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

Neil G Rumachik; Stacy A Malaker; Nicole Poweleit; Lucy H Maynard; Christopher M Adams; Ryan D Leib; Giana Cirolia; Dennis Thomas; Susan Stamnes; Kathleen Holt; Patrick Sinn; Andrew P May; Nicole K Paulk

doi:10.1016/j.omtm.2020.05.018

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

Mol Ther Methods Clin Dev. 2020 May 22:18:98-118. doi: 10.1016/j.omtm.2020.05.018. eCollection 2020 Sep 11.

Authors

Affiliations

¹ Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
² Department of Medicine, University of California San Francisco, San Francisco, CA 94305, USA.
³ Genome Engineering, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
⁴ Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University, Stanford, CA 94305, USA.
⁵ Cryo-EM Core Facility, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
⁶ Viral Vector Core, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
⁷ Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.

Abstract

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.

Keywords: AAV; PTM; adeno-associated virus; baculovirus-Sf9; capsid; human; mass spectrometry; methylation; post-translational modification; potency.

Abstract

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