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Shastry S, Barbieri E, Minzoni A, Chu W, Johnson S, Stoops M, Pancorbo J, Gilleskie G, Ritola K, Crapanzano MS, Daniele MA, Menegatti S. Serotype-agnostic affinity purification of adeno-associated virus (AAV) via peptide-functionalized chromatographic resins. J Chromatogr A 2024; 1734:465320. [PMID: 39217737 DOI: 10.1016/j.chroma.2024.465320] [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: 07/08/2024] [Revised: 08/12/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Adeno-associated viruses (AAVs) have emerged as a prominent family of vectors for gene delivery, providing therapeutic options to diseases once deemed incurable. At the same time, they necessitate efficient and affordable purification methods that can be platformed to serve all AAV serotypes. Current chromatographic tools, while affording high product purity, fail to bind certain serotypes, provide limited yield and lifetime, and impose harsh elution conditions that can compromise the vector's activity and safety. Addressing these challenges, this work demonstrates the application of new peptide ligands as the first serotype-agnostic technology for AAV purification by affinity chromatography. Our study reveals a pH-dependent affinity interaction: AAV2, AAV3, AAV6, AAV9, and AAVrh.10 are effectively captured at neutral pH, while binding AAV1, AAV5, AAV7, and AAV8 is stronger in a slightly acidic environment. The elution of bound AAVs was achieved using magnesium chloride at neutral pH for all serotypes, consistently affording capsid yields above 50% and genome yields above 80%, together with a >100-fold reduction in host cell proteins and nucleic acids. In particular, peptide ligand A10 exhibited remarkable binding capacity (> 1014 vp per mL of resin) and purification performance for all AAV serotypes, demonstrating broad applicability for gene therapy manufacturing. Finally, this work introduces novel alkaline-stable variants of A10 and demonstrates their use as the first affinity ligands capable of performing multiple cycles of AAV2, AAV8, and AAV9 purification with intermediate caustic cleaning without loss of capacity or product quality. Collectively, these results demonstrate the promise of this technology to further the impact and affordability of gene therapy.
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Affiliation(s)
- Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27606, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27606, USA; LigaTrap Technologies LLC, Raleigh, NC 27606, USA
| | - Arianna Minzoni
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27606, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27606, USA
| | - Stephanie Johnson
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
| | - Mark Stoops
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
| | - Jennifer Pancorbo
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
| | - Gary Gilleskie
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
| | - Kimberly Ritola
- Neuroscience Center, Brain Initiative Neurotools Vector Core, University of North Carolina at Chapel Hill, 116 Manning Drive, Chapel Hill, NC 27599; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 911 Oval Dr, Raleigh, NC 27695, USA
| | | | - Michael A Daniele
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 911 Oval Dr, Raleigh, NC 27695, USA; Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27606, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 911 Oval Dr, Raleigh, NC 27695, USA; LigaTrap Technologies LLC, Raleigh, NC 27606, USA.
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2
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Penzes JJ, Holm M, Yost SA, Kaelber JT. Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles. Cell 2024; 187:5604-5619.e14. [PMID: 39208798 DOI: 10.1016/j.cell.2024.07.053] [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: 06/29/2023] [Revised: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
We use cryoelectron microscopy (cryo-EM) as a sequence- and culture-independent diagnostic tool to identify the etiological agent of an agricultural pandemic. For the past 4 years, American insect-rearing facilities have experienced a distinctive larval pathology and colony collapse of farmed Zophobas morio (superworm). By means of cryo-EM, we discovered the causative agent: a densovirus that we named Zophobas morio black wasting virus (ZmBWV). We confirmed the etiology of disease by fulfilling Koch's postulates and characterizing strains from across the United States. ZmBWV is a member of the family Parvoviridae with a 5,542 nt genome, and we describe intersubunit interactions explaining its expanded internal volume relative to human parvoviruses. Cryo-EM structures at resolutions up to 2.1 Å revealed single-strand DNA (ssDNA) ordering at the capsid inner surface pinned by base-binding pockets in the capsid inner surface. Also, we demonstrated the prophylactic potential of non-pathogenic strains to provide cross-protection in vivo.
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Affiliation(s)
- Judit J Penzes
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Martin Holm
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Samantha A Yost
- Research and Early Development, REGENXBIO Inc., Rockville, MD, USA
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
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3
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Ebberink EH, Ruisinger A, Nuebel M, Meyer-Berg H, Ferreira IR, Thomann M, Heck AJ. Probing recombinant AAV capsid integrity and genome release after thermal stress by mass photometry. Mol Ther Methods Clin Dev 2024; 32:101293. [PMID: 39100914 PMCID: PMC11295964 DOI: 10.1016/j.omtm.2024.101293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/21/2024] [Indexed: 08/06/2024]
Abstract
Adeno-associated viruses (AAVs) are gaining traction as delivery vehicles for gene therapy although the molecular understanding of AAV-transgene release is still limited. Typically, the process of viral uncoating is investigated (in vitro) through thermal stress, revealing capsid disintegration at elevated temperatures. To assess the (in)stability of different empty and filled AAV preparations, we used the light-scattering-based interferometric microscopy technique of mass photometry that, on a single-particle basis, determines the molecular weight of AAVs. By introducing a heat-stable DNA plasmid as an internal standard, we quantitatively probed the impact of heat on AAVs. Generally, empty AAVs exhibited greater heat resistance than genome-filled particles. Our data also indicate that upon DNA release, the capsids do not transform into empty AAVs, but seem to aggregate or disintegrate. Strikingly, some AAVs exhibited an intermediate state with disrupted capsids but preserved bound genome, a feature that experimentally only emerged following incubation with a nuclease. Our data demonstrate that the thermal uncoating process is highly AAV specific (i.e., can be influenced by serotype, genome, host system). We argue that nuclease treatment in combination with MP can be used as an additional analytical tool for assessing structural integrity of recombinant and/or clinical AAV vectors.
