1
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La Bella T, Bertin B, Mihaljevic A, Nozi J, Vidal P, Imbeaud S, Nault JC, Zucman-Rossi J, Ronzitti G. Predictive power of deleterious single amino acid changes to infer on AAV2 and AAV2-13 capsids fitness. Mol Ther Methods Clin Dev 2024; 32:101327. [PMID: 39286333 PMCID: PMC11403266 DOI: 10.1016/j.omtm.2024.101327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/15/2024] [Indexed: 09/19/2024]
Abstract
Adeno-associated virus (AAV) is the most widely used vector for in vivo gene transfer. A major limitation of capsid engineering is the incomplete understanding of the consequences of multiple amino acid variations on AAV capsid stability resulting in high frequency of non-viable capsids. In this context, the study of natural AAV variants can provide valuable insights into capsid regions that exhibit greater tolerance to mutations. Here, the characterization of AAV2 variants and the analysis of two public capsid libraries highlighted common features associated with deleterious mutations, suggesting that the impact of mutations on capsid viability is strictly dependent on their 3D location within the capsid structure. We developed a novel prediction method to infer the fitness of AAV2 variants containing multiple amino acid variations with 98% sensitivity, 98% accuracy, and 95% specificity. This novel approach might streamline the development of AAV vector libraries enriched in viable capsids, thus accelerating the identification of therapeutic candidates among engineered capsids.
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Affiliation(s)
- Tiziana La Bella
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Bérangère Bertin
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Ante Mihaljevic
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Justine Nozi
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Patrice Vidal
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Sandrine Imbeaud
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, 75000 Paris, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, 75000 Paris, France
- Avicenne Hospital, Paris-Seine-Saint-Denis University Hospital, APHP, 93000 Bobigny, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, 75000 Paris, France
- Hôpital Européen Georges Pompidou, AP-HP, 75000 Paris, France
| | - Giuseppe Ronzitti
- Genethon, 91000 Evry, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
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2
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Giacomoni J, Åkerblom M, Habekost M, Fiorenzano A, Kajtez J, Davidsson M, Parmar M, Björklund T. Identification and validation of novel engineered AAV capsid variants targeting human glia. Front Neurosci 2024; 18:1435212. [PMID: 39193523 PMCID: PMC11348808 DOI: 10.3389/fnins.2024.1435212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024] Open
Abstract
Direct neural conversion of endogenous non-neuronal cells, such as resident glia, into therapeutic neurons has emerged as a promising strategy for brain repair, aiming to restore lost or damaged neurons. Proof-of-concept has been obtained from animal studies, yet these models do not efficiently recapitulate the complexity of the human brain, and further refinement is necessary before clinical translation becomes viable. One important aspect is the need to achieve efficient and precise targeting of human glial cells using non-integrating viral vectors that exhibit a high degree of cell type specificity. While various naturally occurring or engineered adeno-associated virus (AAV) serotypes have been utilized to transduce glia, efficient targeting of human glial cell types remains an unsolved challenge. In this study, we employ AAV capsid library engineering to find AAV capsids that selectively target human glia in vitro and in vivo. We have identified two families of AAV capsids that induce efficient targeting of human glia both in glial spheroids and after glial progenitor cell transplantation into the rat forebrain. Furthermore, we show the robustness of this targeting by transferring the capsid peptide from the parent AAV2 serotype onto the AAV9 serotype, which facilitates future scalability for the larger human brain.
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Affiliation(s)
- Jessica Giacomoni
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Malin Åkerblom
- Molecular Neuromodulation, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Mette Habekost
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Alessandro Fiorenzano
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Janko Kajtez
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Marcus Davidsson
- Molecular Neuromodulation, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Tomas Björklund
- Molecular Neuromodulation, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
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3
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Zhou X, Liu J, Xiao S, Liang X, Li Y, Mo F, Xin X, Yang Y, Gao C. Adeno-Associated Virus Engineering and Load Strategy for Tropism Modification, Immune Evasion and Enhanced Transgene Expression. Int J Nanomedicine 2024; 19:7691-7708. [PMID: 39099791 PMCID: PMC11296317 DOI: 10.2147/ijn.s459905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/21/2024] [Indexed: 08/06/2024] Open
Abstract
Gene therapy aims to add, replace or turn off genes to help treat disease. To date, the US Food and Drug Administration (FDA) has approved 14 gene therapy products. With the increasing interest in gene therapy, feasible gene delivery vectors are necessary for inserting new genes into cells. There are different kinds of gene delivery vectors including viral vectors like lentivirus, adenovirus, retrovirus, adeno-associated virus et al, and non-viral vectors like naked DNA, lipid vectors, polymer nanoparticles, exosomes et al, with viruses being the most commonly used. Among them, the most concerned vector is adeno-associated virus (AAV) because of its safety, natural ability to efficiently deliver gene into cells and sustained transgene expression in multiple tissues. In addition, the AAV genome can be engineered to generate recombinant AAV (rAAV) containing transgene sequences of interest and has been proven to be a safe gene vector. Recently, rAAV vectors have been approved for the treatment of various rare diseases. Despite these approvals, some major limitations of rAAV remain, namely nonspecific tissue targeting and host immune response. Additional problems include neutralizing antibodies that block transgene delivery, a finite transgene packaging capacity, high viral titer used for per dose and high cost. To deal with these challenges, several techniques have been developed. Based on differences in engineering methods, this review proposes three strategies: gene engineering-based capsid modification (capsid modification), capsid surface tethering through chemical conjugation (surface tethering), and other formulations loaded with AAV (virus load). In addition, the major advantages and limitations encountered in rAAV engineering strategies are summarized.
