Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells

Abstract

10Genome-scale metabolic models describe cellular metabolism with mechanistic detail. 11Given their high complexity, such models need to be parameterized correctly to yield 12 accurate predictions and avoid overfitting. Effective parameterization has been well-13 studied for microbial models, but it remains unclear for higher eukaryotes, including 14 mammalian cells. To address this, we enumerated model parameters that describe key 15 features of cultured mammalian cells -including cellular composition, bioprocess 16 performance metrics, mammalian-specific pathways, and biological assumptions behind 17 model formulation approaches. We tested these parameters by building thousands of 18 metabolic models and evaluating their ability to predict the growth rates of a panel of 19 phenotypically diverse Chinese Hamster Ovary cell clones. We found the following 20 considerations to be most critical for accurate parameterization: (1) cells limit metabolic 21 activity to maintain homeostasis, (2) cell morphology and viability change dynamically 22 during a growth curve, and (3) cellular biomass has a particular macromolecular 23 composition. Depending on parameterization, models predicted different metabolic 24 phenotypes, including contrasting mechanisms of nutrient utilization and energy 25 generation, leading to varying accuracies of growth rate predictions. Notably, accurate 26 parameter values broadly agreed with experimental measurements. These insights will 27 guide future investigations of mammalian metabolism. 28

Error propagation in constraint‐based modeling of Chinese hamster ovary cells

“…These results are specific to the use of biomass objective function. Schinn et al [34] reported that the objective function has a big impact on the prediction accuracy and the biomass objective function was correlated with poor predictions. A suggested alternative was minimization of cytosolic NADPH regeneration, which was correlated with good predictions.…”

A genome‐scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures

“…We used a previously described metabolic network model that is tailored to the investigated CHO clones (Schinn et al, 2020). Experimental measurements for clone and culture day were used to constrain model reactions for biomass production, monoclonal antibody secretion and consumption of glucose, lactate, glutamate, and glutamine.…”

“…We used a previously described metabolic network model that is tailored to the investigated CHO clones (Schinn et al, 2020). Experimental et al, 2014) and COBRApy (Ebrahim et al, 2013).…”

A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures

“…We sought to predict these diverse consumption behaviors using a tailored model of CHO metabolism (Schinn et al, 2020). As input information, we utilized the following routinely measured industrial bioprocess data: (1) viable cell density and titer measurements, from which growth rate and specific productivity are calculated (Methods, equation 1), and (2) bioreactor concentrations of glucose, lactate, glutamate and glutamine, from which their respective consumption rates are calculated.…”