The integrated model of apoptosis EO Kutumova, RN Sharipov, IN Lavrik, FA Kolpakov Design Technological Institute of Digital Techniques SB RAS, Institute of Systems Biology, Institute of Cytology and Genetics SB RAS, German Cancer Research Center (DKFZ) Novosibirsk, Russia

Presentation items Apoptosis is the programmed cell death Materials and methods  The integrated model of apoptosis creation  BioUML - the environment for systems biology modeling  Optimization plug-in of BioUML Results  The integrated model details  Parameters fitting

Apoptosis or programmed cell death MacFarlane M, Williams AC, EMBO Rep : Reactome database: TRANSPATH database:

“Can a biologist fix a radio?—Or, what I learned while studying apoptosis“ Y Lazebnik (2002), Cancer Cell, 2(3): Biologist view of a radio Engineer’s view of a radio

Mathematical models of apoptosis ModelsYearPathways Bentele M, et al2004CD95 induced apoptosis Rangamani P, et al 2007 TNF-alpha induced apoptosis Hua F, et al 2005Fas signaling, type II cells Eissing T, et al2004 Caspases activation Fussenegger M, et al 2000Caspase-function in apoptosis Stucki JW, et al 2005 Caspase-3 activation Legewie S, et al 2006Caspases activation and inhibition Schoeberl B, et al2002 EGF signaling Hoffmann A, et al2002IkB–NF-kB signaling module Hamada H, et al2008 P53 dynamics Bagci EZ, et al2006Mitochondrial level

Decomposition of the integrated model 13 modules 5 compartments 286 species 684 reactions 719 parameters

TRAIL- signaling CD95-signaling TNF-α-signaling Mitochondrial level Activation of effector caspases by caspase-8 Apoptosis execution phase Cleavage of PARP1 by caspase-3, -7 EGF-signaling p53- module Cytochrome C module NF- κB activation Smac module The integrated model overview Activation of effector caspases by caspase-12

BioUML main features Supports access to main biological databases:  catalolgs: Ensembl, UniProt, ChEBI, GO…  pathways: KEGG, Reactome, EHMN, BioModels, SABIO-RK, TRANSPATH, EndoNet, BMOND… Supports main standards used in systems biology: SBML, SBGN, CellML, BioPAX, OBO, PSI-MI… Database search and graph search Visual modeling Data analysis

BioUML workbench

BioUML web Availability Web edition: BMOND database:

Notation RNA Active monomer Inactive monomer Phosphorylated protein Heterodimer Homodimer Multimer Binary reaction Complex reaction Entities Reactions

Caspase-8 dynamics after TRAIL stimulation

Virtual experiments

Experimental data ReferencesCell lines Apoptosis inducers Farfan A, et al, 2004JurkatTRAIL Bentele M, et al, 2004SKW 6.4anti-APO-1 Lavrik IN, et al, 2007SKW 6.4anti-APO-1 Janes KA, et al, 2006HT29TNF Hua F, et al, 2005JurkatCD95L Neumann L, et al, 2010HeLaanti-CD95 Sprick MR, et al, 2002T cells CD95L Scaffidi C, et al, 1998CEManti-APO-1

Optimization plug-in

Main features Diagram parameters estimation Experimental data – time courses or steady states expressed as exact or relative values of substance concentrations Different optimization methods for analysis Multi-experiments optimization Constraint optimization Local/global parameters Parameters optimization using java script

Comparison with COPASI (10,000 simulations) MethodBioUML (4 cores) BioUML (1 core) COPASI (1 core) Evolutionary Programming –– 1 min 58,2sec 1 min 31,3 sec 1 min 16,6 sec Particle swarm7,1 sec 7,7 sec 6,9 sec 22,4 sec 15,3 sec 22,5 sec 1 min 32 sec 1 min 26,4 sec 1 min 07,1 sec Stochastic Ranking Evolution Strategy 7,5 sec 7,47 sec 6,9 sec 23,4 sec 23,5 sec 22,2 sec 1 min 25,0 sec 1 min 5,6 sec 1 min 8,8 sec Cellular genetic algorithm 7,7 sec 7,5 sec 7,2 sec 25,5 sec 22,1 sec 20,8 sec –

Multi-experiments fitting

Analysis diagram Experimental data tables Simulation results for all experiments Optimization document Fitted parameter values for two estimations

Java script for the optimization analysis

Results

Statistics 13 modules 5 compartments 286 species 684 reactions 719 parameters

TRAIL module (BMOND ID: Int_TRAIL signaling) Albeck JG, et al: PLoS Biol 2008 Additions: Trimerization of the TRAIL:TRAIL-R complex with subsequent binding by FADD Procaspase-10 activation pathway Reactions of degradation of FLIP long and FLIP short, casp-8 and casp-10

CD95 module (BMOND ID: Int_CD95 signaling) Bentele M, et al: The Journal of Cell Biology 2004 Additions: Trimerization of the CD95:CD95L complex Procaspase-10 activation pathway Reactions of degradation of FLIP long and FLIP short, casp-8 and casp-10

