Multi-omics analysis reveals the effects of pH on CHO cell bioprocessing

2021_12 Alison Group photo 2
From Left: Dr Alison Lee, Dr Kok Yee Jiun, Dr Meiyappan Lakshmanan and Dr Ho Ying Swan



Chinese hamster ovary (CHO) cells are the most widely used mammalian cell host to produce therapeutic proteins such as monoclonal antibodies. It is important that these therapeutic proteins are of the highest possible product quality. In a typical biomanufacturing process, cells carrying genetic instructions which encode the product of interest are grown in nutrient media inside large stirred-tank bioreactors. High-quality therapeutic proteins can be produced by optimising the process parameters such as pH, temperature, amount of dissolved oxygen, and agitation speed. At present, a comprehensive understanding of the effects of different pH set points on therapeutic protein quality is lacking. To address this, BTI, together with their collaborator, has studied how pH levels can be fine-tuned to further improve the quality of CHO cell therapeutic protein production.


Societal Impact

The impact of bioprocess conditions on product quality profiles has mostly been elucidated by empirical studies. However, investigations on the effects of pH set point are not comprehensive among scientific literature. As a result, regulatory agencies have increasingly encouraged the adoption of the quality by design (QbD) approach to process optimisation and product quality control. The authors have employed a data-driven approach which utilises both systems modelling and untargeted multi-omics data profiling, to effectively identify optimal bioprocess conditions that result in desired product quality attributes (Lakshmanan et al., 2019; Yusufi et al., 2017). The findings from the multi-omics study will provide valuable insights for the refinement of process control strategies.


Technical Summary

The quality profiles of monoclonal antibodies (mAbs) produced by CHO cells are influenced by several cell culture process parameters, including media composition, feeding strategy, pH, temperature and osmolality. pH, a critical parameter that needs to be well-regulated to maintain product quality, has been shown to significantly impact N-glycosylation profiles, aggregation levels and charge variant proportions. However, a comprehensive understanding of how culture pH affects these quality attributes and mAb titre, is currently inadequate.

In this study, the authors set out to apply high-throughput “omics” methodologies to uncover the biological mechanisms in CHO cells that influence process outcomes under different pH set points. The process outcomes include cell-specific productivity, N-glycosylation patterns, charge variants and protein aggregation levels. The authors investigated the effects of culture pH on CHO cell biology and process outcomes by conducting transcriptomics, proteomics and metabolomics time-course analyses of CHO fed-batch cell cultures. Statistical analyses of the multi-omics datasets were conducted to identify specific omics features with expression or abundance levels that correlated with mAb productivity and quality. The analyses revealed how culture pH affects endoplasmic reticulum (ER) homeostasis, N-glycosylation, and the efficiency of vesicle trafficking between the ER and Golgi. This in turn leads to differences in specific productivity, mAb titre and product quality. This multi-omics-based study advances our understanding of cellular processes influenced by culture pH. It can be used as a baseline to improve quality optimization and control strategies of mAb production in CHO cells.


2021_12 Alison Fig 1
Figure 1. Multi-omics data profiling approach to investigate how pH variations affect mAb titre and quality attributes in mAb-producing CHO fed-batch cell cultures.



Lee, A. P., Kok, Y. J., Lakshmanan, M., Leong, D., Zheng, L., Lim, H. L., Chen, S., Mak, S. Y., Ang, K. S., Templeton, N., Salim, T., Wei, X., Gifford, E., Tan, A. H.-M., Bi, X., Ng, S. K., Lee, D.-Y., Ling, W. L. W., Ho, Y. S. (2021) Multi-omics profiling of a CHO cell culture system unravels the effect of culture pH on cell growth, antibody titre, and product quality. Biotechnology and Bioengineering, 118(11), 4305-4316.

Lakshmanan, M., Kok, Y. J., Lee, A. P., Kyriakopoulos, S., Lim, H. L., Teo, G., Poh, S. L., Tang, W. Q., Hong, J., Tan, A. H.‐M., Bi, X., Ho, Y. S., Zhang, P., Ng, S. K., & Lee, D.‐Y. (2019). Multi‐omics profiling of CHO parental hosts reveals cell line‐specific variations in bioprocessing traits. Biotechnology and Bioengineering, 116, 116–2129.

Yusufi, F. N. K., Lakshmanan, M., Ho, Y. S., Loo, B. L. W., Ariyaratne, P., Yang, Y., Ng, S. K., Tan, T. R. M., Yeo, H. C., Lim, H. L., Ng, S. W., Hiu, A. P., Chow, C. P., Wan, C., Chen, S., Teo, G., Song, G., Chin, J. X., Ruan, X., … Lee, D. Y. (2017). Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line. Cell Systems 4, 530–542.e6.