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Mietzsch M, Nelson AR, Hsi J, Zachary J, Potts L, Chipman P, Ghanem M, Khandekar N, Alexander IE, Logan GJ, Huiskonen JT, McKenna R. Structural characterization of antibody-responses from Zolgensma treatment provides the blueprint for the engineering of an AAV capsid suitable for redosing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590489. [PMID: 38746165 PMCID: PMC11092599 DOI: 10.1101/2024.05.01.590489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Monoclonal antibodies (mAbs) are useful tools to dissect the neutralizing antibody response against the adeno-associated virus (AAV) capsids used as gene therapy delivery vectors. This study structurally characterizes the interactions of 21 human-derived antibodies from patients treated with the AAV9 vector, Zolgensma ® , utilizing high-resolution cryo-electron microscopy. The majority of the bound antibodies do not conform to the icosahedral symmetry of the capsid, thus requiring localized reconstructions. These complex structures provide unprecedented details of the mAbs binding interfaces, with some antibodies inducing structural perturbations of the capsid upon binding. Key surface capsid amino acid residues were identified facilitating the design of capsid variants with an antibody escape phenotype, with the potential to expand the patient cohort treatable with AAV9 vectors to include those that were previously excluded due to their pre-existing neutralizing antibodies, and possibly also to those requiring redosing.
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2
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Gonzalez TJ, Mitchell-Dick A, Blondel LO, Fanous MM, Hull JA, Oh DK, Moller-Tank S, Castellanos Rivera RM, Piedrahita JA, Asokan A. Structure-guided AAV capsid evolution strategies for enhanced CNS gene delivery. Nat Protoc 2023; 18:3413-3459. [PMID: 37735235 DOI: 10.1038/s41596-023-00875-y] [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: 07/21/2022] [Accepted: 06/13/2023] [Indexed: 09/23/2023]
Abstract
Over the past 5 years, our laboratory has systematically developed a structure-guided library approach to evolve new adeno-associated virus (AAV) capsids with altered tissue tropism, higher transduction efficiency and the ability to evade pre-existing humoral immunity. Here, we provide a detailed protocol describing two distinct evolution strategies using structurally divergent AAV serotypes as templates, exemplified by improving CNS gene transfer efficiency in vivo. We outline four major components of our strategy: (i) structure-guided design of AAV capsid libraries, (ii) AAV library production, (iii) library cycling in single versus multiple animal models, followed by (iv) evaluation of lead AAV vector candidates in vivo. The protocol spans ~95 d, excluding gene expression analysis in vivo, and can vary depending on user experience, resources and experimental design. A distinguishing attribute of the current protocol is the focus on providing biomedical researchers with 3D structural information to guide evolution of precise 'hotspots' on AAV capsids. Furthermore, the protocol outlines two distinct methods for AAV library evolution consisting of adenovirus-enabled infectious cycling in a single species and noninfectious cycling in a cross-species manner. Notably, our workflow can be seamlessly merged with other RNA transcript-based library strategies and tailored for tissue-specific capsid selection. Overall, the procedures outlined herein can be adapted to expand the AAV vector toolkit for genetic manipulation of animal models and development of human gene therapies.
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Affiliation(s)
- Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Leo O Blondel
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Marco M Fanous
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Joshua A Hull
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Daniel K Oh
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Sven Moller-Tank
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jorge A Piedrahita
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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3
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Hsi J, Mietzsch M, Chipman P, Afione S, Zeher A, Huang R, Chiorini J, McKenna R. Structural and antigenic characterization of the avian adeno-associated virus capsid. J Virol 2023; 97:e0078023. [PMID: 37702486 PMCID: PMC10617571 DOI: 10.1128/jvi.00780-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an alternative to primate-based therapeutic vectors. Despite the high sequence diversity, the AAAV capsid was found to bind to a common glycan receptor, terminal galactose, which is also utilized by other AAVs already being utilized in gene therapy trials. However, contrary to the initial hypothesis, AAAV was recognized by approximately 30% of human sera tested. Structural and sequence comparisons point to conserved epitopes in the fivefold region of the capsid as the reason determinant for the observed cross-reactivity.