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Affiliation(s)
- Eduard H.T.M. Ebberink
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Alisa Ruisinger
- Gene Therapy Technical Development Analytics, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Markus Nuebel
- Gene Therapy Technical Development Analytics, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | | | | | - Marco Thomann
- Gene Therapy Technical Development Analytics, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands
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4
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Patra AT, Tan E, Kok YJ, Ng SK, Bi X. Temporal insights into molecular and cellular responses during rAAV production in HEK293T cells. Mol Ther Methods Clin Dev 2024; 32:101278. [PMID: 39022743 PMCID: PMC11253160 DOI: 10.1016/j.omtm.2024.101278] [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: 12/16/2023] [Accepted: 06/04/2024] [Indexed: 07/20/2024]
Abstract
The gene therapy field seeks cost-effective, large-scale production of recombinant adeno-associated virus (rAAV) vectors for high-dosage therapeutic applications. Although strategies like suspension cell culture and transfection optimization have shown moderate success, challenges persist for large-scale applications. To unravel molecular and cellular mechanisms influencing rAAV production, we conducted an SWATH-MS proteomic analysis of HEK293T cells transfected using standard, sub-optimal, and optimal conditions. Gene Ontology and pathway analysis revealed significant protein expression variations, particularly in processes related to cellular homeostasis, metabolic regulation, vesicular transport, ribosomal biogenesis, and cellular proliferation under optimal transfection conditions. This resulted in a 50% increase in rAAV titer compared with the standard protocol. Additionally, we identified modifications in host cell proteins crucial for AAV mRNA stability and gene translation, particularly regarding AAV capsid transcripts under optimal transfection conditions. Our study identified 124 host proteins associated with AAV replication and assembly, each exhibiting distinct expression pattern throughout rAAV production stages in optimal transfection condition. This investigation sheds light on the cellular mechanisms involved in rAAV production in HEK293T cells and proposes promising avenues for further enhancing rAAV titer during production.
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Affiliation(s)
- Alok Tanala Patra
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Evan Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Say Kong Ng
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore
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5
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Kachanov A, Kostyusheva A, Brezgin S, Karandashov I, Ponomareva N, Tikhonov A, Lukashev A, Pokrovsky V, Zamyatnin AA, Parodi A, Chulanov V, Kostyushev D. The menace of severe adverse events and deaths associated with viral gene therapy and its potential solution. Med Res Rev 2024; 44:2112-2193. [PMID: 38549260 DOI: 10.1002/med.22036] [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: 10/10/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 08/09/2024]
Abstract
Over the past decade, in vivo gene replacement therapy has significantly advanced, resulting in market approval of numerous therapeutics predominantly relying on adeno-associated viral vectors (AAV). While viral vectors have undeniably addressed several critical healthcare challenges, their clinical application has unveiled a range of limitations and safety concerns. This review highlights the emerging challenges in the field of gene therapy. At first, we discuss both the role of biological barriers in viral gene therapy with a focus on AAVs, and review current landscape of in vivo human gene therapy. We delineate advantages and disadvantages of AAVs as gene delivery vehicles, mostly from the safety perspective (hepatotoxicity, cardiotoxicity, neurotoxicity, inflammatory responses etc.), and outline the mechanisms of adverse events in response to AAV. Contribution of every aspect of AAV vectors (genomic structure, capsid proteins) and host responses to injected AAV is considered and substantiated by basic, translational and clinical studies. The updated evaluation of recent AAV clinical trials and current medical experience clearly shows the risks of AAVs that sometimes overshadow the hopes for curing a hereditary disease. At last, a set of established and new molecular and nanotechnology tools and approaches are provided as potential solutions for mitigating or eliminating side effects. The increasing number of severe adverse reactions and, sadly deaths, demands decisive actions to resolve the issue of immune responses and extremely high doses of viral vectors used for gene therapy. In response to these challenges, various strategies are under development, including approaches aimed at augmenting characteristics of viral vectors and others focused on creating secure and efficacious non-viral vectors. This comprehensive review offers an overarching perspective on the present state of gene therapy utilizing both viral and non-viral vectors.
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Affiliation(s)
- Artyom Kachanov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Anastasiya Kostyusheva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Sergey Brezgin
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Ivan Karandashov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Natalia Ponomareva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Andrey Tikhonov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Alexander Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Vadim Pokrovsky
- Laboratory of Biochemical Fundamentals of Pharmacology and Cancer Models, Blokhin Cancer Research Center, Moscow, Russia
- Department of Biochemistry, People's Friendship University, Russia (RUDN University), Moscow, Russia
| | - Andrey A Zamyatnin
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Research, Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alessandro Parodi
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Vladimir Chulanov
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Infectious Diseases, Sechenov University, Moscow, Russia
| | - Dmitry Kostyushev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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6
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Hanlon KS, Cheng M, Ferrer RM, Ryu JR, Lee B, De La Cruz D, Patel N, Espinoza P, Santoscoy MC, Gong Y, Ng C, Nguyen DM, Nammour J, Clark SW, Heine VM, Sun W, Kozarsky K, Maguire CA. In vivo selection in non-human primates identifies AAV capsids for on-target CSF delivery to spinal cord. Mol Ther 2024; 32:2584-2603. [PMID: 38845196 PMCID: PMC11405149 DOI: 10.1016/j.ymthe.2024.05.040] [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: 04/12/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024] Open
Abstract
Systemic administration of adeno-associated virus (AAV) vectors for spinal cord gene therapy has challenges including toxicity at high doses and pre-existing immunity that reduces efficacy. Intrathecal (IT) delivery of AAV vectors into cerebral spinal fluid can avoid many issues, although distribution of the vector throughout the spinal cord is limited, and vector entry to the periphery sometimes initiates hepatotoxicity. Here we performed biopanning in non-human primates (NHPs) with an IT injected AAV9 peptide display library. We identified top candidates by sequencing inserts of AAV DNA isolated from whole tissue, nuclei, or nuclei from transgene-expressing cells. These barcoded candidates were pooled with AAV9 and compared for biodistribution and transgene expression in spinal cord and liver of IT injected NHPs. Most candidates displayed increased retention in spinal cord compared with AAV9. Greater spread from the lumbar to the thoracic and cervical regions was observed for several capsids. Furthermore, several capsids displayed decreased biodistribution to the liver compared with AAV9, providing a high on-target/low off-target biodistribution. Finally, we tested top candidates in human spinal cord organoids and found them to outperform AAV9 in efficiency of transgene expression in neurons and astrocytes. These capsids have potential to serve as leading-edge delivery vehicles for spinal cord-directed gene therapies.
