Mathematical modeling of cell cycle regulation in response to DNA damage: Exploring mechanisms of cell-fate determination

BioSystems

Volumn 103, Issue 3, 2011, Pages 384-391

  Iwamoto, Kazunari ^a,b   Hamada, Hiroyuki ^a   Eguchi, Yukihiro ^a   Okamoto, Masahiro ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b JAPAN SOCIETY FOR THE PROMOTION OF SCIENCE   (Japan)

Author keywords

Cell cycle arrest; Cell fate; P53 oscillation; Whole cell cycle regulation

Indexed keywords

PROTEIN P21; PROTEIN P53;

APOPTOSIS; CYTOLOGY; NUMERICAL MODEL; SIGNAL;

APOPTOSIS; ARTICLE; CELL CYCLE ARREST; CELL CYCLE REGULATION; CELL FATE; DNA DAMAGE; MATHEMATICAL MODEL; PROTEIN EXPRESSION; QUALITATIVE ANALYSIS; SIGNAL TRANSDUCTION; SIMULATION; ULTRAVIOLET IRRADIATION;

EID: 79751531809     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.11.011     Document Type: Article

References (48)

1. Bartek J., Lukas J. Chk1 and Chk2 kinases in checkpoint control and cancer. Cancer Cell 2003, 3(5):421-429.
2. Batchelor E., Mock C.S., Bhan I., Loewer A., Lahav G. Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage. Mol. Cell 2008, 30:277-289.
3. Canman C.E., Lim D.S., Cimprich K.A., Taya Y., Tamai K., Sakaguchi K., Appella E., Kastan M.B., Siliciano J.D. Activation of the ATM kinase by ionizing radiation and phosphorylation of p53. Science 1998, 281(5383):1677-1679.
4. Castro A., Bernis C., Vigneron S., Labbe J.C., Lorca T. The anaphase-promoting complex: a key factor in the regulation of cell cycle. Oncogene 2005, 24:314-325.
5. Chae H.D., Yun J., Bang Y.J., Shin D.Y. Cdk2-dependent phosphorylation of the NF-Y transcription factor is essential for the expression of the cell cycle-regulatory genes and cell cycle G1/S and G2/M transitions. Oncogene 2004, 23:4084-4088.
6. Chang D., Chen F., Zhang F., McKay B.C., Ljungman M. Dose-dependent effects of DNA-damaging agents on p53-mediated cell cycle arrest. Cell Growth Differ. 1999, 10:155-162.
7. Csikasz-Nagy A., Battogtokh D., Chen K.C., Novak B., Tyson J.J. Analysis of a generic model of eukaryotic cell-cycle regulation. Biophys. J. 2006, 90(12):4361-4379.
8. Di Leonardo A., Linke S.P., Clarkin K., Wahl G.M. DNA damage triggers a prolonged p53-dependent G1 arrest and long-term induction of Cip1 in normal human fibroblasts. Genes Dev. 1994, 8:2540-2551.
9. Donjerkovic D., Scott D.W. Regulation of the G1 phase of the mammalian cell cycle. Cell Res. 2000, 10:1-16.
10. Dulic V., Kaufmann W.K., Wilson S.J., Tlsty T.D., Lees E., Harper J.W., Elledge S.J., Reed S.I. p53-dependent inhibition of cyclin-dependent kinase activities in human fibroblasts during radiation-induced G1 arrest. Cell 1994, 76:1013-1023.
11. Ermentrout B. Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAUT for Researchers and Students 2002, Soc. for Industrial and Applied Math, Philadelphia.
12. Furuno N., Elzen N.D., Pines J. Human Cyclin A is required for mitosis until mid prophase. J. Cell Biol. 1999, 147:295-306.
13. Gervais J.L.M., Seth P., Zhang H. Cleavage of CDK inhibitor p21Cip1/Waf1 by caspases is an early event during DNA damage-induced apoptosis. J. Biol. Chem. 1998, 273(30):19207-19212.
14. Gong D., Pomerening J.R., Myers J.W., Gustavsson C., Jones J.T., Hahn A.T., Meyer T., Ferrell J.E. Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of Cyclin B1. Curr. Biol. 2007, 17(1):85-91.
15. Hamada H., Tashima Y., Kisaka Y., Iwamoto K., Hanai T., Eguchi Y., Okamoto M. Sophisticated framework between cell cycle arrest and apoptosis induction based on p53 dynamics. PLoS ONE 2009, 4(3):e4795.
16. Helin K. Regulation of cell proliferation by the E2F transcription factors. Curr. Opin. Genet. 1998, 8:28-35.
17. Hochegger H., Takeda S., Hunt T. Cyclin-dependent kinases and cell-cycle transitions: does one fit all?. Nat. Rev. Mol. Cell Biol. 2008, 9:910-916.
18. Iliakis G., Wang Y., Guan J., Wang H. DNA damage checkpoint control in cells exposed to ionizing radiation. Oncogene 2003, 22:5834-5847.
19. Iwamoto K., Tashima Y., Hamada H., Eguchi Y., Okamoto M. Mathematical modeling and sensitivity analysis of G1/S phase in the cell cycle including the DNA-damage signal transduction pathway. Biosystems 2008, 94:109-117.
20. Kohn K.W. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell 1999, 10:2703-2734.
21. Kong M., Barnes E.A., Ollendorff V., Donoghue D.J. Cyclin F regulates the nuclear localization of cyclin B1 through a cyclin-cyclin interaction. EMBO J. 2000, 19:1378-1388.
