Cancer: A Systems Biology disease

BioSystems

Volumn 83, Issue 2-3 SPEC. ISS., 2006, Pages 81-90

  Hornberg, Jorrit J ^a   Bruggeman, Frank J ^a   Westerhoff, Hans V ^a,b   Lankelma, Jan ^a,c  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c VU UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Complexity; Drug design; Integrative biology; Kinase inhibitor; Signaling network

Indexed keywords

BASIC FIBROBLAST GROWTH FACTOR; DOXORUBICIN; MITOGEN ACTIVATED PROTEIN KINASE; MONOCLONAL ANTIBODY; PROTEIN TYROSINE KINASE INHIBITOR; VASCULOTROPIN;

CANCER;

CANCER; CHEMICAL REACTION KINETICS; CONFERENCE PAPER; DRUG DESIGN; DRUG INHIBITION; ENZYME PHOSPHORYLATION; GENE MUTATION; MATHEMATICAL MODEL; MOLECULE; OUTCOMES RESEARCH; PREDICTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 32044451325     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2005.05.014     Document Type: Conference Paper

References (74)

1. L. Acerenza, H.M. Sauro, and H. Kacser Control analysis of time-dependent metabolic systems J. Theor. Biol. 137 4 1989 423 444
2. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter Cell communication Molecular Biology of the Cell 2002 Garland Science New York, NY pp. 831-906
3. A.R. Asthagiri, and D.A. Lauffenburger A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (mapk) pathway model Biotechnol. Prog. 17 2 2001 227 239
4. B.M. Bakker, H.V. Westerhoff, F.R. Opperdoes, and P.A. Michels Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs Mol. Biochem. Parasitol. 106 1 2000 1 10
5. M. Bentele, I. Lavrik, M. Ulrich, S. Stosser, D.W. Heermann, H. Kalthoff, P.H. Krammer, and R. Eils Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis J. Cell Biol. 166 6 2004 839 851
6. U.S. Bhalla, and R. Iyengar Emergent properties of networks of biological signaling pathways Science 283 5400 1999 381 387
7. F.A. Brightman, and D.A. Fell Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells FEBS Lett. 482 3 2000 169 174
8. G.C. Brown, and B.N. Kholodenko Spatial gradients of cellular phospho-proteins FEBS Lett. 457 3 1999 452 454
9. E.C. Butcher, E.L. Berg, and E.J. Kunkel Systems biology in drug discovery Nat. Biotechnol. 22 10 2004 1253 1259
10. D.P. Cahill, K.W. Kinzler, B. Vogelstein, and C. Lengauer Genetic instability and Darwinian selection in tumours Trends Cell Biol. 9 12 1999 M57 M60
11. S.L. Campbell, R. Khosravi-Far, K.L. Rossman, G.J. Clark, and C.J. Der Increasing complexity of Ras signaling Oncogene 17 1998 1395 1413 11 Reviews
12. M. Cascante, L.G. Boros, B. Comin-Anduix, P. de Atauri, J.J. Centelles, and P.W. Lee Metabolic control analysis in drug discovery and disease Nat. Biotechnol. 20 3 2002 243 249
13. M. Chaplain, and A. Anderson Mathematical modelling of tumour-induced angiogenesis: network growth and structure Cancer Treat. Res. 117 2004 51 75
14. R. Christopher, A. Dhiman, J. Fox, R. Gendelman, T. Haberitcher, D. Kagle, G. Spizz, I.G. Khalil, and C. Hill Data-driven computer simulation of human cancer cell Ann. N. Y. Acad. Sci. 1020 2004 132 153
15. DeVita, V.T., Hellman, S., Rosenberg, S.A. Cancer: Principles and Practice of Oncology, sixth ed. Lippincott Williams & Wilkins, Philidelphia, PA, USA, 2001.
16. R.J. Ellis, and A.P. Minton Cell biology: join the crowd Nature 425 6953 2003 27 28
17. Fell, D.A. Understanding the Control of Metabolism. Portland Press, London, 1997.
18. N. Ferrara Vascular endothelial growth factor as a target for anticancer therapy Oncologist 9 Suppl. 1 2004 2 10
19. J.E. Ferrell Jr. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs Trends Biochem. Sci. 21 12 1996 460 466 [see comments]
20. J.E. Ferrell Jr. Building a cellular switch: more lessons from a good egg Bioessays 21 10 1999 866 870
21. J.E. Ferrell Jr. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability Curr. Opin. Cell Biol. 14 2 2002 140 148
22. J. Folkman Role of angiogenesis in tumor growth and metastasis Semin. Oncol. 29 6 Suppl. 16 2002 15 18