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Affiliation(s)
- Jane Hsi
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Sandra Afione
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Department of Epidemiology, Bloomberg School for Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - John Chiorini
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
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4
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López-Astacio RA, Adu OF, Lee H, Hafenstein SL, Parrish CR. The Structures and Functions of Parvovirus Capsids and Missing Pieces: the Viral DNA and Its Packaging, Asymmetrical Features, Nonprotein Components, and Receptor or Antibody Binding and Interactions. J Virol 2023; 97:e0016123. [PMID: 37367301 PMCID: PMC10373561 DOI: 10.1128/jvi.00161-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Parvoviruses are among the smallest and superficially simplest animal viruses, infecting a broad range of hosts, including humans, and causing some deadly infections. In 1990, the first atomic structure of the canine parvovirus (CPV) capsid revealed a 26-nm-diameter T=1 particle made up of two or three versions of a single protein, and packaging about 5,100 nucleotides of single-stranded DNA. Our structural and functional understanding of parvovirus capsids and their ligands has increased as imaging and molecular techniques have advanced, and capsid structures for most groups within the Parvoviridae family have now been determined. Despite those advances, significant questions remain unanswered about the functioning of those viral capsids and their roles in release, transmission, or cellular infection. In addition, the interactions of capsids with host receptors, antibodies, or other biological components are also still incompletely understood. The parvovirus capsid's apparent simplicity likely conceals important functions carried out by small, transient, or asymmetric structures. Here, we highlight some remaining open questions that may need to be answered to provide a more thorough understanding of how these viruses carry out their various functions. The many different members of the family Parvoviridae share a capsid architecture, and while many functions are likely similar, others may differ in detail. Many of those parvoviruses have not been experimentally examined in detail (or at all in some cases), so we, therefore, focus this minireview on the widely studied protoparvoviruses, as well as the most thoroughly investigated examples of adeno-associated viruses.
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Affiliation(s)
- Robert A. López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Oluwafemi F. Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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5
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Logan GJ, Mietzsch M, Khandekar N, D'Silva A, Anderson D, Mandwie M, Hsi J, Nelson AR, Chipman P, Jackson J, Schofield P, Christ D, Goodnow CC, Reed JH, Farrar MA, McKenna R, Alexander IE. Structural and functional characterization of capsid binding by anti-AAV9 monoclonal antibodies from infants after SMA gene therapy. Mol Ther 2023; 31:1979-1993. [PMID: 37012705 PMCID: PMC10362397 DOI: 10.1016/j.ymthe.2023.03.032] [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: 01/20/2023] [Revised: 03/02/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Success in the treatment of infants with spinal muscular atrophy (SMA) underscores the potential of vectors based on adeno-associated virus (AAV). However, a major obstacle to the full realization of this potential is pre-existing natural and therapy-induced anti-capsid humoral immunity. Structure-guided capsid engineering is one possible approach to surmounting this challenge but necessitates an understanding of capsid-antibody interactions at high molecular resolution. Currently, only mouse-derived monoclonal antibodies (mAbs) are available to structurally map these interactions, which presupposes that mouse and human-derived antibodies are functionally equivalent. In this study, we have characterized the polyclonal antibody responses of infants following AAV9-mediated gene therapy for SMA and recovered 35 anti-capsid mAbs from the abundance of switched-memory B (smB) cells present in these infants. For 21 of these mAbs, seven from each of three infants, we have undertaken functional and structural analysis measuring neutralization, affinities, and binding patterns by cryoelectron microscopy (cryo-EM). Four distinct patterns were observed akin to those reported for mouse-derived mAbs, but with early evidence of differing binding pattern preference and underlying molecular interactions. This is the first human and largest series of anti-capsid mAbs to have been comprehensively characterized and will prove to be powerful tools for basic discovery and applied purposes.
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Affiliation(s)
- Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Neeta Khandekar
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Arlene D'Silva
- School of Women's and Children's Health, University of New South Wales Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Daniel Anderson
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Mawj Mandwie
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Jane Hsi
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Austin R Nelson
- 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
| | - Jennifer Jackson
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Joanne H Reed
- Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Westmead, NSW, Australia
| | - Michelle A Farrar
- School of Women's and Children's Health, University of New South Wales Medicine, UNSW Sydney, Sydney, NSW, Australia; Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia; Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW, Australia.
