1
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Suk Lee Y, Lee J, Fang K, Gee GV, Rogers B, McNally D, Yoon S. Separation of full, empty, and partial adeno-associated virus capsids via anion-exchange chromatography with continuous recycling and accumulation. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1242:124206. [PMID: 38908134 DOI: 10.1016/j.jchromb.2024.124206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024]
Abstract
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, fraction analysis, determination of fluorescence response factors between capsid variants, and validation through comparison with other comparative techniques.
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Affiliation(s)
- Yong Suk Lee
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Jaeweon Lee
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Kun Fang
- MassBiologics, University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
| | - Gretchen V Gee
- MassBiologics, University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
| | - Benjamin Rogers
- MassBiologics, University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
| | - David McNally
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA; MassBiologics, University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA.
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2
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Ma J, Tian Z, Shi Q, Dong X, Sun Y. Affinity chromatography for virus-like particle manufacturing: Challenges, solutions, and perspectives. J Chromatogr A 2024; 1721:464851. [PMID: 38574547 DOI: 10.1016/j.chroma.2024.464851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
The increasing medical application of virus-like particles (VLPs), notably vaccines and viral vectors, has increased the demand for commercial VLP production. However, VLP manufacturing has not yet reached the efficiency level achieved for recombinant protein therapeutics, especially in downstream processing. This review provides a comprehensive analysis of the challenges associated with affinity chromatography for VLP purification with respect to the diversity and complexity of VLPs and the associated upstream and downstream processes. The use of engineered affinity ligands and matrices for affinity chromatography is first discussed. Although several representative affinity ligands are currently available for VLP purification, most of them have difficulty in balancing ligand universality, ligand selectivity and mild operation conditions. Then, phage display technology and computer-assisted design are discussed as efficient methods for the rapid discovery of high-affinity peptide ligands. Finally, the VLP purification by affinity chromatography is analyzed. The process is significantly influenced by virus size and variation, ligand type and chromatographic mode. To address the updated regulatory requirements and epidemic outbreaks, technical innovations in affinity chromatography and process intensification and standardization in VLP purification should be promoted to achieve rapid process development and highly efficient VLP manufacturing, and emphasis is given to the discovery of universal ligands, applications of gigaporous matrices and platform technology. It is expected that the information in this review can provide a better understanding of the affinity chromatography methods available for VLP purification and offer useful guidance for the development of affinity chromatography for VLP manufacturing in the decades to come.
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Affiliation(s)
- Jing Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Zengquan Tian
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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3
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Xie Y, Butler M. N-glycomic profiling of capsid proteins from Adeno-Associated Virus serotypes. Glycobiology 2024; 34:cwad074. [PMID: 37774344 PMCID: PMC10950483 DOI: 10.1093/glycob/cwad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023] Open
Abstract
Adeno-associated virus (AAV) vector has become the leading platform for gene delivery. Each serotype exhibits a different tissue tropism, immunogenicity, and in vivo transduction performance. Therefore, selecting the most suitable AAV serotype is critical for efficient gene delivery to target cells or tissues. Genome divergence among different serotypes is due mainly to the hypervariable regions of the AAV capsid proteins. However, the heterogeneity of capsid glycosylation is largely unexplored. In the present study, the N-glycosylation profiles of capsid proteins of AAV serotypes 1 to 9 have been systemically characterized and compared using a previously developed high-throughput and high-sensitivity N-glycan profiling platform. The results showed that all 9 investigated AAV serotypes were glycosylated, with comparable profiles. The most conspicuous feature was the high abundance mannosylated N-glycans, including FM3, M5, M6, M7, M8, and M9, that dominated the chromatograms within a range of 74 to 83%. Another feature was the relatively lower abundance of fucosylated and sialylated N-glycan structures, in the range of 23%-40% and 10%-17%, respectively. However, the exact N-glycan composition differed. These differences may be utilized to identify potential structural relationships between the 9 AAV serotypes. The current research lays the foundation for gaining better understanding of the importance of N-glycans on the AAV capsid surface that may play a significant role in tissue tropism, interaction with cell surface receptors, cellular uptake, and intracellular processing.