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Affiliation(s)
- Xun Zhou
- School of Pharmacy, Henan University, Kaifeng, People’s Republic of China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Jingzhou Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Shuang Xiao
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
- School of Pharmacy, Guangxi Medical University, Nanning, People’s Republic of China
| | - Xiaoqing Liang
- School of Pharmacy, Henan University, Kaifeng, People’s Republic of China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Yi Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Fengzhen Mo
- School of Pharmacy, Guangxi Medical University, Nanning, People’s Republic of China
| | - Xin Xin
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Yang Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Chunsheng Gao
- School of Pharmacy, Henan University, Kaifeng, People’s Republic of China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
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4
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Pham Q, Glicksman J, Chatterjee A. Chemical approaches to probe and engineer AAV vectors. NANOSCALE 2024; 16:13820-13833. [PMID: 38978480 PMCID: PMC11271820 DOI: 10.1039/d4nr01300j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024]
Abstract
Adeno-associated virus (AAV) has emerged as the most promising vector for in vivo human gene therapy, with several therapeutic approvals in the last few years and countless more under development. Underlying this remarkable success are several attractive features that AAV offers, including lack of pathogenicity, low immunogenicity, long-term gene expression without genomic integration, the ability to infect both dividing and non-dividing cells, etc. However, the commonly used wild-type AAV capsids in therapeutic development present significant challenges, including inadequate tissue specificity and the need for large doses to attain therapeutic effectiveness, raising safety concerns. Additionally, significant preexisting adaptive immunity against most natural capsids, and the development of such anti-capsid immunity after the first treatment, represent major challenges. Strategies to engineer the AAV capsid are critically needed to address these challenges and unlock the full promise of AAV gene therapy. Chemical modification of the AAV capsid has recently emerged as a powerful new approach to engineer its properties. Unlike genetic strategies, which can be more disruptive to the delicate capsid assembly and packaging processes, "late-stage" chemical modification of the assembled capsid-whether at natural amino acid residues or site-specifically installed noncanonical amino acid residues-often enables a versatile approach to introducing new properties to the capsid. This review summarizes the significant recent progress in AAV capsid engineering strategies, with a particular focus on chemical modifications in advancing the next generation of AAV-based gene therapies.
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Affiliation(s)
- Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Jake Glicksman
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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5
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Słyk Ż, Stachowiak N, Małecki M. Recombinant Adeno-Associated Virus Vectors for Gene Therapy of the Central Nervous System: Delivery Routes and Clinical Aspects. Biomedicines 2024; 12:1523. [PMID: 39062095 PMCID: PMC11274884 DOI: 10.3390/biomedicines12071523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/23/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
The Central Nervous System (CNS) is vulnerable to a range of diseases, including neurodegenerative and oncological conditions, which present significant treatment challenges. The blood-brain barrier (BBB) restricts molecule penetration, complicating the achievement of therapeutic concentrations in the CNS following systemic administration. Gene therapy using recombinant adeno-associated virus (rAAV) vectors emerges as a promising strategy for treating CNS diseases, demonstrated by the registration of six gene therapy products in the past six years and 87 ongoing clinical trials. This review explores the implementation of rAAV vectors in CNS disease treatment, emphasizing AAV biology and vector engineering. Various administration methods-such as intravenous, intrathecal, and intraparenchymal routes-and experimental approaches like intranasal and intramuscular administration are evaluated, discussing their advantages and limitations in different CNS contexts. Additionally, the review underscores the importance of optimizing therapeutic efficacy through the pharmacokinetics (PK) and pharmacodynamics (PD) of rAAV vectors. A comprehensive analysis of clinical trials reveals successes and challenges, including barriers to commercialization. This review provides insights into therapeutic strategies using rAAV vectors in neurological diseases and identifies areas requiring further research, particularly in optimizing rAAV PK/PD.