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Affiliation(s)
- Killian S Hanlon
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA; University College London, London, UK
| | - Ming Cheng
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Roberto Montoro Ferrer
- Department of Pediatric Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam Leukodystrophy Center, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, the Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, De Boelelaan, Amsterdam, the Netherlands
| | - Jae Ryun Ryu
- Department of Anatomy, Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul, Republic of Korea
| | - Boram Lee
- Department of Anatomy, Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul, Republic of Korea
| | - Demitri De La Cruz
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Nikita Patel
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Paula Espinoza
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Miguel C Santoscoy
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Carrie Ng
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Diane M Nguyen
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Josette Nammour
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA
| | - Sean W Clark
- SwanBio Therapeutics, Bala Cynwyd, PA 19005, USA
| | - Vivi M Heine
- Department of Child and Adolescent Psychiatry, Emma Center for Personalized Medicine, Emma Children's Hospital, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, the Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, De Boelelaan, Amsterdam, the Netherland
| | - Woong Sun
- Department of Anatomy, Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul, Republic of Korea
| | | | - Casey A Maguire
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02116, USA.
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7
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Matsuzaka Y, Yashiro R. Therapeutic Application and Structural Features of Adeno-Associated Virus Vector. Curr Issues Mol Biol 2024; 46:8464-8498. [PMID: 39194716 DOI: 10.3390/cimb46080499] [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: 06/10/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024] Open
Abstract
Adeno-associated virus (AAV) is characterized by non-pathogenicity, long-term infection, and broad tropism and is actively developed as a vector virus for gene therapy products. AAV is classified into more than 100 serotypes based on differences in the amino acid sequence of the capsid protein. Endocytosis involves the uptake of viral particles by AAV and accessory receptors during AAV infection. After entry into the cell, they are transported to the nucleus through the nuclear pore complex. AAVs mainly use proteoglycans as receptors to enter cells, but the types of sugar chains in proteoglycans that have binding ability are different. Therefore, it is necessary to properly evaluate the primary structure of receptor proteins, such as amino acid sequences and post-translational modifications, including glycosylation, and the higher-order structure of proteins, such as the folding of the entire capsid structure and the three-dimensional (3D) structure of functional domains, to ensure the efficacy and safety of biopharmaceuticals. To further enhance safety, it is necessary to further improve the efficiency of gene transfer into target cells, reduce the amount of vector administered, and prevent infection of non-target cells.
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Affiliation(s)
- Yasunari Matsuzaka
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
| | - Ryu Yashiro
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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8
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Kuz CA, McFarlin S, Qiu J. The Expression and Function of the Small Nonstructural Proteins of Adeno-Associated Viruses (AAVs). Viruses 2024; 16:1215. [PMID: 39205189 PMCID: PMC11359079 DOI: 10.3390/v16081215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Adeno-associated viruses (AAVs) are small, non-enveloped viruses that package a single-stranded (ss)DNA genome of 4.7 kilobases (kb) within their T = 1 icosahedral capsid. AAVs are replication-deficient viruses that require a helper virus to complete their life cycle. Recombinant (r)AAVs have been utilized as gene delivery vectors for decades in gene therapy applications. So far, six rAAV-based gene medicines have been approved by the US FDA. The 4.7 kb ssDNA genome of AAV encodes nine proteins, including three viral structural/capsid proteins, VP1, VP2, and VP3; four large nonstructural proteins (replication-related proteins), Rep78/68 and Rep52/40; and two small nonstructural proteins. The two nonstructured proteins are viral accessory proteins, namely the assembly associated protein (AAP) and membrane-associated accessory protein (MAAP). Although the accessory proteins are conserved within AAV serotypes, their functions are largely obscure. In this review, we focus on the expression strategy and functional properties of the small nonstructural proteins of AAVs.
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Affiliation(s)
| | | | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (C.A.K.); (S.M.)
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9
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Ye X, Hu Y, Qiu H, Li N. Probe capsid structure stability and dynamics of adeno-associated virus as an important viral vector for gene therapy by hydrogen-deuterium exchange-mass spectrometry. Protein Sci 2024; 33:e5074. [PMID: 38888268 PMCID: PMC11184576 DOI: 10.1002/pro.5074] [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: 01/08/2024] [Revised: 04/14/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
Adeno-associated virus (AAV), a widely used gene therapy vector, is a small, nonenveloped virus that contains a single-stranded DNA genome with a maximum length of 4.7 kb. Despite extensive biophysical and structural characterization, many aspects of AAV functions remain elusive. This knowledge gap is primarily due to a lack of structurally resolved dynamic information and the absence of structural coverage of functionally critical segments on the AAV capsid. Here, we developed a protocol to study AAV structural dynamics by hydrogen-deuterium exchange mass spectrometry (HDX-MS), a powerful method for monitoring protein structure stability and dynamics in solution. We performed HDX-MS measurements on AAVs without or with different DNA payloads of different sizes, and obtained detailed dynamic information on the entire AAV sequence including the two functionally important segments not previously structurally characterized. The unique N terminus of the capsid protein VP1 (VP1u) was found to adopt a highly dynamic and unstable conformation with low HDX protection across the entire region, whereas the presence of a DNA payload increased its protection. The VP1 and VP2 shared region (VP1/2) showed no measurable protection, with or without DNA. Differential HDX between empty and full capsid samples allowed us to identify potential new DNA-capsid interaction sites located primarily around the five-fold channel, which differ from the three-fold pocket binding site previously identified. Our HDX-MS method for characterizing AAV structural dynamics opens a new way for future efforts to understand AAV structure-function relationships and engineer next-generation AAV vectors with improved gene delivery properties.
