Methods Matter: Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors

• Published in: Molecular therapy. Methods & clinical development Vol. 18; pp. 98 - 118
• Main Authors: Rumachik, Neil G., Malaker, Stacy A., Poweleit, Nicole, Maynard, Lucy H., Adams, Christopher M., Leib, Ryan D., Cirolia, Giana, Thomas, Dennis, Stamnes, Susan, Holt, Kathleen, Sinn, Patrick, May, Andrew P., Paulk, Nicole K.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 11.09.2020; American Society of Gene & Cell Therapy; Elsevier
• Subjects: AAV; adeno-associated virus; baculovirus-Sf9; capsid; human; mass spectrometry; methylation; Original; post-translational modification; potency; PTM; potency; AAV; methylation; baculovirus-Sf9; capsid; PTM; mass spectrometry; adeno-associated virus; post-translational modification; human
• ISSN: 2329-0501; 2329-0501
• DOI: 10.1016/j.omtm.2020.05.018

Different approaches are used in the production of recombinant adeno-associated virus (rAAV). The two leading approaches are transiently transfected human HEK293 cells and live baculovirus infection of Spodoptera frugiperda (Sf9) insect cells. Unexplained differences in vector performance have been seen clinically and preclinically. Thus, we performed a controlled comparative production analysis varying only the host cell species but maintaining all other parameters. We characterized differences with multiple analytical approaches: proteomic profiling by mass spectrometry, isoelectric focusing, cryo-EM (transmission electron cryomicroscopy), denaturation assays, genomic and epigenomic sequencing of packaged genomes, human cytokine profiling, and functional transduction assessments in vitro and in vivo, including in humanized liver mice. Using these approaches, we have made two major discoveries: (1) rAAV capsids have post-translational modifications (PTMs), including glycosylation, acetylation, phosphorylation, and methylation, and these differ between platforms; and (2) rAAV genomes are methylated during production, and these are also differentially deposited between platforms. Our data show that host cell protein impurities differ between platforms and can have their own PTMs, including potentially immunogenic N-linked glycans. Human-produced rAAVs are more potent than baculovirus-Sf9 vectors in various cell types in vitro (p < 0.05–0.0001), in various mouse tissues in vivo (p < 0.03–0.0001), and in human liver in vivo (p < 0.005). These differences may have clinical implications for rAAV receptor binding, trafficking, expression kinetics, expression durability, vector immunogenicity, as well as cost considerations. [Display omitted] Paulk and colleagues performed an unbiased comparative characterization of rAAV manufactured by transient transfection of HEK293 or baculoviral infection of insect cells. They discovered that rAAV capsids have post-translational modifications, including glycosylation, acetylation, phosphorylation, and methylation, and these differ between platforms. Additionally, rAAV genomes are differentially methylated during production between platforms.