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Affiliation(s)
- Yongjing Xie
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Michael Butler
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin (UCD), Belfield, Dublin 4, D04 V1W8, Ireland
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4
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Kulkarni AA, Seal AG, Sonnet C, Oka K. Streamlined Adeno-Associated Virus Production Using Suspension HEK293T Cells. Bio Protoc 2024; 14:e4931. [PMID: 38379831 PMCID: PMC10875358 DOI: 10.21769/bioprotoc.4931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/28/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) are valuable viral vectors for in vivo gene transfer, also having significant ex vivo therapeutic potential. Continued efforts have focused on various gene therapy applications, capsid engineering, and scalable manufacturing processes. Adherent cells are commonly used for virus production in most basic science laboratories because of their efficiency and cost. Although suspension cells are easier to handle and scale up compared to adherent cells, their use in virus production is hampered by poor transfection efficiency. In this protocol, we developed a simple scalable AAV production protocol using serum-free-media-adapted HEK293T suspension cells and VirusGEN transfection reagent. The established protocol allows AAV production from transfection to quality analysis of purified AAV within two weeks. Typical vector yields for the described suspension system followed by iodixanol purification range from a total of 1 × 1013 to 1.5 × 1013 vg (vector genome) using 90 mL of cell suspension vs. 1 × 1013 to 2 × 1013 vg using a regular adherent cell protocol (10 × 15 cm dishes). Key features • Adeno-associated virus (AAV) production using serum-free-media-adapted HEK293T suspension cells. • Efficient transfection with VirusGEN. • High AAV yield from small-volume cell culture. Graphical overview.
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Affiliation(s)
- Aditi A. Kulkarni
- Gene Vector Core, Advanced Technology Cores, Baylor
College of Medicine, Houston, TX, USA
| | - Austin G. Seal
- Gene Vector Core, Advanced Technology Cores, Baylor
College of Medicine, Houston, TX, USA
| | - Corinne Sonnet
- Gene Vector Core, Advanced Technology Cores, Baylor
College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine,
Houston, TX, USA
| | - Kazuhiro Oka
- Gene Vector Core, Advanced Technology Cores, Baylor
College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor
College of Medicine, Houston, TX, USA
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5
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Barbieri E, Mollica GN, Moore BD, Sripada SA, Shastry S, Kilgore RE, Loudermilk CM, Whitacre ZH, Kilgour KM, Wuestenhagen E, Aldinger A, Graalfs H, Rammo O, Schulte MM, Johnson TF, Daniele MA, Menegatti S. Peptide ligands targeting the vesicular stomatitis virus G (VSV-G) protein for the affinity purification of lentivirus particles. Biotechnol Bioeng 2024; 121:618-639. [PMID: 37947118 DOI: 10.1002/bit.28594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
The recent uptick in the approval of ex vivo cell therapies highlights the relevance of lentivirus (LV) as an enabling viral vector of modern medicine. As labile biologics, however, LVs pose critical challenges to industrial biomanufacturing. In particular, LV purification-currently reliant on filtration and anion-exchange or size-exclusion chromatography-suffers from long process times and low yield of transducing particles, which translate into high waiting time and cost to patients. Seeking to improve LV downstream processing, this study introduces peptides targeting the enveloped protein Vesicular stomatitis virus G (VSV-G) to serve as affinity ligands for the chromatographic purification of LV particles. An ensemble of candidate ligands was initially discovered by implementing a dual-fluorescence screening technology and a targeted in silico approach designed to identify sequences with high selectivity and tunable affinity. The selected peptides were conjugated on Poros resin and their LV binding-and-release performance was optimized by adjusting the flow rate, composition, and pH of the chromatographic buffers. Ligands GKEAAFAA and SRAFVGDADRD were selected for their high product yield (50%-60% of viral genomes; 40%-50% of HT1080 cell-transducing particles) upon elution in PIPES buffer with 0.65 M NaCl at pH 7.4. The peptide-based adsorbents also presented remarkable values of binding capacity (up to 3·109 TU per mL of resin, or 5·1011 vp per mL of resin, at the residence time of 1 min) and clearance of host cell proteins (up to a 220-fold reduction of HEK293 HCPs). Additionally, GKEAAFAA demonstrated high resistance to caustic cleaning-in-place (0.5 M NaOH, 30 min) with no observable loss in product yield and quality.
