Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: Incorporating EGFR signaling pathway and angiogenesis

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Sun, Xiaoqiang ^a,b   Zhang, Le ^c,d   Tan, Hua ^b   Bao, Jiguang ^b   Strouthos, Costas ^e   Zhou, Xiaobo ^a  

^a HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^b BEIJING NORMAL UNIVERSITY   (China)

^c SOUTHWEST UNIVERSITY   (China)

^d MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^e CYPRUS INSTITUTE   (Cyprus)

Author keywords

Agent based modeling; Angiogenesis; EGFR signaling pathway; Multi scale; TKI treatment

Indexed keywords

AGENT-BASED MODELING; ANGIOGENESIS; EGFR SIGNALING; MULTISCALES; TKI TREATMENT;

AMINO ACIDS; BLOOD VESSELS; BRAIN MODELS; CELLS; COMPUTATIONAL METHODS; CYTOLOGY; DISEASES; GLUCOSE; LINEAR EQUATIONS; MATHEMATICAL MODELS; MOLECULAR OXYGEN; SIGNALING; TUMORS;

PIGMENTS;

ANTINEOPLASTIC AGENT; EPIDERMAL GROWTH FACTOR RECEPTOR; PROTEIN KINASE INHIBITOR;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; BRAIN TUMOR; COMPUTER PROGRAM; COMPUTER SIMULATION; DRUG ANTAGONISM; DRUG EFFECT; HUMAN; METABOLISM; METHODOLOGY; NEOVASCULARIZATION (PATHOLOGY); SIGNAL TRANSDUCTION; VASCULARIZATION;

ANTINEOPLASTIC AGENTS; BRAIN NEOPLASMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; NEOVASCULARIZATION, PATHOLOGIC; PROTEIN KINASE INHIBITORS; RECEPTOR, EPIDERMAL GROWTH FACTOR; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 84865477904     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-218     Document Type: Article

References (33)

