Separation of full, empty, and partial adeno-associated virus capsids via anion-exchange chromatography with continuous recycling and accumulation

• Published in: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences Analytical technologies in the biomedical and life sciences, 2024-07, Vol.1242, p.124206, Article 124206
• Main Authors: Suk Lee, Yong, Lee, Jaeweon, Fang, Kun, Gee, Gretchen V., Rogers, Benjamin, McNally, David, Yoon, Seongkyu
• Format: Article
• Language: English
• Subjects: Adeno-associated virus; anion exchange; anion exchange chromatography; capsid; Continuous anion-exchange chromatography; Dependoparvovirus; detection limit; drugs; fluorescence; Full/empty ratio; Gene therapy; high performance liquid chromatography; N-Rich; Partial capsid; transgenes
• ISSN: 1570-0232; 1873-376X; 1873-376X
• DOI: 10.1016/j.jchromb.2024.124206

•Developing a chromatography-based method for the separation of full, partial, and empty adeno-associated viral capsids through the use of continuous recycling and accumulation across two anion-exchange columns.•Introducing a new approach to anion-exchange chromatography aimed at enhancing baseline separation of partial from full and empty capsids.•Observing that partial capsids with intermediate genome size elute at intermediate retention time relative to capsids containing full or no DNAs.•Determining that fluorescence response factor is not only serotype-specific but also dependent on the DNA size inside the capsid.•Evaluating and comparing capsid ratio results from the newly developed method against other orthogonal techniques. The field of recombinant adeno-associated virus (rAAV) gene therapy has attracted increasing attention over decades. Within the ongoing challenges of rAAV manufacturing, the co-production of impurities, such as empty and partial capsids containing no or truncated transgenes, poses a significant challenge. Due to their potential impact on drug efficacy and clinical safety, it is imperative to conduct comprehensive monitoring and characterization of these impurities prior to the release of the final gene therapy product. Nevertheless, existing analytical techniques encounter notable limitations, encompassing low throughput, long turnaround times, high sample consumption, and/or complicated data analysis. Chromatography-based analytical methods are recognized for their current Good Manufacturing Practice (cGMP) alignment, high repeatability, reproducibility, low limit of detection, and rapid turnaround times. Despite these advantages, current anion exchange high pressure liquid chromatography (AEX-HPLC) methods struggle with baseline separation of partial capsids from full and empty capsids, resulting in inaccurate full-to-empty capsid ratio, as partial capsids are obscured within peaks corresponding to empty and full capsids. In this study, we present a unique analytical AEX method designed to characterize not only empty and full capsids but also partial capsids. This method utilizes continuous N-Rich chromatography with recycling between two identical AEX columns for the accumulation and isolation of partial capsids. The development process is comprehensively discussed, covering the preparation of reference materials representing full (rAAV-LacZ), partial (rAAV-GFP), and empty (rAAV-empty) capsids, N-rich method development, frac