Using machine learning surrogate modeling for faster QSP VP cohort generation.

Virtual patients (VPs) are widely used within quantitative systems pharmacology (QSP) modeling to explore the impact of variability and uncertainty on clinical responses. In one method of generating VPs, parameters are sampled randomly from a distribution, and possible VPs are accepted or rejected based on constraints on model output behavior. This approach works but can be inefficient (i.e., the vast majority of model runs typically do not result in valid VPs). Machine learning surrogate models offer an opportunity to improve the efficiency of VP creation significantly. In this approach, surrogate models are trained using the full QSP model and subsequently used to rapidly pre-screen for parameter combinations that result in feasible VPs. The overwhelming majority of parameter combinations pre-vetted using the surrogate models result in valid VPs when tested in the original QSP model. This tutorial presents this novel workflow and demonstrates how a surrogate model software application can be used to select and optimize the surrogate models in a case study. We then discuss the relative efficiency of the methods and scalability of the proposed method.

T160­phosphorylated CDK2 defines threshold for HGF dependent proliferation in primary hepatocytes.

Liver regeneration is a tightly controlled process mainly achieved by proliferation of usually quiescent hepatocytes. The specific molecular mechanisms ensuring cell division only in response to proliferative signals such as hepatocyte growth factor (HGF) are not fully understood. Here, we combined quantitative time-resolved analysis of primary mouse hepatocyte proliferation at the single cell and at the population level with mathematical modeling. We showed that numerous G1/S transition components are activated upon hepatocyte isolation whereas DNA replication only occurs upon additional HGF stimulation. In response to HGF, Cyclin:CDK complex formation was increased, p21 rather than p27 was regulated, and Rb expression was enhanced. Quantification of protein levels at the restriction point showed an excess of CDK2 over CDK4 and limiting amounts of the transcription factor E2F-1. Analysis with our mathematical model revealed that T160 phosphorylation of CDK2 correlated best with growth factor-dependent proliferation, which we validated experimentally on both the population and the single cell level. In conclusion, we identified CDK2 phosphorylation as a gate-keeping mechanism to maintain hepatocyte quiescence in the absence of HGF.

An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes.

During liver regeneration, quiescent hepatocytes re-enter the cell cycle to proliferate and compensate for lost tissue. Multiple signals including hepatocyte growth factor, epidermal growth factor, tumor necrosis factor α, interleukin-6, insulin and transforming growth factor ß orchestrate these responses and are integrated during the G(1) phase of the cell cycle. To investigate how these inputs influence DNA synthesis as a measure for proliferation, we established a large-scale integrated logical model connecting multiple signaling pathways and the cell cycle. We constructed our model based upon established literature knowledge, and successively improved and validated its structure using hepatocyte-specific literature as well as experimental DNA synthesis data. Model analyses showed that activation of the mitogen-activated protein kinase and phosphatidylinositol 3-kinase pathways was sufficient and necessary for triggering DNA synthesis. In addition, we identified key species in these pathways that mediate DNA replication. Our model predicted oncogenic mutations that were compared with the COSMIC database, and proposed intervention targets to block hepatocyte growth factor-induced DNA synthesis, which we validated experimentally. Our integrative approach demonstrates that, despite the complexity and size of the underlying interlaced network, logical modeling enables an integrative understanding of signaling-controlled proliferation at the cellular level, and thus can provide intervention strategies for distinct perturbation scenarios at various regulatory levels.