1
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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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2
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Marwidi Y, Nguyen HOB, Santos D, Wangzor T, Bhardwaj S, Ernie G, Prawdzik G, Lew G, Shivak D, Trias M, Padilla J, Tran H, Meyer K, Surosky R, Ward AM. A robust and flexible baculovirus-insect cell system for AAV vector production with improved yield, capsid ratios and potency. Mol Ther Methods Clin Dev 2024; 32:101228. [PMID: 38524756 PMCID: PMC10959708 DOI: 10.1016/j.omtm.2024.101228] [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: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/26/2024]
Abstract
Manufacturing of adeno-associated viruses (AAV) for gene and cell therapy applications has increased significantly and spurred development of improved mammalian and insect cell-based production systems. We developed a baculovirus-based insect cell production system-the SGMO Helper-with a novel gene architecture and greater flexibility to modulate the expression level and content of individual Rep and Cap proteins. In addition, we incorporated modifications to the AAV6 capsid sequence that improves yield, capsid integrity, and potency. Production of recombinant AAV 6 (rAAV6) using the SGMO Helper had improved yields compared to the Bac-RepCap helper from the Kotin lab. SGMO Helper-derived rAAV6 is resistant to a previously described proteolytic cleavage unique to baculovirus-insect cell production systems and has improved capsid ratios and potency, in vitro and in vivo, compared with rAAV6 produced using Bac-RepCap. Next-generation sequencing sequence analysis demonstrated that the SGMO Helper is stable over six serial passages and rAAV6 capsids contain comparable amounts of non-vector genome DNA as rAAV6 produced using Bac-RepCap. AAV production using the SGMO Helper is scalable using bioreactors and has improved yield, capsid ratio, and in vitro potency. Our studies demonstrate that the SGMO Helper is an improved platform for AAV manufacturing to enable delivery of cutting-edge gene and cell therapies.
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Affiliation(s)
- Yoko Marwidi
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | | | - David Santos
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Tenzin Wangzor
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Sumita Bhardwaj
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Gabriel Ernie
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Gregg Prawdzik
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Garrett Lew
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - David Shivak
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Michael Trias
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Jada Padilla
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Hung Tran
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Kathleen Meyer
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
| | - Richard Surosky
- Sangamo Therapeutics, 501 Canal Boulevard, Richmond, CA 94804, USA
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3
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Moroncini G, Svegliati S, Grieco A, Cuccioloni M, Mozzicafreddo M, Paolini C, Agarbati S, Spadoni T, Amoresano A, Pinto G, Chen Q, Benfaremo D, Tonnini C, Senzacqua M, Alizzi S, Nieto K, Finke D, Viola N, Amico D, Galgani M, Gasparini S, Zuccatosta L, Menzo S, Müller M, Kleinschmidt J, Funaro A, Giordano A, La Cava A, Dorfmüller P, Amoroso A, Pucci P, Pezone A, Avvedimento EV, Gabrielli A. Adeno-Associated Virus Type 5 Infection via PDGFRα Is Associated With Interstitial Lung Disease in Systemic Sclerosis and Generates Composite Peptides and Epitopes Recognized by the Agonistic Immunoglobulins Present in Patients With Systemic Sclerosis. Arthritis Rheumatol 2024; 76:620-630. [PMID: 37975161 DOI: 10.1002/art.42746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/14/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
OBJECTIVE The etiopathogenesis of systemic sclerosis (SSc) is unknown. Platelet-derived growth factor receptors (PDGFRs) are overexpressed in patients with SSc. Because PDGFRα is targeted by the adeno-associated virus type 5 (AAV5), we investigated whether AAV5 forms a complex with PDGFRα exposing epitopes that may induce the immune responses to the virus-PDGFRα complex. METHODS The binding of monomeric human PDGFRα to the AAV5 capsid was analyzed by in silico molecular docking, surface plasmon resonance (SPR), and genome editing of the PDGFRα locus. AAV5 was detected in SSc lungs by in situ hybridization, immunohistochemistry, confocal microscopy, and molecular analysis of bronchoalveolar lavage (BAL) fluid. Immune responses to AAV5 and PDGFRα were evaluated by SPR using SSc monoclonal anti-PDGFRα antibodies and immunoaffinity-purified anti-PDGFRα antibodies from sera of patients with SSc. RESULTS AAV5 was detected in the BAL fluid of 41 of 66 patients with SSc with interstitial lung disease (62.1%) and in 17 of 66 controls (25.75%) (P < 0.001). In SSc lungs, AAV5 localized in type II pneumocytes and in interstitial cells. A molecular complex formed of spatially contiguous epitopes of the AAV5 capsid and of PDGFRα was identified and characterized. In silico molecular docking analysis and binding to the agonistic anti-PDGFRα antibodies identified spatially contiguous epitopes derived from PDGFRα and AAV5 that interacted with SSc agonistic antibodies to PDGFRα. These peptides were also able to bind total IgG isolated from patients with SSc, not from healthy controls. CONCLUSION These data link AVV5 with the immune reactivity to endogenous antigens in SSc and provide a novel element in the pathogenesis of SSc.
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Affiliation(s)
- Gianluca Moroncini
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | | | | | | | | | | | | | | | | | | | - Qingxin Chen
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Devis Benfaremo
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | | | | | - Silvia Alizzi
- Università di Torino and Azienda Ospedaliera Universitaria Città della Salute e della Scienza, di Torino, Torino, Italy
| | - Karen Nieto
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Doreen Finke
- Università Politecnica delle Marche, Ancona, Italy
| | - Nadia Viola
- Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | | | | | - Stefano Gasparini
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Lina Zuccatosta
- Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Stefano Menzo
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Martin Müller
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | - Antonio La Cava
- Federico II University, Napoli, Italy
- University of California, Los Angeles, CA
| | | | - Antonio Amoroso
- Università di Torino and Azienda Ospedaliera Universitaria Città della Salute e della Scienza, di Torino, Torino, Italy
| | | | | | | | - Armando Gabrielli
- Università Politecnica delle Marche, Ancona, Italy, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy, and Heinrich Heine University, Düsseldorf, Germany
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4
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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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5
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Kurth S, Li T, Hausker A, Evans WE, Dabre R, Müller E, Kervinen J. Separation of full and empty adeno-associated virus capsids by anion-exchange chromatography using choline-type salts. Anal Biochem 2024; 686:115421. [PMID: 38061416 DOI: 10.1016/j.ab.2023.115421] [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: 09/15/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Development of clinically desirable adeno-associated virus (AAV) vectors with optimal genome design requires rapid and accurate analytical methods to assess AAV quality. Anion-exchange (AEX) chromatography provides a powerful analytical method for full/empty AAV capsid ratio determination. However, the current AEX methodology for separation of empty and full AAV capsids largely relies on the use of the highly toxic tetramethylammonium chloride (TMAC). Here, we describe a novel analytical AEX method for separation of empty and full AAV capsids that uses only non-toxic, choline-type compounds that contain structural similarity to the quaternary ammonium ligand present on the surface of AEX resin. Choline-Cl gradient, combined with sensitive fluorescence detection, allowed a safe and effective separation of empty and full AAV capsids with reproducible empty/full ratio determination. The choline-based assay was suitable for commonly used serotypes, AAV2, AAV5, AAV6, and AAV8. The limit of detection was ∼3.9 × 108 virus particles in the assay. A gradient-hold step-gradient elution with choline-Cl resulted in enhanced baseline separation of empty and full AAV8 capsids. In summary, the use of choline-Cl in the AEX assay is recommended for empty/full capsid ratio determination and other applications in AAV production, and it eliminates the necessity of using toxic TMAC.
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Affiliation(s)
- Sam Kurth
- Tosoh Bioscience LLC, 3604 Horizon Drive, King of Prussia, PA, 19406, USA
| | - Tianyu Li
- Tosoh Bioscience LLC, 3604 Horizon Drive, King of Prussia, PA, 19406, USA
| | - Alana Hausker
- Tosoh Bioscience LLC, 3604 Horizon Drive, King of Prussia, PA, 19406, USA
| | - William E Evans
- Tosoh Bioscience LLC, 3604 Horizon Drive, King of Prussia, PA, 19406, USA
| | - Romain Dabre
- Tosoh Bioscience GmbH, Im Leuschnerpark 4, 64347, Griesheim, Germany
| | - Egbert Müller
- Tosoh Bioscience GmbH, Im Leuschnerpark 4, 64347, Griesheim, Germany
| | - Jukka Kervinen
- Tosoh Bioscience LLC, 3604 Horizon Drive, King of Prussia, PA, 19406, USA.
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6
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Dai M, Yang N, Xu K, Zhang J, Li X, Zhang Y, Li W. Discovering human cell-compatible gene therapy virus variants via optimized screening in mouse models. Cell Prolif 2024; 57:e13565. [PMID: 37864397 PMCID: PMC10905335 DOI: 10.1111/cpr.13565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
In gene therapy, intravenous injection of viral vectors reigns as the primary administration route. These vectors include adeno-associated viruses, adenoviruses, herpes viruses, rhabdoviruses and others. However, these naturally occurring viruses lack inherent tissue or organ tropism for tailored disease treatment. To address this, we devised an optimized process involving directed viral capsid evolution, organ-specific humanized mouse models and in vitro-in vivo virus screening. Our approach allows for the rapid generation specifically modified adeno-associated virus variants, surpassing the time required for natural evolution, which spans millions of years. Notably, these variants exhibit robust targeting of the liver, favouring chimeric human liver cells over murine hepatocytes. Furthermore, certain variants achieve augmented targeting with reduced off-target organ infection, thereby mitigating dosage requirements and enhancing safety in gene therapy.
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Affiliation(s)
- Moyu Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ning Yang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kai Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
| | - Jingwen Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life ScienceNankai UniversityTianjinChina
| | - Xueke Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijingChina
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7
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Notarte KI, Catahay JA, Macasaet R, Liu J, Velasco JV, Peligro PJ, Vallo J, Goldrich N, Lahoti L, Zhou J, Henry BM. Infusion reactions to adeno-associated virus (AAV)-based gene therapy: Mechanisms, diagnostics, treatment and review of the literature. J Med Virol 2023; 95:e29305. [PMID: 38116715 DOI: 10.1002/jmv.29305] [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: 07/11/2023] [Revised: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
The use of adeno-associated virus (AAV) vectors in gene therapy has demonstrated great potential in treating genetic disorders. However, infusion-associated reactions (IARs) pose a significant challenge to the safety and efficacy of AAV-based gene therapy. This review provides a comprehensive summary of the current understanding of IARs to AAV therapy, including their underlying mechanisms, clinical presentation, and treatment options. Toll-like receptor activation and subsequent production of pro-inflammatory cytokines are associated with IARs, stimulating neutralizing antibodies (Nabs) and T-cell responses that interfere with gene therapy. Risk factors for IARs include high titers of pre-existing Nabs, previous exposure to AAV, and specific comorbidities. Clinical presentation ranges from mild flu-like symptoms to severe anaphylaxis and can occur during or after AAV administration. There are no established guidelines for pre- and postadministration tests for AAV therapies, and routine laboratory requests are not standardized. Treatment options include corticosteroids, plasmapheresis, and supportive medications such as antihistamines and acetaminophen, but there is no consensus on the route of administration, dosage, and duration. This review highlights the inadequacy of current treatment regimens for IARs and the need for further research to improve the safety and efficacy of AAV-based gene therapy.