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6
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Hahn PA, Martins MA. Adeno-associated virus-vectored delivery of HIV biologics: the promise of a "single-shot" functional cure for HIV infection. J Virus Erad 2023; 9:100316. [PMID: 36915910 PMCID: PMC10005911 DOI: 10.1016/j.jve.2023.100316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
The ability of immunoglobulin-based HIV biologics (Ig-HIV), including broadly neutralizing antibodies, to suppress viral replication in pre-clinical and clinical studies illustrates how these molecules can serve as alternatives or adjuncts to antiretroviral therapy for treating HIV infection. However, the current paradigm for delivering Ig-HIVs requires repeated passive infusions, which faces both logistical and economic challenges to broad-scale implementation. One promising way to overcome these obstacles and achieve sustained expression of Ig-HIVs in vivo involves the transfer of Ig-HIV genes to host cells utilizing adeno-associated virus (AAV) vectors. Because AAV vectors are non-pathogenic and their genomes persist in the cell nucleus as episomes, transgene expression can last for as long as the AAV-transduced cell lives. Given the long lifespan of myocytes, skeletal muscle is a preferred tissue for AAV-based immunotherapies aimed at achieving persistent delivery of Ig-HIVs. Consistent with this idea, recent studies suggest that lifelong immunity against HIV can be achieved from a one-time intramuscular dose of AAV/Ig-HIV vectors. However, realizing the promise of this approach faces significant hurdles, including the potential of AAV-delivered Ig-HIVs to induce anti-drug antibodies and the high AAV seroprevalence in the human population. Here we describe how these host immune responses can hinder AAV/Ig-HIV therapies and review current strategies for overcoming these barriers. Given the potential of AAV/Ig-HIV therapy to maintain ART-free virologic suppression and prevent HIV reinfection in people living with HIV, optimizing this strategy should become a greater priority in HIV/AIDS research.
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Affiliation(s)
- Patricia A. Hahn
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
- The Skaggs Graduate School, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Mauricio A. Martins
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
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7
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Large EE, Chapman MS. Adeno-associated virus receptor complexes and implications for adeno-associated virus immune neutralization. Front Microbiol 2023; 14:1116896. [PMID: 36846761 PMCID: PMC9950413 DOI: 10.3389/fmicb.2023.1116896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Adeno-associated viruses (AAV) are among the foremost vectors for in vivo gene therapy. A number of monoclonal antibodies against several serotypes of AAV have previously been prepared. Many are neutralizing, and the predominant mechanisms have been reported as the inhibition of binding to extracellular glycan receptors or interference with some post-entry step. The identification of a protein receptor and recent structural characterization of its interactions with AAV compel reconsideration of this tenet. AAVs can be divided into two families based on which domain of the receptor is strongly bound. Neighboring domains, unseen in the high-resolution electron microscopy structures have now been located by electron tomography, pointing away from the virus. The epitopes of neutralizing antibodies, previously characterized, are now compared to the distinct protein receptor footprints of the two families of AAV. Comparative structural analysis suggests that antibody interference with protein receptor binding might be the more prevalent mechanism than interference with glycan attachment. Limited competitive binding assays give some support to the hypothesis that inhibition of binding to the protein receptor has been an overlooked mechanism of neutralization. More extensive testing is warranted.
