Predictions and Validation of a Model for the Oscillatory Response of P53 to DNA Damage Gustavo Stolovitzky Functional Genomics & Systems Biology, IBM
The tumor suppressor p53 protein is critical to ensure genomic stability when cells are under ionizing radiation (IR) stress. Recently it was observed that single-cell response of p53 to IR is "digital", in that it is number of oscillations (rather than the amplitude) of p53 what shows dependence with the radiation dose. We present a mathematical model of this phenomenon. In our model, double strand break (DSB) sites induced by IR interact with a limiting pool of DNA repair proteins, forming DSB-protein complexes at DNA damage foci. Both the initial number of DSBs and the DNA repair process are modeled taking into account the stochastic nature of the repair process. The model assumes that the persisting complexes are sensed by ataxia telangiectasia mutated (ATM), a kinase with a positive feedback mechanism of autophosphorylation that sensitively transduces the DNA damage information to downstream processes. The ATM sensing module produces a step-like, ON-to-OFF signal as the input to a downstream oscillator consisting of a p53-Mdm2 (Mdm2 is the negative regulator of p53) autoregulatory feedback loop. Our simulation results show that p53 and Mdm2 exhibit a coordinated oscillatory dynamics upon IR stimulation, with a stochastic number of oscillations whose mean increases with IR dosage, in good agreement with the observed response of p53 to DNA-damage in single-cell experiments. The proposed model allows for specific predictions about the range of both p53 and mdm2 transcription rates that support oscillation. At nominal p53 and mdm2 transcription rates, oscillation ensues, but for sufficiently high mdm2, or either low or high p53 levels, oscillation disappears. As a recent report has shown that a single nucleotide polymorphism in the mdm2 gene (SNP309) enhances mdm2 transcription level, the model predicts that in the SNP309 cell line with heighten level of Mdm2, oscillation disappears. To examine the impact of the SNP309 on oscillation, the kinetics of the p53 and Mdm2 levels were measured in cells with different genotype at the SNP309 locus. The results show that the oscillations of p53 and Mdm2 are observed in the cells wild type for mdm2 SNP309 but not in cells homozygous for mdm2 SNP309. By using H1299 cell line expressing wild-type p53 under a tetracycline-regulated promoter, the impact of p53 level on oscillation was tested. We found that only when p53 levels are in a certain range oscillation can be observed, and only after stress. Taken together, our validation results provide support to our model, which predicted that a specific range of the p53 and Mdm2 levels are required for the coordinated p53-Mdm2 oscillation upon stress. A possible physiological use for these oscillations will be discussed. |