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Affiliation(s)
- Żaneta Słyk
- Department of Applied Pharmacy, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland
- Laboratory of Gene Therapy, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Natalia Stachowiak
- Department of Applied Pharmacy, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Maciej Małecki
- Department of Applied Pharmacy, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland
- Laboratory of Gene Therapy, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland
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6
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De Leonardis M, Fernandez-de-Cossio-Diaz J, Uguzzoni G, Pagnani A. Unsupervised modeling of mutational landscapes of adeno-associated viruses viability. BMC Bioinformatics 2024; 25:229. [PMID: 38956474 PMCID: PMC11221173 DOI: 10.1186/s12859-024-05823-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Adeno-associated viruses 2 (AAV2) are minute viruses renowned for their capacity to infect human cells and akin organisms. They have recently emerged as prominent candidates in the field of gene therapy, primarily attributed to their inherent non-pathogenic nature in humans and the safety associated with their manipulation. The efficacy of AAV2 as gene therapy vectors hinges on their ability to infiltrate host cells, a phenomenon reliant on their competence to construct a capsid capable of breaching the nucleus of the target cell. To enhance their infection potential, researchers have extensively scrutinized various combinatorial libraries by introducing mutations into the capsid, aiming to boost their effectiveness. The emergence of high-throughput experimental techniques, like deep mutational scanning (DMS), has made it feasible to experimentally assess the fitness of these libraries for their intended purpose. Notably, machine learning is starting to demonstrate its potential in addressing predictions within the mutational landscape from sequence data. In this context, we introduce a biophysically-inspired model designed to predict the viability of genetic variants in DMS experiments. This model is tailored to a specific segment of the CAP region within AAV2's capsid protein. To evaluate its effectiveness, we conduct model training with diverse datasets, each tailored to explore different aspects of the mutational landscape influenced by the selection process. Our assessment of the biophysical model centers on two primary objectives: (i) providing quantitative forecasts for the log-selectivity of variants and (ii) deploying it as a binary classifier to categorize sequences into viable and non-viable classes.
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Affiliation(s)
- Matteo De Leonardis
- DISAT, Politecnico di Torino, Corso Duca degli Abruzzi, 10129, Torino, Italy.
| | - Jorge Fernandez-de-Cossio-Diaz
- Laboratoire de Physique de l'Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, Universite, Paris-Cité, 75005, Paris, France
| | - Guido Uguzzoni
- Italian Institute for Genomic Medicine, IRCCS Candiolo, SP-142, 10060, Candiolo, Italy
| | - Andrea Pagnani
- DISAT, Politecnico di Torino, Corso Duca degli Abruzzi, 10129, Torino, Italy
- Italian Institute for Genomic Medicine, IRCCS Candiolo, SP-142, 10060, Candiolo, Italy
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7
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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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8
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Wang Y, Fu Q, Park SY, Lee YS, Park SY, Lee DY, Yoon S. Decoding cellular mechanism of recombinant adeno-associated virus (rAAV) and engineering host-cell factories toward intensified viral vector manufacturing. Biotechnol Adv 2024; 71:108322. [PMID: 38336188 DOI: 10.1016/j.biotechadv.2024.108322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is one of the prominent gene delivery vehicles that has opened promising opportunities for novel gene therapeutic approaches. However, the current major viral vector production platform, triple transfection in mammalian cells, may not meet the increasing demand. Thus, it is highly required to understand production bottlenecks from the host cell perspective and engineer the cells to be more favorable and tolerant to viral vector production, thereby effectively enhancing rAAV manufacturing. In this review, we provided a comprehensive exploration of the intricate cellular process involved in rAAV production, encompassing various stages such as plasmid entry to the cytoplasm, plasmid trafficking and nuclear delivery, rAAV structural/non-structural protein expression, viral capsid assembly, genome replication, genome packaging, and rAAV release/secretion. The knowledge in the fundamental biology of host cells supporting viral replication as manufacturing factories or exhibiting defending behaviors against viral production is summarized for each stage. The control strategies from the perspectives of host cell and materials (e.g., AAV plasmids) are proposed as our insights based on the characterization of molecular features and our existing knowledge of the AAV viral life cycle, rAAV and other viral vector production in the Human embryonic kidney (HEK) cells.
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Affiliation(s)
- Yongdan Wang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Qiang Fu
- Department of Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - So Young Park
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America.
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9
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Hoffmann MD, Zdechlik AC, He Y, Nedrud D, Aslanidi G, Gordon W, Schmidt D. Multiparametric domain insertional profiling of adeno-associated virus VP1. Mol Ther Methods Clin Dev 2023; 31:101143. [PMID: 38027057 PMCID: PMC10661864 DOI: 10.1016/j.omtm.2023.101143] [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: 04/17/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023]
Abstract
Several evolved properties of adeno-associated virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Most efforts to re-engineer these properties have focused on variable regions near AAV's 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of six structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. Insertion permissibility depended strongly on insertion position, domain type, and measured fitness phenotype, which clustered into contiguous structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.
