Cross-scale sensitivity analysis of a non-small cell lung cancer model: Linking molecular signaling properties to cellular behavior

BioSystems

Volumn 92, Issue 3, 2008, Pages 249-258

  Wang, Zhihui ^a   Birch, Christina M ^b   Deisboeck, Thomas S ^a  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

Agent based model; Cellular behavior; Epidermal growth factor; Expansion rate; Non small cell lung cancer; Sensitivity analysis

Indexed keywords

EPIDERMAL GROWTH FACTOR; MITOGEN ACTIVATED PROTEIN KINASE 3; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; PROTEIN KINASE C;

CANCER; CELL ORGANELLE; EXPANSION; SENSITIVITY ANALYSIS; SIGNALING;

ARTICLE; CELL ACTIVITY; CELL FUNCTION; LUNG NON SMALL CELL CANCER; MODEL; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS;

EID: 43049167278     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2008.03.002     Document Type: Article

References (50)

1. Akhurst R.J., and Derynck R. TGF-beta signaling in cancer-a double-edged sword. Trends Cell Biol. 11 11 (2001) S44-S51
2. Aldridge B.B., Burke J.M., Lauffenburger D.A., and Sorger P.K. Physicochemical modelling of cell signalling pathways. Nat. Cell Biol. 8 11 (2006) 1195-1203
3. Allen L.F., Sebolt-Leopold J., and Meyer M.B. CI-1040 (PD184352), a targeted signal transduction inhibitor of MEK (MAPKK). Semin. Oncol. 30 5 Suppl. 16 (2003) 105-116
4. Bae K.M., Wang H., Jiang G., Chen M.G., Lu L., and Xiao L. Protein kinase C epsilon is overexpressed in primary human non-small cell lung cancers and functionally required for proliferation of non-small cell lung cancer cells in a p21/Cip1-dependent manner. Cancer Res. 67 13 (2007) 6053-6063
5. Bentele M., Lavrik I., Ulrich M., Stosser S., Heermann D.W., Kalthoff H., Krammer P.H., and Eils R. Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J. Cell Biol. 166 6 (2004) 839-851
6. Butcher E.C., Berg E.L., and Kunkel E.J. Systems biology in drug discovery. Nat. Biotechnol. 22 10 (2004) 1253-1259
7. Calabrese E.J. Cancer biology and hormesis: human tumor cell lines commonly display hormetic (biphasic) dose responses. Crit. Rev. Toxicol. 35 6 (2005) 463-582
8. Cho K.H., Shin S.Y., Lee H.W., and Wolkenhauer O. Investigations into the analysis and modeling of the TNF alpha-mediated NF-kappa B-signaling pathway. Genome Res. 13 11 (2003) 2413-2422
9. Davidson L.A., Aymond C.M., Jiang Y.H., Turner N.D., Lupton J.R., and Chapkin R.S. Non-invasive detection of fecal protein kinase C betaII and zeta messenger RNA: putative biomarkers for colon cancer. Carcinogenesis 19 2 (1998) 253-257
10. de Pillis L.G., Radunskaya A.E., and Wiseman C.L. A validated mathematical model of cell-mediated immune response to tumor growth. Cancer Res. 65 17 (2005) 7950-7958
11. Di Ventura B., Lemerle C., Michalodimitrakis K., and Serrano L. From in vivo to in silico biology and back. Nature 443 7111 (2006) 527-533
12. El-Samad H., Kurata H., Doyle J.C., Gross C.A., and Khammash M. Surviving heat shock: control strategies for robustness and performance. Proc. Natl. Acad. Sci. U.S.A. 102 8 (2005) 2736-2741
13. Frey H.C., and Patil S.R. Identification and review of sensitivity analysis methods. Risk Anal. 22 3 (2002) 553-578
14. Gollob J.A., Wilhelm S., Carter C., and Kelley S.L. Role of Raf kinase in cancer: therapeutic potential of targeting the Raf/MEK/ERK signal transduction pathway. Semin. Oncol. 33 4 (2006) 392-406