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Affiliation(s)
- Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Gina N Mollica
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Sobhana A Sripada
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Casee M Loudermilk
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Zachary H Whitacre
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Katie M Kilgour
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | | | | | | | | | | | - Thomas F Johnson
- Department of Biochemical Engineering, University College London, London, UK
| | - Michael A Daniele
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
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6
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Asarnow D, Becker VA, Bobe D, Dubbledam C, Johnston JD, Kopylov M, Lavoie NR, Li Q, Mattingly JM, Mendez JH, Paraan M, Turner J, Upadhye V, Walsh RM, Gupta M, Eng ET. Recent advances in infectious disease research using cryo-electron tomography. Front Mol Biosci 2024; 10:1296941. [PMID: 38288336 PMCID: PMC10822977 DOI: 10.3389/fmolb.2023.1296941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
With the increasing spread of infectious diseases worldwide, there is an urgent need for novel strategies to combat them. Cryogenic sample electron microscopy (cryo-EM) techniques, particularly electron tomography (cryo-ET), have revolutionized the field of infectious disease research by enabling multiscale observation of biological structures in a near-native state. This review highlights the recent advances in infectious disease research using cryo-ET and discusses the potential of this structural biology technique to help discover mechanisms of infection in native environments and guiding in the right direction for future drug discovery.
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Affiliation(s)
- Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Vada A. Becker
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
| | - Daija Bobe
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Charlie Dubbledam
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jake D. Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Nathalie R. Lavoie
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, United States
| | - Qiuye Li
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Jacob M. Mattingly
- Department of Chemistry, College of Arts and Sciences, Emory University, Atlanta, GA, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Mohammadreza Paraan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jack Turner
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Viraj Upadhye
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology and Harvard Medical School, Boston, MA, United States
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
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7
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Wagner C, Fuchsberger FF, Innthaler B, Pachlinger R, Schrenk I, Lemmerer M, Birner-Gruenberger R. Automated Mass Photometry of Adeno-Associated Virus Vectors from Crude Cell Extracts. Int J Mol Sci 2024; 25:838. [PMID: 38255912 PMCID: PMC10815086 DOI: 10.3390/ijms25020838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Mass photometry (MP) is a fast and simple analysis method for the determination of the proportions of subpopulations in an AAV sample. It is label-free and requires minimal sample volumes between 5-10 µL, which makes it a promising candidate over orthogonal techniques such as analytical ultracentrifugation (AUC), cryo-transmission electron microscopy (Cryo-TEM) or charge-detection mass spectrometry (CDMS). However, these methods are limited in their application to purified samples only. Here we developed a purification step based on single-domain monospecific antibody fragments immobilised on either a poly(styrene-divinylbenzene) resin or on magnetic beads prior to MP analysis that allows the quantification of empty, partially filled, full and overfull AAV vectors in crude cell extracts. This is aimed at identifying potentially promising harvest conditions that yield large numbers of filled AAV vectors during the early stages of the viral vector development platform, e.g., the type of transfection reagent used. Furthermore, we provide a direct comparison of the automated and manual handling of the mass photometer with respect to the quantities of AAV subspecies, molar mass of the capsid and payload, and highlight the differences between the "buffer-free" sample measurement and the "buffer-dilution" mode. In addition, we provide information on which candidates to use for calibration and demonstrate the limitations of the mass photometer with respect to the estimation of the capsid titer.
