Ensemble modeling of cancer metabolism

Frontiers in Physiology

Volumn 3 MAY, Issue , 2012, Pages

  Khazaei, Tahmineh ^a   McGuigan, Alison ^a,b   Mahadevan, Radhakrishnan ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Cancer metabolism; Ensemble modeling; Flux balance analysis; Warburg effect

Indexed keywords

EID: 84866354583     PISSN: None     EISSN: 1664042X     Source Type: Journal    
DOI: 10.3389/fphys.2012.00135     Document Type: Article

References (29)

1. Boros, L. G., Cascante, M., and Lee, W. N. (2002). Metabolic profiling of cell growth and death in cancer: applications in drug discovery. Drug Discov. Today 7, 364-372.
2. Christofk, H. R., Vander Heiden, M. G., Wu, N., Asara, J. M., and Cantley, L. C. (2008). Pyruvate kinase M2 is a phosphotyrosine-binding protein. Nature 452, 181-186.
3. Contador, C. A., Rizk, M. L., Asenjo, J. A., and Liao, J. C. (2009). Ensemble modeling for strain development of L-lysine-producing Escherichia coli. Metab. Eng. 11, 221-233.
4. Curi, R., Newsholme, P., and New-sholme, E. A. (1988). Metabolism of pyruvate by isolated rat mesenteric lymphocytes, lymphocyte mitochondria and isolated mouse macrophages. Biochem. J. 250, 383.
5. Dean, J. T., Rizk, M. L., Tan, Y., Dipple, K. M., and Liao, J. C. (2010). Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxy-late shunt. Biophys. J. 98, 1385-1395.
6. DeBerardinis, R. J., Lum, J. J., Hatzi-vassiliou, G., and Thompson, C. B. (2008). The biology of cancer: metabolic reprogramming fuels cell growth and proliferation. Cell Metab. 7, 11-20.
7. Duarte, N. C.,Becker,S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., and Palsson, B. O. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. U.S.A. 104, 1777-1782.
8. Elliott, W. H., Elliott, D. C., Jefferson, J. R., and Wheldrake, J. (2009). Biochemistry and Molecular Biology. Oxford: Oxford University Press.
9. Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E., and Shlomi, T. (2011). Predicting selective drug targets in cancer through metabolic networks. Mol. Syst. Biol. 7, 527.
10. Frezza, C., Zheng, L., Folger, O., Rajagopalan, K. N., MacKenzie, E. D., Jerby, L., Micaroni, M., Chane-ton, B., Adam, J., Hedley, A., Kalna, G., Tomlinson, I. P. M., Pollard, P. J., Watson, D. G., Deber-ardinis, R. J., Shlomi, T., Rup-pin, E., and Gottlieb, E. (2011). Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature 477, 225-228.
11. Jakoby, W. B. (1979). Cell Culture, Vol. 58. San Diego: Academic Press.
12. Jankowski, M. D., Henry, C. S., Broad-belt, L. J., and Hatzimanikatis, V. (2008). Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys. J. 95, 1487-1499.
13. Lee, D. Y., Yun, C., Cho, A., Hou, B. K., Park, S., and Lee, S. Y. (2006). Web-Cell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioin-formatics 22, 1150-1151.
14. Ma, Y., Peng, J., Huang, L., Liu, W., Zhang, P., and Qin, H. (2009). Searching for serum tumor markers for colorectal cancer using a 2-D DIGE approach. Electrophoresis 30, 2591-2599.
15. Mahadevan, R., and Schilling, C. H. (2003). The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5, 264-276.
16. Michal, G. (1999). Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology. New York: Wiley.
17. Moreno-Sánchez, R., Rodríguez-Enríquez, S., Marín-Hernández, A., and Saavedra, E. (2007). Energy metabolism in tumor cells. FEBS J. 274, 1393-1418.
18. Newsholme, E. A., Crabtree, B., and Ardawi, M. S. (1985). The role of high rates of glycolysis and gluta-mine utilization in rapidly dividing cells. Biosci. Rep. 5, 393-400.
19. Orth, J. D., Thiele, I., and Palsson, B. Ø. (2010). What is flux balance analysis? Nat. Biotechnol. 28, 245-248.
20. Park, K., Millet, L. J., Kim, N., Li, H., Jin, X., Popescu, G., Aluru, N. R., Hsia, K. J., and Bashir, R. (2010). Measurement of adherent cell mass and growth. Proc. Natl. Acad. Sci. U.S.A. 107, 20691-20696.
21. Samland, A. K., and Sprenger, G. A. (2009). Transaldolase: from biochemistry to human disease. Int. J. Biochem. Cell Biol. 41, 1482-1494.
22. Schilling, C. H., Edwards, J. S., and Palsson, B. O. (1999). Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol. Prog. 15, 288-295.
23. Schulz, T. J., Thierbach, R., Voigt, A., Drewes, G., Mietzner, B., Steinberg, P., Pfeiffer, A. F., and Ristow, M. (2006). Induction of oxidative metabolism by mitochondrial frataxin inhibits cancer growth: Otto Warburg revisited. J. Biol. Chem. 281, 977-981.
24. Shlomi, T., Benyamini, T., Gottlieb, E., Sharan, R., and Ruppin, E. (2011). Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Comput. Biol. 7, e1002018. doi:10.1371/jour-nal.pcbi.1002018
25. Tan, Y., Rivera, J. G., Contador, C. A., Asenjo, J. A., and Liao, J. C. (2011). Reducing the allowable kinetic space by constructing ensem-bleof dynamic modelswith the same steady-state flux. Metab. Eng. 13, 60-75.
26. Tran, L. M., Rizk, M. L., and Liao, J. C. (2008). Ensemble modeling of metabolic networks. Biophys. J. 95, 5606-5617.
27. Vander Heiden, M. G., Cantley, L. C., and Thompson, C. B. (2009). Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 324, 1029-1033.
28. Vazquez, A., Liu, J., Zhou, Y., and Olt-vai, Z. N. (2010). Catabolic efficiency of aerobic glycolysis: the Warburg effect revisited. BMC Syst. Biol. 4, 58. doi:10.1186/1752-0509-4-58
29. Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., and Hassanali, M. (2008). DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36, D901-D906.