An omics approach to rational feed

• Published in: Journal of biotechnology 2016-09, Vol.234, p.127-138
• Main Authors: Blondeel, Eric J.M., Ho, Raymond, Schulze, Steffen, Sokolenko, Stanislav, Guillemette, Simon R., Slivac, Igor, Durocher, Yves, Guillemette, J. Guy, McConkey, Brendan J., Chang, David, Aucoin, Marc G.
• Format: Article
• Language: English
• Subjects: 2D-DIGE; CHO cells; Metabolomics; NMR; Proteomics
• ISSN: 0168-1656; 1873-4863
• DOI: 10.1016/j.jbiotec.2016.07.027

•Expression of recombinant proteins exerts resource stresses on cell culture systems.•Between parental cell line and antibody-producing progeny, 34 differentially expressed proteins were identified by 2D-DiGE.•50 nutrients and metabolites tracked by 1D-1H-NMR metabolomics.•Stresses linked to TCA-cycle, THF cofactor conversions, limits to lipid synthesis.•8 nutrients added to medium achieved a ∼75% improvement to peak cell densities. Expression of recombinant proteins exerts stress on cell culture systems, affecting the expression of endogenous proteins, and contributing to the depletion of nutrients and accumulation of waste metabolites. In this work, 2D-DIGE proteomics was employed to analyze differential expression of proteins following stable transfection of a Chinese Hamster Ovary (CHO) cell line to constitutively express a heavy-chain monoclonal antibody. Thirty-four proteins of significant differential expression were identified and cross-referenced with cellular functions and metabolic pathways to identify points of cell stress. Subsequently, 1D-1H NMR metabolomics experiments analyzed cultures to observe nutrient depletion and waste metabolite accumulations to further examine these cell stresses and pathways. From among fifty metabolites tracked in time-course, eight were observed to be completely depleted from the production media, including: glucose, glutamine, proline, serine, cystine, asparagine, choline, and hypoxanthine, while twenty-three excreted metabolites were also observed to accumulate. The differentially expressed proteins, as well as the nutrient depletion and accumulation of these metabolites corresponded with upregulated pathways and cell systems related to anaplerotic TCA-replenishment, NADH/NADPH replenishment, tetrahydrofolate cycle C1 cofactor conversions, limitations to lipid synthesis, and redox modulation. A nutrient cocktail was assembled to improve the growth medium and alleviate these cell stresses to achieve a ∼75% improvement to peak cell densities.