Upon tissue loss or damage, the liver engages in a regenerative response where hepatocytes exit their usually quiescent state and proliferate. Multiple signals including HGF, EGF, TNFα, IL-6, Insulin and TGFβ orchestrate progression through this process and are integrated during the G1 phase of the cell cycle. Mathematical models describing signaling pathways or the cell cycle have been developed separately in the past. Integrative studies however are rare due to the complexity of the underlying network.
To cope with this issue, based upon established literature knowledge we built an integrated large-scale logical model that connects signaling events as well as transcriptional and cell cycle regulation in hepatocytes with DNA synthesis as model output. To estimate and improve its quality, distinct model scenarios were compared to hepatocyte-specific literature data. The models’ input/output behavior was validated by measuring induction of DNA synthesis revealing that (i) HGF, EGF, and IL-6 could promote DNA synthesis alone, (ii) TNFα and Insulin only did so in combination, and (iii) TGFβ had priority over any growth signal. Minimal intervention set analysis showed that activation of the PI3K and MAPK pathways was sufficient and necessary for triggering DNA synthesis. The validated model was employed to predict single protein species whose inhibition abrogates HGF-induced DNA replication, and these hypotheses were experimentally confirmed by employing small molecule inhibitors targeting Akt1/2, PI3K, MEK1/2, PDK1, CRM1 and CDK4/6.Our large-scale integrated logical model allows parallel evaluation of various inputs regarding their effect on hepatocyte DNA synthesis and hence represents the in vivo situation, where multiple factors simultaneously influence the process of liver regeneration.