23. P.A. Futreal, L. Coin, M. Marshall, T. Down, T. Hubbard, R. Wooster, N. Rahman, and M.R. Stratton A census of human cancer genes Nat. Rev. Cancer 4 3 2004 177 183
24. R.A. Gatenby, and P.K. Maini Mathematical oncology: cancer summed up Nature 421 6921 2003 321
25. A. Goldbeter, and D.E. Koshland Jr. Sensitivity amplification in biochemical systems Q. Rev. Biophys. 15 3 1982 555 591
26. D. Hanahan, and J. Folkman Patterns and emerging mechanisms of the angiogenic switch during tumorigenesis Cell 86 3 1996 353 364
27. D. Hanahan, and R.A. Weinberg The hallmarks of cancer Cell 100 1 2000 57 70
28. R. Heinrich, and T.A. Rapoport A linear steady-state treatment of enzymatic chains: general properties, control and effector strength Eur. J. Biochem. 42 1 1974 89 95
29. R. Heinrich, and S. Schuster The Regulation of Cellular Systems 2001 Chapman & Hall New York
30. R. Heinrich, B.G. Neel, and T.A. Rapoport Mathematical models of protein kinase signal transduction Mol. Cell 9 5 2002 957 970
31. M.H. Hoefnagel, M.J. Starrenburg, D.E. Martens, J. Hugenholtz, M. Kleerebezem, S. Van II, R. Bongers, H.V. Westerhoff, and J.L. Snoep Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis Microbiology 148 Pt. 4 2002 1003 1013
32. J.J. Hornberg, M.R. Tijssen, and J. Lankelma Synergistic activation of signalling to extracellular signal-regulated kinases 1 and 2 by epidermal growth factor and 4beta-phorbol 12-myristate 13-acetate Eur. J. Biochem. 271 19 2004 3905 3913
33. J.J. Hornberg, F.J. Bruggeman, B. Binder, C.R. Geest, A.J.M. Bij de Vaate, J. Lankelma, R. Heinrich, and H.V. Westerhoff Principles behind the multifarious control of signal transduction: ERK phosphorylation and kinase/phosphatase control FEBS J. 272 1 2005 244 258
34. J.J. Hornberg, B. Binder, F.J. Bruggeman, B. Schoeberl, R. Heinrich, and H.V. Westerhoff Control of MAPK signalling: from complexity to what really matters Oncogene 24 36 2005 5533 5542
35. C.Y. Huang, and J.E. Ferrell Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade Proc. Natl. Acad. Sci. U.S.A. 93 19 1996 10078 10783
36. B.P. Ingalls, and H.M. Sauro Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories J. Theor. Biol. 222 1 2003 23 36
37. H. Kacser, and J.A. Burns The control of flux Symp. Soc. Exp. Biol. 27 1973 65 104
38. D. Kahn, and H.V. Westerhoff Control theory of regulatory cascades J. Theor. Biol. 153 2 1991 255 285
39. I.G. Khalil, and C. Hill Systems biology for cancer Curr. Opin. Oncol. 17 1 2005 44 48
40. B.N. Kholodenko Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades Eur. J. Biochem. 267 6 2000 1583 1588
41. B.N. Kholodenko, O.V. Demin, and H.V. Westerhoff Control analysis of periodic phenomena in biological systems J. Phys. Chem. B 101 11 1997 2070 2081
42. B.N. Kholodenko, O.V. Demin, G. Moehren, and J.B. Hoek Quantification of short term signaling by the epidermal growth factor receptor J. Biol. Chem. 274 42 1999 30169 30181
43. H. Kitano Cancer robustness: tumour tactics Nature 426 6963 2003 125
44. N. Klauber-DeMore, K.J. Van Zee, I. Linkov, P.I. Borgen, and W.L. Gerald Biological behavior of human breast cancer micrometastases Clin. Cancer Res. 7 8 2001 2434 2439
45. W. Kolch Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions Biochem. J. 351 Pt. 2 2000 289 305
46. J.G. Koster, O.H. Destree, and H.V. Westerhoff Kinetics of histone gene expression during early development of Xenopus laevis J. Theor. Biol. 135 2 1988 139 167
47. J. Lankelma Tissue transport of anti-cancer drugs Curr. Pharm. Des. 8 22 2002 1987 1993
48. J. Lankelma, H. Dekker, F.R. Luque, S. Luykx, K. Hoekman, P. van der Valk, P.J. van Diest, and H.M. Pinedo Doxorubicin gradients in human breast cancer Clin. Cancer Res. 5 7 1999 1703 1707
49. J. Lankelma, R. Fernandez Luque, H. Dekker, and H.M. Pinedo Simulation model of doxorubicin activity in islets of human breast cancer cells Biochim. Biophys. Acta 1622 3 2003 169 178