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Affiliation(s)
- Kin Israel Notarte
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jesus Alfonso Catahay
- Department of Medicine, Saint Peter's University Hospital, New Brunswick, New Jersey, USA
| | - Raymart Macasaet
- Department of Medicine, Monmouth Medical Center, Long Branch, New Jersey, USA
| | - Jin Liu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Jolaine Vallo
- Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | | | - Lokesh Lahoti
- Department of Medicine, Saint Peter's University Hospital, New Brunswick, New Jersey, USA
| | - Jiayan Zhou
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Brandon Michael Henry
- Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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8
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Casy W, Garza IT, Chen X, Dong T, Hu Y, Kanchwala M, Trygg CB, Shyng C, Xing C, Bunnell BA, Braun SE, Gray SJ. SMRT Sequencing Enables High-Throughput Identification of Novel AAVs from Capsid Shuffling and Directed Evolution. Genes (Basel) 2023; 14:1660. [PMID: 37628711 PMCID: PMC10454592 DOI: 10.3390/genes14081660] [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: 07/21/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The use of AAV capsid libraries coupled with various selection strategies has proven to be a remarkable approach for generating novel AAVs with enhanced and desired features. The inability to reliably sequence the complete capsid gene in a high-throughput manner has been the bottleneck of capsid engineering. As a result, many library strategies are confined to localized and modest alterations in the capsid, such as peptide insertions or single variable region (VR) alterations. The caveat of short reads by means of next-generation sequencing (NGS) hinders the diversity of capsid library construction, shifting the field away from whole-capsid modifications. We generated AAV capsid shuffled libraries of naturally occurring AAVs and applied directed evolution in both mice and non-human primates (NHPs), with the goal of yielding AAVs that are compatible across both species for translational applications. We recovered DNA from the tissues of injected animal and used single molecule real-time (SMRT) sequencing to identify variants enriched in the central nervous system (CNS). We provide insights and considerations for variant identification by comparing bulk tissue sequencing to that of isolated nuclei. Our work highlights the potential advantages of whole-capsid engineering, as well as indispensable methodological improvements for the analysis of recovered capsids, including the nuclei-enrichment step and SMRT sequencing.
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Affiliation(s)
- Widler Casy
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Irvin T. Garza
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
- Graduate School of Basic Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xin Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Thomas Dong
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Yuhui Hu
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.K.)
| | - Cynthia B. Trygg
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA (B.A.B.); (S.E.B.)
| | - Charles Shyng
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.K.)
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce A. Bunnell
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA (B.A.B.); (S.E.B.)
| | - Stephen E. Braun
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA (B.A.B.); (S.E.B.)
| | - Steven J. Gray
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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9
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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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10
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Rana J, Marsic D, Zou C, Muñoz-Melero M, Li X, Kondratov O, Li N, de Jong YP, Zolotukhin S, Biswas M. Characterization of a Bioengineered AAV3B Capsid Variant with Enhanced Hepatocyte Tropism and Immune Evasion. Hum Gene Ther 2023; 34:289-302. [PMID: 36950804 PMCID: PMC10125406 DOI: 10.1089/hum.2022.176] [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: 08/28/2022] [Accepted: 02/25/2023] [Indexed: 03/24/2023] Open
Abstract
Capsid engineering of adeno-associated virus (AAV) can surmount current limitations to gene therapy such as broad tissue tropism, low transduction efficiency, or pre-existing neutralizing antibodies (NAb) that restrict patient eligibility. We previously generated an AAV3B combinatorial capsid library by integrating rational design and directed evolution with the aim of improving hepatotropism. A potential isolate, AAV3B-DE5, gained a selective proliferative advantage over five rounds of iterative selection in hepatocyte spheroid cultures. In this study, we reanalyzed our original dataset derived from the AAV3B combinatorial library and isolated variants from earlier (one to three) rounds of selection, with the assumption that variants with faster replication kinetics are not necessarily the most efficient transducers. We identified a potential candidate, AAV3B-V04, which demonstrated significantly enhanced transduction in mouse-passaged primary human hepatocytes as well as in humanized liver chimeric mice, compared to the parental AAV3B or the previously described isolate, AAV3B-DE5. Interestingly, the AAV3B-V04 capsid variant exhibited significantly reduced seroreactivity to pooled or individual human serum samples. Forty-four percent of serum samples with pre-existing NAbs to AAV3B had 5- to 20-fold lower reciprocal NAb titers to AAV3B-V04. AAV3B-V04 has only nine amino acid substitutions, clustered in variable region IV compared to AAV3B, indicating the importance of the loops at the top of the three-fold protrusions in determining both transduction efficiency and immunogenicity. This study highlights the effectiveness of rational design combined with targeted selection for enhanced AAV transduction via molecular evolution approaches. Our findings support the concept of limiting selection rounds to isolate the best transducing AAV3B variant without outgrowth of faster replicating candidates. We conclude that AAV3B-V04 provides advantages such as improved human hepatocyte tropism and immune evasion and propose its utility as a superior candidate for liver gene therapy.
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Affiliation(s)
- Jyoti Rana
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Damien Marsic
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
- Porton Biologics, Jiangsu, China
| | - Chenhui Zou
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Maite Muñoz-Melero
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Xin Li
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Oleksandr Kondratov
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Ning Li
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ype P. de Jong
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Sergei Zolotukhin
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Moanaro Biswas
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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11
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Boye SL, O’Riordan C, Morris J, Lukason M, Compton D, Baek R, Elmore DM, Peterson J, Fajardo D, McCullough KT, Scaria A, McVie-Wylie A, Boye SE. Preclinical studies in support of phase I/II clinical trials to treat GUCY2D-associated Leber congenital amaurosis. Mol Ther Methods Clin Dev 2023; 28:129-145. [PMID: 36654798 PMCID: PMC9830033 DOI: 10.1016/j.omtm.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Mutations in GUCY2D are associated with severe early-onset retinal dystrophy, Leber congenital amaurosis type 1 (LCA1), a leading cause of blindness in children. Despite a high degree of visual disturbance stemming from photoreceptor dysfunction, patients with LCA1 largely retain normal photoreceptor structure, suggesting that they are good candidates for gene replacement therapy. The purpose of this study was to conduct the preclinical and IND-enabling experiments required to support clinical application of AAV5-hGRK1-GUCY2D in patients harboring biallelic recessive mutations in GUCY2D. Preclinical studies were conducted in mice to evaluate the effect of vector manufacturing platforms and transgene species on the therapeutic response. Dose-ranging studies were conducted in cynomolgus monkeys to establish the minimum dose required for efficient photoreceptor transduction. Good laboratory practice (GLP) studies evaluated systemic biodistribution in rats and toxicology in non-human primates (NHPs). These results expanded our knowledge of dose response for an AAV5-vectored transgene under control of the human rhodopsin kinase (hGRK1) promoter in NHPs with respect to photoreceptor transduction and safety and, in combination with the rat biodistribution and mouse efficacy studies, informed the design of a first-in-human clinical study in patients with LCA1.
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Affiliation(s)
- Sanford L. Boye
- Powell Gene Therapy Center, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Shannon E. Boye
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, PO Box 100296, Gainesville, FL 32610, USA
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12
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Large EE, Silveria MA, Weerakoon O, White TA, Chapman MS. Cross-Species Permissivity: Structure of a Goat Adeno-Associated Virus and Its Complex with the Human Receptor AAVR. J Virol 2022; 96:e0148422. [PMID: 36453885 PMCID: PMC9769368 DOI: 10.1128/jvi.01484-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 12/05/2022] Open
Abstract
Adeno-associated virus (AAV) is a small ssDNA satellite virus of high interest (in recombinant form) as a safe and effective gene therapy vector. AAV's human cell entry receptor (AAVR) contains polycystic kidney disease (PKD) domains bound by AAV. Seeking understanding of the spectrum of interactions, goat AAVGo.1 is investigated, because its host is the species most distant from human with reciprocal cross-species cell susceptibility. The structure of AAVGo.1, solved by cryo-EM to 2.9 Å resolution, is most similar to AAV5. Through ELISA (enzyme-linked immunosorbent assay) studies, it is shown that AAVGo.1 binds to human AAVR more strongly than do AAV2 or AAV5, and that it joins AAV5 in a class that binds exclusively to PKD domain 1 (PKD1), in contrast to other AAVs that interact primarily with PKD2. The AAVGo.1 cryo-EM structure of a complex with a PKD12 fragment of AAVR at 2.4 Å resolution shows PKD1 bound with minimal change in virus structure. There are only minor conformational adaptations in AAVR, but there is a near-rigid rotation of PKD1 with maximal displacement of the receptor domain by ~1 Å compared to PKD1 bound to AAV5. AAVGo.1 joins AAV5 as the second member of an emerging class of AAVs whose mode of receptor-binding is completely different from other AAVs, typified by AAV2. IMPORTANCE Adeno-associated virus (AAV) is a small ssDNA satellite parvovirus. As a recombinant vector with a protein shell encapsidating a transgene, recombinant AAV (rAAV) is a leading delivery vehicle for gene therapy, with two FDA-approved treatments and 150 clinical trials for 30 diseases. The human entry receptor AAVR has five PKD domains. To date, all serotypes, except AAV5, have interacted primarily with the second PKD domain, PKD2. Goat is the AAV host most distant from human with cross-species cell infectivity. AAVGo.1 is similar in structure to AAV5, the two forming a class with a distinct mode of receptor-binding. Within the two classes, binding interactions are mostly conserved, giving an indication of the latitude available in modulating delivery vectors.
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Affiliation(s)
- Edward E. Large
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Mark A. Silveria
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Onellah Weerakoon
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Tommi A. White
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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13
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Zinn E, Unzu C, Schmit PF, Turunen HT, Zabaleta N, Sanmiguel J, Fieldsend A, Bhatt U, Diop C, Merkel E, Gurrala R, Peacker B, Rios C, Messemer K, Santos J, Estelien R, Andres-Mateos E, Wagers AJ, Tipper C, Vandenberghe LH. Ancestral library identifies conserved reprogrammable liver motif on AAV capsid. Cell Rep Med 2022; 3:100803. [PMID: 36327973 PMCID: PMC9729830 DOI: 10.1016/j.xcrm.2022.100803] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/18/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
Gene therapy is emerging as a modality in 21st-century medicine. Adeno-associated viral (AAV) gene transfer is a leading technology to achieve efficient and durable expression of a therapeutic transgene. However, the structural complexity of the capsid has constrained efforts to engineer the particle toward improved clinical safety and efficacy. Here, we generate a curated library of barcoded AAVs with mutations across a variety of functionally relevant motifs. We then screen this library in vitro and in vivo in mice and nonhuman primates, enabling a broad, multiparametric assessment of every vector within the library. Among the results, we note a single residue that modulates liver transduction across all interrogated models while preserving transduction in heart and skeletal muscles. Moreover, we find that this mutation can be grafted into AAV9 and leads to profound liver detargeting while retaining muscle transduction-a finding potentially relevant to preventing hepatoxicities seen in clinical studies.
