Chinese Hamster Ovary (CHO) cells are cell factories for a variety of pharmaceutical outputs, namely monoclonal antibody production and biotherapeutics. Having been utilised for the synthesis of biological compounds for over a century, CHO cells facilitate a wide range of post-translational modifications, including glycosylation, making them a popular choice for human drug development. Furthermore, CHO cells can tolerate shifts in their culture conditions, such as pH, oxygen levels, temperature and cell density. These characteristics can be predicted and explained using constraint-based modelling, which through the integration of ‘omics data, invites the simulation of changing environmental conditions favouring improved productivity.
Here, the recently published iCHO2441 genome-scale model (GEM) (Strain et al, 2023) has been modified to closely match a specific cell line used for production by FUJIFILM Diosynth Biotechnologies (FDB), as part of our industry partnership. A wealth of time-course ‘omics data (transcriptomics, proteomics and metabolomics) has been generated to enable constraint-based modelling and provide opportunities for creative model inputs and validations. Initial work has seen the flux sampling of models constrained using transcriptomics data to represent specific time points over a two-week culture period. Flux sampling for bioengineering is a novel approach, and here we have used it in conjunction with both unsupervised and supervised methods to identify metabolic signatures of low- and high-producing cell lines. Results from this analysis suggested a range of metabolic subsystems associated with high productivity, including bile, eicosanoid and steroid metabolism, fatty acid metabolism and vitamin metabolism, amongst others. Furthermore, we have used these models as a framework for media simulations, to validate predictions against experimental metabolite uptake rates, production rates and growth measurements. From here we have been able to begin predicting media supplements which could favour high productivity.
Results generated here could have exciting implications for bioengineering, expanding our knowledge of CHO cell metabolism and pathways underlying recombinant protein production. In addition, we are developing a workflow involving more unconventional ‘omics constraints and the interpretation of complex flux sampling results. This project could be translated to other bioengineering systems and our simulations aim to maximise the efficiency, cost-effectiveness and predictive potential of sample-specific constraint-based models.

Strain, B. et al. (2023) ‘How reliable are Chinese hamster ovary (CHO) cell genome-scale metabolic models?’, Biotechnology and Bioengineering [Preprint]. Available at: https://doi.org/10.1002/bit.28366.