Uncovering the cell fate decision in lysis-lysogeny transition and stem cell development via Markov state modeling

Understanding the behavior of a complex gene regulatory network is a fundamental but challenging task in systems biology. How to reduce the large number of degrees of freedom of a specific network and identify its main biological pathway is the key issue. In this paper, we utilized the transition path theory (TPT) and Markov state modeling (MSM) framework to numerically study two typical cell fate decision processes: the lysis-lysogeny transition and stem cell development. The application of TPT to the lysis-lysogeny decision-making system reveals that the competitions of CI and Cro dimer binding play the major role in determining the cell fates. We also quantified the transition rates from the lysogeny to lysis state under different conditions. The overall computational results are consistent with biological intuitions but with more detailed information. For the stem cell developmental system, we applied the MSM to reduce the original dynamics to a moderate-size Markov chain. Further spectral analysis showed that the reduced system exhibits nine metastable states, which correspond to the refinement of the five known typical cell types in development. We further investigated the dominant transition pathways corresponding to the cell differentiation, reprogramming, and trans-differentiation. A similar approach can be applied to study other biological systems.