Towards abstraction of computational modelling of mammalian cell cycle: Model reduction pipeline incorporating multi-level hybrid petri nets. (7th July 2020)

• Record Type: Journal Article
• Authors: Abroudi, Ali; Samarasinghe, Sandhya; Kulasiri, Don
• Is Part Of: Journal of theoretical biology. Volume 496(2020)
• Publication Date: 2020-07-07
• Subjects: Complex systems -- Computational systems biology -- Model reduction -- Mammalian cell cycle -- Hybrid petri nets -- DNA damage -- Checkpoint efficiency -- Robustness; Biology -- Periodicals; Biological Science Disciplines -- Periodicals; Biology -- Periodicals; Biologie -- Périodiques; Theoretische biologie; Biology; Periodicals; 571.05
• DOI: 10.1016/j.jtbi.2020.110212
• Languages: English
• ISSNs: 0022-5193

Abstract

Highlights: Presents an abstraction of a minimalist yet comprehensive model of mammalian cell cycle controller system from a full ODE cell cycle model using an advanced petri nets (PN) approach which is intuitive, transparent and easy to understand and analyse. Contributes a new hybrid petri net model for mammalian cell cycle as well as a model abstraction pipeline. The PN model was based on the significant parameters/elements found from the original ODE full model of cell cycle. The proposed model is hybrid (discrete and continuous), hierarchical (high-level and low level representation of elements) and temporal (Stage level representing cell cycle stages). The model is based on Cyc-Cdk complexes as drivers at high level representation and it retains the concepts of interacting sub-systems in the original model and the system dynamics of the PN model including response to parameter perturbations closely approximates the original model. DNA damage checkpoint efficiency of the PN model is also similar to the original model. The PN model captures cell cycle response in a compact model of 14 elements and 31 parameters (containing 4 ODEs and rules for 10 discrete variables) compared to 61 ODEs and 148 parameters in the full model. Abstract: Cell cycle is a large biochemical network and it is crucial to simplify it to gain a clearer understanding and insights into the cell cycle. This is also true for other biochemical networks. In this study, we present a model abstraction scheme/pipeline to create a minimal abstract model of the whole mammalian cell cycle system from a large Ordinary Differential Equation model of cell cycle we published previously (Abroudi et al., 2017). The abstract model is developed in a way that it captures the main characteristics (dynamics of key controllers), responses (G1-S and G2-M transitions and DNA damage) and the signalling subsystems (Growth Factor, G1-S and G2-M checkpoints, and DNA damage) of the original model (benchmark). Further, our model exploits: (i) separation of time scales (slow and fast reactions), (ii) separation of levels of complexity (high-level and low-level interactions), (iii) cell-cycle stages (temporality), (iv) functional subsystems (as mentioned above), and (v) represents the whole cell cycle - within a Multi-Level Hybrid Petri Net (MLHPN) framework. Although hybrid Petri Nets is not new, the abstraction of interactions and timing we introduced here is new to cell cycle and Petri Nets. Importantly, our models builds on the significant elements, representing the core cell cycle system, found through a novel Global Sensitivity Analysis on the benchmark model, using Self Organising Maps and Correlation Analysis that we introduced in (Abroudi et al., 2017). Taken the two aspects together, our study proposes a 2-stage model reduction pipeline for large systems and the main focus of this paper is on stage 2, Petri Net model, put in the context of the pipeline. With the MLHPN model, the benchmark model with 61 continuous variables (ODEs) and 148 parameters were reduced to 14 variables (4 continuous (Cyc_Cdks - the main controllers of cell cycle) and 10 discrete (regulators of Cyc_Cdks)) and 31 parameters. Additional 9 discrete elements represented the temporal progression of cell cycle. Systems dynamics simulation results of the MLHPN model were in close agreement with the benchmark model with respect to the crucial metrics selected for comparison: order and pattern of Cyc_Cdk activation, timing of G1-S and G2-M transitions with or without DNA damage, efficiency of the two cell cycle checkpoints in arresting damaged cells and passing healthy cells, and response to two types of global parameter perturbations. The results show that the MLHPN provides a close approximation to the comprehensive benchmark model in robustly representing systems dynamics and emergent properties while presenting the core cell cycle controller in an intuitive, transparent and subsystems format.