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Affiliation(s)
- Mareike D. Hoffmann
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alina C. Zdechlik
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yungui He
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Nedrud
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Wendy Gordon
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
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10
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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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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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12
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Kwak G, Lee D, Suk JS. Advanced approaches to overcome biological barriers in respiratory and systemic routes of administration for enhanced nucleic acid delivery to the lung. Expert Opin Drug Deliv 2023; 20:1531-1552. [PMID: 37946533 PMCID: PMC10872418 DOI: 10.1080/17425247.2023.2282535] [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: 07/11/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION Numerous delivery strategies, primarily novel nucleic acid delivery carriers, have been developed and explored to enable therapeutically relevant lung gene therapy. However, its clinical translation is yet to be achieved despite over 30 years of efforts, which is attributed to the inability to overcome a series of biological barriers that hamper efficient nucleic acid transfer to target cells in the lung. AREAS COVERED This review is initiated with the fundamentals of nucleic acid therapy and a brief overview of previous and ongoing efforts on clinical translation of lung gene therapy. We then walk through the nature of biological barriers encountered by nucleic acid carriers administered via respiratory and/or systemic routes. Finally, we introduce advanced strategies developed to overcome those barriers to achieve therapeutically relevant nucleic acid delivery efficiency in the lung. EXPERT OPINION We are now stepping close to the clinical translation of lung gene therapy, thanks to the discovery of novel delivery strategies that overcome biological barriers via comprehensive preclinical studies. However, preclinical findings should be cautiously interpreted and validated to ultimately realize meaningful therapeutic outcomes with newly developed delivery strategies in humans. In particular, individual strategies should be selected, tailored, and implemented in a manner directly relevant to specific therapeutic applications and goals.
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Affiliation(s)
- Gijung Kwak
- Department of Neurosurgery and Medicine Institute for Neuroscience Discovery (UM-MIND), University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daiheon Lee
- Department of Neurosurgery and Medicine Institute for Neuroscience Discovery (UM-MIND), University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jung Soo Suk
- Department of Neurosurgery and Medicine Institute for Neuroscience Discovery (UM-MIND), University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
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13
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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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14
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Hoffmann MD, Zdechlik AC, He Y, Nedrud D, Aslanidi G, Gordon W, Schmidt D. Multiparametric domain insertional profiling of Adeno-Associated Virus VP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537549. [PMID: 37131661 PMCID: PMC10153220 DOI: 10.1101/2023.04.19.537549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Evolved properties of Adeno-Associated Virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Previous efforts to re-engineer these properties have focused on variable regions near AAV’s 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of large, structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. There was strong positional, domain-type, and fitness phenotype dependence of insertion permissibility, which clustered into correlated structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified new engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.
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15
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Moreno-Gutierrez DS, Del Toro-Ríos X, Martinez-Sulvaran NJ, Perez-Altamirano MB, Hernandez-Garcia A. Programming the Cellular Uptake of Protein-Based Viromimetic Nanoparticles for Enhanced Delivery. Biomacromolecules 2023; 24:1563-1573. [PMID: 36877960 DOI: 10.1021/acs.biomac.2c01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Viral mimetics is a noteworthy strategy to design efficient delivery systems without the safety drawbacks and engineering difficulties of modifying viral vectors. The triblock polypeptide CSB was previously designed de novo to self-assemble with DNA into nanocomplexes called artificial virus-like particles (AVLPs) due to their similarities to viral particles. Here, we show how we can incorporate new blocks into the CSB polypeptide to enhance its transfection without altering its self-assembly capabilities and the stability and morphology of the AVLPs. The addition of a short peptide (aurein) and/or a large protein (transferrin) to the AVLPs improved their internalization and specific targeting to cells by up to 11 times. Overall, these results show how we can further program the cellular uptake of the AVLPs with a wide range of bioactive blocks. This can pave the way to develop programmable and efficient gene delivery systems.
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Affiliation(s)
- David S Moreno-Gutierrez
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Ximena Del Toro-Ríos
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Natalia J Martinez-Sulvaran
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Mayra B Perez-Altamirano
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Armando Hernandez-Garcia
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
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Ghauri MS, Ou L. AAV Engineering for Improving Tropism to the Central Nervous System. BIOLOGY 2023; 12:186. [PMID: 36829465 PMCID: PMC9953251 DOI: 10.3390/biology12020186] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023]
Abstract
Adeno-associated virus (AAV) is a non-pathogenic virus that mainly infects primates with the help of adenoviruses. AAV is being widely used as a delivery vector for in vivo gene therapy, as evidenced by five currently approved drugs and more than 255 clinical trials across the world. Due to its relatively low immunogenicity and toxicity, sustained efficacy, and broad tropism, AAV holds great promise for treating many indications, including central nervous system (CNS), ocular, muscular, and liver diseases. However, low delivery efficiency, especially for the CNS due to the blood-brain barrier (BBB), remains a significant challenge for more clinical application of AAV gene therapy. Thus, there is an urgent need for utilizing AAV engineering to discover next-generation capsids with improved properties, e.g., enhanced BBB penetrance, lower immunogenicity, and higher packaging efficiency. AAV engineering methods, including directed evolution, rational design, and in silico design, have been developed, resulting in the discovery of novel capsids (e.g., PhP.B, B10, PAL1A/B/C). In this review, we discuss key studies that identified engineered CNS capsids and/or established methodological improvements. Further, we also discussed important issues that need to be addressed, including cross-species translatability, cell specificity, and modular engineering to improve multiple properties simultaneously.
