. Med. 233, 109-122 (Pubitemid 351231543)
4. Lu, P., Takai, K., Weaver, V. M., and Werb, Z. (2011) Extracellular matrix degradation and remodeling in development and disease. Cold Spring Harb. Perspect. Biol. 3:a005058
5. Suki, B., and Bates, J. H. (2008) Extracellular matrix mechanics in lung parenchymal diseases. Resp. Physiol. Neurobiol. 163, 33-43
6. Wight, T. N., and Potter-Perigo, S. (2011) The extracellular matrix: an active or passive player in fibrosis? Am. J. Physiol. Gastrointest. Liver Physiol. 301, G950-G955
7. Wynn, T. A., and Ramalingam, T. R. (2012) Mechanisms of fibrosis: therapeutic translation for fibrotic disease. Nat. Med. 18, 1028-1040
8. Cowan, M. L., Rahman, T. M., and Krishna, S. (2010) Proteomic approaches in the search for biomarkers of liver fibrosis. Trends Mol. Med. 16, 171-183
9. Noble, P. W., Barkauskas, C. E., and Jiang, D. (2012) Pulmonary fibrosis: patterns and perpetrators. J. Clin. Invest. 122, 2756-2762
10. Ueha, S., Shand, F. H., and Matsushima, K. (2012) Cellular and molecular mechanisms of chronic inflammation-associated organ fibrosis. Frontiers Immunol. 3, 71
11. Booth, A. J., Hadley, R., Cornett, A. M., Dreffs, A. A., Matthes, S. A., Tsui, J. L., Weiss, K., Horowitz, J. C., Fiore, V. F., Barker, T. H., Moore, B. B., Martinez, F. J., Niklason, L. E., and White, E. S. (2012) Acellular normal and fibrotic human lung matrices as a culture system for in vitro investigation. Am. J. Resp. Crit. Care Med. 186, 866-876
12. Smits, N. C., Shworak, N. W., Dekhuijzen, P. N., and van Kuppevelt, T. H. (2010) Heparan sulfates in the lung: structure, diversity, and role in pulmonary emphysema. Anat. Rec. 293, 955-967
13. Kim, S. H., Turnbull, J., and Guimond, S. (2011) Extracellular matrix and cell signalling: the dynamic cooperation of integrin, proteoglycan and growth factor receptor. J. Endocrinol. 209, 139-151
14. Price, J. C., Holmes, W. E., Li, K. W., Floreani, N. A., Neese, R. A., Turner, S. M., and Hellerstein, M. K. (2012) Measurement of human plasma proteome dynamics with (2)H(2)O and liquid chromatography tandem mass spectrometry. Anal. Biochem. 420, 73-83
15. Hellerstein, M. K. (2004) New stable isotope-mass spectrometric techniques for measuring fluxes through intact metabolic pathways in mammalian systems: introduction of moving pictures into functional genomics and biochemical phenotyping. Metab. Eng. 6, 85-100
16. Hellerstein, M. K., and Neese, R. A. (1999) Mass isotopomer distribution analysis at eight years: theoretical, analytic, and experimental considerations. Am. J. Physiol. 276, E1146-E1170 (Pubitemid 29323432)
17. Crapo, P. M., Gilbert, T. W., and Badylak, S. F. (2011) An overview of tissue and whole organ decellularization processes. Biomaterials 32, 3233-3243
18. Barallobre-Barreiro, J., Didangelos, A., Schoendube, F. A., Drozdov, I., Yin, X., Fernandez-Caggiano, M., Willeit, P., Puntmann, V. O., Aldama-Lopez, G., Shah, A. M., Domenech, N., and Mayr, M. (2012) Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury. Circulation 125, 789-802
19. 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
20. 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, M111.014647
21. Gardner, J. L., Turner, S. M., Bautista, A., Lindwall, G., Awada, M., and Hellerstein, M. K. (2007) Measurement of liver collagen synthesis by heavy water labeling: effects of profibrotic toxicants and antifibrotic interventions. Am. J. Physiol. Gastrointest. Liver Physiol. 292, G1695-G1705 (Pubitemid 47080614)
22. Atabai, K., Jame, S., Azhar, N., Kuo, A., Lam, M., McKleroy, W., Dehart, G., Rahman, S., Xia, D. D., Melton, A. C., Wolters, P., Emson, C. L., Turner, S. M., Werb, Z., and Sheppard, D. (2009) Mfge8 diminishes the severity of tissue fibrosis in mice by binding and targeting collagen for uptake by macrophages. J. Clin. Invest. 119, 3713-3722
23. Didangelos, A., Yin, X., and Mayr, M. (2012) Method for protein subfractionation of cardiovascular tissues before DIGE analysis. Methods Mol. Biol. 854, 287-297
24. McCabe, B. J., Bederman, I. R., Croniger, C., Millward, C., Norment, C., and Previs, S. F. (2006) Reproducibility of gas chromatography-mass spectrometry measurements of 2H labeling of water: application for measuring body composition in mice. Anal. Biochem. 350, 171-176 (Pubitemid 43332816)
25. Boutten, B., Brazier, M., Morche, N., Morel, A., and Vendeuvre, J. L. (2000) Effects of animal and muscle characteristics on collagen and consequences for ham production. Meat Sci. 55, 233-238