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Affiliation(s)
- Christina Wagner
- Pharmaceutical Sciences, Baxalta Innovations (Part of Takeda), 1220 Vienna, Austria
| | - Felix F. Fuchsberger
- Pharmaceutical Sciences, Baxalta Innovations (Part of Takeda), 1220 Vienna, Austria
| | - Bernd Innthaler
- Pharmaceutical Sciences, Baxalta Innovations (Part of Takeda), 1220 Vienna, Austria
| | - Robert Pachlinger
- Pharmaceutical Sciences, Baxalta Innovations (Part of Takeda), 1220 Vienna, Austria
| | - Irene Schrenk
- Pharmaceutical Sciences, Baxalta Innovations (Part of Takeda), 1220 Vienna, Austria
| | - Martin Lemmerer
- Pharmaceutical Sciences, Baxalta Innovations (Part of Takeda), 1220 Vienna, Austria
| | - Ruth Birner-Gruenberger
- Institute of Chemical Technologies and Analytics, Technical University of Vienna, 1040 Vienna, Austria
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8
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Shastry S, Chu W, Barbieri E, Greback-Clarke P, Smith WK, Cummings C, Minzoni A, Pancorbo J, Gilleskie G, Ritola K, Daniele MA, Johnson TF, Menegatti S. Rational design and experimental evaluation of peptide ligands for the purification of adeno-associated viruses via affinity chromatography. Biotechnol J 2024; 19:e2300230. [PMID: 37728197 DOI: 10.1002/biot.202300230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/21/2023]
Abstract
Adeno-associated viruses (AAVs) have acquired a central role in modern medicine as delivery agents for gene therapies targeting rare diseases. While new AAVs with improved tissue targeting, potency, and safety are being introduced, their biomanufacturing technology is lagging. In particular, the AAV purification pipeline hinges on protein ligands for the affinity-based capture step. While featuring excellent AAV binding capacity and selectivity, these ligands require strong acid (pH <3) elution conditions, which can compromise the product's activity and stability. Additionally, their high cost and limited lifetime has a significant impact on the price tag of AAV-based therapies. Seeking to introduce a more robust and affordable affinity technology, this study introduces a cohort of peptide ligands that (i) mimic the biorecognition activity of the AAV receptor (AAVR) and anti-AAV antibody A20, (ii) enable product elution under near-physiological conditions (pH 6.0), and (iii) grant extended reusability by withstanding multiple regenerations. A20-mimetic CYIHFSGYTNYNPSLKSC and AAVR-mimetic CVIDGSQSTDDDKIC demonstrated excellent capture of serotypes belonging to distinct clones/clades - namely, AAV1, AAV2, AAV5, AAV6, AAV8, and AAV9. This corroborates the in silico models documenting their ability to target regions of the viral capsid that are conserved across all serotypes. CVIDGSQSTDDDKIC-Toyopearl resin features binding capacity (≈1014 vp mL-1 ) and product yields (≈60%-80%) on par with commercial adsorbents, and purifies AAV2 from HEK293 and Sf9 cell lysates with high recovery (up to 78%), reduction of host cell proteins (up to 700-fold), and high transduction activity (up to 65%).