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Affiliation(s)
- Muhammad S. Ghauri
- School of Medicine, California University of Science and Medicine, Colton, CA 92324, USA
| | - Li Ou
- Genemagic Biosciences, Media, PA 19086, USA
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA
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17
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Xie YL, Wang JY, He Y, Yu XM, Zheng QY, Ling C, Feng XL, Zhu LQ. The use of melittin to enhance transgene expression mediated by recombinant adeno-associated virus serotype 2 vectors both in vitro and in vivo. JOURNAL OF INTEGRATIVE MEDICINE 2023; 21:106-115. [PMID: 36333178 DOI: 10.1016/j.joim.2022.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/26/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Melittin, a cell-penetrating peptide, improves the efficiency of many non-viral gene delivery vectors, yet its application in viral vectors has not been well studied. The non-pathogenic recombinant adeno-associated virus (rAAV) vector is an ideal in vivo gene delivery vector. However, its full potential will only be achieved after improvement of its transduction efficiency. To improve the transduction efficiency of rAAV2 vectors, we attempted to develop a melittin-based rAAV2 vector delivery strategy. METHODS The melittin peptide was inserted into the rAAV2 capsid either in the loop VIII of all viral proteins (VPs) or at the N terminus of VP2. Various rAAV2-gfp or -fluc vectors were subjected to quantitative real-time polymerase chain reaction and Western blot assays to determine their titers and integrity of capsid proteins, respectively. Alternatively, the vectors based on wild-type capsid were pre-incubated with melittin, followed by transduction of cultured cells or tail vein administration of the mixture to C57BL/6 and BALB/c nude mice. In vivo bioluminescence imaging was performed to evaluate the transgene expression. RESULTS rAAV2 vectors with melittin peptide inserted in the loop VIII of VPs had low transduction efficiency, probably due to dramatically reduced ability to bind to the target cells. Fusing the melittin peptide at the N-terminus of VP2 produced vectors without the VP2 subunit. Interestingly, among the commonly used rAAV vectors, pre-incubation of rAAV2 and rAAV6 vectors with melittin significantly enhanced their transduction efficiency in HEK293 and Huh7 cells in vitro. Melittin also had the ability to increase the rAAV2-mediated transgene expression in mouse liver in vivo. Mechanistically, melittin did not change the vector-receptor interaction. Moreover, cell counting kit-8 assays of cultured cells and serum transaminase levels indicated melittin had little cytotoxicity. CONCLUSION Pre-incubation with melittin, but not insertion of melittin into the rAAV2 capsid, significantly enhanced rAAV2-mediated transgene expression. Although further in vivo evaluations are required, this research not only expands the pharmacological potential of melittin, but also provides a new strategy to improve gene therapy mediated by rAAV vectors.
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Affiliation(s)
- Yi-Lin Xie
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Ji-Yao Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China
| | - Yun He
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Xiao-Min Yu
- Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China
| | - Qing-Yun Zheng
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Chen Ling
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China
| | - Xi-Lin Feng
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Yantai Fuheng Biological Technology Co., Ltd., Yantai 264006, Shandong Province, China.
| | - Li-Qing Zhu
- Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China.
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18
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Pupo A, Fernández A, Low SH, François A, Suárez-Amarán L, Samulski RJ. AAV vectors: The Rubik's cube of human gene therapy. Mol Ther 2022; 30:3515-3541. [PMID: 36203359 PMCID: PMC9734031 DOI: 10.1016/j.ymthe.2022.09.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 12/12/2022] Open
Abstract
Defective genes account for ∼80% of the total of more than 7,000 diseases known to date. Gene therapy brings the promise of a one-time treatment option that will fix the errors in patient genetic coding. Recombinant viruses are highly efficient vehicles for in vivo gene delivery. Adeno-associated virus (AAV) vectors offer unique advantages, such as tissue tropism, specificity in transduction, eliciting of a relatively low immune responses, no incorporation into the host chromosome, and long-lasting delivered gene expression, making them the most popular viral gene delivery system in clinical trials, with three AAV-based gene therapy drugs already approved by the US Food and Drug Administration (FDA) or European Medicines Agency (EMA). Despite the success of AAV vectors, their usage in particular scenarios is still limited due to remaining challenges, such as poor transduction efficiency in certain tissues, low organ specificity, pre-existing humoral immunity to AAV capsids, and vector dose-dependent toxicity in patients. In the present review, we address the different approaches to improve AAV vectors for gene therapy with a focus on AAV capsid selection and engineering, strategies to overcome anti-AAV immune response, and vector genome design, ending with a glimpse at vector production methods and the current state of recombinant AAV (rAAV) at the clinical level.