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Affiliation(s)
- Xiang Ye
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Yunli Hu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Haibo Qiu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Ning Li
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
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10
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Smith J, Carillo S, Kulkarni A, Redman E, Yu K, Bones J. Rapid characterization of adeno-associated virus (AAV) capsid proteins using microchip ZipChip CE-MS. Anal Bioanal Chem 2024; 416:1069-1084. [PMID: 38102410 PMCID: PMC10800304 DOI: 10.1007/s00216-023-05097-5] [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: 11/08/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Adeno-associated viruses (AAVs) are viral vectors used as delivery systems for gene therapies. Intact protein characterization of AAV viral capsid proteins (VPs) and their post-translational modifications is critical to ensuring product quality. In this study, microchip-based ZipChip capillary electrophoresis-mass spectrometry (CE-MS) was applied for the rapid characterization of AAV intact VPs, specifically full and empty viral capsids of serotypes AAV6, AAV8 and AAV9, which was accomplished using 5 min of analysis time. Low levels of dimethyl sulfoxide (4%) in the background electrolyte (BGE) improved MS signal quality and component detection. A sensitivity evaluation revealed consistent detection of VP proteoforms when as little as 2.64 × 106 viral particles (≈26.4 picograms) were injected. Besides the traditional VP proteoforms used for serotype identification, multiple VP3 variants were detected, including truncated VP3 variants most likely generated by leaky scanning as well as unacetylated and un-cleaved VP3 proteoforms. Phosphorylation, known to impact AAV transduction efficiency, was also seen in all serotypes analysed. Additionally, low abundant fragments originating from either N- or C-terminus truncation were detected. As the aforementioned VP components can impact product quality and efficacy, the ZipChip's ability to rapidly characterize them illustrates its strength in monitoring product quality during AAV production.
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Affiliation(s)
- Josh Smith
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, A94 X099, Co. Dublin, Ireland
| | - Sara Carillo
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, A94 X099, Co. Dublin, Ireland
| | - Aditya Kulkarni
- 908 Devices Inc., 645 Summer Street #201, Boston, MA, 02210, USA
| | - Erin Redman
- 908 Devices Inc., 511 Davis Dr Suite 450, Morrisville, NC, 27560, USA
| | - Kate Yu
- 908 Devices Inc., 645 Summer Street #201, Boston, MA, 02210, USA
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, A94 X099, Co. Dublin, Ireland.
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland.
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11
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Smith J, Guapo F, Strasser L, Millán-Martín S, Milian SG, Snyder RO, Bones J. Development of a Rapid Adeno-Associated Virus (AAV) Identity Testing Platform through Comprehensive Intact Mass Analysis of Full-Length AAV Capsid Proteins. J Proteome Res 2023; 23:161-174. [PMID: 38123456 PMCID: PMC10775144 DOI: 10.1021/acs.jproteome.3c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Adeno-associated viruses (AAVs) are commonly used as vectors for the delivery of gene therapy targets. Characterization of AAV capsid proteins (VPs) and their post-translational modifications (PTMs) have become a critical attribute monitored to evaluate product quality. Liquid chromatography-mass spectrometry (LC-MS) analysis of intact AAV VPs provides both quick and reliable serotype identification as well as proteoform information on each VP. Incorporating these analytical strategies into rapid good manufacturing practice (GMP)-compliant workflows containing robust, but simplified, data processing methods is necessary to ensure effective product quality control (QC) during production. Here, we present a GMP-compliant LC-MS workflow for the rapid identification and in-depth characterization of AAVs. Hydrophilic interaction liquid chromatography (HILIC) MS with difluoroacetic acid as a mobile phase modifier is utilized to achieve the intact separation and identification of AAV VPs and their potential proteoforms. Peptide mapping is performed to confirm PTMs identified during intact VP analysis and for in-depth PTM characterization. The intact separations platform is then incorporated into a data processing workflow developed using GMP-compliant software capable of rapid AAV serotype identification and, if desired, specific serotype PTM monitoring and characterization. Such a platform provides product QC capabilities that are easily accessible in a regulatory setting.
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Affiliation(s)
- Josh Smith
- Characterisation
and Comparability Laboratory, The National
Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Dublin A94 X099, Ireland
| | - Felipe Guapo
- Characterisation
and Comparability Laboratory, The National
Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Dublin A94 X099, Ireland
| | - Lisa Strasser
- Characterisation
and Comparability Laboratory, The National
Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Dublin A94 X099, Ireland
| | - Silvia Millán-Martín
- Characterisation
and Comparability Laboratory, The National
Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Dublin A94 X099, Ireland
| | - Steven G. Milian
- Patheon
Viral Vector Services, 13859 Progress Blvd, Alachua, Florida 32615, United States
| | - Richard O. Snyder
- Patheon
Viral Vector Services, 13859 Progress Blvd, Alachua, Florida 32615, United States
| | - Jonathan Bones
- Characterisation
and Comparability Laboratory, The National
Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Dublin A94 X099, Ireland
- School
of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin D04 V1W8.F, Ireland
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12
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Yost SA, Firlar E, Glenn JD, Carroll HB, Foltz S, Giles AR, Egley JM, Firnberg E, Cho S, Nguyen T, Henry WM, Janczura KJ, Bruder J, Liu Y, Danos O, Karumuthil-Melethil S, Pannem S, Yost V, Engelson Y, Kaelber JT, Dimant H, Smith JB, Mercer AC. Characterization and biodistribution of under-employed gene therapy vector AAV7. J Virol 2023; 97:e0116323. [PMID: 37843374 PMCID: PMC10688378 DOI: 10.1128/jvi.01163-23] [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: 07/31/2023] [Accepted: 08/27/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The use of adeno-associated viruses (AAVs) as gene delivery vectors has vast potential for the treatment of many severe human diseases. Over one hundred naturally existing AAV capsid variants have been described and classified into phylogenetic clades based on their sequences. AAV8, AAV9, AAVrh.10, and other intensively studied capsids have been propelled into pre-clinical and clinical use, and more recently, marketed products; however, less-studied capsids may also have desirable properties (e.g., potency differences, tissue tropism, reduced immunogenicity, etc.) that have yet to be thoroughly described. These data will help build a broader structure-function knowledge base in the field, present capsid engineering opportunities, and enable the use of novel capsids with unique properties.