1. Patel AA, Gawlinski ET, Lemieux SK, Gatenby RA. A cellular automaton model of early tumor growth and invasion: the effects of native tissue vascularity and increased anaerobic tumor metabolism. J Theor Biol 2001, 213(3):315-331. 10.1006/jtbi.2001.2385, 11735284.
2. Kansal A, Torquato S, Harsh Iv G, Chiocca E, Deisboeck T. Cellular automaton of idealized brain tumor growth dynamics. Biosystems 2000, 55(1-3):119-127.
3. Zheng X, Wise SM, Cristini V. Nonlinear simulation of tumor necrosis, neo-vascularization and tissue invasion via an adaptive finite-element/level-set method. Bull Math Biol 2005, 67(2):211-259. 10.1016/j.bulm.2004.08.001, 15710180.
4. Macklin P, McDougall S, Anderson ARA, Chaplain MAJ, Cristini V, Lowengrub J. Multiscale modelling and nonlinear simulation of vascular tumour growth. J Math Biol 2009, 58(4):765-798. 10.1007/s00285-008-0216-9, 3037282, 18781303.
5. Anderson ARA. A hybrid mathematical model of solid tumour invasion: the importance of cell adhesion. Math Med Biol 2005, 22(2):163-186. 10.1093/imammb/dqi005, 15781426.
6. Rejniak KA, Anderson ARA. Hybrid models of tumor growth. Wiley Interdiscip Rev Syst Biol Med 2011, 3(1):115-125. 10.1002/wsbm.102, 3057876, 21064037.
7. Chen P, Xie H, Sekar MC, Gupta K, Wells A. Epidermal growth factor receptor-mediated cell motility: phospholipase C activity is required, but mitogen-activated protein kinase activity is not sufficient for induced cell movement. J Cell Biol 1994, 127(3):847-857. 10.1083/jcb.127.3.847, 2120228, 7962064.
8. Piccolo E, Innominato PF, Mariggio MA, Maffucci T, Iacobelli S, Falasca M. The mechanism involved in the regulation of phospholipase Cgamma1 activity in cell migration. Oncogene 2002, 21(42):6520-6529. 10.1038/sj.onc.1205821, 12226755.
9. Wang Z, Gluck S, Zhang L, Moran MF. Requirement for phospholipase C-gamma1 enzymatic activity in growth factor-induced mitogenesis. Mol Cell Biol 1998, 18(1):590-597. 121526, 9418905.
10. Zhang L, Athale CA, Deisboeck TS. Development of a three-dimensional multiscale agent-based tumor model: Simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer. J Theor Biol 2007, 244(1):96-107. 10.1016/j.jtbi.2006.06.034, 16949103.
11. Zhang L, Chen LL, Deisboeck TS. Multi-scale, multi-resolution brain cancer modeling. Math Comput Simulat 2009, 79(7):2021-2035.
12. Wang ZH, Zhang L, Sagotsky J, Deisboeck TS. Simulating non-small cell lung cancer with a multiscale agent-based model. Theor Biol Med Model 2007, 4:50. 10.1186/1742-4682-4-50, 2259313, 18154660.
13. Zhang L, Wang ZH, Sagotsky JA, Deisboeck TS. Multiscale agent-based cancer modeling. J Math Biol 2009, 58(4-5):545-559.
14. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000, 100(1):57-70. 10.1016/S0092-8674(00)81683-9, 10647931.
15. Graziano L, Preziosi L, Mollica F, Preziosi L, Rajagopal KR. Modeling of Biological Materials. Mechanics in tumor growth 2007, 263-321. Boston: Birkhäuser, Mollica F, Preziosi L, Rajagopal KR.
16. Risau W. Mechanisms of angiogenesis. Nature 1997, 386(6626):671-674.
17. Zhang L, Strouthos CG, Wang Z, Deisboeck TS. Simulating brain tumor heterogeneity with a multiscale agent-based model: Linking molecular signatures, phenotypes and expansion rate. Math Comput Model 2009, 49(1-2):307-319. 2653254, 20047002.
18. Ellis P, Morzycki W, Melosky B, Butts C, Hirsh V, Krasnoshtein F, Murray N, Shepherd FA, Soulieres D, Tsao MS. The role of the epidermal growth factor receptor tyrosine kinase inhibitors as therapy for advanced, metastatic, and recurrent non-small-cell lung cancer: a Canadian national consensus statement. Curr Oncol 2009, 16(1):27. 2644627, 19229369.
19. Anderson ARA, Chaplain MAJ. Continuous and discrete mathematical models of tumor-induced angiogenesis. Bull Math Biol 1998, 60(5):857-899. 10.1006/bulm.1998.0042, 9739618.
20. Araujo RP, Petricoin EF, Liotta LA. A mathematical model of combination therapy using the EGFR signaling network. Biosystems 2005, 80(1):57-69. 10.1016/j.biosystems.2004.10.002, 15740835.
21. Alarcon T. A mathematical model of the effects of hypoxia on the cell-cycle of normal and cancer cells. J Theor Biol 2004, 229(3):395-411. 10.1016/j.jtbi.2004.04.016, 15234206.
22. Mansury YD. T: The impact of " search precision" in an agent-based tumor model. J Theor Biol 2003, 224:25-337.
23. Shvartsman SY, Wiley HS, Deen WM, Lauffenburger DA. Spatial range of autocrine signaling: modeling and computational analysis. Biophys J 2001, 81(4):1854-1867. 10.1016/S0006-3495(01)75837-7, 1301661, 11566760.
24. Morton KW, Mayers DF. Numerical solution of partial differential equations: an introduction 2005, Cambridge: Univ Pr.
25. Stokes CL, Lauffenburger DA. Analysis of the roles of microvessel endothelial cell random motility and chemotaxis in angiogenesis. J Theor Biol 1991, 152(3):377-403. 10.1016/S0022-5193(05)80201-2, 1721100.
26. Zhu XW, Zhou XB, Lewis MT, Xia L, Wong S. Cancer stem cell, niche and EGFR decide tumor development and treatment response: A bio-computational simulation study. J Theor Biol 2011, 269(1):138-149. 10.1016/j.jtbi.2010.10.016, 3153880, 20969880.
27. Griffero F, Daga A, Marubbi D, Capra MC, Melotti A, Pattarozzi A, Gatti M, Bajetto A, Porcile C, Barbieri F. Different response of human glioma tumor-initiating cells to epidermal growth factor receptor kinase inhibitors. J Biol Chem 2009, 284(11):7138. 2652334, 19147502.
28. Liu G, Swihart MT, Neelamegham S. Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling. Bioinformatics 2005, 21(7):1194-1202. 10.1093/bioinformatics/bti118, 15531606.
29. Peng H, Wen J, Li H, Chang J, Zhou X. Drug inhibition profile prediction for NFkB pathway in multiple myeloma. PLoS One 2011, 6(3):e14750. 10.1371/journal.pone.0014750, 3051063, 21408099.
30. Sun X, Su J, Bao J, Peng T, Zhang L, Zhang Y, Yang Y, Zhou X. Cytokine combination therapy prediction for bone remodeling in tissue engineering based on the intracellular signaling pathway. Biomaterials 2012, 33(33):8265-8276. 10.1016/j.biomaterials.2012.07.041, 22910219.
31. Rabitz H, Kramer M, Dacol D. Sensitivity analysis in chemical kinetics. Annu Rev Phys Chem 1983, 34(1):419-461.
32. Petersen WP, Arbenz P. Introduction to parallel computing, vol. 9 2004, USA: Oxford University Press.
33. Anderson ARA, Weaver AM, Cummings PT, Quaranta V. Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell 2006, 127(5):905-915. 10.1016/j.cell.2006.09.042, 17129778.