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Affiliation(s)
- Edward E. Large
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
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8
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Lakshmanan R, Mietzsch M, Jimenez Ybargollin A, Chipman P, Fu X, Qiu J, Söderlund-Venermo M, McKenna R. Capsid Structure of Aleutian Mink Disease Virus and Human Parvovirus 4: New Faces in the Parvovirus Family Portrait. Viruses 2022; 14:2219. [PMID: 36298773 PMCID: PMC9612331 DOI: 10.3390/v14102219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022] Open
Abstract
Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. Aleutian mink disease virus (AMDV), a pathogen in minks, and human parvovirus 4 (PARV4), infecting humans, are parvoviruses belonging to the genera Amdoparvovirus and Tetraparvovirus, respectively. While Aleutian mink disease caused by AMDV is a major threat to mink farming, no clear clinical manifestations have been established following infection with PARV4 in humans. Here, the capsid structures of AMDV and PARV4 were determined via cryo-electron microscopy at 2.37 and 3.12 Å resolutions, respectively. Despite low amino acid sequence identities (10-30%) both viruses share the icosahedral nature of parvovirus capsids, with 60 viral proteins (VPs) assembling the capsid via two-, three-, and five-fold symmetry VP-related interactions, but display major structural variabilities in the surface loops when the capsid structures are superposed onto other parvoviruses. The capsid structures of AMDV and PARV4 will add to current knowledge of the structural platform for parvoviruses and permit future functional annotation of these viruses, which will help in understanding their infection mechanisms at a molecular level for the development of diagnostics and therapeutics.
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Affiliation(s)
- Renuk Lakshmanan
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Alberto Jimenez Ybargollin
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Xiaofeng Fu
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
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9
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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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10
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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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11
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Hull JA, Mietzsch M, Chipman P, Strugatsky D, McKenna R. Structural characterization of an envelope-associated adeno-associated virus type 2 capsid. Virology 2022; 565:22-28. [PMID: 34638006 PMCID: PMC9911311 DOI: 10.1016/j.virol.2021.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 01/28/2023]
Abstract
Adeno-associated virus (AAV) are classified as non-enveloped ssDNA viruses. However, AAV capsids embedded within exosomes have been observed, and it has been suggested that the AAV membrane associated accessory protein (MAAP) may play a role in envelope-associated AAV (EA-AAV) capsid formation. Here, we observed and selected sufficient homogeneous EA-AAV capsids of AAV2, produced using the Sf9 baculoviral expression system, to determine the cryo-electron microscopy (cryo-EM) structure at 3.14 Å resolution. The reconstructed map confirmed that the EA-AAV capsid, showed no significant structural variation compared to the non-envelope capsid. In addition, the Sf9 expression system used implies the notion that MAAP may enhance exosome AAV encapsulation. Furthermore, we speculate that these EA-AAV capsids may have therapeutic benefits over the currently used non-envelope AAV capsids, with advantages in immune evasion and/or improved infectivity.
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Affiliation(s)
- Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA
| | - David Strugatsky
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA.
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12
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Zolotukhin S, Vandenberghe L. AAV capsid design: A Goldilocks challenge. Trends Mol Med 2022; 28:183-193. [DOI: 10.1016/j.molmed.2022.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/16/2022]
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13
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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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Mietzsch M, Yu JC, Hsi J, Chipman P, Broecker F, Fuming Z, Linhardt RJ, Seeberger PH, Heilbronn R, McKenna R, Agbandje-McKenna M. Structural Study of Aavrh.10 Receptor and Antibody Interactions. J Virol 2021; 95:e0124921. [PMID: 34549984 PMCID: PMC8577363 DOI: 10.1128/jvi.01249-21] [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: 07/23/2021] [Accepted: 09/13/2021] [Indexed: 11/20/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors are one of the leading tools for the delivery of therapeutic genes in human gene therapy applications. For a successful transfer of their payload, the AAV vectors have to circumvent potential preexisting neutralizing host antibodies and bind to the receptors of the target cells. Both of these aspects have not been structurally analyzed for AAVrh.10. Here, cryo-electron microscopy and three-dimensional image reconstruction were used to map the binding site of sulfated N-acetyllactosamine (LacNAc; previously shown to bind AAVrh.10) and a series of four monoclonal antibodies (MAbs). LacNAc was found to bind to a pocket located on the side of the 3-fold capsid protrusion that is mostly conserved to AAV9 and equivalent to its galactose-binding site. As a result, AAVrh.10 was also shown to be able to bind to cell surface glycans with terminal galactose. For the antigenic characterization, it was observed that several anti-AAV8 MAbs cross-react with AAVrh.10. The binding sites of these antibodies were mapped to the 3-fold capsid protrusions. Based on these observations, the AAVrh.10 capsid surface was engineered to create variant capsids that escape these antibodies while maintaining infectivity. IMPORTANCE Gene therapy vectors based on adeno-associated virus rhesus isolate 10 (AAVrh.10) have been used in several clinical trials to treat monogenetic diseases. However, compared to other AAV serotypes little is known about receptor binding and antigenicity of the AAVrh.10 capsid. Particularly, preexisting neutralizing antibodies against capsids are an important challenge that can hamper treatment efficiency. This study addresses both topics and identifies critical regions of the AAVrh.10 capsid for receptor and antibody binding. The insights gained were utilized to generate AAVrh.10 variants capable of evading known neutralizing antibodies. The findings of this study could further aid the utilization of AAVrh.10 vectors in clinical trials and help the approval of the subsequent biologics.
