Analysis of inhibition of HER2 signaling to apoptotic transcription factors Marc Fink & Yan Liu & Shangying Wang Student Project Proposal Computational Cell Biology 2012

Goals Modeling the signaling pathway of HER2 inhibitor, Lapatinib, in Breast Cancer Cells Analyze the influence factors of cell apoptosis Explanation of cell survival rate after treatment

Outline Brief review Boolean network model and results Modeling with ODEs in VCell and COPASI Analysis of simulation results Summary and outlook

Mechanistic (process) diagrams Death Lapatinib ?????? HER2 Survival PI3K PDK1 p AKT (PKB) Protein Translation p ER FoxO p FoxO p 14-3-3 Translocation Translocation Transcription FoxO FoxO Apoptotic genes Apoptosis FoxO FoxO Survival genes 01/13

Flow chart and strategies Lapatinib HER2 IGF1R FASL AKT FoxO apoptosis RAF MEK ERK RSK BAD BIM Lack of experimental parameters => Boolean network Better understanding of dynamics => ODEs Analysis of survival rate => Stochastic simulation 02/13

Boolean network model HER2 AKT FoxO apoptosis BIM Lapatinib IGF1R Apoptosis Time steps => Average value of apoptosis is around 0.5 with simplification. 03/13

Boolean network model HER2 FASL AKT FoxO apoptosis BIM Lapatinib IGF1R Apoptosis Time steps => Average apoptosis is around 0.6 with additional information. 03/13

Boolean network model HER2 FASL AKT FoxO apoptosis RAF MEK ERK RSK BAD BIM Lapatinib IGF1R Apoptosis Time steps => Results depend on the complexity, adding weights not possible. 03/13

Modeling with ODEs => 22 species and 32 reactions, reasonable rates???!!! 04/13

Model reduction and modification Due to the importance of FOXO => Neglect the downstream and add the self regulation 05/13

Model reduction and modification Lapatinib HER2 IGF1R FASL AKT FoxO apoptosis RAF MEK ERK RSK BAD BIM 05/13

Model reduction and modification Due to the importance of FOXO => Neglect the downstream and add the self regulation AKT HER2_dimer HER2_dimer* PI3K H_PI3K PIP2 PIP3 AKT* Lapatinib HER2 AKT FoxO Apoptosis FoxO_gene FoxO_mRNA (x) FoxO (y) FoxO* (z) Φ

Model reduction and modification Due to the importance of FOXO => Neglect the downstream and add the self regulation AKT HER2_dimer HER2_dimer* PI3K H_PI3K PIP2 PIP3 AKT* Lapatinib HER2 AKT FoxO [Birtwistle et al., 2007] Apoptosis FoxO_gene FoxO_mRNA (x) FoxO (y) FoxO* (z) Φ

Self regulation of FOXO FoxO_gene FoxO_mRNA (x) FoxO (y) FoxO* (z) Φ => Bistability of the positive feedback loop 06/13

Modified model => 14 species and 16 reactions 07/13

Sensitivity analysis in COPASI Binding of Laptinib to HER2 Dimerization of HER2 FOXO => Laptinib is important for cancer cell apoptosis 08/13

Analysis of simulation results Deterministic simulations with parameter scan (Laptinib) FOXO concentration With increasing initial Laptinib concentration 0 -> 400 nM 09/13

Analysis of simulation results Deterministic simulations with parameter scan (Laptinib) Phosphorylation => Laptinib is able to stimulate FOXO, crucial to apoptosis 09/13

Analysis of simulation results Random initial concentrations and constant Laptinib (200nM) FOXO concentration => Initial concentrations influence the effect of Laptinib. 10/13

Analysis of simulation results Stochastic simulation using Gillespie algorithm (in VCell & C) High Laptinib Low Laptinib 11/13

Summary and outlook Inhibition of HER2 signaling to apoptotic transcription factors is studied. Models with different complexities are analyzed. Laptinib induced inhibition of HER2 is simulated. Outlook Improve the stochastic study Improve the pathway model with more details by getting more rates from experiments Measurement of concentrations within small time scale before and after treatment will help to understand the whole signaling process and validate the model. 12/13

Experience with the softwares COPASI vs VCell Writing reactions + +++ Checking parameters + +++ Deterministic simulation +++ + Stochastic simulation ++ + Parameter scan +++ ++ Sensitivity analysis +++ - Visualization - +++ 13/13

Happy Birthday to Nina!