Systems Biology Modeling For The Signaling Pathways Involved In Somitogenesis

Somites are epithelial cell group budding off periodically from the rostral end of thepresocratic mesoderm (PSM). Somitogenesis is the process by which somites form.Somitogenesis is strictly regulated in time and space by which somites can be formed atregular intervals in the right position. If the somitogenesis is disturbed, normal somiteformation will be destroyed which results in abnormal physical growth thereby bringingabout various congenital diseases. Consequently, it is important for ensuring the normaldevelopment of vertebrate bodies as well as the diagnosis and treatment to related diseases toresearch into somitogenesis and then to reveal its regulation mechanisms.Somitogenesis has rhythm in time and it is regulated by a periodic oscillatorysegmentation clock in the PSM. The segmentation clock is formed by the crosstlak of theNotch, Wnt and fibroblast growth factors (FGF) pathways and the oscillatory expression oftheir target genes is essential to normal somite formation. A lot of experiments of molecularbiology proved that there are many periodic expressing genes in the segmentation clock andthere are regulations among these genes. However, it is very difficult to uncover themolecular mechanisms of the oscillatory expression of genes in the segmentation clock insystematic level only through the methods of the biological experiment. In recent years,systems biology modeling methods are widely used in the research on the segmentation clockand some models have been proposed. Unfortunately, most of these models contained onlypart of the signaling pathways in the segmentation clock and the model structures as well asformulae representing biochemical reactions are too simple and abstract. Moreover, the goalof modeling is only to simulate the oscillatory expression of genes. The research findingsabout simulating the signal transduction process of pathways through differential equations,modeling multiple pathways by integrating multi-levels of crosstalk and exploring themechanisms of the oscillatory expression of genes through model analyses are still lacking.In this thesis, first of all, we constructed the mathematical models of the signaltransduction process of the Notch and Wnt pathways in isolation using systems biologymethods. Every biochemical reaction in the signaling pathway, from the activation ofreceptors to the transcription of target genes, is modeled by ordinary differential equations.On that basis, we constructed a crosstalk model by integrating the Notch and Wnt pathwaysthrough introducing three levels of crosstalk between the pathways. These models canaccurately reproduce the oscillatory expression of the target genes in the segmentation clockand the simulation results are in accord with biological experimental findings. The simulationresults indicated that the negative feedback loop centered on Hes7in the Notch pathway and the negative feedback loop centered on Axin2in the Wnt pathway are essential to theoscillation of the target genes in the single pathway. The transcriptional regulation of Wntsignals to the Notch ligand Dll1and the transcriptional repression of the Notch target geneHes7to the Wnt inhibitor Nkd1gene are essential to the oscillation of the target genes in thecrosstalk model. In addition, multiple negative feedback loops in the pathways are alsoessential to the oscillation of the target genes but the mechanisms are different. Among them,the negative feedback loop centered on Lfng gene in the Notch pathway is very important toregulate the oscillatory period of the segmentation clock.On the basis of our previous research, we constructed a comprehensive model of thesegmentation clock that contains the Notch, Wnt and FGF pathways through adding the FGFpathway as well as the regulations among the Notch, Wnt and FGF pathways. The modelsimulated the transcriptional activation of the Wnt and FGF signals to the Hes7gene, thetranscriptional activation of the Wnt signal to the Notch activator Msgn1and thetranscriptional repression of the Notch target gene Hes7to the FGF inhibitor Dusp4for thefirst time. The results of model analyses indicated that the concentration of Wnt and FGFsignals changing from high level to low level along PSM corresponds to the process fromstart to stop of the oscillation of the segmentation clock. Moreover, the stable oscillation ofthe segmentation clock depends not only on the negative feedback loops in the pathways butalso on the reaction parameters related to the regulations among pathways. In addition, thereare many complementary mechanisms in the pathways that ensure the segmentation clock canmaintain stable oscillation under perturbations.In this thesis, we proposed a number of models of the signal transduction pathwaysinvolved in somitogenesis in different level and studied the molecular mechanisms by whichthe target genes in the segmentation clock maintain stable oscillation. These models canprovide guidance for the experimental research on somitogenesis and provide reference forexploring the pathogenesis of the diseases related to somitogenesis.