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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, Florida, USA
| | - Jennifer C. Yu
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jane Hsi
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Felix Broecker
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Zhang Fuming
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Robert J. Linhardt
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Regine Heilbronn
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
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Wec AZ, Lin KS, Kwasnieski JC, Sinai S, Gerold J, Kelsic ED. Overcoming Immunological Challenges Limiting Capsid-Mediated Gene Therapy With Machine Learning. Front Immunol 2021; 12:674021. [PMID: 33986759 PMCID: PMC8112259 DOI: 10.3389/fimmu.2021.674021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/09/2021] [Indexed: 12/11/2022] Open
Abstract
A key hurdle to making adeno-associated virus (AAV) capsid mediated gene therapy broadly beneficial to all patients is overcoming pre-existing and therapy-induced immune responses to these vectors. Recent advances in high-throughput DNA synthesis, multiplexing and sequencing technologies have accelerated engineering of improved capsid properties such as production yield, packaging efficiency, biodistribution and transduction efficiency. Here we outline how machine learning, advances in viral immunology, and high-throughput measurements can enable engineering of a new generation of de-immunized capsids beyond the antigenic landscape of natural AAVs, towards expanding the therapeutic reach of gene therapy.
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Affiliation(s)
- Anna Z. Wec
- Applied Biology, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Kathy S. Lin
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | | | - Sam Sinai
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Jeff Gerold
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Eric D. Kelsic
- Applied Biology, Dyno Therapeutics Inc, Cambridge, MA, United States
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
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Abstract
Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and image reconstruction, the HBoV2 capsid structure was determined to 2.7 Å resolution at pH 7.4 and compared to the previously determined HBoV1, HBoV3, and HBoV4 structures. Consistent with previous findings, surface variable region (VR) III of the capsid protein VP3, proposed as a host tissue-tropism determinant, was structurally similar among the gastrointestinal strains HBoV2-4, but differed from HBoV1 with its tropism for the respiratory tract. Towards understanding the entry and trafficking properties of these viruses, HBoV1 and HBoV2 were further analyzed as species representatives of the two HBoV tropisms. Their cell surface glycan-binding characteristics were analyzed, and capsid structures determined to 2.5-2.7 Å resolution at pH 5.5 and 2.6, conditions normally encountered during infection. The data showed that glycans with terminal sialic acid, galactose, GlcNAc or heparan sulfate moieties do not facilitate HBoV1 or HBoV2 cellular attachment. With respect to trafficking, conformational changes common to both viruses were observed at low pH conditions localized to the VP N-terminus under the 5-fold channel, in the surface loops VR-I and VR-V and specific side-chain residues such as cysteines and histidines. The 5-fold conformational movements provide insight into the potential mechanism of VP N-terminal dynamics during HBoV infection and side-chain modifications highlight pH-sensitive regions of the capsid.IMPORTANCE Human bocaviruses (HBoVs) are associated with disease in humans. However, the lack of an animal model and a versatile cell culture system to study their life cycle limits the ability to develop specific treatments or vaccines. This study presents the structure of HBoV2, at 2.7 Å resolution, determined for comparison to the existing HBoV1, HBoV3, and HBoV4 structures, to enable the molecular characterization of strain and genus-specific capsid features contributing to tissue tropism and antigenicity. Furthermore, HBoV1 and HBoV2 structures determined under acidic conditions provide insight into capsid changes associated with endosomal and gastrointestinal acidification. Structural rearrangements of the capsid VP N-terminus, at the base of the 5-fold channel, demonstrate a disordering of a "basket" motif as pH decreases. These observations begin to unravel the molecular mechanism of HBoV infection and provide information for control strategies.