15. Green L.J., Marder P., Ray C., Cook C.A., Jaken S., Musib L.C., Herbst R.S., Carducci M., Britten C.D., Basche M., Eckhardt S.G., and Thornton D. Development and validation of a drug activity biomarker that shows target inhibition in cancer patients receiving enzastaurin, a novel protein kinase C-beta inhibitor. Clin. Cancer Res. 12 11 Pt 1 (2006) 3408-3415
16. Han S.W., Hwang P.G., Chung D.H., Kim D.W., Im S.A., Kim Y.T., Kim T.Y., Heo D.S., Bang Y.J., and Kim N.K. Epidermal growth factor receptor (EGFR) downstream molecules as response predictive markers for gefitinib (Iressa, ZD1839) in chemotherapy-resistant non-small cell lung cancer. Int. J. Cancer 113 1 (2005) 109-115
17. Hatakeyama M., Kimura S., Naka T., Kawasaki T., Yumoto N., Ichikawa M., Kim J.H., Saito K., Saeki M., Shirouzu M., Yokoyama S., and Konagaya A. A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochem. J. 373 Pt 2 (2003) 451-463
18. Hirsch F.R., Varella-Garcia M., Bunn Jr. P.A., Di Maria M.V., Veve R., Bremmes R.M., Baron A.E., Zeng C., and Franklin W.A. Epidermal growth factor receptor in non-small-cell lung carcinomas: correlation between gene copy number and protein expression and impact on prognosis. J. Clin. Oncol. 21 20 (2003) 3798-3807
19. Hirsch F.R., Varella-Garcia M., Bunn Jr. P.A., Franklin W.A., Dziadziuszko R., Thatcher N., Chang A., Parikh P., Pereira J.R., Ciuleanu T., von Pawel J., Watkins C., Flannery A., Ellison G., Donald E., Knight L., Parums D., Botwood N., and Holloway B. Molecular predictors of outcome with gefitinib in a phase III placebo-controlled study in advanced non-small-cell lung cancer. J. Clin. Oncol. 24 31 (2006) 5034-5042
20. Hornberg J.J., Binder B., Bruggeman F.J., Schoeberl B., Heinrich R., and Westerhoff H.V. Control of MAPK signalling: from complexity to what really matters. Oncogene 24 36 (2005) 5533-5542
21. Ihekwaba A.E., Broomhead D.S., Grimley R.L., Benson N., and Kell D.B. Sensitivity analysis of parameters controlling oscillatory signalling in the NF-kappaB pathway: the roles of IKK and IkappaBalpha. Syst. Biol. (Stevenage) 1 1 (2004) 93-103
22. Ingalls B.P., and Sauro H.M. Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J. Theor. Biol. 222 1 (2003) 23-36
23. Jemal A., Siegel R., Ward E., Murray T., Xu J., and Thun M.J. Cancer statistics, 2007. CA Cancer J. Clin. 57 1 (2007) 43-66
24. Kharait S., Hautaniemi S., Wu S., Iwabu A., Lauffenburger D.A., and Wells A. Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst. Biol. 1 (2007) 9
25. Kholodenko B.N., Demin O.V., Moehren G., and Hoek J.B. Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274 42 (1999) 30169-30181
26. Kitano H. Systems biology: a brief overview. Science 295 5560 (2002) 1662-1664
27. Kodama Y., Baxter R.C., and Martin J.L. Insulin-like growth factor-I inhibits cell growth in the a549 non-small lung cancer cell line. Am. J. Respir. Cell Mol. Biol. 27 3 (2002) 336-344
28. Lee E., Salic A., Kruger R., Heinrich R., and Kirschner M.W. The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biol. 1 1 (2003) E10
29. Liu G., Swihart M.T., and Neelamegham S. Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling. Bioinformatics 21 7 (2005) 1194-1202
30. Mahdavi A., Davey R.E., Bhola P., Yin T., and Zandstra P.W. Sensitivity analysis of intracellular signaling pathway kinetics predicts targets for stem cell fate control. PLoS Comput. Biol. 3 7 (2007) e130
31. Martin M.J., and Buckland-Wright J.C. Sensitivity analysis of a novel mathematical model identifies factors determining bone resorption rates. Bone 35 4 (2004) 918-928