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Affiliation(s)
- Eric Zinn
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Carmen Unzu
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Pauline F Schmit
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Heikki T Turunen
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Julio Sanmiguel
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Allegra Fieldsend
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Urja Bhatt
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Cheikh Diop
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Erin Merkel
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Rakesh Gurrala
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Bryan Peacker
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Rios
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Kathleen Messemer
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer Santos
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Reynette Estelien
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Eva Andres-Mateos
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Amy J Wagers
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA; Joslin Diabetes Center, Boston, MA 02215, USA
| | - Christopher Tipper
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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14
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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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15
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Wang Y, Yang C, Hu H, Chen C, Yan M, Ling F, Wang KC, Wang X, Deng Z, Zhou X, Zhang F, Lin S, Du Z, Zhao K, Xiao X. Directed evolution of adeno-associated virus 5 capsid enables specific liver tropism. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:293-306. [PMID: 35474733 PMCID: PMC9010518 DOI: 10.1016/j.omtn.2022.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/18/2022] [Indexed: 02/07/2023]
Abstract
Impressive achievements in clinical trials to treat hemophilia establish a milestone in the development of gene therapy. It highlights the significance of AAV-mediated gene delivery to liver. AAV5 is a unique serotype featured by low neutralizing antibody prevalence. Nevertheless, its liver infectivity is relatively weak. Consequently, it is vital to exploit novel AAV5 capsid mutants with robust liver tropism. To this aim, we performed AAV5-NNK library and barcode screening in mice, from which we identified one capsid variant, called AAVzk2. AAVzk2 displayed a similar yield but divergent post-translational modification sites compared with wild-type serotypes. Mice intravenously injected with AAVzk2 demonstrated a stronger liver transduction than AAV5, roughly comparable with AAV8 and AAV9, with undetectable transduction of other tissues or organs such as heart, lung, spleen, kidney, brain, and skeletal muscle, indicating a liver-specific tropism. Further studies showed a superior human hepatocellular transduction of AAVzk2 to AAV5, AAV8 and AAV9, whereas the seroreactivity of AAVzk2 was as low as AAV5. Overall, we provide a novel AAV serotype that facilitates a robust and specific liver gene delivery to a large population, especially those unable to be treated by AAV8 and AAV9.
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Affiliation(s)
- Yuqiu Wang
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chen Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hanyang Hu
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chen Chen
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Mengdi Yan
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Feixiang Ling
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kathy Cheng Wang
- Department of Biology, New York University, 24 Waverly Pl, New York, NY 10003, USA
| | - Xintao Wang
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhe Deng
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xinyue Zhou
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Feixu Zhang
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Sen Lin
- Department of Ophthalmology, Daping Hospital, Army Medical Center of PLA, Army Medical University, Chongqing 400042, China
| | - Zengmin Du
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kai Zhao
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Corresponding author Kai Zhao, School of Bioengineering and School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Xiao Xiao
- School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Corresponding author Xiao Xiao, School of Bioengineering and School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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16
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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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17
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Katsikis G, Hwang IE, Wang W, Bhat VS, McIntosh NL, Karim OA, Blus BJ, Sha S, Agache V, Wolfrum JM, Springs SL, Sinskey AJ, Barone PW, Braatz RD, Manalis SR. Weighing the DNA Content of Adeno-Associated Virus Vectors with Zeptogram Precision Using Nanomechanical Resonators. NANO LETTERS 2022; 22:1511-1517. [PMID: 35148107 DOI: 10.1021/acs.nanolett.1c04092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantifying the composition of viral vectors used in vaccine development and gene therapy is critical for assessing their functionality. Adeno-associated virus (AAV) vectors, which are the most widely used viral vectors for in vivo gene therapy, are typically characterized using PCR, ELISA, and analytical ultracentrifugation which require laborious protocols or hours of turnaround time. Emerging methods such as charge-detection mass spectroscopy, static light scattering, and mass photometry offer turnaround times of minutes for measuring AAV mass using optical or charge properties of AAV. Here, we demonstrate an orthogonal method where suspended nanomechanical resonators (SNR) are used to directly measure both AAV mass and aggregation from a few microliters of sample within minutes. We achieve a precision near 10 zeptograms which corresponds to 1% of the genome holding capacity of the AAV capsid. Our results show the potential of our method for providing real-time quality control of viral vectors during biomanufacturing.
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Affiliation(s)
- Georgios Katsikis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Iris E Hwang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wade Wang
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Vikas S Bhat
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Nicole L McIntosh
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Omair A Karim
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Bartlomiej J Blus
- BioMarin Pharmaceutical, Inc., San Rafael, California 94901, United States
| | - Sha Sha
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vincent Agache
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Richard D Braatz
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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18
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Stiles K, Frenk EZ, Kaminsky SM, Crystal RG. Genetic Modification of the AAV5 Capsid with Lysine Residues Results in a Lung-tropic, Liver-detargeted Gene Transfer Vector. Hum Gene Ther 2022; 33:148-154. [PMID: 35018834 DOI: 10.1089/hum.2021.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Intravenous (IV) administration of naturally occurring adeno-associated virus (AAV) vectors are liver tropic, with a significant proportion of the total vector dose mediating gene expression in liver hepatocytes. AAV capsids that are directed towards other organs such as lung may be useful for therapy of non-liver-based diseases. Based on the knowledge that the lung capillary endothelium is the first capillary bed encountered by an intravenously administered AAV vector, and that the lung endothelium glycocalyx is enriched in negatively charged sialic acid, we hypothesized that adding positively changed lysine residues to the AAV capsid would enhance AAV biodistribution to the lung following intravenous administration. Using site directed mutagenesis, two lysine residues were inserted into variable loop VIII of the AAV serotype 5 capsid vector (AAV5-PK2). Organ distribution of AAV5-PK2 was compared to AAV5, AAVrh.10, AAV2, and AAV2-7m8 4 wk after intravenous administration (1011 gc) to C57Bl/6 male mice. As predicted, following intravenous administration, AAAV5-PK2 had the highest biodistribution in the lung (p<0.02 compared to AAV5, AAVrh.10, AAV2 and AAV2-7m8). Further, biodistribution to liver of AAV5-PK2 was 2-logs decreased compared to AAV5 (p<10-4) with a ratio of AAV5-PK2 lung to liver of 62-fold compared to AAV5 of 0.2-fold (p<0.0003). The AAV5-PK2 capsid represents a lung-tropic AAV vector that is also significantly detargeted from the liver, a property that may be useful in lung directed gene therapies.
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Affiliation(s)
- Katie Stiles
- Weill Cornell Medicine, 12295, New York, New York, United States;
| | - Esther Z Frenk
- Weill Cornell Medical College, 12295, 1300 York Avenue, New York, New York, United States, 10065;
| | | | - Ronald G Crystal
- Weill Medical College of Cornell University, Department of Genetic Medicine, 1300 York Avenue, Box 96, New York, New York, United States, 10021;
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19
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Salegio EA, Cukrov M, Lortz R, Green A, Lambert E, Copeland S, Gonzalez M, Stockinger DE, Yeung JM, Hwa GGC. Feasibility of Targeted Delivery of AAV5-GFP into the Cerebellum of Nonhuman Primates Following a Single Convection-Enhanced Delivery Infusion. Hum Gene Ther 2022; 33:86-93. [PMID: 34779239 DOI: 10.1089/hum.2021.163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In this study, we built upon our previous work to demonstrate the distribution and transport of AAV5-green fluorescent protein (GFP) following a single convection-enhanced delivery infusion into the nonhuman primate cerebellum, with no untoward side effects noted. Dosing under magnetic resonance imaging guidance revealed a sixfold larger volume of distribution compared with the volume of infusion, with no evidence of reflux underscoring the convective properties of the cerebellum and step design of the cannula. Postmortem tissue analysis, 4 weeks post-adeno-associated viral (AAV) delivery, revealed the robust presence of the transgene in situ, with GFP detection in secondary regions not directly targeted by the infusion, denoting distal transport of the vector. Irrespective of tropism, a twofold larger area of transgene expression was found and was corroborated against the presence of contrast on T1-weighted images. Different levels of transduction were detected between animals, which were negatively correlated with the level of antibody titer against the GFP construct, whereby the higher the antibody titer, the lower the level of transgene expression. These findings support the use of the posterior fossa as a potential target site for direct delivery of gene-based therapeutics for cerebellar diseases.
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Affiliation(s)
| | - Mira Cukrov
- Valley Biosystems, Inc., West Sacramento, California, USA
| | - Rachel Lortz
- Valley Biosystems, Inc., West Sacramento, California, USA
| | - Abigail Green
- Valley Biosystems, Inc., West Sacramento, California, USA
| | - Emily Lambert
- Valley Biosystems, Inc., West Sacramento, California, USA
| | | | - Marc Gonzalez
- Valley Biosystems, Inc., West Sacramento, California, USA
| | | | - Jeremy M Yeung
- Valley Biosystems, Inc., West Sacramento, California, USA
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20
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Khatri A, Shelke R, Guan S, Somanathan S. Higher seroprevalence of anti-AAV NAb among racial minorities in the United States. Hum Gene Ther 2021; 33:442-450. [PMID: 34861783 PMCID: PMC9063129 DOI: 10.1089/hum.2021.243] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Anti-AAV neutralizing antibodies (NAbs) can ablate efficacy of transgene expression following intravenous vector administration. This observation in both preclinical and clinical trials has led to exclusion of NAb positive patients from receiving AAV gene therapy. AAV drug development includes selection of capsids with lower NAb seroprevalence, that also possess other favorable traits. Often a limited number of healthy volunteers are screened to gauge NAb seroprevalence. However, limited data sets can be biased leading to inaccurate estimates of NAb incidence. Here we evaluated AAV NAbs against a panel of vectors among healthy donors within the United States. While the overall seroprevalence against most AAVs was lower, we did observe increased NAb incidence among Black and Hispanic donors. These findings of increased NAb seroprevalence among the minority races were confirmed in a second set of donors that also demonstrated higher seroprevalence among these races. Interracial-and intraracial differences within genders was also observed among donors. The increased incidence of AAV NAb among racial minorities was unexpected. Our findings underscore the need for removing bias in sample data sets and evaluating seroprevalence within the patient population while selecting capsids.