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Affiliation(s)
- Samantha A. Yost
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Emre Firlar
- Institute of Quantitative Biomedicine and Rutgers CryoEM & Nanoimaging Facility, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Justin D. Glenn
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Hayley B. Carroll
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Steven Foltz
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - April R. Giles
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Jenny M. Egley
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Elad Firnberg
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Sungyeon Cho
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Trang Nguyen
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - William M. Henry
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | | | - Joseph Bruder
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Ye Liu
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Olivier Danos
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | | | | | | | | | - Jason T. Kaelber
- Institute of Quantitative Biomedicine and Rutgers CryoEM & Nanoimaging Facility, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Hemi Dimant
- Invicro LLC, Needham, Massachusetts, USA
- Emit Imaging, Baltimore, Maryland, USA
| | - Jared B. Smith
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Andrew C. Mercer
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
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13
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Hanlon KS, Cheng M, De La Cruz D, Patel N, Santoscoy MC, Gong Y, Ng C, Nguyen DM, Nammour J, Clark SW, Kozarsky K, Maguire CA. In vivo selection in non-human primates identifies superior AAV capsids for on-target CSF delivery to spinal cord. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557506. [PMID: 37745398 PMCID: PMC10515928 DOI: 10.1101/2023.09.13.557506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Systemic administration of adeno-associated virus (AAV) vectors for spinal cord gene therapy has challenges including toxicity at high doses and pre-existing immunity that reduces efficacy. Intrathecal delivery of AAV vectors into the cerebral spinal fluid (CSF) can avoid many of the issues of systemic delivery, although achieving broad distribution of the vector and transgene expression throughout the spinal cord is challenging and vector entry to the periphery occurs, sometimes initiating hepatotoxicity. Here we performed two rounds of in vivo biopanning in non-human primates (NHPs) with an AAV9 peptide display library injected intrathecally and performed insert sequencing on DNA isolated from either whole tissue (conventional selection), isolated nuclei, or nuclei from transgene-expressing cells. A subsequent barcoded pool of candidates and AAV9 was compared at the DNA (biodistribution) and RNA (expression) level in spinal cord and liver of intrathecally injected NHPs. Most of the candidates displayed enhanced biodistribution compared to AAV9 at all levels of spinal cord ranging from 2 to 265-fold. Nuclear isolation or expression-based selection yielded 4 of 7 candidate capsids with enhanced transgene expression in spinal cord (up to 2.4-fold), while no capsid obtained by conventional selection achieved that level. Furthermore, several capsids displayed lower biodistribution to the liver of up to 1,250-fold, compared to AAV9, providing a remarkable on target/off target biodistribution ratio. These capsids may have potential for gene therapy programs directed at the spinal cord and the selection method described here should be useful in clinically relevant large animal models.
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Affiliation(s)
- Killian S. Hanlon
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | - Ming Cheng
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | - Demitri De La Cruz
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | - Nikita Patel
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | - Miguel C. Santoscoy
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Carrie Ng
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | - Diane M. Nguyen
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | - Josette Nammour
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
| | | | | | - Casey A. Maguire
- Department of Neurology, Massachusetts General Hospital, Boston, MA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA
- Harvard Medical School, Boston, MA
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14
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Grossen P, Skaripa Koukelli I, van Haasteren J, H E Machado A, Dürr C. The ice age - A review on formulation of Adeno-associated virus therapeutics. Eur J Pharm Biopharm 2023; 190:1-23. [PMID: 37423416 DOI: 10.1016/j.ejpb.2023.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Gene therapies offer promising therapeutic alternatives for many disorders that currently lack efficient treatment options. Due to their chemical nature and physico-chemical properties, delivery of polynucleic acids into target cells and subcellular compartments remains a significant challenge. Adeno-associated viruses (AAV) have gained a lot of interest for the efficient delivery of therapeutic single-stranded DNA (ssDNA) genomes over the past decades. More than a hundred products have been tested in clinical settings and three products have received market authorization by the US FDA in recent years. A lot of effort is being made to generate potent recombinant AAV (rAAV) vectors that show favorable safety and immunogenicity profiles for either local or systemic administration. Manufacturing processes are gradually being optimized to deliver a consistently high product quality and to serve potential market needs beyond rare indications. In contrast to protein therapeutics, most rAAV products are still supplied as frozen liquids within rather simple formulation buffers to enable sufficient product shelf life, significantly hampering global distribution and access. In this review, we aim to outline the hurdles of rAAV drug product development and discuss critical formulation and composition aspects of rAAV products under clinical evaluation. Further, we highlight recent development efforts in order to achieve stable liquid or lyophilized products. This review therefore provides a comprehensive overview on current state-of-the-art rAAV formulations and can further serve as a map for rational formulation development activities in the future.
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Affiliation(s)
- Philip Grossen
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland.
| | - Irini Skaripa Koukelli
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Joost van Haasteren
- F.Hoffmann-La Roche AG, Cell and Gene Therapy Unit, Gene Therapy Development Clinical Manufacturing, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Alexandra H E Machado
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christoph Dürr
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland
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15
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Chu W, Shastry S, Barbieri E, Prodromou R, Greback-Clarke P, Smith W, Moore B, Kilgore R, Cummings C, Pancorbo J, Gilleskie G, Daniele MA, Menegatti S. Peptide ligands for the affinity purification of adeno-associated viruses from HEK 293 cell lysates. Biotechnol Bioeng 2023; 120:2283-2300. [PMID: 37435968 PMCID: PMC10440015 DOI: 10.1002/bit.28495] [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: 02/21/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/13/2023]
Abstract
Adeno-associated viruses (AAVs) are the vector of choice for delivering gene therapies that can cure inherited and acquired diseases. Clinical research on various AAV serotypes significantly increased in recent years alongside regulatory approvals of AAV-based therapies. The current AAV purification platform hinges on the capture step, for which several affinity resins are commercially available. These adsorbents rely on protein ligands-typically camelid antibodies-that provide high binding capacity and selectivity, but suffer from low biochemical stability and high cost, and impose harsh elution conditions (pH < 3) that can harm the transduction activity of recovered AAVs. Addressing these challenges, this study introduces peptide ligands that selectively capture AAVs and release them under mild conditions (pH = 6.0). The peptide sequences were identified by screening a focused library and modeled in silico against AAV serotypes 2 and 9 (AAV2 and AAV9) to select candidate ligands that target homologous sites at the interface of the VP1-VP2 and VP2-VP3 virion proteins with mild binding strength (KD ~ 10-5 -10- 6 M). Selected peptides were conjugated to Toyopearl resin and evaluated via binding studies against AAV2 and AAV9, demonstrating the ability to target both serotypes with values of dynamic binding capacity (DBC10% > 1013 vp/mL of resin) and product yields (~50%-80%) on par with commercial adsorbents. The peptide-based adsorbents were finally utilized to purify AAV2 from a HEK 293 cell lysate, affording high recovery (50%-80%), 80- to 400-fold reduction of host cell proteins (HCPs), and high transduction activity (up to 80%) of the purified viruses.