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Affiliation(s)
- Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Paul Greback-Clarke
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - William K Smith
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Christopher Cummings
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Arianna Minzoni
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Jennifer Pancorbo
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Gary Gilleskie
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Kimberly Ritola
- Neuroscience Center, Brain Initiative Neurotools Vector Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
| | - Michael A Daniele
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Thomas F Johnson
- Department of Biochemical Engineering, University College London, London, UK
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
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9
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Di W, Koczera K, Zhang P, Chen DP, Warren JC, Huang C. Improved adeno-associated virus empty and full capsid separation using weak partitioning multi-column AEX chromatography. Biotechnol J 2024; 19:e2300245. [PMID: 38013662 DOI: 10.1002/biot.202300245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/10/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Recombinant adeno-associated virus (rAAV) empty and full capsid separation has been a topic of interest in the rAAV gene therapy community for many years and the anion exchange chromatography (AEX) step has undergone various process optimizations to improve rAAV empty capsid separation, including AEX stationary phase, mobile phase, and process parameters. Here, we present a new AEX method that employs both weak partitioning chromatography (WPC) and multi-column chromatography (MCC) to achieve improved full rAAV percentage in the AEX pool. The WPC technology allows empty rAAV to be displaced by full rAAV during loading, while the MCC technology enables parallel column processing which further increases AEX step productivity. Our results show that, compared to baseline AEX batch chromatography, the AEX-WPC-MCC method demonstrated improvements in both AEX pool full rAAV percentage (∼ 20% increase) and rAAV genome recovery (∼ 20% increase). As a result, the productivity (full capsid generated per liter of AEX column per hour of processing time) of the AEX step increased by ∼34-fold from the baseline AEX batch run to the AEX-WPC-MCC run. It is foreseeable that this AEX-WPC-MCC method could find applications in large-scale rAAV manufacturing processes to improve AEX yield and reduce the cost of goods of rAAV manufacturing.
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Affiliation(s)
- Wenjun Di
- Pharmaceutical Development, Ultragenyx Pharmaceutical Inc., Woburn, Massachusetts, USA
| | - Kyle Koczera
- Pharmaceutical Development, Ultragenyx Pharmaceutical Inc., Woburn, Massachusetts, USA
| | - Peilun Zhang
- Pharmaceutical Development, Ultragenyx Pharmaceutical Inc., Woburn, Massachusetts, USA
| | - Dennis P Chen
- Pharmaceutical Development, Ultragenyx Pharmaceutical Inc., Woburn, Massachusetts, USA
| | - James C Warren
- Pharmaceutical Development, Ultragenyx Pharmaceutical Inc., Woburn, Massachusetts, USA
| | - Chao Huang
- Pharmaceutical Development, Ultragenyx Pharmaceutical Inc., Woburn, Massachusetts, USA
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10
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Heckel J, Martinez A, Elger C, Haindl M, Leiss M, Ruppert R, Williams C, Hubbuch J, Graf T. Fast HPLC-based affinity method to determine capsid titer and full/empty ratio of adeno-associated viral vectors. Mol Ther Methods Clin Dev 2023; 31:101148. [PMID: 38046198 PMCID: PMC10690635 DOI: 10.1016/j.omtm.2023.101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Recombinant adeno-associated viruses (rAAVs) are promising gene delivery vectors in the emerging field of in vivo gene therapies. To ensure their consistent quality during manufacturing and process development, multiple analytical techniques have been proposed for the characterization and quantification of rAAV capsids. Despite their indisputable capabilities for performing this task, current analytical methods are rather time-consuming, material intensive, complicated, and costly, restricting their suitability for process development in which time and sample throughput are severe constraints. To eliminate this bottleneck, we introduce here an affinity-based high-performance liquid chromatography method that allows the determination of the capsid titer and the full/empty ratio of rAAVs within less than 5 min. By packing the commercially available AAVX affinity resin into small analytical columns, the rAAV fraction of diverse serotypes can be isolated from process-related impurities and analyzed by UV and fluorescence detection. As demonstrated by both method qualification data and side-by-side comparison with AAV enzyme-linked immunosorbent assay results for rAAV8 samples as well as by experiments using additional rAAV2, rAAV8, and rAAV9 constructs, our approach showed good performance, indicating its potential as a fast, simple and efficient tool for supporting the development of rAAV gene therapies.