TNF-α module (BMOND ID: Int_TNF signaling) Rangamani P & Sirovich L: Biotechnology and Bioengineering 2007, Cho K-H, et al: Genome research 2003 Additions: Downregulation of FLIP by FOXO3a* Deactivation of FOXO3a by Akt-PP* Synthesis of procaspase-8 and its processing to the active form under the influence of IFN-gamma** *Kim H-S, et al: The FASEB Journal 2005 **Ossina NK, et al: J Biol Chem 1997

p53 module (BMOND ID: Int_p53 pathway) Hamada H, et al: PLoS One 2008 Additions: Upregulation of mdm- 2 by Akt-PP * * Gottlieb TM, et al: Oncogene 2002

NF-κB module (BMOND ID: Int_NF-κB module) Hoffmann A, et al: Science 2002 Werner SL, et al: Science 2005 Cheong R, et al: J Biol Chem 2006 Kearns JD, et al: J Cell Biol 2006 O’Dea EL, et al:Mol Syst Biol 2007 Additions: Regulation of cIAP by NF- κ B* Upregulation of NF- κ B by Akt-PP and ERK-PP** * Salvesen GS, Duckett CS: Nat Rev Mol Cell Biol 2002 ** Meng F, et al: J Biol Chem 2002

EGF module ( BMOND ID: Int_EGF signaling) Schoeberl B, et al: Nature Biotechnology 2002 Borisov N, et al: Molecular Systems Biology 2009 Additions: Reactions of protein syntheses and degradations

Mitochondria module (BMOND ID: Int_mitochondria) Bagci EZ, et al, Biophysical J 2006 Albeck JG, et al, PLoS Biol 2008 Additions: Activation of CREB and deactivation of BAD by Akt-PP and ERK-PP Upregulation of Bcl-2 by CREB Bcl-2 suppression by p53

Cytochrome C module (BMOND ID: Int_Cyt C response) Bagci EZ, et al, Biophysical Journal 2006 Legewie S, et al, PLoS Computational Biology 2006

SMAC module ( BMOND ID: Int_Smac response) Salvesen GS, Duckett CS: Nat Rev Mol Cell Biol 2002

Type I cells module ( BMOND ID: Int_type I cells) Bentele M, et al: The Journal of Cell Biology 2004

Caspase-12 module (BMOND ID: Int_casp-12 response) Fan T-Y, et al: Acta Biochimica et Biophysica Sinica 2005

PARP module ( BMOND ID: Int_PARP cleavage ) Bentele M, et al: The Journal of Cell Biology 2004 Albeck JG, et al: PLoS Biol 2008

Apoptosis execution phase module ( BMOND ID : Int_execution phase ) Fan T-Y, et al: Acta Biochimica et Biophysica Sinica 2005

Fitting results

Experimental data for the CD95 module was found in the papers: Neumann L, et al: Molecular Systems Biology, 2010 Bentele M, et al: The Journal of Cell Biology, 2004 Hua F, et al: The Journal of Immunology, 2005 Scaffidi C, et al: The EMBO Journal, 1998

Fitting results for the CD95L module Bentele M, 2004 Neumann L, 2010Scaffidi C, 1998 Hua F, 2005

Fitting of the TNF module parameters was based on the experimental data of Janes KA et al Janes KA, et al: Cell 2006

Fitting results for the TNF-α module Untreated cells 5 ng/ml of TNF-α 100 ng/ml of TNF-α

TRAIL module fitting Farfan A, et al: Cell Notes, 2004 Vilimanovich U and Bumbasirevic V: Cell. Mol. Life Sci., 2008

Fitting results for the TRAIL module Farfan, et al, Jurkat cellsVilimanovich, et al, LN-71 cells Vilimanovich, et al, U343MG cells

TRAIL- signaling CD95-signaling TNF-α-signaling Mitochondrial level Activation of effector caspases by caspase-8 Activation of effector caspases by caspase-12 Apoptosis execution phase Cleavage of PARP1 by caspase-3, -7 EGF-signaling p53- module Cytochrome C module NF- κB activation Smac module Conclusions

The integrated model of apoptosis is one of the most complex models existing at the moment. Modular representation for apoptosis models have never seen before. Effective optimization plug-in allowing to parallelize calculations was developed for the model parameters estimation. Availability: BioUML Home page: Web edition: BMOND database:

Acknowledgements Part of this work was partially supported by the grant: European Committee grant № “Net2Drug” European Committee grant № “LipidomicNet” BioUML author: Fedor Kolpakov Useful comments, discussions and technical support: Alexander Kel and Sergey Zhatchenko Software developers Annotator Nikita TolstyhAlexey Shadrin Ruslan Sharipov Elena KutumovaTatyana Leonova Ilya KiselevMikhail Puzanov

Experimental data of Bentele M et al (CD95L concentration – 79.6 nM) Time (min) p43 (p43/p41)p55 (pro-8)p18 (casp-8) BLU% % %

Experimental data of Hua F et al (CD95L concentration – 2 nM) Time (h)procaspase-8 ( S.E.) , , , , , , , , ,

Experimental data of Janes KA, et al Time (h) Untreated cells TNF (100 ng/ml) TNF (5 ng/ml) pro-8 casp-8 pro-8casp-8pro-8casp