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Affiliation(s)
- Amaury Pupo
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Audry Fernández
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Siew Hui Low
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Achille François
- Viralgen. Parque Tecnológico de Guipuzkoa, Edificio Kuatro, Paseo Mikeletegui, 83, 20009 San Sebastián, Spain
| | - Lester Suárez-Amarán
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Richard Jude Samulski
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Corresponding author: Richard Jude Samulski, R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, NC 27709, USA.
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Determination of AAV properties by single amino acids: Go(o)d is in the details. Mol Ther Methods Clin Dev 2022; 27:93-95. [PMID: 36212908 PMCID: PMC9529493 DOI: 10.1016/j.omtm.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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20
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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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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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22
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Jäschke N, Büning H. Adeno-Associated Virus Vector Design-Moving the Adeno-Associated Virus to a Bioengineered Therapeutic Nanoparticle. Hematol Oncol Clin North Am 2022; 36:667-685. [PMID: 35778330 DOI: 10.1016/j.hoc.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Although the number of market-approved gene therapies is still low, this new class of therapeutics has become an integral part of modern medicine. The success and safety of gene therapy depend on the vectors used to deliver the therapeutic material. Adeno-associated virus (AAV) vectors have emerged as the most frequently used delivery system for in vivo gene therapy. This success was achieved with first-generation vectors, using capsids derived from natural AAV serotypes. Their broad tropism, the high seroprevalence for many of the AAV serotypes in the human population, and the high vector doses needed to transduce a sufficient number of therapy-relevant target cells are challenges that are addressed by engineering the capsid and the vector genome, improving the efficacy of these biological nanoparticles.
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Affiliation(s)
- Nico Jäschke
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover 30625, Germany
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover 30625, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Carl-Neuberg-Str.1, Hannover 30625, Germany; German Center for Infection Research, Partner Site Hannover-Braunschweig.
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23
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Becker J, Fakhiri J, Grimm D. Fantastic AAV Gene Therapy Vectors and How to Find Them—Random Diversification, Rational Design and Machine Learning. Pathogens 2022; 11:pathogens11070756. [PMID: 35890005 PMCID: PMC9318892 DOI: 10.3390/pathogens11070756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Parvoviruses are a diverse family of small, non-enveloped DNA viruses that infect a wide variety of species, tissues and cell types. For over half a century, their intriguing biology and pathophysiology has fueled intensive research aimed at dissecting the underlying viral and cellular mechanisms. Concurrently, their broad host specificity (tropism) has motivated efforts to develop parvoviruses as gene delivery vectors for human cancer or gene therapy applications. While the sum of preclinical and clinical data consistently demonstrates the great potential of these vectors, these findings also illustrate the importance of enhancing and restricting in vivo transgene expression in desired cell types. To this end, major progress has been made especially with vectors based on Adeno-associated virus (AAV), whose capsid is highly amenable to bioengineering, repurposing and expansion of its natural tropism. Here, we provide an overview of the state-of-the-art approaches to create new AAV variants with higher specificity and efficiency of gene transfer in on-target cells. We first review traditional and novel directed evolution approaches, including high-throughput screening of AAV capsid libraries. Next, we discuss programmable receptor-mediated targeting with a focus on two recent technologies that utilize high-affinity binders. Finally, we highlight one of the latest stratagems for rational AAV vector characterization and optimization, namely, machine learning, which promises to facilitate and accelerate the identification of next-generation, safe and precise gene delivery vehicles.
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Affiliation(s)
- Jonas Becker
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Center for Integrative Infectious Diseases Research (CIID), BioQuant, 69120 Heidelberg, Germany;
- Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - Julia Fakhiri
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
- Correspondence: (J.F.); (D.G.); Tel.: +49-174-3486203 (J.F.); +49-6221-5451331 (D.G.)
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Center for Integrative Infectious Diseases Research (CIID), BioQuant, 69120 Heidelberg, Germany;
- German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (J.F.); (D.G.); Tel.: +49-174-3486203 (J.F.); +49-6221-5451331 (D.G.)
