Abstract
Excessive vascularization is a hallmark of many diseases including cancer, rheumatoid arthritis, diabetic nephropathy, pathologic obesity, age-related macular degeneration, and asthma. Compounds that inhibit angiogenesis represent potential therapeutics for many diseases. Karagiannis and Popel [Proc. Natl. Acad. Sci. USA 105(37):13775–13780, 2008] used a bioinformatics approach to identify more than 100 peptides with sequence homology to known angiogenesis inhibitors. The peptides could be grouped into families by the conserved domain of the proteins they were derived from. The families included type IV collagen fibrils, CXC chemokine ligands, and type I thrombospondin domain-containing proteins. The relationships between these families have received relatively little attention. To investigate these relationships, we approached the problem by placing the families of proteins in the context of the human interactome including >120,000 physical interactions among proteins, genes, and transcripts. We built on a graph theoretic approach to identify proteins that may represent conduits of crosstalk between protein families. We validated these findings by statistical analysis and analysis of a time series gene expression data set taken during angiogenesis. We identified six proteins at the center of the angiogenesis-associated network including three syndecans, MMP9, CD44, and versican. These findings shed light on the complex signaling networks that govern angiogenesis phenomena.
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Albig, A. R., J. R. Neil, and W. P. Schiemann. Fibulins 3 and 5 antagonize tumor angiogenesis in vivo. Cancer Res. 66(5):2621–2629, 2006.
Ashburner, M., C. A. Ball, J. A. Blake, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25(1):25–29, 2000.
Bauer, S., S. Grossmann, M. Vingron, et al. Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24(14):1650–1651, 2008.
Breitkreutz, B. J., C. Stark, T. Reguly, et al. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res. 36(Database issue):D637–D640, 2008.
Cano Mdel, V., E. D. Karagiannis, M. Soliman, et al. A peptide derived from type 1 thrombospondin repeat-containing protein WISP-1 inhibits corneal and choroidal neovascularization. Invest. Ophthalmol. Vis. Sci. 50(8):3840–3845, 2009.
Cao, G., R. C. Savani, M. Fehrenbach, et al. Involvement of endothelial CD44 during in vivo angiogenesis. Am. J. Pathol. 169(1):325–336, 2006.
Folkman, J. Tumor angiogenesis: therapeutic implications. N. Engl. J. Med. 285(21):1182–1186, 1971.
Folkman, J. Angiogenesis: an organizing principle for drug discovery? Nat. Rev. Drug Discov. 6(4):273–286, 2007.
Gioia, M., S. Monaco, P. E. Van Den Steen, et al. The collagen binding domain of gelatinase A modulates degradation of collagen IV by gelatinase B. J. Mol. Biol. 386(2):419–434, 2009.
Jayapandian, M., A. Chapman, V. G. Tarcea, et al. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 35(Database issue):D566–D571, 2007.
Karagiannis, E. D., and A. S. Popel. A theoretical model of type I collagen proteolysis by matrix metalloproteinase (MMP) 2 and membrane type 1 MMP in the presence of tissue inhibitor of metalloproteinase 2. J. Biol. Chem. 279(37):39105–39114, 2004.
Karagiannis, E. D., and A. S. Popel. Anti-angiogenic peptides identified in thrombospondin type I domains. Biochem. Biophys. Res. Commun. 359(1):63–69, 2007.
Karagiannis, E. D., and A. S. Popel. Peptides derived from type I thrombospondin repeat-containing proteins of the CCN family inhibit proliferation and migration of endothelial cells. Int. J. Biochem. Cell Biol. 39(12):2314–2323, 2007.
Karagiannis, E. D., and A. S. Popel. A systematic methodology for proteome-wide identification of peptides inhibiting the proliferation and migration of endothelial cells. Proc. Natl. Acad. Sci. USA 105(37):13775–13780, 2008.
Karagiannis, E. D., and A. S. Popel. Novel anti-angiogenic peptides derived from ELR-containing CXC chemokines. J. Cell. Biochem. 104(4):1356–1363, 2008.
Keshava Prasad, T. S., R. Goel, K. Kandasamy, et al. Human Protein Reference Database—2009 update. Nucleic Acids Res. 37(Database issue):D767–D772, 2009.
Killcoyne, S., G. W. Carter, J. Smith, et al. Cytoscape: a community-based framework for network modeling. Methods Mol. Biol. 563:219–239, 2009.