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Affiliation(s)
- Jakob Heckel
- Pharma Technical Development Analytics, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Andres Martinez
- Gene Therapy Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Carsten Elger
- Gene Therapy Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Markus Haindl
- Gene Therapy Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Michael Leiss
- Pharma Technical Development Analytics, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Raphael Ruppert
- Gene Therapy Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Chris Williams
- Gene Therapy Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Jürgen Hubbuch
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Tobias Graf
- Pharma Technical Development Analytics, Roche Diagnostics GmbH, 82377 Penzberg, Germany
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11
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Onishi T, Nonaka M, Maruno T, Yamaguchi Y, Fukuhara M, Torisu T, Maeda M, Abbatiello S, Haris A, Richardson K, Giles K, Preece S, Yamano-Adachi N, Omasa T, Uchiyama S. Enhancement of recombinant adeno-associated virus activity by improved stoichiometry and homogeneity of capsid protein assembly. Mol Ther Methods Clin Dev 2023; 31:101142. [PMID: 38027055 PMCID: PMC10663676 DOI: 10.1016/j.omtm.2023.101142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023]
Abstract
Studies of recombinant adeno-associated virus (rAAV) revealed the mixture of full particles with different densities in rAAV. There are no conclusive results because of the lack of quantitative stoichiometric viral proteins, encapsidated DNA, and particle level analyses. We report the first comprehensive characterization of low- and high-density rAAV serotype 2 particles. Capillary gel electrophoresis showed high-density particles possessing a designed DNA encapsidated in the capsid composed of (VP1 + VP2)/VP3 = 0.27, whereas low-density particles have the same DNA but with a different capsid composition of (VP1 + VP2)/VP3 = 0.31, supported by sedimentation velocity-analytical ultracentrifugation and charge detection-mass spectrometry. In vitro analysis demonstrated that the low-density particles had 8.9% higher transduction efficacy than that of the particles before fractionation. Further, based on our recent findings of VP3 clip, we created rAAV2 single amino acid variants of the transcription start methionine of VP3 (M203V) and VP3 clip (M211V). The rAAV2-M203V variant had homogeneous particles with higher (VP1+VP2)/VP3 values (0.35) and demonstrated 24.7% higher transduction efficacy compared with the wild type. This study successfully provided highly functional rAAV by the extensive fractionation from the mixture of rAAV2 full particles or by the single amino acid replacement.
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Affiliation(s)
- Takayuki Onishi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Michika Nonaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- U-Medico Inc, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Yamaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mitsuko Fukuhara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- U-Medico Inc, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuo Torisu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masaharu Maeda
- Osaka Consolidated Laboratory, Manufacturing Technology Association of Biologics, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | | - Keith Richardson
- Waters Corporation (Micromass UK Ltd), Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | | | - Steve Preece
- Waters Corporation (Micromass UK Ltd), Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Noriko Yamano-Adachi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Omasa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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12
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Kilgore R, Minzoni A, Shastry S, Smith W, Barbieri E, Wu Y, LeBarre JP, Chu W, O'Brien J, Menegatti S. The downstream bioprocess toolbox for therapeutic viral vectors. J Chromatogr A 2023; 1709:464337. [PMID: 37722177 DOI: 10.1016/j.chroma.2023.464337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/20/2023]
Abstract
Viral vectors are poised to acquire a prominent position in modern medicine and biotechnology owing to their role as delivery agents for gene therapies, oncolytic agents, vaccine platforms, and a gateway to engineer cell therapies as well as plants and animals for sustainable agriculture. The success of viral vectors will critically depend on the availability of flexible and affordable biomanufacturing strategies that can meet the growing demand by clinics and biotech companies worldwide. In this context, a key role will be played by downstream process technology: while initially adapted from protein purification media, the purification toolbox for viral vectors is currently undergoing a rapid expansion to fit the unique biomolecular characteristics of these products. Innovation efforts are articulated on two fronts, namely (i) the discovery of affinity ligands that target adeno-associated virus, lentivirus, adenovirus, etc.; (ii) the development of adsorbents with innovative morphologies, such as membranes and 3D printed monoliths, that fit the size of viral vectors. Complementing these efforts are the design of novel process layouts that capitalize on novel ligands and adsorbents to ensure high yield and purity of the product while safeguarding its therapeutic efficacy and safety; and a growing panel of analytical methods that monitor the complex array of critical quality attributes of viral vectors and correlate them to the purification strategies. To help explore this complex and evolving environment, this study presents a comprehensive overview of the downstream bioprocess toolbox for viral vectors established in the last decade, and discusses present efforts and future directions contributing to the success of this promising class of biological medicines.
