141
Views
4
CrossRef citations to date
0
Altmetric
Original Articles

Robustness of complex feedback systems: application to oncological biochemical networks

, , , , &
Pages 1304-1321 | Received 23 Oct 2012, Accepted 25 Apr 2013, Published online: 14 Jun 2013

References

  • Bader, A.G., Kang, S., Zhao, L., & Vogt, P.K. (2005). Oncogenic PI3K deregulates transcription and translation. Nature Reviews Cancer, 5, 921–929.
  • Becker, M.A., & Yee, D. (2008). EGFR signaling networks in cancer therapy. J.D. Haley & W.J. Gullick (Eds.), Business, pp. 155–168.
  • Bianconi, F., Baldelli, E., Ludovini, V., Crinò, L., & Valigi, P. (2012). Computational model of EGFR and IGF1R pathways in lung cancer: A systems biology approach for translational oncology. Biotechnology Advances, 142–153.
  • Bianconi, F., Lillacci, G., & Valigi, P. (2007). A hybrid model of nucleotide excision repair in neoplastic diseases: The identification problem. European Control Conference, Kios 2007, 30(1) (pp. 2603–2610). Greece, July.
  • Bianconi, F., Lillacci, G., & Valigi, P. (2010). Dynamic modeling and parameter identification for biological networks: Application to the DNA damage and repair processes. In L.A. Liu, D. Wei, and Y. Li (Eds.), Handbook of research on computational and systems biology: Interdisciplinary applications.
  • Boguski, M., & McCormick, F. (1993). Proteins regulating Ras and its relatives. Nature, 366, 643–654.
  • Brown, K.S., Hill, C.C., Calero, G.A., Myers, C.R., Lee, K.H., Sethna, J.P., & Cerione, R.A. (2004). The statistical mechanics of complex signaling networks: Nerve growth factor signaling. Physical Biology, 1, 184–195.
  • Chaves, M., Sengupta, A., & Sontag, E. (2009). Geometry and topology of parameter space: Investigating measures of robustness in regulatory networks. Journal of Mathematical Biology, 50, 315–358.
  • Chen, D., Waters, S.B., Holt, K.H., & Pessin, J.E. (1996). SOS phosphorylation and disassociation of the Grb2-SOS complex by the ERK and JNK signaling pathways. The Journal of Biological Chemistry, 271, 6328–6332.
  • Citri, A., Skaria, K.B., & Yarden, Y. (2003). The deaf and the dumb: The biology of ErbB-2 and ErbB-3. Experimental Cell Research, 284, 54–65.
  • Clermont, G., Auffray, C., Moreau, Y., Rocke, D.M., Dalevi, D., Dubhashi, D., … Benson, M. (2009). Bridging the gap between systems biology and medicine. Genome Medicine, 1, 88.
  • Daniels, B.C., Chen, Y.J., Sethna, J.P., Gutenkunst, R.N., & Myers, C.R. (2008). Sloppiness, robustness, and evolvability in systems biology. arXiv.org, q-bio.QM.
  • Dayarian, A., Chaves, M., Sontag, E.D., & Sengupta, A.M. (2009). Shape, size, and robustness: Feasible regions in the parameter space of biochemical networks. PLoS Computational Biology, 5, e1000256.
  • Del Vecchio, D., Ninfa, A.J., & Sontag, E.D. (2008). Modular cell biology: Retroactivity and insulation. Molecular Systems Biology, 4, 161.
  • Denley, A., Cosgrove, L.J., Booker, G.W., Wallace, J.C., & Forbes, B.E. (2005). Molecular interactions of the IGF system. Cytokine & Growth Factor Reviews, 16, 421–439.
  • Donzé, A., Fanchon, E., Gattepaille, L., Maler, O., & Tracqui, P. (2011). Robustness analysis and behavior discrimination in enzymatic reaction networks. PLOS One, 6(9), e24246.
  • Frödin, M., & Gammeltoft, S. (1999). Role and regulation of 90 kDa ribosomal S6 kinase (RSK) in signal transduction. Molecular and Cellular Endocrinology, 151(1–2), 6.
  • Gonzalez-Angulo, A., Hennessy, B., & Mills, G. (2010). Future of personalized medicine in oncology: A systems biology approach. Journal of Clinical Oncology, 28, 2777.
  • Guan, K.L., Figueroa, C., Brtva, T.R., Zhu, T., Taylor, J., Barber, T.D., & Vojtek, A.B. (2000). Negative regulation of the serine/threonine kinase B-Raf by Akt. The Journal of Biological Chemistry, 275, 27354–27359.
  • Hafner, M., Koeppl, H., Hasler, M., & Wagner, A. (2009). ‘Glocal’ robustness analysis and model discrimination for circadian oscillators. PLoS Computational Biology, 5, e1000534.
  • Heng, H.H. (2007). Cancer genome sequencing: The challenges ahead. BioEssays, 29, 783–794.
  • Hennessy, B.T., Smith, D.L., Ram, P.T., Lu, Y., & Mills, G.B. (2005). Exploiting the PI3K/AKT pathway for cancer drug discovery. Nature Reviews Drug Discovery, 4, 988–1004.
  • Jiang, Y., Rom, W.N., Yie, T.A., Chi, C.X., & Tchou-Wong, K.M. (1999). Induction of tumor suppression and glandular differentiation of A549 lung carcinoma cells by dominant-negative IGF-I receptor. Oncogene, 18, 6071–6077.
  • Johnson, Gary L., & Lapadat, R. (2002). Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases. Science, 298(5600), 1911–1912.
  • Jones JI, C.D. (1995). Insulin-like growth factors and their binding proteins: Biological actions. Endocrine Reviews, 16, 3–34.