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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: 40] [Impact Index Per Article: 13.3] [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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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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19
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Havlik LP, Simon KE, Smith JK, Klinc KA, Tse LV, Oh DK, Fanous MM, Meganck RM, Mietzsch M, Kleinschmidt J, Agbandje-McKenna M, Asokan A. Coevolution of Adeno-associated Virus Capsid Antigenicity and Tropism through a Structure-Guided Approach. J Virol 2020; 94:e00976-20. [PMID: 32669336 PMCID: PMC7495376 DOI: 10.1128/jvi.00976-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
Adeno-associated viruses (AAV) are composed of nonenveloped, icosahedral protein shells that can be adapted to package and deliver recombinant therapeutic DNA. Approaches to engineer recombinant capsids for gene therapy applications have focused on rational design or library-based approaches that can address one or two desirable attributes; however, there is an unmet need to comprehensively improve AAV vector properties. Such cannot be achieved by utilizing sequence data alone but requires harnessing the three-dimensional (3D) structural properties of AAV capsids. Here, we solve the structures of a natural AAV isolate complexed with antibodies using cryo-electron microscopy and harness this structural information to engineer AAV capsid libraries through saturation mutagenesis of different antigenic footprints. Each surface loop was evolved by infectious cycling in the presence of a helper adenovirus to yield a new AAV variant that then serves as a template for evolving the next surface loop. This stepwise process yielded a humanized AAV8 capsid (AAVhum.8) displaying nonnatural surface loops that simultaneously display tropism for human hepatocytes, increased gene transfer efficiency, and neutralizing antibody evasion. Specifically, AAVhum.8 can better evade neutralizing antisera from multiple species than AAV8. Further, AAVhum.8 displays robust transduction in a human liver xenograft mouse model with expanded tropism for both murine and human hepatocytes. This work supports the hypothesis that critical properties, such as AAV capsid antibody evasion and tropism, can be coevolved by combining rational design and library-based evolution for clinical gene therapy.IMPORTANCE Clinical gene therapy with recombinant AAV vectors has largely relied on natural capsid isolates. There is an unmet need to comprehensively improve AAV tissue tropism, transduction efficiency, and antibody evasion. Such cannot be achieved by utilizing capsid sequence data alone but requires harnessing the 3D structural properties of AAV capsids. Here, we combine rational design and library-based evolution to coevolve multiple, desirable properties onto AAV by harnessing 3D structural information.
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Affiliation(s)
- L Patrick Havlik
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Katherine E Simon
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - J Kennon Smith
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Kelli A Klinc
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Longping V Tse
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel K Oh
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Marco M Fanous
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rita M Meganck
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Jürgen Kleinschmidt
- German Cancer Research Center, Research Program Infection and Cancer, Heidelberg, Germany
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Aravind Asokan
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Regeneration Next, Duke University, Durham, North Carolina, USA
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20
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Mietzsch M, McKenna R, Väisänen E, Yu JC, Ilyas M, Hull JA, Kurian J, Smith JK, Chipman P, Lasanajak Y, Smith D, Söderlund-Venermo M, Agbandje-McKenna M. Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology. Viruses 2020; 12:E653. [PMID: 32560452 PMCID: PMC7354515 DOI: 10.3390/v12060653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 12/15/2022] Open
Abstract
Several members of the Protoparvovirus genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens.
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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 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - Elina Väisänen
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.V.); (M.S.-V.)
| | - Jennifer C. Yu
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - Maria Ilyas
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - Joshua A. Hull
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - Justin Kurian
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - J. Kennon Smith
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
| | - Yi Lasanajak
- Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA; (Y.L.); (D.S.)
| | - David Smith
- Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA; (Y.L.); (D.S.)
| | | | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.); (R.M.); (J.C.Y.); (M.I.); (J.A.H.); (J.K.); (J.K.S.); (P.C.)
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