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Affiliation(s)
- Arpana Khatri
- Pfizer Inc, 2253, Rare disease research unit, Cambridge, Massachusetts, United States;
| | - Rajani Shelke
- Pfizer Inc, 2253, Rare Diseases Research Unit, Cambridge, Massachusetts, United States;
| | - Shunjie Guan
- Pfizer Inc, 2253, Rare Diseases Research Unit, Cambridge, Massachusetts, United States.,Pfizer Inc, 2253, Early Clinical Development, Cambridge, Massachusetts, United States;
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21
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Structurally Mapping Antigenic Epitopes of Adeno-Associated Virus 9: Development of Antibody Escape Variants. J Virol 2021; 96:e0125121. [PMID: 34757842 DOI: 10.1128/jvi.01251-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adeno-associated viruses (AAV) serve as vectors for therapeutic gene delivery. AAV9 vectors have been FDA approved, as Zolgensma®, for the treatment of spinal muscular atrophy and is being evaluated in clinical trials for the treatment of neurotropic and musculotropic diseases. A major hurdle for AAV-mediated gene delivery is the presence of pre-existing neutralizing antibodies in 40 to 80% of the general population. These pre-existing antibodies can reduce therapeutic efficacy through viral neutralization, and the size of the patient cohort eligible for treatment. In this study, cryo-electron microscopy and image reconstruction was used to define the epitopes of five anti-AAV9 monoclonal antibodies (MAbs); ADK9, HL2368, HL2370, HL2372, and HL2374, on the capsid surface. Three of these, ADK9, HL2370, and HL2374, bound on or near the icosahedral 3-fold axes, HL2368 to the 2/5-fold wall, and HL2372 to the region surrounding the 5-fold axes. Pseudo-atomic modeling enabled the mapping and identification of antibody contact amino acids on the capsid, including S454 and P659. These epitopes overlap with previously defined parvovirus antigenic sites. Capsid amino acids critical for the interactions were confirmed by mutagenesis followed by biochemical assays testing recombinant AAV9 (rAAV9) variants capable of escaping recognition and neutralization by the parental MAbs. These variants retained parental tropism and had similar or improved transduction efficiency compared to AAV9. These engineered rAAV9 variants could expand the patient cohort eligible for AAV9-mediated gene delivery by avoiding pre-existing circulating neutralizing antibodies. IMPORTANCE The use of recombinant AAVs (rAAVs) as delivery vectors for therapeutic genes is becoming increasingly popular, especially following the FDA approval of Luxturna® and Zolgensma®, based on serotypes AAV2 and AAV9, respectively. However, high titer anti-AAV neutralizing antibodies in the general population, exempts patients from treatment. The goal of this study is to circumvent this issue by creating AAV variant vectors not recognized by pre-existing neutralizing antibodies. The mapping of the antigenic epitopes of five different monoclonal antibodies (MAbs) on AAV9, to recapitulate a polyclonal response, enabled the rational design of escape variants with minimal disruption to cell tropism and gene expression. This study, which included four newly developed and now commercially available MAbs, provides a platform for the engineering of rAAV9 vectors that can be used to deliver genes to patients with pre-exiting AAV antibodies.
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22
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Frederick A, Sullivan J, Liu L, Adamowicz M, Lukason M, Raymer J, Luo Z, Jin X, Rao KN, O'Riordan C. Engineered Capsids for Efficient Gene Delivery to the Retina and Cornea. Hum Gene Ther 2021; 31:756-774. [PMID: 32578442 DOI: 10.1089/hum.2020.070] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Adeno-associated viral (AAV) vectors represent an ideal vehicle for human gene transfer. One advantage to the AAV vector system is the availability of multiple naturally occurring serotypes that provide selective tropisms for various target cells. Strategies to enhance the properties of the natural AAV isolates have been developed and can be divided into two approaches, rational design or directed evolution. The rational design approach utilizes knowledge of AAV capsids to make targeted changes to the capsid to alter transduction efficiency or specificity, while the directed evolution approach does not require a priori knowledge of capsid structure and includes random mutagenesis, capsid shuffling, or random peptide insertion. In this study, we describe the generation of novel variants for both AAV2 and AAV5 using a rational design approach and knowledge of AAV receptor binding, surface charge, and AAV capsid protein posttranslational modifications. The novel AAV2 and AAV5 variants demonstrate improved transduction properties in both the mouse retina and cornea. The translational fidelity of the novel AAV2 variant was confirmed in the context of the nonhuman primate (NHP) retina, whereas a NHP tissue explant model was established to allow the rapid assessment of translational fidelity between species for the AAV5 variants. The capsid-modified AAV2 and AAV5 variants described in this study have novel attributes that will add to the efficacy and specificity of their potential use in gene therapy for a range of human ocular diseases.
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Affiliation(s)
- Amy Frederick
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
| | - Jennifer Sullivan
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
| | - Lin Liu
- Department of BioAnalytics, Sanofi, Framingham, Massachusetts, USA
| | - Matthew Adamowicz
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
| | - Michael Lukason
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
| | - Jasmine Raymer
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
| | - Zhengyu Luo
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
| | - Xiaoying Jin
- Department of BioAnalytics, Sanofi, Framingham, Massachusetts, USA
| | - Kollu Nageswara Rao
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
| | - Catherine O'Riordan
- Department of Gene Therapy Research, Rare and Neurologic Diseases Therapeutic Area, Sanofi, Framingham, Massachusetts, USA
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23
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Large EE, Silveria MA, Zane GM, Weerakoon O, Chapman MS. Adeno-Associated Virus (AAV) Gene Delivery: Dissecting Molecular Interactions upon Cell Entry. Viruses 2021; 13:1336. [PMID: 34372542 PMCID: PMC8310307 DOI: 10.3390/v13071336] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Human gene therapy has advanced from twentieth-century conception to twenty-first-century reality. The recombinant Adeno-Associated Virus (rAAV) is a major gene therapy vector. Research continues to improve rAAV safety and efficacy using a variety of AAV capsid modification strategies. Significant factors influencing rAAV transduction efficiency include neutralizing antibodies, attachment factor interactions and receptor binding. Advances in understanding the molecular interactions during rAAV cell entry combined with improved capsid modulation strategies will help guide the design and engineering of safer and more efficient rAAV gene therapy vectors.
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Affiliation(s)
| | | | | | | | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65201, USA; (E.E.L.); (M.A.S.); (G.M.Z.); (O.W.)
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24
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Negrini M, Wang G, Heuer A, Björklund T, Davidsson M. AAV Production Everywhere: A Simple, Fast, and Reliable Protocol for In-house AAV Vector Production Based on Chloroform Extraction. ACTA ACUST UNITED AC 2021; 93:e103. [PMID: 32865885 DOI: 10.1002/cpns.103] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recombinant adeno-associated virus (rAAV) is a mammalian virus that has been altered to be used as a gene delivery vehicle. Several changes to the viral genome have made them replication deficient so that this aspect of the viral infection cycle is under full control of the experimenter, while maintaining gene expression machinery. Over the last decades, rAAVs have become the gold standard for studying in vivo gene function and are especially favorable for gene transfer in the central nervous system. AAVs have been proven safe and provide stable gene expression over a long period of time. They are extensively used in preclinical experiments and show great potential for clinical applications. However, the use of AAVs in preclinical settings are often held back due to availability. Waiting lines are long at commercial production facilities, and in-lab production is hindered due to lack of specific laboratory equipment needed. Here we present a novel production method that can be carried out in any molecular biology laboratory using standard laboratory equipment. We provide a simple, fast, and streamlined protocol for production that can result in titers comparable with the more time-consuming iodixanol gradient ultracentrifugation method. The yield using this protocol is high enough for any type of study where AAV is the vector of choice. © 2020 The Authors.
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Affiliation(s)
- Matilde Negrini
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Gang Wang
- Molecular Neuromodulation, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Andreas Heuer
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Tomas Björklund
- Molecular Neuromodulation, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Marcus Davidsson
- Molecular Neuromodulation, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
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25
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Khatwani SL, Pavlova A, Pirot Z. Anion-exchange HPLC assay for separation and quantification of empty and full capsids in multiple adeno-associated virus serotypes. Mol Ther Methods Clin Dev 2021; 21:548-558. [PMID: 33997103 PMCID: PMC8099603 DOI: 10.1016/j.omtm.2021.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022]
Abstract
Gene therapy has entered a new era where numerous therapies for severe and rare diseases are generating robust and compelling clinical results. The rapid improvements in gene therapies over the past few years can be attributed to better scientific understanding of the critical quality attributes that contribute to a safe and efficacious product, as well as a better understanding of the manufacturing processes that are required to yield consistent products, which routinely meet the quality standards required for clinical studies. Of particular concern is the need for an effective, quality control (QC)-compatible, and versatile test method for the quantification of empty and full capsids in recombinant adeno-associated virus (rAAV) samples from multiple serotypes. In that regard, we describe the development of a QC-compatible anion-exchange chromatography method consisting of a modular discontinuous gradient to achieve full baseline peak separation and quantification of empty and full AAV capsids. Using an rAAV6 vector, our assay was shown to be precise, linear, robust, and accurate-correlating well with orthogonal methods such as analytical ultracentrifugation (AUC) and cryogenic transmission electron microscopy (Cryo-TEM). Additionally, we demonstrate the versatility of our approach by adapting the method to separate and quantify empty/full capsids in samples from several rAAV serotypes.
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Affiliation(s)
| | - Anna Pavlova
- Sangamo Therapeutics, Inc., 7000 Marina Blvd., Brisbane, CA 94005, USA
| | - Zhu Pirot
- Sangamo Therapeutics, Inc., 7000 Marina Blvd., Brisbane, CA 94005, USA
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26
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Srivastava A, Mallela KMG, Deorkar N, Brophy G. Manufacturing Challenges and Rational Formulation Development for AAV Viral Vectors. J Pharm Sci 2021; 110:2609-2624. [PMID: 33812887 DOI: 10.1016/j.xphs.2021.03.024] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
Adeno-associated virus (AAV) has emerged as a leading platform for gene delivery for treating various diseases due to its excellent safety profile and efficient transduction to various target tissues. However, the large-scale production and long-term storage of viral vectors is not efficient resulting in lower yields, moderate purity, and shorter shelf-life compared to recombinant protein therapeutics. This review provides a comprehensive analysis of upstream, downstream and formulation unit operation challenges encountered during AAV vector manufacturing, and discusses how desired product quality attributes can be maintained throughout product shelf-life by understanding the degradation mechanisms and formulation strategies. The mechanisms of various physical and chemical instabilities that the viral vector may encounter during its production and shelf-life because of various stressed conditions such as thermal, shear, freeze-thaw, and light exposure are highlighted. The role of buffer, pH, excipients, and impurities on the stability of viral vectors is also discussed. As such, the aim of this review is to outline the tools and a potential roadmap for improving the quality of AAV-based drug products by stressing the need for a mechanistic understanding of the involved processes.