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Affiliation(s)
- Wenning Chu
- 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
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Raphael Prodromou
- 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
| | - Will Smith
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Brandyn Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Christopher Cummings
- Biomanufacturing Training and Education Center (BTEC), 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
| | - 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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16
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Pénzes JJ, Pham HT, Chipman P, Smith EW, McKenna R, Tijssen P. Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus. Nat Commun 2023; 14:3515. [PMID: 37316488 DOI: 10.1038/s41467-023-38875-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, "pinning" the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.
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Affiliation(s)
- Judit J Pénzes
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada.
- The McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
- Institute for Quantitative Biomedicine, Rutgers, the Sate University of New Jersey, Piscataway, NJ, 08854, USA.
| | - Hanh T Pham
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada
- HTG Molecular Diagnostics, 3430 E Global Loop, Tucson, AZ, 85706, USA
| | - Paul Chipman
- The McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Emmanuel W Smith
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA
- JEOL USA Inc., Peabody, MA, 01960, USA
| | - Robert McKenna
- The McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Peter Tijssen
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada.
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17
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Santoscoy MC, Espinoza P, De La Cruz D, Mahamdeh M, Starr JR, Patel N, Maguire CA. An AAV capsid increases transduction of striatum and a ChAT promoter allows selective cholinergic neuron transduction. Mol Ther Methods Clin Dev 2023; 29:532-540. [PMID: 37359416 PMCID: PMC10285237 DOI: 10.1016/j.omtm.2023.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/04/2023] [Indexed: 06/28/2023]
Abstract
Adeno-associated virus (AAV) vectors are currently the most efficient option for intracranial gene therapies to treat neurodegenerative disease. Increased efficacy and safety will depend upon robust and specific expression of therapeutic genes into target cell-types within the human brain. In this study, we set out with two objectives: (1) to identify capsids with broader transduction of the striatum upon intracranial injection in mice and (2) to test a truncated human choline acetyltransferase (ChAT) promoter that would allow efficient and selective transduction of cholinergic neurons. We compared AAV9 and an engineered capsid, AAV-S, to mediate widespread reporter gene expression throughout the striatum. We observed that AAV-S transduced a significantly greater area of the injected hemisphere primarily in the rostral direction compared with AAV9 (CAG promoter). We tested AAV9 vectors packaging a reporter gene expression cassette driven by either the ChAT or CAG promoter. Specificity of transgene expression of ChAT neurons over other cells was 7-fold higher, and efficiency was 3-fold higher for the ChAT promoter compared with the CAG promoter. The AAV-ChAT transgene expression cassette should be a useful tool for the study of cholinergic neurons in mice, and the broader transduction area of AAV-S warrants further evaluation of this capsid.
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Affiliation(s)
- Miguel C. Santoscoy
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Paula Espinoza
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Demitri De La Cruz
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Mohammed Mahamdeh
- Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jacqueline R. Starr
- Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Nikita Patel
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Casey A. Maguire
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
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18
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Xiang YS, Hao GG. Biophysical characterization of adeno-associated virus capsid through the viral transduction life cycle. J Genet Eng Biotechnol 2023; 21:62. [PMID: 37195476 DOI: 10.1186/s43141-023-00518-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/11/2023] [Indexed: 05/18/2023]
Abstract
Adeno-associated virus (AAV) vectors have emerged as the leading delivery platforms for gene therapy. Throughout the life cycle of the virions, the capsid vector carries out diverse functions, ranging from cell surface receptor engagement, cellular entry, endosomal escape, nuclear import to new particle packaging, and assembly. Each of these steps is mediated by exquisite structure features of the viral capsid and its interaction with viral genome, Rep proteins, and cellular organelle and apparatus. In this brief review, we provide an overview of results from over a decade of extensive biophysical studies of the capsid employing various techniques. The remaining unaddressed questions and perspective are also discussed. The detailed understanding of the structure and function interplay would provide insight to the strategy for improving the efficacy and safety of the viral vectors.
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Affiliation(s)
| | - Gang Gary Hao
- Weston Biomedical Reviews, 65 Autumn Road, Weston, MA, 02493, USA.
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19
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Golm SK, Hübner W, Müller KM. Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses 2023; 15:v15051174. [PMID: 37243260 DOI: 10.3390/v15051174] [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: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.
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Affiliation(s)
- Susanne K Golm
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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20
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Shay TF, Sullivan EE, Ding X, Chen X, Ravindra Kumar S, Goertsen D, Brown D, Crosby A, Vielmetter J, Borsos M, Wolfe DA, Lam AW, Gradinaru V. Primate-conserved carbonic anhydrase IV and murine-restricted LY6C1 enable blood-brain barrier crossing by engineered viral vectors. SCIENCE ADVANCES 2023; 9:eadg6618. [PMID: 37075114 PMCID: PMC10115422 DOI: 10.1126/sciadv.adg6618] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The blood-brain barrier (BBB) presents a major challenge for delivering large molecules to study and treat the central nervous system. This is due in part to the scarcity of targets known to mediate BBB crossing. To identify novel targets, we leverage a panel of adeno-associated viruses (AAVs) previously identified through mechanism-agnostic directed evolution for improved BBB transcytosis. Screening potential cognate receptors for enhanced BBB crossing, we identify two targets: murine-restricted LY6C1 and widely conserved carbonic anhydrase IV (CA-IV). We apply AlphaFold-based in silico methods to generate capsid-receptor binding models to predict the affinity of AAVs for these identified receptors. Demonstrating how these tools can unlock target-focused engineering strategies, we create an enhanced LY6C1-binding vector, AAV-PHP.eC, that, unlike our prior PHP.eB, also works in Ly6a-deficient mouse strains such as BALB/cJ. Combined with structural insights from computational modeling, the identification of primate-conserved CA-IV enables the design of more specific and potent human brain-penetrant chemicals and biologicals, including gene delivery vectors.
