DECIPHERING THE ROLE OF CLOCK GENES IN OSTEOPOROSIS PATHWAYS USING HYBRID PETRI NET MODELING

Bone remodeling is a tightly regulated process influenced by various cellular mechanisms, including circadian rhythm and autophagy. Circadian rhythm governs multiple physiological processes, including bone remodeling, by modulating key signaling pathways. Similarly, autophagy plays a crucial role in maintaining cellular homeostasis and regulating bone turnover. In this study, we constructed a biological regulatory network to investigate the cross-talk between circadian rhythm and autophagy in bone remodeling. Then, a verified set of parameters was obtained through model checking by modeling biological observations in Computational Tree Logic (CTL). Based on the Biological Regulatory Network (BRN) and the deduced set of parameters, a qualitative model was developed in the GINsim tool. The analysis of the qualitative model shows the cyclic behavior of the circadian rhythm, which does not have a stable state. This model was then exported to Hybrid Petri Net (HPN) for quantitative simulation to investigate the cross-talk between circadian rhythm and autophagy in bone remodeling. The results show that in a normal sleep/wake cycle, Per/Cry and Reverb inhibit osteoclast differentiation, whereas Clock/Bmal inhibits osteoblast differentiation. Moreover, the simulation results predict that dysregulation of Per/Cry, Reverb, Clock/Bmal due to shift work or sleep restriction, changes the expression level of Atgs and Rankl that may lead to bone related disorders. Thus, maintaining a normal circadian rhythm is crucial for bone homeostasis. Furthermore, our results show that Rankl is up-regulated during daytime and down-regulated in night. On the contrary, Atgs are up-regulated at night and down-regulated in the daytime, so time is a crucial factor while considering therapeutic targets. We validated these simulation results on real-time data using statistical z-tests and multiple linear regression, whose outcomes align with the simulation results. In conclusion, this study suggests that factors influencing circadian rhythm, such as adequate sleep, regular sunlight exposure, and balanced diet, play a crucial role in supporting bone homeostasis and are particularly beneficial for patients suffering from osteoporosis.