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24
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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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25
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Bennett A, Hull J, Jolinon N, Tordo J, Moss K, Binns E, Mietzsch M, Hagemann C, Linden RM, Serio A, Chipman P, Sousa D, Broecker F, Seeberger P, Henckaerts E, McKenna R, Agbandje-McKenna M. Comparative structural, biophysical, and receptor binding study of true type and wild type AAV2. J Struct Biol 2021; 213:107795. [PMID: 34509611 PMCID: PMC9918372 DOI: 10.1016/j.jsb.2021.107795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/27/2021] [Accepted: 09/05/2021] [Indexed: 01/25/2023]
Abstract
Adeno-associated viruses (AAV) are utilized as gene transfer vectors in the treatment of monogenic disorders. A variant, rationally engineered based on natural AAV2 isolates, designated AAV-True Type (AAV-TT), is highly neurotropic compared to wild type AAV2 in vivo, and vectors based on it, are currently being evaluated for central nervous system applications. AAV-TT differs from AAV2 by 14 amino acids, including R585S and R588T, two residues previously shown to be essential for heparan sulfate binding of AAV2. The capsid structures of AAV-TT and AAV2 visualized by cryo-electron microscopy at 3.4 and 3.0 Å resolution, respectively, highlighted structural perturbations at specific amino acid differences. Differential scanning fluorimetry (DSF) performed at different pH conditions demonstrated that the melting temperature (Tm) of AAV2 was consistently ∼5 °C lower than AAV-TT, but both showed maximal stability at pH 5.5, corresponding to the pH in the late endosome, proposed as required for VP1u externalization to facilitate endosomal escape. Reintroduction of arginines at positions 585 and 588 in AAV-TT caused a reduction in Tm, demonstrating that the lack of basic amino acids at these positions are associated with capsid stability. These results provide structural and thermal annotation of AAV2/AAV-TT residue differences, that account for divergent cell binding, transduction, antigenic reactivity, and transduction of permissive tissues between the two viruses. Specifically, these data indicate that AAV-TT may not utilize a glycan receptor mediated pathway to enter cells and may have lower antigenic properties as compared to AAV2.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Joshua Hull
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nelly Jolinon
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | | | - Katie Moss
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Enswert Binns
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mario Mietzsch
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Cathleen Hagemann
- Centre for Craniofacial & Regenerative Biology, King's College London, London SE19RT, UK; The Francis Crick Institute, London NW1 1AT, UK
| | | | - Andrea Serio
- Centre for Craniofacial & Regenerative Biology, King's College London, London SE19RT, UK; The Francis Crick Institute, London NW1 1AT, UK
| | - Paul Chipman
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Duncan Sousa
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, 89 Chieftan Way Rm 119, Tallahassee, FL 32306, USA
| | - Felix Broecker
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Peter Seeberger
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Els Henckaerts
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK; Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.
| | - Robert McKenna
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - Mavis Agbandje-McKenna
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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26
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Macdonald J, Marx J, Büning H. Capsid-Engineering for Central Nervous System-Directed Gene Therapy with Adeno-Associated Virus Vectors. Hum Gene Ther 2021; 32:1096-1119. [PMID: 34662226 DOI: 10.1089/hum.2021.169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Closing the gap in knowledge on the cause of neurodegenerative disorders is paving the way toward innovative treatment strategies, among which gene therapy has emerged as a top candidate. Both conventional gene therapy and genome editing approaches are being developed, and a great number of human clinical trials are ongoing. Already 2 years ago, the first gene therapy for a neurodegenerative disease, spinal muscular atrophy type 1 (SMA1), obtained market approval. To realize such innovative strategies, gene therapy delivery tools are key assets. Here, we focus on recombinant adeno-associated virus (AAV) vectors and report on strategies to improve first-generation vectors. Current efforts focus on the viral capsid to modify the host-vector interaction aiming at increasing the efficacy of target cell transduction, at simplifying vector administration, and at reducing the risk of vector dose-related side effects.
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Affiliation(s)
- Josephine Macdonald
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Jennifer Marx
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
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27
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AAV9 Structural Rearrangements Induced by Endosomal Trafficking pH and Glycan Attachment. J Virol 2021; 95:e0084321. [PMID: 34260280 DOI: 10.1128/jvi.00843-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adeno-associated viruses (AAVs) are small non-enveloped ssDNA viruses, that are currently being developed as gene therapy biologics. After cell entry, AAVs traffic to the nucleus using the endo-lysosomal pathway. The subsequent decrease in pH triggers conformational changes to the capsid that enables the externalization of the capsid protein (VP) N-termini, including the unique domain of the minor capsid protein VP1 (VP1u), which permits phospholipase activity required for the capsid lysosomal egress. Here, we report the AAV9 capsid structure, determined at the endosomal pHs (7.4, 6.0, 5.5, and 4.0) and terminal galactose-bound AAV9 capsids at pHs 7.4 and 5.5 using cryo-electron microscopy and three-dimensional image reconstruction. Taken together these studies provide insight into AAV9 capsid conformational changes at the 5-fold pore during endosomal trafficking, both in the presence and absence of its cellular glycan receptor. We visualized, for the first time, that acidification induces the externalization of the VP3 and possibly VP2 N-termini, presumably in prelude to the externalization of VP1u at pH 4.0, that is essential for lysosomal membrane disruption. In addition, the structural study of AAV9-galactose interactions demonstrates AAV9 remains attached to its glycan receptor at the late endosome pH 5.5. This interaction significantly alters the conformational stability of the variable region I of the VPs, as well as the dynamics associated with VP N-terminus externalization. Importance There are 13 distinct Adeno-associated virus (AAV) serotypes that are structurally homologous and whose capsid proteins (VP1-3) are similar in amino acid sequence. However, AAV9 is one of the most commonly studied and used as gene therapy vector. This is part because, AAV9 is capable of crossing the blood brain barrier as well as readily transduces a wide array of tissues, including the central nervous system. In this study we provide AAV9 capsid structural insight during intracellular trafficking. Although the AAV capsid has been shown to externalize the N-termini of its VPs, to enzymatically disrupt the lysosome membrane at low pH, there was no structural evidence to confirm this. By utilizing AAV9 as our model, we provide the first structural evidence that the externalization process occurs at the protein interface at the icosahedral 5-fold symmetry axis and can be triggered by lowering pH.