Koskimaki, J. E., E. D. Karagiannis, E. V. Rosca, et al. Peptides derived from type IV collagen, CXC chemokines, and thrombospondin-1 domain-containing proteins inhibit neovascularization and suppress tumor growth in MDA-MB-231 breast cancer xenografts. Neoplasia 11(12):1285–1291, 2009.
Koskimaki, J. E., E. D. Karagiannis, B. C. Tang, et al. Pentastatin-1, a collagen IV derived 20-mer peptide, suppresses tumor growth in a small cell lung cancer xenograft model. BMC Cancer 10:29, 2010.
Kuo, H. J., C. L. Maslen, D. R. Keene, et al. Type VI collagen anchors endothelial basement membranes by interacting with type IV collagen. J. Biol. Chem. 272(42):26522–26529, 1997.
Li, Y., P. Agarwal, and D. Rajagopalan. A global pathway crosstalk network. Bioinformatics 24(12):1442–1447, 2008.
McCarty, M. F. Toward prevention of Alzheimers disease—potential nutraceutical strategies for suppressing the production of amyloid beta peptides. Med. Hypotheses 67(4):682–697, 2006.
Mellberg, S., A. Dimberg, F. Bahram, et al. Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis. FASEB J. 23(5):1490–1502, 2009.
Mira, E., R. A. Lacalle, J. M. Buesa, et al. Secreted MMP9 promotes angiogenesis more efficiently than constitutive active MMP9 bound to the tumor cell surface. J. Cell Sci. 117(Pt 9):1847–1857, 2004.
Nagase, H., and J. F. Woessner, Jr. Matrix metalloproteinases. J. Biol. Chem. 274(31):21491–21494, 1999.
Natarajan, M., K. M. Lin, R. C. Hsueh, et al. A global analysis of cross-talk in a mammalian cellular signalling network. Nat. Cell Biol. 8(6):571–580, 2006.
Opdenakker, G., P. E. Van den Steen, B. Dubois, et al. Gelatinase B functions as regulator and effector in leukocyte biology. J. Leukoc. Biol. 69(6):851–859, 2001.
Ruoslahti, E. Fibronectin. J. Oral Pathol. 10(1):3–13, 1981.
Schonherr, E., C. Sunderkotter, L. Schaefer, et al. Decorin deficiency leads to impaired angiogenesis in injured mouse cornea. J. Vasc. Res. 41(6):499–508, 2004.
Silva, R., G. D’Amico, K. M. Hodivala-Dilke, et al. Integrins: the keys to unlocking angiogenesis. Arterioscler. Thromb. Vasc. Biol. 28(10):1703–1713, 2008.
Subramanian, A., P. Tamayo, V. K. Mootha, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102(43):15545–15550, 2005.
Suo, Z., J. Humphrey, A. Kundtz, et al. Soluble Alzheimers beta-amyloid constricts the cerebral vasculature in vivo. Neurosci. Lett. 257(2):77–80, 1998.
Tarcea, V. G., T. Weymouth, A. Ade, et al. Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res. 37(Database issue):D642–D646, 2009.
Tkachenko, E., J. M. Rhodes, and M. Simons. Syndecans: new kids on the signaling block. Circ. Res. 96(5):488–500, 2005.
Tony, J. C. Alzheimer’s disease and angiogenesis. Lancet 361(9365):1300, 2003.
Tsuda, K., and W. S. Noble. Learning kernels from biological networks by maximizing entropy. Bioinformatics 20(Suppl. 1):326–333, 2004.
Vastrik, I., P. D’Eustachio, E. Schmidt, et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 8(3):R39, 2007.
Zielinski, R., P. F. Przytycki, J. Zheng, et al. The crosstalk between EGF, IGF, and Insulin cell signaling pathways—computational and experimental analysis. BMC Syst. Biol. 3:88, 2009.
Acknowledgments
The work was supported by NIH grants R01 HL101200 and R01 CA138264. The authors would like to thank Emmanouil Karagiannis for helpful discussions at the initial stage of the project. We would also like to thank Sofie Mellberg and Lena Claesson-Welsh for use of their time series gene expression dataset. CGR implemented the method, performed the analysis, generated the images and wrote the paper. ASP and JSB designed the study and edited the paper.
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The authors declare no competing interests.
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Associate Editor Sriram Neelamegham oversaw the review of this article.
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Rivera, C.G., Bader, J.S. & Popel, A.S. Angiogenesis-Associated Crosstalk Between Collagens, CXC Chemokines, and Thrombospondin Domain-Containing Proteins. Ann Biomed Eng 39, 2213–2222 (2011). https://doi.org/10.1007/s10439-011-0325-2
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DOI: https://doi.org/10.1007/s10439-011-0325-2