A genome-scale dynamic constraint-based modelling (gDCBM) framework predicts growth dynamics, medium composition and intracellular flux distributions in CHO clonal variations

Abstract

Optimizing mammalian cell growth and bioproduction is a tedious task. However, due to the inherent complexity of eukaryotic cells, heuristic experimental approaches such as, metabolic engineering and bioprocess design, are frequently integrated with mathematical models of cell culture to improve biological process efficiency and find paths for improvement. Constraint-based metabolic models have evolved over the last two decades to be used for dynamic modelling in addition to providing a linear description of steady-state metabolic systems. Formulation and implementation of the underlying optimization problems require special attention to the model's performance and feasibility, lack of defects in the definition of system components, and consideration of optimal alternate solutions, in addition to processing power limitations. Here, the time-resolved dynamics of a genome-scale metabolic network of Chinese hamster ovary (CHO) cell metabolism are shown using a genome-scale dynamic constraint-based modelling framework (gDCBM). The metabolic network was adapted from a reference model of CHO genome-scale metabolic model (GSMM), iCHO_DG44_v1, and dynamic restrictions were imposed to its exchange fluxes based on experimental results. We used this framework for predicting physiological changes in CHO clonal variants. Because of the methodical creation of the components for the flux balance analysis optimization problem and the integration of a switch time, this model can generate sequential predictions of intracellular fluxes during growth and non-growth phases (per hour of culture time) and transparently reveal the shortcomings in such practice. As a result of the differences exploited by various clones, we can understand the relevance of changes in intracellular flux distribution and exometabolomics. The integration of various omics data into the given gDCBM framework, as well as the reductionist analysis of the model, can further help bioprocess optimization.