26. Chaudhary, N. I., Schnapp, A., and Park, J. E. (2006) Pharmacologic differentiation of inflammation and fibrosis in the rat bleomycin model. Am. J. Resp. Crit. Care Med. 173, 769-776
27. Peng, R., Sridhar, S., Tyagi, G., Phillips, J. E., Garrido, R., Harris, P., Burns, L., Renteria, L., Woods, J., Chen, L., Allard, J., Ravindran, P., Bitter, H., Liang, Z., Hogaboam, C. M., Kitson, C., Budd, D. C., Fine, J. S., Bauer, C. M., and Stevenson, C. S. (2013) Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: a model for "active" disease. PLoS One 8, e59348
28. Okamoto, O., and Fujiwara, S. (2006) Dermatopontin, a novel player in the biology of the extracellular matrix. Connective Tissue Res. 47, 177-189 (Pubitemid 44463524)
29. Molleken, C., Sitek, B., Henkel, C., Poschmann, G., Sipos, B., Wiese, S., Warscheid, B., Broelsch, C., Reiser, M., Friedman, S. L., Tornoe, I., Schlosser, A., Kloppel, G., Schmiegel, W., Meyer, H. E., Holmskov, U., and Stuhler, K. (2009) Detection of novel biomarkers of liver cirrhosis by proteomic analysis. Hepatology 49, 1257-1266
30. Blaauboer, M. E., Emson, C. L., Verschuren, L., van Erk, M., Turner, S. M., Everts, V., Hanemaaijer, R., and Stoop, R. (2013) Novel combination of collagen dynamics analysis and transcriptional profiling reveals fibrosisrelevant genes and pathways. Matrix Biol. 32, 424-431
31. Popov, Y., Sverdlov, D. Y., Sharma, A. K., Bhaskar, K. R., Li, S., Freitag, T. L., Lee, J., Dieterich, W., Melino, G., and Schuppan, D. (2011) Tissue transglutaminase does not affect fibrotic matrix stability or regression of liver fibrosis in mice. Gastroenterology 140, 1642-1652
32. Baranova, A., Lal, P., Birerdinc, A., and Younossi, Z. M. (2011) Non-invasive markers for hepatic fibrosis. BMC Gastroenterol. 11, 91
33. Lorena, D., Darby, I. A., Reinhardt, D. P., Sapin, V., Rosenbaum, J., and Desmouliere, A. (2004) Fibrillin-1 expression in normal and fibrotic rat liver and in cultured hepatic fibroblastic cells: modulation by mechanical stress and role in cell adhesion. Lab. Invest. 84, 203-212 (Pubitemid 41656501)
34. Kolb, M., Margetts, P. J., Sime, P. J., and Gauldie, J. (2001) Proteoglycans decorin and biglycan differentially modulate TGF-beta-mediated fibrotic responses in the lung. Am. J. Physiol. Lung Cell. Mol. Physiol. 280, L1327-L1334
35. Kalamajski, S., and Oldberg, A. (2010) The role of small leucine-rich proteoglycans in collagen fibrillogenesis. Matrix Biol. 29, 248-253
36. Hernnas, J., Nettelbladt, O., Bjermer, L., Sarnstrand, B., Malmstrom, A., and Hallgren, R. (1992) Alveolar accumulation of fibronectin and hyaluronan precedes bleomycin-induced pulmonary fibrosis in the rat. Eur. Resp. J. 5, 404-410
37. Okamoto, O., Fujiwara, S., Abe, M., and Sato, Y. (1999) Dermatopontin interacts with transforming growth factor beta and enhances its biological activity. Biochem. J. 337, 537-541
38. Gauldie, J., and Kolb, M. (2008) Animal models of pulmonary fibrosis: how far from effective reality? Am. J. Physiol. Lung Cell. Mol. Physiol. 294, L151 (Pubitemid 351253352)
39. Moeller, A., Ask, K., Warburton, D., Gauldie, J., and Kolb, M. (2008) The bleomycin animal model: a useful tool to investigate treatment options for idiopathic pulmonary fibrosis? Int. J. Biochem. Cell Biol. 40, 362-382 (Pubitemid 351249887)
40. Veidal, S. S., Bay-Jensen, A. C., Tougas, G., Karsdal, M. A., and Vainer, B. (2010) Serum markers of liver fibrosis: combining the BIPED classification and the neo-epitope approach in the development of new biomarkers. Dis. Markers 28, 15-28
41. Veidal, S. S., Karsdal, M. A., Nawrocki, A., Larsen, M. R., Dai, Y., Zheng, Q., Hagglund, P., Vainer, B., Skjot-Arkil, H., and Leeming, D. J. (2011) Assessment of proteolytic degradation of the basement membrane: a fragment of type IV collagen as a biochemical marker for liver fibrosis. Fibrogenesis Tissue Repair 4, 22
42. Veidal, S. S., Karsdal, M. A., Vassiliadis, E., Nawrocki, A., Larsen, M. R., Nguyen, Q. H., Hagglund, P., Luo, Y., Zheng, Q., Vainer, B., and Leeming, D. J. (2011) MMP mediated degradation of type VI collagen is highly associated with liver fibrosis-identification and validation of a novel biochemical marker assay. PLoS One 6, e24753
43. Veidal, S. S., Vassiliadis, E., Bay-Jensen, A. C., Tougas, G., Vainer, B., and Karsdal, M. A. (2010) Procollagen type I N-terminal propeptide (PINP) is a marker for fibrogenesis in bile duct ligation-induced fibrosis in rats. Fibrogenesis Tissue Repair 3, 5
44. Arthur, M. J. (2000) Fibrogenesis II. Metalloproteinases and their inhibitors in liver fibrosis. Am. J. Physiol. Gastrointest. Liver Physiol. 279, G245-G249