Discovery of Chemical Tools for Polysorbate-Degradative Enzyme Control in the Biopharmaceutical Upstream Process via Multi-Omic Profiling of Host Cell Clones

Host cell proteins are process-related impurities in
biotherapeutics
and can potentially pose risks to patient safety and product quality.
Specifically, certain host cell–derived enzymes, including
lipases, can degrade the formulation excipient polysorbate (PS) in
biopharmaceutical formulations, affecting drug product stability in
liquid formulations. We leveraged multiomics approaches, including
transcriptomics, proteomics, and activity-based protein profiling
(ABPP), to identify mechanisms that regulate PS-degradative enzyme
(PSDE) abundance and to develop strategies for their control. Comparative
multiomics analysis of two monoclonal antibody (mAb)-producing host
cell clones revealed differential lipase profiles at the mRNA, protein,
and enzyme activity levels and associated increased lipase activity
with upregulated lipid catabolic pathways such as the fatty acid beta
oxidation pathway. Further, for the first time in the literature,
we identified peroxisome proliferator–activated receptor γ
(PPARγ) as a key regulator of PSDEs in manufacturing Chinese
Hamster Ovary (CHO) cells. Downregulation of the PPARγ pathway
with its antagonists resulted in a selective reduction of PSDE levels
and improved PS stability without compromising mAb productivity or
quality. This study highlights the potential of PPARγ modulators
as chemical tools for PSDE control at the gene regulation level, offering
significant implications for biopharmaceutical process development
and control.