(284f) From Ligand Binding to Transcription Activation: Insilico Simulation of Tumor Necrosis Factor-Induced Nuclear Factor Kappa B Activation Using Ibrena Software Package

Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function, including proliferation, differentiation and apoptosis. This cytokine also plays an important role in normal immune response and in controlling the pathogenesis of inflammatory diseases like rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module. Insilico simulation and analysis were performed using a novel software package called: Insilico Biochemical Reaction Network Analysis (IBReNA). The package combines subroutines written in FORTRAN and MATLAB into a stand-alone application. A graphical user interface is provided for dynamical simulation, sensitivity analysis, principal component analysis and singular value decomposition analysis of reaction networks. Simulations of TNF induced signaling performed using this package are validated using experimental data on mRNA levels, protein expression, protein kinase activity and NF-κB transcription function. Sensitivity analysis of reaction network demonstrates how two negative feedback loops in this pathway, due to A20 and IκB, regulate the time dependent oscillatory behavior of nuclear NF-κB. The rate constants regulating the negative feedbacks are observed to have a linear effect on nuclear NF-κB levels during the first oscillation. The sensitivity of NF-κB levels to these rate constants at later oscillations and when NF-κB levels approach steady state is however greater than one. This suggests that signal amplification and damping may be important features regulating TNF mediated cell function. Overall, we demonstrate the successful application of IBReNA and the utility of implemented analysis methods for investigation of complex biochemical signal transduction networks.