A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

Abstract

SUMMARY Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells, provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show the metabolic resources in CHO are >3 times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.

Mechanisms driving the lactate switch in Chinese hamster ovary cells

“…Advances such as the sequencing of the CHO cell genome (Xu et al, 2011) and the development of a genome scale metabolic model (Hefzi et al, 2016) mean new enzymes and pathways can be targeted rationally. Advances such as the sequencing of the CHO cell genome (Xu et al, 2011) and the development of a genome scale metabolic model (Hefzi et al, 2016) mean new enzymes and pathways can be targeted rationally.…”

Improvements in protein production in mammalian cells from targeted metabolic engineering

“…This will be accomplished by the development of detailed metabolic pathway and interaction maps of the major cell processes, and identifying the genes associated with the pathways [45, 52]. These metabolic networks can be converted into mathematical models that can guide engineering efforts by quantifying the connection of cellular processes to desired phenotypes and protein production using metabolic flux analysis [44, 45, 53]. Furthermore, these models will allow the analysis and integration of the avalanche of high-throughput data available at the genomic, transcriptomic, proteomic, and metabolomic levels thanks to innovations in these fields [54].…”

Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures

“…For a range of microbial systems and some eukaryotic cell factories, genome‐scale networks have already been configured and can be readily obtained from databases, such as KEGG (kegg.jp), BioCyc Databases (https://biocyc.org), MetaCyc database (https://MetaCyc.org), and BRENDA (https://brenda-enzymes.org). An important development is the recent construction of the first genome‐scale metabolic model for CHO cells (Hefzi et al, ). Commonly used CHO genome‐scale model before 2016 was usually an extrapolation from mouse model and treated as a generic model for mammalian cells (Selvarasu et al, ).…”

“…A new developed genome‐scale CHO model, iCHO1766, contains 1,766 genes and 6,663 reactions involving 4,456 metabolites specifically to CHO cells. Further genome‐scale models specifically featured for CHO‐K, CHO‐S, and CHO‐DG44 were built with the integration of omics data (Hefzi et al, ).…”