  • Kim, E.K., & Choi, E.J. (2010). Pathological roles of MAPK signaling pathways in human diseases. Biochimica et Biophysica Acta, 1802, 396–405.
  • Kitano, H. (2004). Cancer as a robust system: Implications for anticancer therapy. Nature Reviews Cancer, 4, 227–235.
  • Kitano, H. (2007). Towards a theory of biological robustness. Molecular Systems Biology, 3, 137.
  • Kwon, Y.K., & Cho, K.H. (2008). Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics. Bioinformatics (Oxford, England), 24, 987–994.
  • LeRoith, D., Werner, H., Beitner-Johnson, D., & Roberts, C.T. (1995). Molecular and cellular aspects of the insulin-like growth factor I receptor. Endocrine Reviews, 16, 143–163.
  • López-Calderero, I., Chávez, E.S., & García-Carbonero, R. (2010). The insulin-like growth factor pathway as a target for cancer therapy. Clinical and Translational Oncology, 12, 326–338.
  • Ludovini, V., Bellezza, G., Pistola, L., Bianconi, F., Carlo, L.D., Sidoni, A.,  … Crinò, L. (2009). High coexpression of both insulin-like growth factor receptor-1 (IGFR-1) and epidermal growth factor receptor (EGFR) is associated with shorter disease-free survival in resected non-small-cell lung cancer patients. Annals of Oncology, 20(5), 842–849.
  • Markevich, N.I., Hoek, J.B., & Kholodenko, B.N. (2004). Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. The Journal of Cell Biology, 164, 353–359.
  • Mendelsohn, J., & Baselga, J. (2006). Epidermal growth factor receptor targeting in cancer. Seminars in Oncology, 33, 369–385.
  • Mitsudomi, T., & Yatabe, Y. (2010). Epidermal growth factor receptor in relation to tumor development: EGFR gene and cancer. The FEBS Journal, 277, 301–308.
  • Morohashi, M., Winn, A.E., Borisuk, M.T., Bolouri, H., Doyle, J., & Kitano, H. (2002). Robustness as a measure of plausibility in models of biochemical networks. Journal of Theoretical Biology, 216, 19–30.
  • Orton, R.J., Adriaens, M.E., Gormand, A., Sturm, O.E., Kolch, W., & Gilbert, D.R. (2009). Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Systems Biology, 3, 100.
  • Pearson, G. (2001). Mitogen-activated protein (MAP) kinase pathways: Regulation and physiological functions. Endocrine Reviews, 22, 153–183.
  • Qi, M., & Elion, E.A. (2005). MAP kinase pathways. Journal of Cell Science, 118, 3569–3572.
  • Riedemann, J., & Macaulay, V.M. (2006). IGF1R signalling and its inhibition. Endocrine-Related Cancer, 13(Suppl 1), S33–S43.
  • Rizk, A., Batt, G., Fages, F., & Soliman, S. (2009). A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics, 25, i169–i178.
  • Roberts, P.J., & Der, C.J. (2007). Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer. Oncogene, 26, 3291–3310.
  • Rodriguez-Fernandez, M., Banga, J., & Doyle, III, F. (2011). Novel global sensitivity analysis methodology accounting for the crucial role of the distribution of input parameters: Application to systems biology models. International Journal of Robust and Nonlinear Control, 22, 1082–1102.
  • Scaltriti, M., & Baselga, J. (2006). The epidermal growth factor receptor pathway: A model for targeted therapy. Clinical Cancer Research, 12, 5268–5272.
  • Schlessinger, J. (2002). Ligand-induced, receptor-mediated dimerization and activation of EGF receptor. Cell, 110, 669–672.
  • Schubbert, S., Shannon, K., & Bollag, G. (2007). Hyperactive Ras in developmental disorders and cancer. Nature Reviews Cancer, 7, 295–308.
  • Shane Donovana, K.M.S., & Bollagb, G. (2002). GTPase activating proteins: Critical regulators of intracellular signaling. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 1602(1), 23–45.
  • Shinar, G., Alon, U., & Feinberg, M. (2009). Sensitivity and robustness in chemical reaction networks. SIAM Journal on Applied Mathematics, 69, 977–998.
  • Vivanco, I., & Sawyers, C.L. (2002). The phosphatidylinositol 3-Kinase-AKT pathway in human cancer. Nature Reviews Cancer, 2, 489–501.
  • Von Dassow, G., Meir, E., Munro, E., & Odell, G. (2000). The segment polarity network is a robust developmental module. Nature, 406, 188–192.
  • Yarden, Y. (2001). The EGFR family and its ligands in human cancer. Signalling mechanisms and therapeutic opportunities. European Journal of Cancer (Oxford, England : 1990), 37(Suppl 4), S3–S8.
  • Yoon, J., & Deisboeck, T.S. (2009). Investigating differential dynamics of the MAPK signaling cascade using a multi-parametric global sensitivity analysis. PLoS ONE, 4, e4560.
  • Yoon, S., & Seger, R. (2006). The extracellular signal-regulated kinase: Multiple substrates regulate diverse cellular functions. Growth Factors, 24, 21–44.
  • Zi, Z. (2011). Sensitivity analysis approaches applied to systems biology models. IET Systems Biology, 5, 336–336.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.