ON/OFF and beyond - A Boolean model of apoptosis

PLoS Computational Biology

Volumn 5, Issue 12, 2009, Pages

  Schlatter, Rebekka ^a   Schmich, Kathrin ^b   Vizcarra, Ima Avalos ^a,c   Scheurich, Peter ^a   Sauter, Thomas ^d   Borner, Christoph ^b   Ederer, Michael ^a,e   Merfort, Irmgard ^b   Sawodny, Oliver ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

^c ETH ZURICH   (Switzerland)

^d UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^e MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX NETWORKS; CROSSTALK; SIGNALING;

APOPTOSIS PATHWAYS; BOOLEAN MODELING; EXTERNAL STIMULUS; FAS LIGAND; INTERLEUKIN 1Β; LARGE-SCALES; LOGICAL MODELS; QUALITATIVE BEHAVIOR; SIGNALLING PATHWAYS; TNF Α;

CELL DEATH;

FAS LIGAND; INSULIN; INTERLEUKIN 1BETA; TUMOR NECROSIS FACTOR ALPHA;

ANIMAL CELL; APOPTOSIS; ARTICLE; BOOLEN MODEL; LIVER CELL; MODEL; MOUSE; NONHUMAN; ULTRAVIOLET B RADIATION; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; HUMAN; RADIATION EXPOSURE; SIGNAL TRANSDUCTION;

ANIMALS; APOPTOSIS; COMPUTATIONAL BIOLOGY; HUMANS; MICE; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION;

EID: 74549172058     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000595     Document Type: Article

References (55)