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Affiliation(s)
- Arvind Srivastava
- Biopharma Production, Avantor, Inc., 1013 US Highway, 202/206, Bridgewater, NJ, United States.
| | - Krishna M G Mallela
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, MS C238-V20, Aurora, CO 80045, United States.
| | - Nandkumar Deorkar
- Biopharma Production, Avantor, Inc., 1013 US Highway, 202/206, Bridgewater, NJ, United States
| | - Ger Brophy
- Biopharma Production, Avantor, Inc., 1013 US Highway, 202/206, Bridgewater, NJ, United States
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27
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Completion of the AAV Structural Atlas: Serotype Capsid Structures Reveals Clade-Specific Features. Viruses 2021; 13:v13010101. [PMID: 33450892 PMCID: PMC7828300 DOI: 10.3390/v13010101] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of AAV7, AAV11, AAV12, and AAV13 determined by cryo-electron microscopy and three-dimensional image reconstruction to 2.96, 2.86, 2.54, and 2.76 Å resolution, respectively. These structures complete the structural atlas of the AAV serotype capsids. AAV7 represents the first clade D capsid structure; AAV11 and AAV12 are of a currently unassigned clade that would include AAV4; and AAV13 represents the first AAV2-AAV3 hybrid clade C capsid structure. These newly determined capsid structures all exhibit the AAV capsid features including 5-fold channels, 3-fold protrusions, 2-fold depressions, and a nucleotide binding pocket with an ordered nucleotide in genome-containing capsids. However, these structures have viral proteins that display clade-specific loop conformations. This structural characterization completes our three-dimensional library of the current AAV serotypes to provide an atlas of surface loop configurations compatible with capsid assembly and amenable for future vector engineering efforts. Derived vectors could improve gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity or receptor retargeting.
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28
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Silveria MA, Large EE, Zane GM, White TA, Chapman MS. The Structure of an AAV5-AAVR Complex at 2.5 Å Resolution: Implications for Cellular Entry and Immune Neutralization of AAV Gene Therapy Vectors. Viruses 2020; 12:E1326. [PMID: 33218165 PMCID: PMC7698955 DOI: 10.3390/v12111326] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/28/2022] Open
Abstract
Adeno-Associated Virus is the leading vector for gene therapy. Although it is the vector for all in vivo gene therapies approved for clinical use by the US Food and Drug Administration, its biology is still not yet fully understood. It has been shown that different serotypes of AAV bind to their cellular receptor, AAVR, in different ways. Previously we have reported a 2.4Å structure of AAV2 bound to AAVR that shows ordered structure for only one of the two AAVR domains with which AAV2 interacts. In this study we present a 2.5Å resolution structure of AAV5 bound to AAVR. AAV5 binds to the first polycystic kidney disease (PKD) domain of AAVR that was not ordered in the AAV2 structure. Interactions of AAV5 with AAVR are analyzed in detail, and the implications for AAV2 binding are explored through molecular modeling. Moreover, we find that binding sites for the antibodies ADK5a, ADK5b, and 3C5 on AAV5 overlap with the binding site of AAVR. These insights provide a structural foundation for development of gene therapy agents to better evade immune neutralization without disrupting cellular entry.
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Affiliation(s)
- Mark A. Silveria
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Edward E. Large
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Tommi A. White
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
- Electron Microscopy Core, University of Missouri, Columbia, MO 65211, USA
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
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29
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Biswas M, Marsic D, Li N, Zou C, Gonzalez-Aseguinolaza G, Zolotukhin I, Kumar SRP, Rana J, Butterfield JSS, Kondratov O, de Jong YP, Herzog RW, Zolotukhin S. Engineering and In Vitro Selection of a Novel AAV3B Variant with High Hepatocyte Tropism and Reduced Seroreactivity. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:347-361. [PMID: 33145371 PMCID: PMC7591349 DOI: 10.1016/j.omtm.2020.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/29/2020] [Indexed: 01/04/2023]
Abstract
Limitations to successful gene therapy with adeno-associated virus (AAV) can comprise pre-existing neutralizing antibodies to the vector capsid that can block cellular entry, or inefficient transduction of target cells that can lead to sub-optimal expression of the therapeutic transgene. Recombinant serotype 3 AAV (AAV3) is an emerging candidate for liver-directed gene therapy. In this study, we integrated rational design by using a combinatorial library derived from AAV3B capsids with directed evolution by in vitro selection for liver-targeted AAV variants. The AAV3B-DE5 variant described herein was undetectable in the original viral library but gained a selective advantage upon in vitro passaging in human hepatocarcinoma spheroid cultures. AAV3B-DE5 contains 24 capsid amino acid substitutions compared with AAV3B, distributed among all five variable regions, with strong selective pressure on VR-IV, VR-V, and VR-VII. In vivo, AAV3B-DE5 demonstrated improved human hepatocyte tropism in a liver chimeric mouse model. Importantly, this variant exhibited reduced seroreactivity to human intravenous immunoglobulin (i.v. Ig), as well as individual serum samples from 100 healthy human donors. Therefore, molecular evolution using a combinatorial library platform generated a viral capsid with high hepatocyte tropism and enhanced evasion of pre-existing AAV neutralizing antibodies.
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Affiliation(s)
- Moanaro Biswas
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Damien Marsic
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL 32610, USA.,Porton Biologics, Building 3, Ascendas Park, No. 388 Xinping Street, Suzhou Industrial Park, Jiangsu 215021, China
| | - Ning Li
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chenhui Zou
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10065, USA.,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Irene Zolotukhin
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL 32610, USA
| | - Sandeep R P Kumar
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jyoti Rana
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - John S S Butterfield
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL 32610, USA
| | - Oleksandr Kondratov
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL 32610, USA
| | - Ype P de Jong
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Roland W Herzog
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sergei Zolotukhin
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL 32610, USA
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30
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Mietzsch M, Smith JK, Yu JC, Banala V, Emmanuel SN, Jose A, Chipman P, Bhattacharya N, McKenna R, Agbandje-McKenna M. Characterization of AAV-Specific Affinity Ligands: Consequences for Vector Purification and Development Strategies. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:362-373. [PMID: 33145372 PMCID: PMC7591348 DOI: 10.1016/j.omtm.2020.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023]
Abstract
Affinity-based purification of adeno-associated virus (AAV) vectors has replaced density-based methods for vectors used in clinical settings. This method utilizes camelid single-domain antibodies recognizing AAV capsids. These include AVB Sepharose (AVB) and POROS CaptureSelect affinity ligand for AAV8 (CSAL8) and AAV9 (CSAL9). In this study, we utilized cryo-electron microscopy and 3D image reconstruction to map the binding sites of these affinity ligands on the capsids of several AAV serotypes, including AAV1, AAV2, AAV5, AAV8, and AAV9, representing the range of sequence and structure diversity among AAVs. The AAV-ligand complex structures showed that AVB and CSAL9 bound to the 5-fold capsid region, although in different orientations, and CSAL8 bound to the side of the 3-fold protrusion. The AAV contact residues required for ligand binding, and thus AAV purification, and the ability of the ligands to neutralize infection were analyzed. The data show that only a few residues within the epitopes served to block affinity ligand binding. Neutralization was observed for AAV1 and AAV5 with AVB, for AAV1 with CSAL8, and for AAV9 with CSAL9, associated with regions that overlap with epitopes for neutralizing monoclonal antibodies against these capsids. This information is critical and could be generally applicable in the development of novel AAV vectors amenable to affinity column purification.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - J Kennon Smith
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jennifer C Yu
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Vibhu Banala
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Shanan N Emmanuel
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Ariana Jose
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Nilakshee Bhattacharya
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
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31
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McNally DJ, Piras BA, Willis CM, Lockey TD, Meagher MM. Development and Optimization of a Hydrophobic Interaction Chromatography-Based Method of AAV Harvest, Capture, and Recovery. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:275-284. [PMID: 33102619 PMCID: PMC7569186 DOI: 10.1016/j.omtm.2020.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022]
Abstract
With many ongoing clinical trials utilizing adeno-associated virus (AAV) gene therapy, it is necessary to find scalable and serotype-independent primary capture and recovery methods to allow for efficient and robust manufacturing processes. Here, we demonstrate the ability of a hydrophobic interaction chromatography membrane to capture and recover AAV1, AAV5, AAV8, and AAV “Mutant C” (a novel serotype incorporating elements of AAV3B and AAV8) particles from cell culture media and cell lysate with recoveries of 76%–100% of loaded material, depending on serotype. A simple, novel technique that integrates release and recovery of cell-associated AAV capsids is demonstrated. We show that by the addition of lyotropic salts to AAV-containing cell suspensions, AAV is released at an equivalent efficiency to mechanical lysis. The addition of the lyotropic salt also promotes a phase separation, which allows physical removal of large amounts of DNA and insoluble cellular debris from the AAV-containing aqueous fraction. The AAV is then captured and eluted from a hydrophobic interaction chromatography membrane. This integrated lysis and primary capture and recovery technique facilitates substantial removal of host-cell DNA and host-cell protein impurities.
