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
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Apoptosis is the programmed cell death
Materials and methods
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The integrated model of apoptosis creation
BioUML - the environment for systems
biology modeling
Optimization plug-in of BioUML
Results
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The integrated model details
Parameters fitting
Apoptosis or programmed cell death
MacFarlane M, Williams AC, EMBO Rep. 2004. 5:674-678
Reactome database:
TRANSPATH database:
http://www.reactome.org/
http://www.gene-regulation.com/
“Can a biologist fix a radio?—Or, what I
learned while studying apoptosis“
Biologist view of a radio
Engineer’s view of a radio
Y Lazebnik (2002),
Cancer Cell, 2(3):
179-182.
Mathematical models of apoptosis
Models
Bentele M, et al
Rangamani P, et al
Hua F, et al
Eissing T, et al
Fussenegger M, et
al
Stucki JW, et al
Legewie S, et al
Schoeberl B, et al
Hoffmann A, et al
Hamada H, et al
Bagci EZ, et al
Year
2004
2007
2005
2004
2000
Pathways
CD95 induced apoptosis
TNF-alpha induced apoptosis
Fas signaling, type II cells
Caspases activation
Caspase-function in apoptosis
2005
2006
2002
2002
2008
2006
Caspase-3 activation
Caspases activation and inhibition
EGF signaling
IkB–NF-kB signaling module
P53 dynamics
Mitochondrial level
Decomposition of the integrated model
• 13 modules
•
•
•
•
5 compartments
286 species
684 reactions
719 parameters
The integrated model overview
EGF-signaling
TRAILsignaling
CD95-signaling
Activation of
effector caspases
by caspase-8
Activation of
effector caspases
by caspase-12
p53module
TNF-α-signaling
NF- κB
activation
Mitochondrial
level
Cytochrome C
module
Apoptosis
execution phase
Smac module
Cleavage of PARP1
by caspase-3, -7
BioUML main features
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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
http://www.biouml.org/
BioUML web
Availability
Web edition:
BMOND database:
http://www.server.biouml.org/webedition
http://www.bmond.biouml.org
Notation
Entities
RNA
Heterodimer
Active monomer
Homodimer
Inactive monomer
Multimer
Phosphorylated protein
Reactions
Binary reaction
Complex reaction
Caspase-8 dynamics after TRAIL stimulation
Virtual experiments
Experimental data
References
Farfan A, et al, 2004
Bentele M, et al, 2004
Lavrik IN, et al, 2007
Janes KA, et al, 2006
Hua F, et al, 2005
Neumann L, et al, 2010
Sprick MR, et al, 2002
Scaffidi C, et al, 1998
Cell lines
Jurkat
SKW 6.4
SKW 6.4
HT29
Jurkat
HeLa
T cells
CEM
Apoptosis
inducers
TRAIL
anti-APO-1
anti-APO-1
TNF
CD95L
anti-CD95
CD95L
anti-APO-1
Optimization plug-in
Optimization plug-in
Optimization plug-in
Optimization plug-in
Main features
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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
Method
Evolutionary
Programming
Particle swarm
BioUML
(4 cores)
–
7,1 sec
7,7 sec
6,9 sec
(10,000 simulations)
BioUML
(1 core)
–
COPASI
(1 core)
1 min 58,2sec
1 min 31,3 sec
1 min 16,6 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
7,5 sec
Ranking Evolution 7,47 sec
Strategy
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
25,5 sec
22,1 sec
20,8 sec
7,7 sec
7,5 sec
7,2 sec
–
Multi-experiments fitting
Multi-experiments fitting
Analysis diagram
Experimental data tables
Optimization document
Fitted parameter values
for two estimations
Simulation results for all experiments
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-κB*
Upregulation of NF-κB 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
Hua F, 2005
Neumann L, 2010
Scaffidi C, 1998
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
100 ng/ml of TNF-α
5 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
Vilimanovich, et al, LN-71 cells
Vilimanovich, et al, U343MG cells
Farfan, et al, Jurkat cells
Conclusions
TRAILsignaling
EGF-signaling
CD95-signaling
Activation of
effector caspases
by caspase-8
Activation of
effector caspases
by caspase-12
p53module
TNF-α-signaling
NF- κB
activation
Mitochondrial
level
Cytochrome C
module
Apoptosis
execution phase
Smac module
Cleavage of PARP1
by caspase-3, -7
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:
http://www.biouml.org
http://www.server.biouml.org/webedition
http://www.bmond.biouml.org
Acknowledgements
Part of this work was partially supported by the grant:
European Committee grant №037590 “Net2Drug”
European Committee grant №202272 “LipidomicNet”
BioUML author:
Fedor Kolpakov
Useful comments, discussions and technical support:
Alexander Kel and Sergey Zhatchenko
Software developers
Nikita Tolstyh
Alexey Shadrin
Elena Kutumova
Tatyana Leonova
Ilya Kiselev
Mikhail Puzanov
Annotator
Ruslan Sharipov
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Experimental data of Bentele M et al
(CD95L concentration – 79.6 nM)
Time
(min)
p43 (p43/p41)
p55 (pro-8)
p18 (casp-8)
BLU
%
BLU
%
BLU
%
0
1
1
4405
100
0
0
5
16
18
4312
98
0
0
10
19
21
3123
71
0
0
20
34
38
3440
78
7
3
30
38
43
3580
81
4
2
60
55
62
2930
67
50
21
120
206
231
2340
53
387
163
180
151
170
1465
33
471
198
240
89
100
927
21
238
100
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Experimental data of Hua F et al
(CD95L concentration – 2 nM)
Time (h)
0.5
1
1.5
2
3
4
5
6
7
8
procaspase-8 ( S.E.)
1
0,768717209793586
0,773312261257627
0,508999000649146
0,337764699869925
0,285381219211975
0,18596448144249
0,177879408426172
0,189180280994578
0,239456408757187
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Experimental data of Janes KA, et al
Time
(h)
0
0.083
0.25
0.5
1
1.5
2
4
8
12
16
20
24
Untreated cells
pro-8 casp-8
100
2
89
23
110
33
101
1
103
7
117
38
102
36
108
44
127
63
143
46
140
60
128
92
151
100
TNF (100 ng/ml)
pro-8
casp-8
100
0
159
0
174
0
184
0
173
2
151
1
200
7
145
13
135
72
131
90
132
92
123
98
99
100
TNF (5 ng/ml)
pro-8
casp-8
100
7
92
7
98
13
105
13
118
19
130
20
127
14
75
12
89
23
84
42
85
58
89
76
91
100