50. E. Lee, A. Salic, R. Kruger, R. Heinrich, and M.W. Kirschner The roles of APC and axin derived from experimental and theoretical analysis of the Wnt pathway PLoS Biol. 1 1 2003 e10
51. A. Mantovani, S. Sozzani, M. Locati, P. Allavena, and A. Sica Macrophage polarization: tumor-associated macrophages as a paradigm for polarized M2 mononuclear phagocytes Trends Immunol. 23 11 2002 549 555
52. J. Mendelsohn, and J. Baselga The EGF receptor family as targets for cancer therapy Oncogene 19 56 2000 6550 6565
53. P. Mendes Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3 Trends Biochem. Sci. 22 9 1997 361 363
54. P. Mendes, and D. Kell Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation Bioinformatics 14 10 1998 869 883
55. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon Network motifs: simple building blocks of complex networks Science 298 5594 2002 824 827
56. D.E. Nelson, A.E. Ihekwaba, M. Elliott, J.R. Johnson, C.A. Gibney, B.E. Foreman, G. Nelson, V. See, C.A. Horton, and D.G. Spiller Oscillations in NF-kappaB signaling control the dynamics of gene expression Science 306 5696 2004 704 708
57. D. Noble Modeling the heart Physiology (Bethesda) 19 2004 191 197
58. M.A. Peletier, H.V. Westerhoff, and B.N. Kholodenko Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law J. Theor. Biol. 225 4 2003 477 487
59. J. Pouyssegur, and P. Lenormand Fidelity and spatio-temporal control in MAP kinase (ERKs) signalling Eur. J. Biochem. 270 16 2003 3291 3299
60. J. Rak, J. Filmus, G. Finkenzeller, S. Grugel, D. Marme, and R.S. Kerbel Oncogenes as inducers of tumor angiogenesis Cancer Metastasis Rev. 14 4 1995 263 277
61. K.A. Reijenga, H.V. Westerhoff, B.N. Kholodenko, and J.L. Snoep Control analysis for autonomously oscillating biochemical networks Biophys. J. 82 1 Pt. 1 2002 99 108
62. B. Schoeberl, C. Eichler-Jonsson, E.D. Gilles, and G. Muller Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors Nat. Biotechnol. 20 4 2002 370 375
63. R. Schuster, and H.G. Holzhütter Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations: application to enzyme deficiencies of red blood cells Eur. J. Biochem. 229 2 1995 403 418
64. J.S. Sebolt-Leopold Development of anticancer drugs targeting the MAP kinase pathway Oncogene 19 56 2000 6594 6599
65. L.K. Shawver, D. Slamon, and A. Ullrich Smart drugs: tyrosine kinase inhibitors in cancer therapy Cancer Cell 1 2 2002 117 123
66. M.P. Shekhar, J. Werdell, S.J. Santner, R.J. Pauley, and L. Tait Breast stroma plays a dominant regulatory role in breast epithelial growth and differentiation: implications for tumor development and progression Cancer Res. 61 4 2001 1320 1326
67. J.L. Snoep, and H.V. Westerhoff The silicon cell initiative Curr. Genomics 5 8 2004 687 697
68. J.W. Stucki, and H.U. Simon Mathematical modeling of the regulation of caspase-3 activation and degradation J. Theor. Biol. 234 1 2005 123 131
69. I. Swameye, T.G. Muller, J. Timmer, O. Sandra, and U. Klingmüller Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modelling Proc. Natl. Acad. Sci. U.S.A. 100 3 2003 1028 1033
70. B. Teusink, J. Passarge, C.A. Reijenga, E. Esgalhado, C.C. van der Weijden, M. Schepper, M.C. Walsh, B.M. Bakker, K. van Dam, and H.V. Westerhoff Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry Eur. J. Biochem. 267 17 2000 5313 5329
71. B. Vogelstein, and K.W. Kinzler Cancer genes and the pathways they control Nat. Med. 10 8 2004 789 799
72. G. Weng, U.S. Bhalla, and R. Iyengar Complexity in biological signaling systems Science 284 5411 1999 92 96
73. Westerhoff, H.V., Van Dam, K. Thermodynamics and Control of Biological Free-Energy Transduction. Elsevier, Amsterdam, 1987.
74. E. Yeger-Lotem, S. Sattath, N. Kashtan, S. Itzkovitz, R. Milo, R.Y. Pinter, U. Alon, and H. Margalit Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction Proc. Natl. Acad. Sci. U.S.A. 101. 16 2004 5934 5939