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Affiliation(s)
- David J McNally
- Department of Therapeutics Production & Quality, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Bryan A Piras
- Department of Therapeutics Production & Quality, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | | | - Timothy D Lockey
- Department of Therapeutics Production & Quality, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Michael M Meagher
- Department of Therapeutics Production & Quality, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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32
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Mietzsch M, Li Y, Kurian J, Smith JK, Chipman P, McKenna R, Yang L, Agbandje-McKenna M. Structural characterization of a bat Adeno-associated virus capsid. J Struct Biol 2020; 211:107547. [PMID: 32522552 PMCID: PMC9744130 DOI: 10.1016/j.jsb.2020.107547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/04/2020] [Indexed: 02/08/2023]
Abstract
Adeno-associated viruses (AAVs) are widespread among vertebrates. AAVs isolated from bats display low capsid protein sequence identities (<60%) to AAV2, AAV5, and other primate AAVs. Here we report the first capsid structure of a non-primate AAV which was isolated from bats. The capsid structure of BtAAV-10HB (10HB) was determined by cryo-electron microscopy and three-dimensional image reconstruction to 3.03 Å resolution. Comparison of empty and genome-containing capsids showed that the capsid structures are almost identical except for an ordered nucleotide in a previously described nucleotide-binding pocket, the density in the 5-fold channel, and several amino acids with altered side chain conformations. Compared to other dependoparvoviruses, for example AAV2 and AAV5, 10HB displays unique structural features including insertions and deletions in capsid surface loops. Overall, the 10HB capsid structure superposes with an RMSD of 1.7 Å and 1.8 Å to AAV2 and AAV5, respectively. Currently all approved AAV human gene therapy biologics and vectors in clinical trials are based on primate isolates. However, pre-existing neutralizing antibodies in the human population represents a hurdle to their use. 10HB capsids are capable of packaging AAV2 vector genomes and thus have potential as gene delivery vectors. Significantly, a screen with human sera showed lack of recognition by the 10HB capsid. Thus, the different capsid surface of 10HB vectors likely renders it "invisible" to potential pre-existing neutralizing human anti-AAV antibodies especially because this virus or similar variants do not exist in primate populations.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Ya Li
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Justin Kurian
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - James Kennon Smith
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Lin Yang
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, USA,Address correspondence to Mavis Agbandje-McKenna,
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33
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Hsu HL, Brown A, Loveland AB, Lotun A, Xu M, Luo L, Xu G, Li J, Ren L, Su Q, Gessler DJ, Wei Y, Tai PWL, Korostelev AA, Gao G. Structural characterization of a novel human adeno-associated virus capsid with neurotropic properties. Nat Commun 2020; 11:3279. [PMID: 32606306 PMCID: PMC7327033 DOI: 10.1038/s41467-020-17047-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 05/27/2020] [Indexed: 02/05/2023] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) are currently considered the safest and most reliable gene delivery vehicles for human gene therapy. Three serotype capsids, AAV1, AAV2, and AAV9, have been approved for commercial use in patients, but they may not be suitable for all therapeutic contexts. Here, we describe a novel capsid identified in a human clinical sample by high-throughput, long-read sequencing. The capsid, which we have named AAVv66, shares high sequence similarity with AAV2. We demonstrate that compared to AAV2, AAVv66 exhibits enhanced production yields, virion stability, and CNS transduction. Unique structural properties of AAVv66 visualized by cryo-EM at 2.5-Å resolution, suggest that critical residues at the three-fold protrusion and at the interface of the five-fold axis of symmetry likely contribute to the beneficial characteristics of AAVv66. Our findings underscore the potential of AAVv66 as a gene therapy vector.
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Affiliation(s)
- Hung-Lun Hsu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Alexander Brown
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Anna B Loveland
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anoushka Lotun
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Meiyu Xu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Li Luo
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R., China
| | - Guangchao Xu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R., China
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lingzhi Ren
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Dominic J Gessler
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yuquan Wei
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R., China
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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34
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Cabanes-Creus M, Westhaus A, Navarro RG, Baltazar G, Zhu E, Amaya AK, Liao SHY, Scott S, Sallard E, Dilworth KL, Rybicki A, Drouyer M, Hallwirth CV, Bennett A, Santilli G, Thrasher AJ, Agbandje-McKenna M, Alexander IE, Lisowski L. Attenuation of Heparan Sulfate Proteoglycan Binding Enhances In Vivo Transduction of Human Primary Hepatocytes with AAV2. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:1139-1154. [PMID: 32490035 PMCID: PMC7260615 DOI: 10.1016/j.omtm.2020.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/07/2020] [Indexed: 12/19/2022]
Abstract
Use of the prototypical adeno-associated virus type 2 (AAV2) capsid delivered unexpectedly modest efficacy in an early liver-targeted gene therapy trial for hemophilia B. This result is consistent with subsequent data generated in chimeric mouse-human livers showing that the AAV2 capsid transduces primary human hepatocytes in vivo with low efficiency. In contrast, novel variants generated by directed evolution in the same model, such as AAV-NP59, transduce primary human hepatocytes with high efficiency. While these empirical data have immense translational implications, the mechanisms underpinning this enhanced AAV capsid transduction performance in primary human hepatocytes are yet to be fully elucidated. Remarkably, AAV-NP59 differs from the prototypical AAV2 capsid by only 11 aa and can serve as a tool to study the correlation between capsid sequence/structure and vector function. Using two orthogonal vectorological approaches, we have determined that just 2 of the 11 changes present in AAV-NP59 (T503A and N596D) account for the enhanced transduction performance of this capsid variant in primary human hepatocytes in vivo, an effect that we have associated with attenuation of heparan sulfate proteoglycan (HSPG) binding affinity. In support of this hypothesis, we have identified, using directed evolution, two additional single amino acid substitution AAV2 variants, N496D and N582S, which are highly functional in vivo. Both substitution mutations reduce AAV2's affinity for HSPG. Finally, we have modulated the ability of AAV8, a highly murine-hepatotropic serotype, to interact with HSPG. The results support our hypothesis that enhanced HSPG binding can negatively affect the in vivo function of otherwise strongly hepatotropic variants and that modulation of the interaction with HSPG is critical to ensure maximum efficiency in vivo. The insights gained through this study can have powerful implications for studies into AAV biology and capsid development for preclinical and clinical applications targeting liver and other organs.
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Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erhua Zhu
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Sophia H Y Liao
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Suzanne Scott
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia.,Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Erwan Sallard
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Kimberley L Dilworth
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Arkadiusz Rybicki
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Giorgia Santilli
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Adrian J Thrasher
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, 24-100 Puławy, Poland
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35
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Comparative Analysis of the Capsid Structures of AAVrh.10, AAVrh.39, and AAV8. J Virol 2020; 94:JVI.01769-19. [PMID: 31826994 DOI: 10.1128/jvi.01769-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022] Open
Abstract
Adeno-associated viruses (AAVs) from clade E are often used as vectors in gene delivery applications. This clade includes rhesus isolate 10 (AAVrh.10) and 39 (AAVrh.39) which, unlike representative AAV8, are capable of crossing the blood-brain barrier (BBB), thereby enabling the delivery of therapeutic genes to the central nervous system. Here, the capsid structures of AAV8, AAVrh.10 and AAVrh.39 have been determined by cryo-electron microscopy and three-dimensional image reconstruction to 3.08-, 2.75-, and 3.39-Å resolution, respectively, to enable a direct structural comparison. AAVrh.10 and AAVrh.39 are 98% identical in amino acid sequence but only ∼93.5% identical to AAV8. However, the capsid structures of all three viruses are similar, with only minor differences observed in the previously described surface variable regions, suggesting that specific residues S269 and N472, absent in AAV8, may confer the ability to cross the BBB in AAVrh.10 and AAVrh.39. Head-to-head comparison of empty and genome-containing particles showed DNA ordered in the previously described nucleotide-binding pocket, supporting the suggested role of this pocket in DNA packaging for the Dependoparvovirus The structural characterization of these viruses provides a platform for future vector engineering efforts toward improved gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity, or receptor retargeting.IMPORTANCE Recombinant adeno-associated virus vectors (rAAVs), based on AAV8 and AAVrh.10, have been utilized in multiple clinical trials to treat different monogenetic diseases. The closely related AAVrh.39 has also shown promise in vivo As recently attained for other AAV biologics, e.g., Luxturna and Zolgensma, based on AAV2 and AAV9, respectively, the vectors in this study will likely gain U.S. Food and Drug Administration approval for commercialization in the near future. This study characterized the capsid structures of these clinical vectors at atomic resolution using cryo-electron microscopy and image reconstruction for comparative analysis. The analysis suggested two key residues, S269 and N472, as determinants of BBB crossing for AAVrh.10 and AAVrh.39, a feature utilized for central nervous system delivery of therapeutic genes. The structure information thus provides a platform for engineering to improve receptor retargeting or tissue specificity. These are important challenges in the field that need attention. Capsid structure information also provides knowledge potentially applicable for regulatory product approval.
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36
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Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2. J Struct Biol 2019; 209:107433. [PMID: 31859208 DOI: 10.1016/j.jsb.2019.107433] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022]
Abstract
The AAV2.7m8 vector is an engineered capsid with a 10-amino acid insertion in adeno-associated virus (AAV) surface variable region VIII (VR-VIII) resulting in the alteration of an antigenic region of AAV2 and the ability to efficiently transduce retina cells following intravitreal administration. Directed evolution and in vivo screening in the mouse retina isolated this vector. In the present study, we sought to identify the structural differences between a recombinant AAV2.7m8 (rAAV2.7m8) vector packaging a GFP genome and its parental serotype, AAV2, by cryo-electron microscopy (cryo-EM) and image reconstruction. The structures of rAAV2.7m8 and AAV2 were determined to 2.91 and 3.02 Å resolution, respectively. The rAAV2.7m8 amino acid side-chains for residues 219-745 (the last C-terminal residue) were interpretable in the density map with the exception of the 10 inserted amino acids. While observable in a low sigma threshold density, side-chains were only resolved at the base of the insertion, likely due to flexibility at the top of the loop. A comparison to parental AAV2 (ordered from residues 217-735) showed the structures to be similar, except at some side-chains that had different orientations and, in VR-VIII containing the 10 amino acid insertion. VR-VIII is part of an AAV2 antigenic epitope, and the difference is consistent with rAAV2.7m8's escape from a known AAV2 monoclonal antibody, C37-B. The observations provide valuable insight into the configuration of inserted surface peptides on the AAV capsid and structural differences to be leveraged for future AAV vector rational design, especially for retargeted tropism and antibody escape.
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37
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Pipe S, Leebeek FWG, Ferreira V, Sawyer EK, Pasi J. Clinical Considerations for Capsid Choice in the Development of Liver-Targeted AAV-Based Gene Transfer. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 15:170-178. [PMID: 31660419 PMCID: PMC6807344 DOI: 10.1016/j.omtm.2019.08.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As gene transfer with adeno-associated virus (AAV) vectors is starting to enter clinical practice, this review examines the impact of vector capsid choice in liver-directed gene transfer for hemophilia. Given that there are multiple clinical trials completed and ongoing in this field, it is important to review the clinical evidence, particularly as a range of AAV-vector serotypes including AAV2, AAV5, AAV8, and AAV10 have been tested. Although there have been a number of successful trials, the development of two investigational AAV vectors for hemophilia B has been discontinued because they did not meet efficacy and/or safety expectations. Whether this difference between success and failure of gene transfer approaches reflects capsid choice, vector design, manufacturing system, or other variables is a question of great interest. Here, we examine the body of evidence across trials to determine the possible influences of serotype choice on key clinical outcomes such as safety, vector clearance, treatment eligibility, occurrence of transaminase elevations, activation of capsid-directed cytotoxic T cell responses, and clinical efficacy. In summary, gene transfer requires a balance between achieving sufficient transgene expression and minimizing destructive immune responses, which may be affected by AAV-vector serotype choice.
