Dynamic Mechanism For The P53-mediated Cellular Response To DNA Damage

Combining the regulation of gene transcription with signal transduction has been a focus of intensive research.The p53 protein is one of the most important tumor sup-pressors,mediating the cellular response to a multitude of stress signals such as DNA damage and oncogene activation.Constrained by the current technique available,it still remains challenging to reveal the underlying mechanisms of cellular response at the single-cell level.A new paradigm has recently appeared involving building math-ematical models,characterizing the dynamics of cellular processing,and providing an integrative dynamic picture of cellular response.It has proved an important supple-ment to experimental research and increasingly plays a critical role in cell research.This thesis builds p53-centered network models characterizing the cellular DNA dam-age response(DDR),focusing on the mechanism for variability in p53 oscillations and how the TFG-? and p53 pathways are orchestrated to modulate the cell-fate decision.Recently,it has been shown experimentally that upon DNA damage induced by ionizing radiation(IR),the concentration of p53 can undergo sustained oscillations with large variability in amplitude.Its underlying mechanism still remains elusive.Here,we construct a simplified network model,characterizing the activation of ATM and p53,production of Mdm2 and Wip1 and their regulation of ATM and p53 activities.In the deterministic model of the network,ordinary differential equations govern the rates of change in concentrations of network components.We find that the ATM-p53-Wipl negative feedback is indispensable for p53 oscillation,compared with the p53-Mdm2 negative feedback.The system can undergo oscillation in a relatively wide parameter range.It is well known that cells function in a noisy environment.We build a stochastic model of the network based on biochemical reactions therein,and propose a new stochastic simulation algorithm to simulate the evolution of the numbers of molecules.Given the number of p53 during the DDR is on the order of 105,the coefficient of variation(CV)in amplitude for p53 oscillation is rather small when only intrinsic noise is present.There is large noise in gene transcription,and we add colored noise to the basal and maximum transcription rates of genes.Consequently,the CVs rise evidently,and the correlation time and intensity of colored noise play different roles in inducing p53 fluctuations.When cellular heterogeneity,intrinsic noise and extrinsic colored noise are combined together,both the CVs and the histograms for quantities characterizing p53 oscillations agree well with the experimental data.At the cell population level,cellular heterogeneity contributes mostly to p53 variability.Thus,this study clarifies the previous viewpoints and provides a clear picture of fluctuations in p53 oscillation,enriching our understanding of p53 oscillation.TGF-?,secreted in the extracellular matrix layers,often exists in an inactive pre-cursor form.Activated by IR,TGF-,? then specifically binds to the membrane receptor Tf ?-R,which can recruit Smad proteins and transmit signals to the nucleus,affecting the cellular sensitivity to IR.How the TGF-,? and p53 pathways interact to modulate the cellular response is still poorly understood.Here,we propose an integrative net-work model,characterizing the induction and repair of DNA damage,p53 activation,transmission of TFG signaling,and cell-fate decision.The model describes the activa-tion of ATM and p53,induction of Mdm2,Bax,and p21 by p53,release of cytochrome c(Cyt c)from mitochondria to the cytoplasm induced by Bax,Smad2/3 activation,transcription of Smad7 and miR-21 by Smad:Cmplex as well as its role in coactivating Mdm2 and p21,the positive feedback between Cyt c release and Caspas3 activation,and the double-negative feedback between p21 and Caspase3 activation.We find that at low damage levels,p53 can remain in the activated state for some time and induces p21 to arrest the cell cycle,providing time for DNA repair.After the damage is fixed,the cell resumes proliferation.At high damage levels,p53 can be persistently main-tained in the activated state,and apoptosis is induced.Weakening the phosphorylation of Smad2/3,production of miR-21,and transcription of Mdm2 via Smad.Complex can enhance the induction of apoptosis.Therefore,coupling the two pathways improves the modulation of cell fate.Our simulation results are in good agreement with the ex-perimental data,and testable predictions are also made.This study provides a possible mechanism for how inhibiting TGF-? activation can enhance the cellular sensitivity to IR and provides clues to p53-based cancer treatment.The paper is organized as follows.Chapter 1 introduces the related background of biology,basic nonlinear dynamics theory,and stochastic simulation methods.It de-scribes the p53 protein,microRNAs,TGF-? signaling,stability analysis of nonlinear systems,and stochastic simulation algorithms.Chapter 2 explores the effects of net-work feedback loops,intrinsic and extrinsic noise,and cellular heterogeneity on vari-ability in p53 oscillations.Chapter 3 probes how the coupled TGF-? and p53 signaling pathways modulate the cellular response to DNA damage.Chapter 4 summarizes the main results and presents some outlooks for further research.