32. Mouneimne G., Soon L., DesMarais V., Sidani M., Song X., Yip S.C., Ghosh M., Eddy R., Backer J.M., and Condeelis J. Phospholipase C and cofilin are required for carcinoma cell directionality in response to EGF stimulation. J. Cell Biol. 166 5 (2004) 697-708
33. Nagashima T., Shimodaira H., Ide K., Nakakuki T., Tani Y., Takahashi K., Yumoto N., and Hatakeyama M. Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation. J. Biol. Chem. 282 6 (2007) 4045-4056
34. Paez J.G., Janne P.A., Lee J.C., Tracy S., Greulich H., Gabriel S., Herman P., Kaye F.J., Lindeman N., Boggon T.J., Naoki K., Sasaki H., Fujii Y., Eck M.J., Sellers W.R., Johnson B.E., and Meyerson M. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 304 5676 (2004) 1497-1500
35. Piccolo E., Innominato P.F., Mariggio M.A., Maffucci T., Iacobelli S., and Falasca M. The mechanism involved in the regulation of phospholipase Cgamma1 activity in cell migration. Oncogene 21 42 (2002) 6520-6529
36. Rabitz H., Kramer M., and Dacol D. Sensitivity analysis in chemical kinetics. Annu. Rev. Phys. Chem. 34 (1983) 419-461
37. Ritchie C.K., Andrews L.R., Thomas K.G., Tindall D.J., and Fitzpatrick L.A. The effects of growth factors associated with osteoblasts on prostate carcinoma proliferation and chemotaxis: implications for the development of metastatic disease. Endocrinology 138 3 (1997) 1145-1150
38. Schoeberl B., Eichler-Jonsson C., Gilles E.D., and Muller G. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat. Biotechnol. 20 4 (2002) 370-375
39. Shuryak I., Sachs R.K., Hlatky L., Little M.P., Hahnfeldt P., and Brenner D.J. Radiation-induced leukemia at doses relevant to radiation therapy: modeling mechanisms and estimating risks. J. Natl. Cancer Inst. 98 24 (2006) 1794-1806
40. Swameye I., Muller T.G., Timmer J., Sandra O., and Klingmuller U. 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
41. van Riel N.A. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinform. 7 4 (2006) 364-374
42. Vicent S., Lopez-Picazo J.M., Toledo G., Lozano M.D., Torre W., Garcia-Corchon C., Quero C., Soria J.C., Martin-Algarra S., Manzano R.G., and Montuenga L.M. ERK1/2 is activated in non-small-cell lung cancer and associated with advanced tumours. Br. J. Cancer 90 5 (2004) 1047-1052
43. Vivanco I., and Sawyers C.L. The phosphatidylinositol 3-kinase AKT pathway in human cancer. Nat. Rev. Cancer 2 7 (2002) 489-501
44. von Dassow G., Meir E., Munro E.M., and Odell G.M. The segment polarity network is a robust developmental module. Nature 406 6792 (2000) 188-192
45. Wakeling A.E. Inhibitors of growth factor signalling. Endocr. Relat. Cancer 12 Suppl. 1 (2005) S183-S187
46. Wang Z., Zhang L., Sagotsky J., and Deisboeck T.S. Simulating non-small cell lung cancer with a multiscale agent-based model. Theor. Biol. Med. Model 4 1 (2007) 50
47. Wijeratne N.S., and Hoo K.A. Understanding the role of the tumour vasculature in the transport of drugs to solid cancer tumours. Cell Prolif. 40 3 (2007) 283-301
48. Zhang Y., and Rundell A. Comparative study of parameter sensitivity analyses of the TCR-activated Erk-MAPK signalling pathway. IEE Proc. Syst. Biol. 153 4 (2006) 201-211
49. Zhang J., Anastasiadis P.Z., Liu Y., Thompson E.A., and Fields A.P. Protein kinase C (PKC) betaII induces cell invasion through a Ras/Mek-, PKC iota/Rac 1-dependent signaling pathway. J. Biol. Chem. 279 (2004) 22118-22123
50. Zi Z., Cho K.H., Sung M.H., Xia X., Zheng J., and Sun Z. In silico identification of the key components and steps in IFN-gamma induced JAK-STAT signaling pathway. FEBS Lett. 579 5 (2005) 1101-1108