Decades of bioprocess optimization have resulted in substantial improvements in CHO-based recombinant protein production. However, some proteins remain difficult to express, and there is a need for improved control of critical quality attributes of biopharmaceuticals. To enable cell engineering efforts to enhance protein production and control product quality, we have sequenced the genomes of the Chinese hamster and several cell lines, and used these to develop a genome-scale metabolic network reconstruction for CHO. Using these models, which account for the activities of ~1700 genes, we have approached questions relevant to bioprocessing and guided cell engineering efforts. First, 59 years ago, CHO cells were derived from a single hamster, and over the decades numerous mutants have been obtained and propagated. We recently sequenced CHO cells from three main lineages and identified millions of mutations. Using these data, along with transcriptomic, proteomic and metabolomic data, we have constructed metabolic network models for different CHO cell lines (e.g., CHO-K1, CHO-S, etc.) and demonstrate unique metabolic characteristics and capabilities of different CHO cell lines, thus potentially aiding in cell line selection. Second, several bioprocess treatments have increased CHO cell specific productivity, but the yields still pale in comparison to professional secretory cells. Have these bioprocess treatments maximized specific productivity? Using our cell-line specific models we demonstrate that while common bioprocess treatments, such as NaBu and decreased temperature increase the titers, they do so inefficiently. However, by engineering apoptosis and the secretory system, targeted cell engineering efforts allow for specific productivities much closer to the theoretical maximum. In summary, the genome-scale model serves as valuable platforms for data analysis and simulation, and is providing insights into the molecular basis of various bioprocess phenotypes and guiding cell engineering efforts.

Guiding CHO cell engineering for biopharmaceutical development using genome-scale models of CHO cell metabolism

251st National Meeting (2016)

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