Genome‐Scale Modeling of CHO Cells Unravel the Critical Role of Asparagine in Cell Culture Feed Media

• Published in: Biotechnology journal 2024-11, Vol.19 (11), p.e202400072-n/a
• Main Authors: Pang, Kuin Tian, Hong, Yi Fan, Shozui, Fumi, Furomitsu, Shunpei, Myint, Matthew, Ho, Ying Swan, Silberberg, Yaron R., Walsh, Ian, Lakshmanan, Meiyappan
• Format: Article
• Language: English
• Subjects: Animals; Asparagine - metabolism; Aspartic Acid - metabolism; Cell Culture Techniques - methods; Chinese hamster ovary (CHO) cells; CHO Cells; Computer Simulation; Cricetinae; Cricetulus; Culture Media - chemistry; enzyme capacity constrained flux balance analysis (ecFBA); genome‐scale model (GEM); Glutamic Acid - metabolism; Glutamine - metabolism; mammalian systems biotechnology; Models, Biological
• ISSN: 1860-6768; 1860-7314; 1860-7314
• DOI: 10.1002/biot.202400072

ABSTRACT Amino acids, including asparagine, aspartate, glutamine, and glutamate, play important roles in purine and pyrimidine biosynthesis as well as serve as anaplerotic sources fueling the tricarboxylic acid (TCA) cycle for mitochondrial energy generation. Despite extensive studies on glutamine and glutamate in CHO cell cultures, the roles of asparagine and aspartate, especially in feed media, remain underexplored. In this study, we utilized a CHO genome scale model to first deeply characterize the intracellular metabolic states of CHO cells cultured in different combinations of basal and feed media to understand the traits of asparagine/aspartate‐dependent and glutamate‐dependent feeds. Subsequently, we identified the critical role of asparagine and aspartate in the feed media as anaplerotic sources and conducted in silico simulations to ascertain their optimal ratios to improve cell culture performance. Finally, based on the model simulations, we reformulated the feed media by tailoring the concentrations of asparagine and aspartate. Our experimental data reveal a CHO cell preference for asparagine compared with aspartate, and thus maintaining an optimal ratio of these amino acids is a key factor for achieving optimal CHO cell culture performance in biopharmaceutical production. Graphical and Lay Summary A genome scale model driven approach is proposed to characterize the CHO cell metabolism during cell culture, identifying the critical role of asparagine and aspartate as anaplerotic sources in cell culture media. Based on this observation, further model simulations were then conducted to determine the optimal ratio of asparagine to aspartate in cell culture media for improved performance. The finalized reformulation with optimal asparagine to aspartate ratio was then validated experimentally, demonstrating the efficacy of computational model‐driven approach for (re)formulating cell culture media.