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Affiliation(s)
- Timothy F. Shay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Corresponding author. (T.F.S.); (V.G.)
| | - Erin E. Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xiaozhe Ding
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sripriya Ravindra Kumar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Goertsen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Brown
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anaya Crosby
- California State Polytechnic University, Pomona, Pomona, CA, USA
| | - Jost Vielmetter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Máté Borsos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Damien A. Wolfe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Annie W. Lam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Corresponding author. (T.F.S.); (V.G.)
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21
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Large EE, Chapman MS. Adeno-associated virus receptor complexes and implications for adeno-associated virus immune neutralization. Front Microbiol 2023; 14:1116896. [PMID: 36846761 PMCID: PMC9950413 DOI: 10.3389/fmicb.2023.1116896] [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: 12/05/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Adeno-associated viruses (AAV) are among the foremost vectors for in vivo gene therapy. A number of monoclonal antibodies against several serotypes of AAV have previously been prepared. Many are neutralizing, and the predominant mechanisms have been reported as the inhibition of binding to extracellular glycan receptors or interference with some post-entry step. The identification of a protein receptor and recent structural characterization of its interactions with AAV compel reconsideration of this tenet. AAVs can be divided into two families based on which domain of the receptor is strongly bound. Neighboring domains, unseen in the high-resolution electron microscopy structures have now been located by electron tomography, pointing away from the virus. The epitopes of neutralizing antibodies, previously characterized, are now compared to the distinct protein receptor footprints of the two families of AAV. Comparative structural analysis suggests that antibody interference with protein receptor binding might be the more prevalent mechanism than interference with glycan attachment. Limited competitive binding assays give some support to the hypothesis that inhibition of binding to the protein receptor has been an overlooked mechanism of neutralization. More extensive testing is warranted.
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Affiliation(s)
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
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22
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Lin Y, Li C, Wang W, Li J, Huang C, Zheng X, Liu Z, Song X, Chen Y, Gao J, Wu J, Wu J, Tu Z, Lai L, Li XJ, Li S, Yan S. Intravenous AAV9 administration results in safe and widespread distribution of transgene in the brain of mini-pig. Front Cell Dev Biol 2023; 10:1115348. [PMID: 36762127 PMCID: PMC9902950 DOI: 10.3389/fcell.2022.1115348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/13/2022] [Indexed: 01/26/2023] Open
Abstract
Animal models are important for understanding the pathogenesis of human diseases and for developing and testing new drugs. Pigs have been widely used in the research on the cardiovascular, skin barrier, gastrointestinal, and central nervous systems as well as organ transplantation. Recently, pigs also become an attractive large animal model for the study of neurodegenerative diseases because their brains are very similar to human brains in terms of mass, gully pattern, vascularization, and the proportions of the gray and white matters. Although adeno-associated virus type 9 (AAV9) has been widely used to deliver transgenes in the brain, its utilization in large animal models remains to be fully characterized. Here, we report that intravenous injection of AAV9-GFP can lead to widespread expression of transgene in various organs in the pig. Importantly, GFP was highly expressed in various brain regions, especially the striatum, cortex, cerebellum, hippocampus, without detectable inflammatory responses. These results suggest that intravenous AAV9 administration can be used to establish large animal models of neurodegenerative diseases caused by gene mutations and to treat these animal models as well.
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Affiliation(s)
- Yingqi Lin
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Caijuan Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Wei Wang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jiawei Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Chunhui Huang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiao Zheng
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Zhaoming Liu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xichen Song
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Yizhi Chen
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jiale Gao
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jianhao Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jiaxi Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Zhuchi Tu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Liangxue Lai
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China,*Correspondence: Shihua Li, ; Sen Yan,
| | - Sen Yan
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China,*Correspondence: Shihua Li, ; Sen Yan,
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23
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Abstract
Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.
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Affiliation(s)
- Scott
M. Stagg
- Department
of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States
- Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department
of Biomedical Engineering, Oregon Health
& Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S. Chapman
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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24
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Xu G, Zhang R, Li H, Yin K, Ma X, Lou Z. Structural basis for the neurotropic AAV9 and the engineered AAVPHP.eB recognition with cellular receptors. Mol Ther Methods Clin Dev 2022; 26:52-60. [PMID: 35755945 PMCID: PMC9198364 DOI: 10.1016/j.omtm.2022.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/25/2022] [Indexed: 11/19/2022]
Abstract
Clade F adeno-associated virus (AAV) 9 has been utilized as therapeutic gene delivery vector, and it is capable of crossing blood brain barrier (BBB). Recently, an AAV9-based engineering serotype AAVPHP.eB with enhanced BBB crossing ability further expanded clade F AAVs' usages in the murine central nervous system (CNS) gene delivery. In this study, we determined the cryo-electron microscopy (cryo-EM) structures of the AAVPHP.eB and its parental serotype AAV9 in native form or in complex with their essential receptor AAV receptor (AAVR). These structures reveal the molecular details of their AAVR recognition, where the polycystic kidney disease repeat domain 2 (PKD2) of AAVR interacts with AAV9 and AAVPHP.eB virions at the 3-fold protrusions and the raised capsid regions between the 2- and 5-fold axes, termed the 2/5-fold wall. The interacting patterns of AAVR to AAV9 and AAVPHP.eB are similar to what was observed in AAV1/AAV2-AAVR complexes. Moreover, we found that the AAVPHP.eB variable region VIII (VR-VIII) may independently facilitate the new receptor recognition responsible for enhanced CNS transduction. Our study provides insights into the recognition principles of multiple receptors for engineered AAVPHP.eB and parental serotype AAV9, and further reveal the potential molecular basis underlying their different tropisms.
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Affiliation(s)
- Guangxue Xu
- MOE Key Laboratory of Protein Science & Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China
- Corresponding author Guangxue Xu, MOE Key Laboratory of Protein Science & Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China.
| | - Ran Zhang
- MOE Key Laboratory of Protein Science & Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Huapeng Li
- PackGene Biotech, Guangzhou, Guangdong, China
| | - Kaixin Yin
- International School of Beijing, Beijing, China
| | - Xinyi Ma
- Beijing No.8 High School, Beijing, China
| | - Zhiyong Lou
- MOE Key Laboratory of Protein Science & Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China
- Corresponding author Zhiyong Lou, MOE Key Laboratory of Protein Science & Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China.
