Coagulation factor IX analysis in bioreactor cell culture supernatant predicts quality of the purified product

• Published in: Communications biology Vol. 4; no. 1; p. 390
• Main Authors: Zacchi, Lucia F., Roche-Recinos, Dinora, Pegg, Cassandra L., Phung, Toan K., Napoli, Mark, Aitken, Campbell, Sandford, Vanessa, Mahler, Stephen M., Lee, Yih Yean, Schulz, Benjamin L., Howard, Christopher B.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.03.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/475; 631/61/51; 82/58; 82/83; Biology; Biomedical and Life Sciences; Biopharmaceuticals; Bioreactors; Carboxylation; Cell culture; Coagulation; Coagulation factor IX; Coagulation factors; Glycoproteins; Life Sciences; Mass spectroscopy; Post-translation; Protein purification; Proteomics; Quality control; Translation
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-021-01903-x

Coagulation factor IX (FIX) is a complex post-translationally modified human serum glycoprotein and high-value biopharmaceutical. The quality of recombinant FIX (rFIX), especially complete γ-carboxylation, is critical for rFIX clinical efficacy. Bioreactor operating conditions can impact rFIX production and post-translational modifications (PTMs). With the goal of optimizing rFIX production, we developed a suite of Data Independent Acquisition Mass Spectrometry (DIA-MS) proteomics methods and used these to investigate rFIX yield, γ-carboxylation, other PTMs, and host cell proteins during bioreactor culture and after purification. We detail the dynamics of site-specific PTM occupancy and structure on rFIX during production, which correlated with the efficiency of purification and the quality of the purified product. We identified new PTMs in rFIX near the GLA domain which could impact rFIX GLA-dependent purification and function. Our workflows are applicable to other biologics and expression systems, and should aid in the optimization and quality control of upstream and downstream bioprocesses. Zacchi et al. attempt to bridge the gap between understanding the impact of process variables and determination of critical post-translational modifications on a highly complex glycoprotein, factor IX. They implement an LC-MS/MS approach based on data independent acquisition which allows measurement of all detectable peptides, even with heterogeneous modifications.