title: Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway.
abstract: Mutation and/or dysfunction of signaling proteins in the mitogen activated protein kinase (MAPK) signal transduction pathway are frequently observed in various kinds of human cancer. Consistent with this fact, in the present study, we experimentally observe that the epidermal growth factor (EGF) induced activation profile of MAP kinase signaling is not straightforward dose-dependent in the PC3 prostate cancer cells. To find out what parameters and reactions in the pathway are involved in this departure from the normal dose-dependency, a model-based pathway analysis is performed. The pathway is mathematically modeled with 28 rate equations yielding those many ordinary differential equations (ODE) with kinetic rate constants that have been reported to take random values in the existing literature. This has led to us treating the ODE model of the pathways kinetics as a random differential equations (RDE) system in which the parameters are random variables. We show that our RDE model captures the uncertainty in the kinetic rate constants as seen in the behavior of the experimental data and more importantly, upon simulation, exhibits the abnormal EGF dose-dependency of the activation profile of MAP kinase signaling in PC3 prostate cancer cells. The most likely set of values of the kinetic rate constants obtained from fitting the RDE model into the experimental data is then used in a direct transcription based dynamic optimization method for computing the changes needed in these kinetic rate constant values for the restoration of the normal EGF dose response. The last computation identifies the parameters, i.e., the kinetic rate constants in the RDE model, that are the most sensitive to the change in the EGF dose response behavior in the PC3 prostate cancer cells. The reactions in which these most sensitive parameters participate emerge as candidate drug targets on the signaling pathway.
authors.affiliation: Supercomputer Education and Research Centre, Indian Institute of Science (IISc), Bangalore 560012, India. saswatid@rishi.serc.iisc.ernet.in
authors.forename: Saswati
authors.initials: S
authors.lastname: Dana
authors.forename: Takashi
authors.initials: T
authors.lastname: Nakakuki
authors.forename: Mariko
authors.initials: M
authors.lastname: Hatakeyama
authors.forename: Shuhei
authors.initials: S
authors.lastname: Kimura
authors.forename: Soumyendu
authors.initials: S
authors.lastname: Raha
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D007700:Kinetics; D008024:Ligands; D008297:Male; D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D010766:Phosphorylation; D011467:Prostate / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000378:metabolism*; D015398:Signal Transduction; D014407:Tumor Cells, Cultured
chemical_list: D008024:Ligands; D020928:Mitogen-Activated Protein Kinases