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25
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Jang S, Shen HK, Ding X, Miles TF, Gradinaru V. Structural basis of receptor usage by the engineered capsid AAV-PHP.eB. Mol Ther Methods Clin Dev 2022; 26:343-354. [PMID: 36034770 PMCID: PMC9382559 DOI: 10.1016/j.omtm.2022.07.011] [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: 04/29/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
Adeno-associated virus serotype 9 (AAV9) is a promising gene therapy vector for treating neurodegenerative diseases due to its ability to penetrate the blood-brain barrier. PHP.eB was engineered from AAV9 by insertion of a 7-amino acid peptide and point mutation of neighboring residues, thereby enhancing potency in the central nervous system. Here, we report a 2.24-Å resolution cryo-electron microscopy structure of PHP.eB, revealing conformational differences from other 7-mer insertion capsid variants. In PHP.eB, the 7-mer loop adopts a bent conformation, mediated by an interaction between engineered lysine and aspartate residues. Further, we identify PKD2 as the main AAV receptor (AAVR) domain recognizing both AAV9 and PHP.eB and find that the PHP.eB 7-mer partially destabilizes this interaction. Analysis of previously reported AAV structures together with our pull-down data demonstrate that the 7-mer topology determined by the lysine-aspartate interaction dictates AAVR binding strength. Our results suggest that PHP.eB's altered tropism may arise from both an additional interaction with LY6A and weakening of its AAVR interaction. Changing the insertion length, but not sequence, modifies PKD2 binding affinity, suggesting that a steric clash impedes AAVR binding. This research suggests improved library designs for future AAV selections to identify non-LY6A-dependent vectors and modulate AAVR interaction strength.
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Affiliation(s)
- Seongmin Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hao K Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xiaozhe Ding
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Timothy F Miles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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26
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Sutter SO, Lkharrazi A, Schraner EM, Michaelsen K, Meier AF, Marx J, Vogt B, Büning H, Fraefel C. Adeno-associated virus type 2 (AAV2) uncoating is a stepwise process and is linked to structural reorganization of the nucleolus. PLoS Pathog 2022; 18:e1010187. [PMID: 35816507 PMCID: PMC9302821 DOI: 10.1371/journal.ppat.1010187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/21/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
Nucleoli are membrane-less structures located within the nucleus and are known to be involved in many cellular functions, including stress response and cell cycle regulation. Besides, many viruses can employ the nucleolus or nucleolar proteins to promote different steps of their life cycle such as replication, transcription and assembly. While adeno-associated virus type 2 (AAV2) capsids have previously been reported to enter the host cell nucleus and accumulate in the nucleolus, both the role of the nucleolus in AAV2 infection, and the viral uncoating mechanism remain elusive. In all prior studies on AAV uncoating, viral capsids and viral genomes were not directly correlated on the single cell level, at least not in absence of a helper virus. To elucidate the properties of the nucleolus during AAV2 infection and to assess viral uncoating on a single cell level, we combined immunofluorescence analysis for detection of intact AAV2 capsids and capsid proteins with fluorescence in situ hybridization for detection of AAV2 genomes. The results of our experiments provide evidence that uncoating of AAV2 particles occurs in a stepwise process that is completed in the nucleolus and supported by alteration of the nucleolar structure.
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Affiliation(s)
| | - Anouk Lkharrazi
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | | | - Kevin Michaelsen
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | | | - Jennifer Marx
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Bernd Vogt
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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27
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Canuti M, Pénzes JJ, Lang AS. A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics. Virus Evol 2022; 8:veac056. [PMID: 35783582 PMCID: PMC9242002 DOI: 10.1093/ve/veac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/13/2022] [Accepted: 06/13/2022] [Indexed: 12/11/2022] Open
Abstract
Amdoparvoviruses (genus Amdoparvovirus, family Parvoviridae) are primarily viruses of carnivorans, but recent studies have indicated that their host range might also extend to rodents and chiropterans. While their classification is based on the full sequence of the major nonstructural protein (NS1), several studies investigating amdoparvoviral diversity have been focused on partial sequences, leading to difficulties in accurately determining species demarcations and leaving several viruses unclassified. In this study, while reporting the complete genomic sequence of a novel amdoparvovirus identified in an American mink (British Columbia amdoparvovirus, BCAV), we studied the phylogenetic relationships of all amdoparvovirus-related sequences and provide a comprehensive reevaluation of their diversity and evolution. After excluding recombinant sequences, phylogenetic and pairwise sequence identity analyses allowed us to define fourteen different viruses, including the five currently classified species, BCAV, and four additional viruses that fulfill the International Committee on Taxonomy of Viruses criteria to be classified as species. We show that the group of viruses historically known as Aleutian mink disease virus (species Carnivore amdoparvovirus 1) should be considered as a cluster of at least four separate viral species that have been co-circulating in mink farms, facilitating the occurrence of inter-species recombination. Genome organization, splicing donor and acceptor sites, and protein sequence motifs were surprisingly conserved within the genus. The sequence of the major capsid protein virus protein 2 (VP2) was significantly more conserved between and within species compared to NS1, a phenomenon possibly linked to antibody-dependent enhancement (ADE). Homology models suggest a remarkably high degree of conservation of the spikes located near the icosahedral threefold axis of the capsid, comprising the surface region associated with ADE. A surprisingly high number of divergent amino acid positions were found in the luminal threefold and twofold axes of the capsid, regions of hitherto unknown function. We emphasize the importance of complete genome analyses and, given the marked phylogenetic inconsistencies across the genome, advise to obtain the complete coding sequences of divergent strains. Further studies on amdoparvovirus biology and structure as well as epidemiological and virus discovery investigations are required to better characterize the ecology and evolution of this important group of viruses.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
| | - Judit J Pénzes
- Institute for Quantitative Biomedicine, Rutgers the State University of New Jersey, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
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28
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Characterization of the Serpentine Adeno-Associated Virus (SAAV) Capsid Structure: Receptor Interactions and Antigenicity. J Virol 2022; 96:e0033522. [DOI: 10.1128/jvi.00335-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AAVs are widely studied therapeutic gene delivery vectors. However, preexisting antibodies and their detrimental effect on therapeutic efficacy are a primary challenge encountered during clinical trials.
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