1. Hakem R, Hakem A, Duncan GS, Henderson JT, Woo M, et al. (1998) Differential requirement for caspase 9 in apoptotic pathways in vivo. Cell 94: 339-352.
2. Kerr JF, Wyllie AH, Currie AR (1972) Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer 26: 239-257.
3. Kuida K, Zheng TS, Na S, Kuan C, Yang D, et al. (1996) Decreased apoptosis in the brain and premature lethality in CPP32-deficient mice. Nature 384: 368-372.
4. Kuida K, Haydar TF, Kuan CY, Gu Y, Taya C, et al. (1998) Reduced apoptosis and cytochrome c-mediated caspase activation in mice lacking caspase 9. Cell 94: 325-337.
5. Varfolomeev EE, Schuchmann M, Luria V, Chiannilkulchai N, Beckmann JS, et al. (1998) Targeted disruption of the mouse Caspase 8 gene ablates cell death induction by the TNF receptors, Fas/Apo1, and DR3 and is lethal prenatally. Immunity 9: 267-276.
6. Thompson CB (1995) Apoptosis in the pathogenesis and treatment of disease. Science 267: 1456-1462.
7. Cory S, Huang DCS, Adams JM (2003) The Bcl-2 family: roles in cell survival and oncogenesis. Oncogene 22: 8590-8607.
8. Huber HJ, Rehm M, Plchut M, Düssmann H, Prehn JHM (2007) APOPTO-CELL - a simulation tool and interactive database for analyzing cellular susceptibility to apoptosis. Bioinformatics 23: 648-650.
9. Heiner M, Koch I, Will J (2004) Model validation of biological pathways using Petri nets - demonstrated for apoptosis. Biosystems 75: 15-28.
10. Li C, Ge QW, Nakata M, Matsuno H, Miyano S (2007) Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. J Biosci 32: 113-127.
11. Boole G (1854) An Investigation of the Laws of Thought onWhich are Founded the Mathematical Theories of Logic and Probabilities. London: Walten and Maberly.
12. Shannon C (1940) A symbolic analysis of relay and switching circuits. PhD thesis Massachusetts Institute of Technology Dept of Electrical Engineering.
13. Thomas R, D'Ari R (1990) Biological Feedback. Boca Raton, FL: CRC Press Inc.
14. Thomas R (1998) Laws for the dynamics of regulatory networks. Int J Dev Biol 42: 479-485.
15. Chaves M, Eissing T, Allgöwer F (2009) Regulation of Apoptosis via the NFkappaB Pathway: Modeling and Analysis. In: Ganguly N, Deutsch A, Mukherjee A, eds. Dynamics on and of Complex Networks. Boston: Birkhauser. pp 19-33.
16. Calzolari D, Paternostro G, Harrington PL, Piermarocchi C, Duxbury PM (2007) Selective control of the apoptosis signaling network in heterogeneous cell populations. PloS one 2: e547.
17. Zhang R, Shah MV, Yang J, Nyland SB, Liu X, et al. (2008) Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci U S A 105: 16308-16313.
18. Mai Z, Liu H (2009) Boolean network-based analysis of the apoptosis network: Irreversible apoptosis and stable surviving. J Theor Biol 259: 760-769.
19. Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED (2006) A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7: 56.
20. Klamt S, Saez-Rodriguez J, Gilles ED (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 1: 2.
21. Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, et al. (2007) A logical model provides insights into T cell receptor signaling. PLoS Comput Biol 3: e163.
22. Li L, Thomas RM, Suzuki H, De Brabander JK, Wang X, et al. (2004) A small molecule Smac mimic potentiates TRAIL- and TNFalpha-mediated cell death. Science 305: 1471-1474.
23. Wang L, Du F, Wang X (2008) TNF-alpha induces two distinct caspase-8 activation pathways. Cell 133: 693-703.
24. Scaffidi C, Fulda S, Srinivasan A, Friesen C, Li F, et al. (1998) Two CD95 (APO-1/Fas) signaling pathways. EMBO J 17: 1675-1687.
25. Walter D, Schmich K, Vogel S, Pick R, Kaufmann T, et al. (2008) Switch from type II to I Fas/CD95 death signaling on in vitro culturing of primary hepatocytes. Hepatology 48: 1942-1953.
26. Bentele M, Lavrik I, Ulrich M, Stösser S, Heermann DW, et al. (2004) Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J Cell Biol 166: 839-851.
27. Legewie S, Blüthgen N, Herzel H (2006) Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput Biol 2: e120.
28. Callus BA, Moujallad DM, Silke J, Gerl R, Jabbour AM, et al. (2008) Triggering of apoptosis by Puma is determined by the threshold set by prosurvival Bcl-2 family proteins. J Mol Biol 384: 313-323.
29. Lavrik IN, Golks A, Riess D, Bentele M, Eils R, et al. (2007) Analysis of CD95 threshold signaling: triggering of CD95 (FAS/APO-1) at low concentrations primarily results in survival signaling. J Biol Chem 282: 13664-13671.
30. Kreuz S, Siegmund D, Scheurich P, Wajant H (2001) NF-kappaB inducers upregulate cFLIP, a cycloheximide-sensitive inhibitor of death receptor signaling. Mol Cell Biol 21: 3964-3973.
31. Stehlik C, de Martin R, Kumabashiri I, Schmid JA, Binder BR, et al. (1998) Nuclear factor (NF)-kappaB-regulated X-chromosome-linked iap gene expression protects endothelial cells from tumor necrosis factor alpha-induced apoptosis. J Exp Med 188: 211-216.
32. O'Dea EL, Kearns JD, Hoffmann A (2008) UV as an amplifier rather than inducer of NF-kappaB activity. Mol Cell 30: 632-641.
33. Thomas R (1981) On the relation between the logical structure of systems and their ability to generate multiple steady states of sustained oscillations. Springer Series Synergetics 9. pp 180-193.
34. Delbrück M (1949) In Unités biologiques douées de continuité génétique. Editions du Centre National de la Recherche Scientifique Paris. 33-35.
35. Gouzé J (1998) Positive and negative circuits in dynamical systems. J Biol Systems 6: 11-15.
36. Snoussi E (1998) Necessary conditions for multistationarity and stable periodicity. J Biol Systems 6: 3-9.
37. Angeli D, Ferrell JE, Sontag ED (2004) Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci U S A 101: 1822-1827.
38. Brandman O, Meyer T (2008) Feedback loops shape cellular signals in space and time. Science 322: 390-395.
39. Ferrel JJ (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Biology 14: 140-148.
40. Eissing T, Conzelmann H, Gilles ED, Allgöwer F, Bullinger E, et al. (2004) Bistability analyses of a caspase activation model for receptor-induced apoptosis. J Biol Chem 279: 36892-36897.
41. Cheong R, Hoffmann A, Levchenko A (2008) Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol 4: 192.
42. Kearns JD, Basak S, Werner SL, Huang CS, Hoffmann A (2006) IkappaBepsilon provides negative feedback to control NF-kappaB oscillations, signaling dynamics, and inflammatory gene expression. J Cell Biol 173: 659-664.
43. Cowling V, Downward J (2002) Caspase-6 is the direct activator of caspase-8 in the cytochrome c-induced apoptosis pathway: absolute requirement for removal of caspase-6 prodomain. Cell Death Differ 9: 1046-1056.
44. Fujita E, Egashira J, Urase K, Kuida K, Momoi T (2001) Caspase-9 processing by caspase-3 via a feedback amplification loop in vivo. Cell Death Differ 8: 335-344.
45. Vince JE, Wong WWL, Khan N, Feltham R, Chau D, et al. (2007) IAP antagonists target cIAP1 to induce TNFalpha-dependent apoptosis. Cell 131: 682-693.
46. Wu H, Tschopp J, Lin SC (2007) Smac mimetics and TNFalpha: a dangerous liaison? Cell 131: 655-658.
47. Kothny-Wilkes G, Kulms D, Luger TA, Kubin M, Schwarz T (1999) Interleukin-1 protects transformed keratinocytes from tumor necrosis factor-related apoptosis-inducing ligand- and CD95-induced apoptosis but not from ultraviolet radiation-induced apoptosis. J Biol Chem 274: 28916-28921.
48. Gross J, Yellen J (2004) Handbook of graph theory. Boca Raton. FL: CRC Press Inc.
49. Zeigarnik A (2000) On hypercycles and hypercircuits in hypergraphs. In: Hansen P, Fowler P, Zheng M, eds. Discrete Mathematical Chemistry. pp 377-383.
50. Gagneur J, Klamt S (2004) Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5: 175.
51. Klamt S, Gagneur J, von Kamp A (2005) Algorithmic approaches for computing elementary modes in large biochemical reaction networks. Syst Biol (Stevenage) 152: 249-255.
52. Urbanczik R, Wagner C (2005) An improved algorithm for stoichiometric network analysis: theory and applications. Bioinformatics 21: 1203-1210.
53. Devloo V, Hansen P, Labbé M (2003) Identification of all steady states in large networks by logical analysis. Bull Math Biol 65: 1025-1051.
54. Klingmüller U, Bauer A, Bohl S, Nickel PJ, Breitkopf K, et al. (2006) Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways. Syst Biol (Stevenage) 153: 433-447.
55. Schmidt C, Fronza M, Goettert M, Geller F, Luik S, et al. (2009) Biological studies on Brazilian plants used in wound healing. J Ethnopharmacol 122: 523-532.