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Affiliation(s)
- Steven Pipe
- Pediatrics and Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Frank W G Leebeek
- Frank W. G. Leebeek, Erasmus University Medical Centre, Department of Hematology, Rotterdam, the Netherlands
| | | | | | - John Pasi
- Haemophilia Centre, The Royal London Hospital, Barts and The London School of Medicine and Dentistry, London, UK
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38
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Divergent engagements between adeno-associated viruses with their cellular receptor AAVR. Nat Commun 2019; 10:3760. [PMID: 31434885 PMCID: PMC6704107 DOI: 10.1038/s41467-019-11668-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/27/2019] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, revealing the molecular details by which PKD1 recognizes AAV5 and PKD2 is solely engaged with AAV1. PKD2 lies on the plateau region of the AAV1 capsid. However, the AAV5-AAVR interface is strikingly different, in which PKD1 is bound at the opposite side of the spike of the AAV5 capsid than the PKD2-interacting region of AAV1. Residues in strands F/G and the CD loop of PKD1 interact directly with AAV5, whereas residues in strands B/C/E and the BC loop of PKD2 make contact with AAV1. These findings further the understanding of the distinct mechanisms by which AAVR recognizes various AAV serotypes and provide an example of a single receptor engaging multiple viral serotypes with divergent rules. Multiple adeno-associated viruses (AAV) use the same receptor (AAVR), but the binding mode is not clear. Here, the authors determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, identify residues necessary for virus entry and compare the receptor interfaces of different AAV capsids.
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39
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Mietzsch M, Pénzes JJ, Agbandje-McKenna M. Twenty-Five Years of Structural Parvovirology. Viruses 2019; 11:E362. [PMID: 31010002 PMCID: PMC6521121 DOI: 10.3390/v11040362] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Parvoviruses, infecting vertebrates and invertebrates, are a family of single-stranded DNA viruses with small, non-enveloped capsids with T = 1 icosahedral symmetry. A quarter of a century after the first parvovirus capsid structure was published, approximately 100 additional structures have been analyzed. This first structure was that of Canine Parvovirus, and it initiated the practice of structure-to-function correlation for the family. Despite high diversity in the capsid viral protein (VP) sequence, the structural topologies of all parvoviral capsids are conserved. However, surface loops inserted between the core secondary structure elements vary in conformation that enables the assembly of unique capsid surface morphologies within individual genera. These variations enable each virus to establish host niches by allowing host receptor attachment, specific tissue tropism, and antigenic diversity. This review focuses on the diversity among the parvoviruses with respect to the transcriptional strategy of the encoded VPs, the advances in capsid structure-function annotation, and therapeutic developments facilitated by the available structures.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Judit J Pénzes
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
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40
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Adeno-associated virus 2 bound to its cellular receptor AAVR. Nat Microbiol 2019; 4:675-682. [DOI: 10.1038/s41564-018-0356-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]
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41
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High-Resolution Structural Characterization of a New Adeno-associated Virus Serotype 5 Antibody Epitope toward Engineering Antibody-Resistant Recombinant Gene Delivery Vectors. J Virol 2018; 93:JVI.01394-18. [PMID: 30333169 PMCID: PMC6288331 DOI: 10.1128/jvi.01394-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/09/2018] [Indexed: 11/20/2022] Open
Abstract
Adeno-associated virus serotype 5 (AAV5) is being developed as a gene delivery vector for several diseases, including hemophilia and Huntington's disease, and has a demonstrated efficient transduction in liver, lung, skeletal muscle, and the central nervous system. One limitation of AAV gene delivery is preexisting neutralizing antibodies, which present a significant challenge for vector effectiveness in therapeutic applications. Here, we report the cryo-electron microscopy (cryo-EM) and image-reconstructed structure of AAV5 in complex with a newly generated monoclonal antibody, HL2476, at 3.1-Å resolution. Unlike other available anti-AAV5 capsid antibodies, ADK5a and ADK5b, with epitopes surrounding the 5-fold channel of the capsid, HL2476 binds to the 3-fold protrusions. To elucidate the capsid-antibody interactions, the heavy and light chains were sequenced and their coordinates, along with the AAV5 viral protein, assigned to the density map. The high resolution of the complex enabled the identification of interacting residues at the 3-fold protrusions of the capsid, including R483, which forms two hydrogen bonds with the light chain of HL2476. A panel of AAV5 variants was generated and analyzed by native dot immunoblot and transduction assays. This identified variants with antibody escape phenotypes that maintain infectivity.IMPORTANCE Biologics based on recombinant AAVs (rAAVs) are increasingly becoming attractive human gene delivery vehicles, especially after the approval of Glybera in Europe and Luxturna in the United States. However, preexisting neutralizing antibodies against the AAV capsids in a large percentage of the human population limit wide-spread utilization of these vectors. To circumvent this problem, stealth vectors must be generated that are undetectable by these antibodies. This study details the high-resolution characterization of a new antigenic region on AAV5, a vector being developed for numerous delivery applications. The structure of AAV5 complexed with HL2476, a novel antibody, was determined by cryo-EM to 3.1-Å resolution. The resolution of the density map enabled the identification of interacting residues between capsid and antibody and the determinants of neutralization. Thus, the information obtained from this study can facilitate the generation of host immune escape vectors.
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Giles AR, Sims JJ, Turner KB, Govindasamy L, Alvira MR, Lock M, Wilson JM. Deamidation of Amino Acids on the Surface of Adeno-Associated Virus Capsids Leads to Charge Heterogeneity and Altered Vector Function. Mol Ther 2018; 26:2848-2862. [PMID: 30343890 DOI: 10.1016/j.ymthe.2018.09.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/19/2022] Open
Abstract
Post-translational modification of the adeno-associated virus capsids is a poorly understood factor in the development of these viral vectors into pharmaceutical products. Here we report the extensive capsid deamidation of adeno-associated virus serotype 8 and seven other diverse adeno-associated virus serotypes, with supporting evidence from structural, biochemical, and mass spectrometry approaches. The extent of deamidation at each site depended on the vector's age and multiple primary-sequence and three-dimensional structural factors. However, the extent of deamidation was largely independent of the vector recovery and purification conditions. We demonstrate the potential for deamidation to impact transduction activity and, moreover, correlate an early time point loss in vector activity to rapidly progressing spontaneous deamidation at several adeno-associated virus 8 asparagines. We explore mutational strategies that stabilize side-chain amides, improving vector transduction and reducing the lot-to-lot molecular variability that presents a key concern in biologics manufacturing. This study illuminates a previously unknown aspect of adeno-associated virus capsid heterogeneity and highlights its importance in the development of these vectors for gene therapy.
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Affiliation(s)
- April R Giles
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua J Sims
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin B Turner
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lakshmanan Govindasamy
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mauricio R Alvira
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin Lock
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Burg M, Rosebrough C, Drouin LM, Bennett A, Mietzsch M, Chipman P, McKenna R, Sousa D, Potter M, Byrne B, Samulski RJ, Agbandje-McKenna M. Atomic structure of a rationally engineered gene delivery vector, AAV2.5. J Struct Biol 2018; 203:236-241. [PMID: 29775653 PMCID: PMC9908299 DOI: 10.1016/j.jsb.2018.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 01/25/2023]
Abstract
AAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 (AAV2) with the muscle tropic properties of AAV1, and exhibited an antibody escape phenotype because of a modified antigenic epitope. To confirm the design, the structure of the vector was determined to a resolution of 2.78 Å using cryo-electron microscopy and image reconstruction. The structure of the major viral protein (VP), VP3, was ordered from residue 219 to 736, as reported for other AAV structures, and the five AAV2.5 residues exchanged from AAV2 to AAV1, Q263A, T265 (insertion), N706A, V709A, and T717N, were readily interpretable. Significantly, the surface loops containing these residues adopt the AAV1 conformation indicating the importance of amino acid residues in dictating VP structure.
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Affiliation(s)
- Matthew Burg
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Claire Rosebrough
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lauren M. Drouin
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Duncan Sousa
- Biological Science Imaging Resource, Department of Biological Sciences, The Florida State University, 89 Chieftan Way, Rm 119, Tallahassee, FL 32306, USA
| | - Mark Potter
- Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Barry Byrne
- Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - R. Jude Samulski
- Department of Pharmacology, Gene Therapy Center, University of North Carolina at Chapel Hill Chapel Hill NC, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
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Sullivan JA, Stanek LM, Lukason MJ, Bu J, Osmond SR, Barry EA, O'Riordan CR, Shihabuddin LS, Cheng SH, Scaria A. Rationally designed AAV2 and AAVrh8R capsids provide improved transduction in the retina and brain. Gene Ther 2018; 25:205-219. [PMID: 29785047 DOI: 10.1038/s41434-018-0017-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/25/2018] [Accepted: 03/27/2018] [Indexed: 01/18/2023]
Abstract
The successful application of adeno-associated virus (AAV) gene delivery vectors as a therapeutic paradigm will require efficient gene delivery to the appropriate cells in affected organs. In this study, we utilized a rational design approach to introduce modifications to the AAV2 and AAVrh8R capsids and the resulting variants were evaluated for transduction activity in the retina and brain. The modifications disrupted either capsid/receptor binding or altered capsid surface charge. Specifically, we mutated AAV2 amino acids R585A and R588A, which are required for binding to its receptor, heparan sulfate proteoglycans, to generate a variant referred to as AAV2-HBKO. In contrast to parental AAV2, the AAV2-HBKO vector displayed low-transduction activity following intravitreal delivery to the mouse eye; however, following its subretinal delivery, AAV2-HBKO resulted in significantly greater photoreceptor transduction. Intrastriatal delivery of AAV2-HBKO to mice facilitated widespread striatal and cortical expression, in contrast to the restricted transduction pattern of the parental AAV2 vector. Furthermore, we found that altering the surface charge on the AAVrh8R capsid by modifying the number of arginine residues on the capsid surface had a profound impact on subretinal transduction. The data further validate the potential of capsid engineering to improve AAV gene therapy vectors for clinical applications.
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Affiliation(s)
| | - Lisa M Stanek
- Sanofi, 49 New York Avenue, Framingham, MA, 01701-9322, USA
| | | | - Jie Bu
- Sanofi, 49 New York Avenue, Framingham, MA, 01701-9322, USA
| | | | | | | | | | - Seng H Cheng
- Sanofi, 49 New York Avenue, Framingham, MA, 01701-9322, USA
| | - Abraham Scaria
- Sanofi, 49 New York Avenue, Framingham, MA, 01701-9322, USA
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Lykken EA, Shyng C, Edwards RJ, Rozenberg A, Gray SJ. Recent progress and considerations for AAV gene therapies targeting the central nervous system. J Neurodev Disord 2018; 10:16. [PMID: 29776328 PMCID: PMC5960126 DOI: 10.1186/s11689-018-9234-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/01/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders, as a class of diseases, have been particularly difficult to treat even when the underlying cause(s), such as genetic alterations, are understood. What treatments do exist are generally not curative and instead seek to improve quality of life for affected individuals. The advent of gene therapy via gene replacement offers the potential for transformative therapies to slow or even stop disease progression for current patients and perhaps minimize or prevent the appearance of symptoms in future patients. MAIN BODY This review focuses on adeno-associated virus (AAV) gene therapies for diseases of the central nervous system. An overview of advances in AAV vector design for therapy is provided, along with a description of current strategies to develop AAV vectors with tailored tropism. Next, progress towards treatment of neurodegenerative diseases is presented at both the pre-clinical and clinical stages, focusing on a few select diseases to highlight broad categories of therapeutic parameters. Special considerations for more challenging cases are then discussed in addition to the immunological aspects of gene therapy. CONCLUSION With the promising clinical trial results that have been observed for the latest AAV gene therapies and continued pre-clinical successes, the question is no longer whether a therapy can be developed for certain neurodevelopmental disorders, but rather, how quickly.
