A systems biology approach to DNA damage repair

Abstract

The presence of DNA double-stranded breaks in a mammalian cell typically activates the Non-Homologous End Joining (NHEJ) pathway to repair the damage and signal to downstream systems that govern cellular decisions such as apoptosis or senescence. The signalling system also stimulates effects such as the generation of reactive oxygen species (ROS) which in turn feed back into the damage response. Although the overall process of NHEJ is well documented, and much is known about downstream processes that together constitute the DNA damage response (DDR), we know little of the dynamics and how the system operates as a whole. To further our understanding of this we have constructed computational models which integrate current knowledge of the DNA repair process and key downstream signalling systems. The models are coded in Systems Biology Mark-up Language and BioNetGen Language and are quantified as far as possible with experimental data generated within our own laboratories or otherwise gathered from the literature. They are designed to simulate the observed stochastic dynamics of repair by DNA Protein Kinase (DNA-PK) dependent NHEJ (D-NHEJ) and back-up NHEJ mechanisms (B-NHEJ) following damage induced by gamma irradiation in human fibroblasts and the response this causes in the p53-p21 senescence signalling pathway. We have used the models to investigate a number of issues relevant to the study of ageing cells. Our work suggests that this observed heterogeneity in the repair of DNA damage foci that is influenced by levels of damage cannot be explained solely by inherent stochasticity in the NHEJ system. We find that the presence of multiple repair mechanisms and the modulation of key repair factors by oxidation along with further damage inducing feedback triggered by p53 and changes brought about by cellular processes such as senescence all play a cumulative role in causing the differences between stressed and unstressed cells. Our model highlights the importance of Ku oxidation which leads to increased Ku dissociation rates from DNA damage foci and shifts in favour of the less efficient B-NHEJ system. Furthermore we have utilised the model to investigate the role that various levels of DNA damage and repair have on the maintenance of the important p53 oscillations in a cell. We find that, contrary to the current view, p53 levels are affected by temporal dynamics of DNA damage and have used our model to inform the design of further experimental work to investigate the effect of iii maintained low levels of DNA damage induced by frequent low pulses of γ irradiation on the p53 mediated DDR.