22. LaBaer I., Garrett M.D., Stevenson L.F., Slingerland J.M., Sandhu C., Chou H.S., Fattaey A., Harlow E. New functional activities for the p21 family of CDK inhibitors. Genes Dev. 1997, 11(7):847-862.
23. Lev Bar-Or R., Maya R., Lee A.S., Uri A., Arnold J.L., Moshe O. Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:11250-11255.
24. Li G., Ho V.C. p53-dependent DNA repair and apoptosis respond differently to high- and low-dose ultraviolet radiation. Br. J. Dermatol. 1998, 139:3-10.
25. Li J., Meyer A.N., Donoghue D.J. Nuclear localization of cyclin B1 mediates its biological activity and is regulated by phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:502-507.
26. Ling H., Kulasiri D., Samarasinghe S. Robustness of G1/S checkpoint pathways in cell cycle regulation based on probability of DNA-damaged cells passing as healthy cells. Biosystems 2010, 101:213-221.
27. Matsumura I., Tanaka H., Kanakura Y. E2F1 and c-Myc in cell growth and death. Cell Cycle 2003, 2(4):333-338.
28. Novak B., Tyson J.J. A model for restriction point control of the mammalian cell cycle. J. Theor. Biol. 2004, 230:563-579.
29. Ohtsubo M., Theodoras A.M., Schumacher J., Roberts J.M., Pagano M. Human cyclin E, a nuclear protein essential for the G1-to-S phase transition. Mol. Cell. Biol. 1995, 15:2612-2624.
30. Parry D., Bates S., Mann D.J., Peters G. Lack of cyclin D-Cdk complexes in Rb-negative cells correlates with high levels of p16INK4/MTS1 tumour suppressor gene product. EMBO J. 1995, 14(3):503-511.
31. Pellegata N.S., Antoniono R.J., Redpath J.L., Stanbridge E.J. DNA damage and p53-mediated cell cycle arrest: a reevaluation. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:15209-15214.
32. Qu Z., Weiss J.N., MacLellan W.R. Regulation of the mammalian cell cycle: a model of the G1-to-S transition. Am. J. Physiol. Cell Physiol. 2003, 284:349-364.
33. Ragione F.D., Russo G.L., Oliva A., Mercurio C., Mastropietro S., Pietra V.D., Zappia V. Biochemical characterization of p16INK4- and p18-containing complexes in human cell lines. J. Biol. Chem. 1996, 271:15942-15949.
34. Roos W.P., Kaina B. DNA damage-induced cell death by apoptosis. Trends Mol. Med. 2006, 12(9):440-450.
35. Sheaff R.J., Groudine M., Gordon M., Roberts J.M., Clurman B.E. Cyclin E-CDK2 is a regulator of p27kip1. Genes Dev. 1997, 11:1464-1478.
36. Takizawa C.G., Morgan D.O. Control of mitosis by changes in the subcellular location of cyclin-B1-Cdk1 and Cdc25C. Curr. Opin. Cell Biol. 2000, 12:658-665.
37. Tashima Y., Kisaka Y., Hanai T., Hamada H., Eguchi Y., Okamoto M. Mathematical modeling of G2/M phase in cell cycle with involving the p53/Mdm2 oscillation system. Proc. Int. Fed. Med. Biomed. Eng. 2006, 14:195-198.
38. Tashima Y., Hamada H., Okamoto M., Hanai T. Prediction of key factor controlling G1/S phase in the mammalian cell cycle using system analysis. J. Biosci. Bioeng. 2008, 106(4):368-374.
39. Tessema M., Lehmann U., Kreipe H. Cell cycle and no end. Virchows Archiv. 2004, 444:313-323.
40. Toettcher J.E., Loewerc A., Ostheimerd G.J., Yaffe M.B., Tidor B., Lahav G. Distinct mechanisms act in concert to mediate cell cycle arrest. Proc. Natl. Acad. Sci. U.S.A. 2009, 106(3):785-790.
41. Toyoshima H., Hunter T. p27, a novel inhibitor of G1 cyclin-Cdk protein kinase activity, is related to p21. Cell 1994, 78(1):67-74.
42. Wee K.B., Surana U., Aguda B.D. Oscillations of the p53-Akt network: implications on cell survival and death. PLoS ONE 2009, 4(2):e4407.
43. Woo R.A., Poon R.Y. Cyclin-dependent kinases and S phase control in mammalian cells. Cell Cycle 2003, 2(4):316-324.
44. Xiong Y., Hannon G.J., Zhang H., Casso D., Kobayashi R., Beach D. p21 is a universal inhibitor of cyclin kinases. Nature 1993, 366:701-704.
45. Xu N., Chang D.C. Different thresholds of MPF inactivation are responsible for controlling different mitotic events in mammalian cell division. Cell Cycle 2007, 6(13):1639-1645.
46. Xu M., Sheppard K.A., Peng C.Y., Yee A.S., Piwnica-Worms H. Cyclin A/CDK2 binds directly to E2F-1 and inhibits the DNA-binding activity of E2F-1/DP-1 by phosphorylation. Mol. Cell Biol. 1994, 14:8420-8431.
47. Zachariae W., Nasmyth K. Whose end is destruction: cell division and the anaphase-promoting complex. Genes Dev. 1999, 13:2039-2058.
48. Zhu W., Giangrande P.H., Nevins J.R. E2Fs link the control of G1/S and G2/M transcription. EMBO J. 2004, 23:4615-4626.