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Affiliation(s)
- Ryan Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States.
| | - Arianna Minzoni
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, United States
| | - Will Smith
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Yuxuan Wu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Jacob P LeBarre
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Juliana O'Brien
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, United States; North Carolina Viral Vector Initiative in Research and Learning, North Carolina State University, Raleigh, NC 27695, United States
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13
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Turco F, Wegelius A, Lind O, Norrman N, Magnusson AC, Sund-Lundström C, Norén B, Hedberg J, Palmgren R. Combined clarification and affinity capture using magnetic resin enables efficient separation of rAAV5 from cell lysate. Mol Ther Methods Clin Dev 2023; 30:394-402. [PMID: 37637382 PMCID: PMC10457685 DOI: 10.1016/j.omtm.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Recombinant adeno-associated virus (rAAV) vectors have displayed enormous potential as a platform for delivery of gene therapies. Purification of rAAV at industrial scale involves a series of elaborate, material, and time-consuming midstream steps, such as clarification by depth filtration and concentration/buffer exchange by tangential flow filtration. In this study, we developed a filter-less flow capture method for purification of rAAV serotype 5, using a high-gradient magnetic separator and magnetic Mag Sepharose beads coupled to an AVB affinity ligand. In under 2 h, we captured and eluted rAAV5 directly from ∼5 L of cell lysate with a recovery yield of 63% (±5%, n = 3). Compared to cell lysate, the eluate showed a 3-log reduction of host cell DNA and host cell proteins. The process developed eliminates the need for filtration and column chromatography in the early steps of industrial rAAV purification. This will be of high value for industrial-scale manufacturing of rAAVs by reducing time and material in the purification process, without compromising product recovery and purity.
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Affiliation(s)
- Federico Turco
- Cytiva, Björkgatan 30, 753 23 Uppsala, Sweden
- Testa Center, Björkgatan 30, 753 23 Uppsala, Sweden
| | - Adam Wegelius
- Cytiva, Björkgatan 30, 753 23 Uppsala, Sweden
- Testa Center, Björkgatan 30, 753 23 Uppsala, Sweden
| | - Ola Lind
- Cytiva, Björkgatan 30, 753 23 Uppsala, Sweden
| | | | | | | | - Björn Norén
- Cytiva, Björkgatan 30, 753 23 Uppsala, Sweden
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14
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Lothert K, Wolff MW. Affinity and Pseudo-Affinity Membrane Chromatography for Viral Vector and Vaccine Purifications: A Review. MEMBRANES 2023; 13:770. [PMID: 37755191 PMCID: PMC10537005 DOI: 10.3390/membranes13090770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
Several chromatographic approaches have been established over the last decades for the production of pharmaceutically relevant viruses. Due to the large size of these products compared to other biopharmaceuticals, e.g., proteins, convective flow media have proven to be superior to bead-based resins in terms of process productivity and column capacity. One representative of such convective flow materials is membranes, which can be modified to suit the particular operating principle and are also suitable for economical single-use applications. Among the different membrane variants, affinity surfaces allow for the most selective separation of the target molecule from other components in the feed solution, especially from host cell-derived DNA and proteins. A successful membrane affinity chromatography, however, requires the identification and implementation of ligands, which can be applied economically while at the same time being stable during the process and non-toxic in the case of any leaching. This review summarizes the current evaluation of membrane-based affinity purifications for viruses and virus-like particles, including traditional resin and monolith approaches and the advantages of membrane applications. An overview of potential affinity ligands is given, as well as considerations of suitable affinity platform technologies, e.g., for different virus serotypes, including a description of processes using pseudo-affinity matrices, such as sulfated cellulose membrane adsorbers.
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Affiliation(s)
| | - Michael W. Wolff
- Institute of Bioprocess Engineering and Pharmaceutical Technology, Department Life Science Engineering, University of Applied Sciences Mittelhessen (THM), 35390 Giessen, Germany
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