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Affiliation(s)
- Erik Allen Lykken
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Charles Shyng
- University of North Carolina at Chapel Hill, Gene Therapy Center, Chapel Hill, NC 27599 USA
| | - Reginald James Edwards
- University of North Carolina at Chapel Hill, Gene Therapy Center, Chapel Hill, NC 27599 USA
| | - Alejandra Rozenberg
- University of North Carolina at Chapel Hill, Gene Therapy Center, Chapel Hill, NC 27599 USA
| | - Steven James Gray
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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Bennett A, Mietzsch M, Agbandje-McKenna M. Understanding capsid assembly and genome packaging for adeno-associated viruses. Future Virol 2017; 12:283-297. [PMID: 36776482 PMCID: PMC9910337 DOI: 10.2217/fvl-2017-0011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Adeno-associated viruses (AAVs) are promising therapeutic viral vectors. Their capsid is assembled from viral proteins VP1, VP2 and VP3, aided by an assembly-activating protein, followed by replication protein mediated packaging of their 4.7-kb genome with inverted terminal repeats as packaging signals. To aid improvement of AAV vectors, knowledge of viral determinants of successful capsid assembly and genome packaging is important. We review the current knowledge of these two processes and efforts to overcome limited DNA packaging capacity and limit the packaging of unwanted foreign DNA in vector development. Residues involved in essential capsid assembly and genome packaging interactions cannot be manipulated in vector engineering. This information thus aids strategies to improve vector production and to increase AAV packaging capacity toward improved efficacy of this vector system.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry & Molecular Biology, Center for Structure Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA
| | - Mario Mietzsch
- Department of Biochemistry & Molecular Biology, Center for Structure Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry & Molecular Biology, Center for Structure Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA,Author for correspondence: Tel.: +1 352 294 8393;
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Cryo-electron Microscopy Reconstruction and Stability Studies of the Wild Type and the R432A Variant of Adeno-associated Virus Type 2 Reveal that Capsid Structural Stability Is a Major Factor in Genome Packaging. J Virol 2016; 90:8542-51. [PMID: 27440903 DOI: 10.1128/jvi.00575-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 07/12/2016] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED The adeno-associated viruses (AAV) are promising therapeutic gene delivery vectors and better understanding of their capsid assembly and genome packaging mechanism is needed for improved vector production. Empty AAV capsids assemble in the nucleus prior to genome packaging by virally encoded Rep proteins. To elucidate the capsid determinants of this process, structural differences between wild-type (wt) AAV2 and a packaging deficient variant, AAV2-R432A, were examined using cryo-electron microscopy and three-dimensional image reconstruction both at an ∼5.0-Å resolution (medium) and also at 3.8- and 3.7-Å resolutions (high), respectively. The high resolution structures showed that removal of the arginine side chain in AAV2-R432A eliminated hydrogen bonding interactions, resulting in altered intramolecular and intermolecular interactions propagated from under the 3-fold axis toward the 5-fold channel. Consistent with these observations, differential scanning calorimetry showed an ∼10°C decrease in thermal stability for AAV2-R432A compared to wt-AAV2. In addition, the medium resolution structures revealed differences in the juxtaposition of the less ordered, N-terminal region of their capsid proteins, VP1/2/3. A structural rearrangement in AAV2-R432A repositioned the βA strand region under the icosahedral 2-fold axis rather than antiparallel to the βB strand, eliminating many intramolecular interactions. Thus, a single amino acid substitution can significantly alter the AAV capsid integrity to the extent of reducing its stability and possibly rendering it unable to tolerate the stress of genome packaging. Furthermore, the data show that the 2-, 3-, and 5-fold regions of the capsid contributed to producing the packaging defect and highlight a tight connection between the entire capsid in maintaining packaging efficiency. IMPORTANCE The mechanism of AAV genome packaging is still poorly understood, particularly with respect to the capsid determinants of the required capsid-Rep interaction. Understanding this mechanism may aid in the improvement of AAV packaging efficiency, which is currently ∼1:10 (10%) genome packaged to empty capsid in vector preparations. This report identifies regions of the AAV capsid that play roles in genome packaging and that may be important for Rep recognition. It also demonstrates the need to maintain capsid stability for the success of this process. This information is important for efforts to improve AAV genome packaging and will also inform the engineering of AAV capsid variants for improved tropism, specific tissue targeting, and host antibody escape by defining amino acids that cannot be altered without detriment to infectious vector production.
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Madigan VJ, Asokan A. Engineering AAV receptor footprints for gene therapy. Curr Opin Virol 2016; 18:89-96. [PMID: 27262111 PMCID: PMC6537878 DOI: 10.1016/j.coviro.2016.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/03/2016] [Accepted: 05/08/2016] [Indexed: 11/24/2022]
Abstract
Adeno-associated viruses (AAV) are currently at the forefront of human gene therapy clinical trials as recombinant vectors. Significant progress has been made in elucidating the structure, biology and tropisms of different naturally occurring AAV isolates in the past decade. In particular, a spectrum of AAV capsid interactions with host receptors have been identified and characterized. These studies have enabled a better understanding of key determinants of AAV cell recognition and entry in different hosts. This knowledge is now being applied toward engineering new, lab-derived AAV capsids with favorable transduction profiles. The current review conveys a structural perspective of capsid-glycan interactions and provides a roadmap for generating synthetic strains by engineering AAV receptor footprints.
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Affiliation(s)
- Victoria J Madigan
- Gene Therapy Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Aravind Asokan
- Gene Therapy Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Biochemistry & Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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Boye SL, Bennett A, Scalabrino ML, McCullough KT, Van Vliet K, Choudhury S, Ruan Q, Peterson J, Agbandje-McKenna M, Boye SE. Impact of Heparan Sulfate Binding on Transduction of Retina by Recombinant Adeno-Associated Virus Vectors. J Virol 2016; 90:4215-4231. [PMID: 26865709 PMCID: PMC4810560 DOI: 10.1128/jvi.00200-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Adeno-associated viruses (AAVs) currently are being developed to efficiently transduce the retina following noninvasive, intravitreal (Ivt) injection. However, a major barrier encountered by intravitreally delivered AAVs is the inner limiting membrane (ILM), a basement membrane rich in heparan sulfate (HS) proteoglycan. The goal of this study was to determine the impact of HS binding on retinal transduction by Ivt-delivered AAVs. The heparin affinities of AAV2-based tyrosine-to-phenylalanine (Y-F) and threonine-to-valine (T-V) capsid mutants, designed to avoid proteasomal degradation during cellular trafficking, were established. In addition, the impact of grafting HS binding residues onto AAV1, AAV5, and AAV8(Y733F) as well as ablation of HS binding by AAV2-based vectors on retinal transduction was investigated. Finally, the potential relationship between thermal stability of AAV2-based capsids and Ivt-mediated transduction was explored. The results show that the Y-F and T-V AAV2 capsid mutants bind heparin but with slightly reduced affinity relative to that of AAV2. The grafting of HS binding increased Ivt transduction by AAV1 but not by AAV5 or AAV8(Y733F). The substitution of any canonical HS binding residues ablated Ivt-mediated transduction by AAV2-based vectors. However, these same HS variant vectors displayed efficient retinal transduction when delivered subretinally. Notably, a variant devoid of canonical HS binding residues, AAV2(4pMut)ΔHS, was remarkably efficient at transducing photoreceptors. The disparate AAV phenotypes indicate that HS binding, while critical for AAV2-based vectors, is not the sole determinant for transduction via the Ivt route. Finally, Y-F and T-V mutations alter capsid stability, with a potential relationship existing between stability and improvements in retinal transduction by Ivt injection. IMPORTANCE AAV has emerged as the vector of choice for gene delivery to the retina, with attention focused on developing vectors that can mediate transduction following noninvasive, intravitreal injection. HS binding has been postulated to play a role in intravitreally mediated transduction of retina. Our evaluation of the HS binding of AAV2-based variants and other AAV serotype vectors and the correlation of this property with transduction points to HS affinity as a factor controlling retinal transduction following Ivt delivery. However, HS binding is not the only requirement for improved Ivt-mediated transduction. We show that AAV2-based vectors lacking heparin binding transduce retina by subretinal injection and display a remarkable ability to transduce photoreceptors, indicating that other receptors are involved in this phenotype.
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Affiliation(s)
- Sanford L Boye
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Miranda L Scalabrino
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - K Tyler McCullough
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Kim Van Vliet
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Shreyasi Choudhury
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Qing Ruan
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - James Peterson
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Shannon E Boye
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
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Nance ME, Duan D. Perspective on Adeno-Associated Virus Capsid Modification for Duchenne Muscular Dystrophy Gene Therapy. Hum Gene Ther 2015; 26:786-800. [PMID: 26414293 PMCID: PMC4692109 DOI: 10.1089/hum.2015.107] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/01/2015] [Indexed: 12/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a X-linked, progressive childhood myopathy caused by mutations in the dystrophin gene, one of the largest genes in the genome. It is characterized by skeletal and cardiac muscle degeneration and dysfunction leading to cardiac and/or respiratory failure. Adeno-associated virus (AAV) is a highly promising gene therapy vector. AAV gene therapy has resulted in unprecedented clinical success for treating several inherited diseases. However, AAV gene therapy for DMD remains a significant challenge. Hurdles for AAV-mediated DMD gene therapy include the difficulty to package the full-length dystrophin coding sequence in an AAV vector, the necessity for whole-body gene delivery, the immune response to dystrophin and AAV capsid, and the species-specific barriers to translate from animal models to human patients. Capsid engineering aims at improving viral vector properties by rational design and/or forced evolution. In this review, we discuss how to use the state-of-the-art AAV capsid engineering technologies to overcome hurdles in AAV-based DMD gene therapy.
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MESH Headings
- Animals
- Capsid/chemistry
- Capsid/metabolism
- Capsid Proteins/genetics
- Capsid Proteins/metabolism
- Dependovirus/genetics
- Dependovirus/metabolism
- Dystrophin/deficiency
- Dystrophin/genetics
- Gene Expression
- Genetic Therapy/methods
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Animal/genetics
- Muscular Dystrophy, Animal/metabolism
- Muscular Dystrophy, Animal/pathology
- Muscular Dystrophy, Animal/therapy
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Muscular Dystrophy, Duchenne/therapy
- Mutation
- Protein Engineering
- Species Specificity
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Affiliation(s)
- Michael E. Nance
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri
| | - Dongsheng Duan
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri
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