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28
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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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29
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Tissue and cell-type-specific transduction using rAAV vectors in lung diseases. J Mol Med (Berl) 2021; 99:1057-1071. [PMID: 34021360 DOI: 10.1007/s00109-021-02086-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Gene therapy of genetically determined diseases, including some pathologies of the respiratory system, requires an efficient method for transgene delivery. Recombinant adeno-associated viral (rAAV) vectors are well studied and employed in gene therapy, as they are relatively simple and low immunogenic and able to efficiently transduce eukaryotic cells. To date, many natural and artificial (with modified capsids) AAV serotypes have been isolated, demonstrating preferential tropism toward different tissues and cells in accordance with the prevalent receptors on the cell surface. However, rAAV-mediated delivery is not strictly specific due to wide tropism of some viral serotypes. Thus, the development of the methods allowing modulating specificity of these vectors could be beneficial in some cases. This review describes various approaches for retargeting rAAV to respiratory cells, for example, using different types of capsid modifications and regulation of a transgene expression by tissue-specific promoters. Part of the review is devoted to the issues of transduction of stem and progenitor lung cells using AAV, which is a complicated task today.
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30
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Korneyenkov MA, Zamyatnin AA. Next Step in Gene Delivery: Modern Approaches and Further Perspectives of AAV Tropism Modification. Pharmaceutics 2021; 13:pharmaceutics13050750. [PMID: 34069541 PMCID: PMC8160765 DOI: 10.3390/pharmaceutics13050750] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Today, adeno-associated virus (AAV) is an extremely popular choice for gene therapy delivery. The safety profile and simplicity of the genome organization are the decisive advantages which allow us to claim that AAV is currently among the most promising vectors. Several drugs based on AAV have been approved in the USA and Europe, but AAV serotypes’ unspecific tissue tropism is still a serious limitation. In recent decades, several techniques have been developed to overcome this barrier, such as the rational design, directed evolution and chemical conjugation of targeting molecules with a capsid. Today, all of the abovementioned approaches confer the possibility to produce AAV capsids with tailored tropism, but recent data indicate that a better understanding of AAV biology and the growth of structural data may theoretically constitute a rational approach to most effectively produce highly selective and targeted AAV capsids. However, while we are still far from this goal, other approaches are still in play, despite their drawbacks and limitations.
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Affiliation(s)
- Maxim A. Korneyenkov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: ; Tel.: +7-495-622-9843
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31
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Wagner HJ, Weber W, Fussenegger M. Synthetic Biology: Emerging Concepts to Design and Advance Adeno-Associated Viral Vectors for Gene Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004018. [PMID: 33977059 PMCID: PMC8097373 DOI: 10.1002/advs.202004018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/18/2020] [Indexed: 05/28/2023]
Abstract
Three recent approvals and over 100 ongoing clinical trials make adeno-associated virus (AAV)-based vectors the leading gene delivery vehicles in gene therapy. Pharmaceutical companies are investing in this small and nonpathogenic gene shuttle to increase the therapeutic portfolios within the coming years. This prospect of marking a new era in gene therapy has fostered both investigations of the fundamental AAV biology as well as engineering studies to enhance delivery vehicles. Driven by the high clinical potential, a new generation of synthetic-biologically engineered AAV vectors is on the rise. Concepts from synthetic biology enable the control and fine-tuning of vector function at different stages of cellular transduction and gene expression. It is anticipated that the emerging field of synthetic-biologically engineered AAV vectors can shape future gene therapeutic approaches and thus the design of tomorrow's gene delivery vectors. This review describes and discusses the recent trends in capsid and vector genome engineering, with particular emphasis on synthetic-biological approaches.
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Affiliation(s)
- Hanna J. Wagner
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Faculty of BiologyUniversity of FreiburgSchänzlestraße 1Freiburg79104Germany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgSchänzlestraße 18Freiburg79104Germany
| | - Wilfried Weber
- Faculty of BiologyUniversity of FreiburgSchänzlestraße 1Freiburg79104Germany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgSchänzlestraße 18Freiburg79104Germany
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 50Basel4056Switzerland
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32
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Ito M, Takino N, Nomura T, Kan A, Muramatsu SI. Engineered adeno-associated virus 3 vector with reduced reactivity to serum antibodies. Sci Rep 2021; 11:9322. [PMID: 33927271 PMCID: PMC8084969 DOI: 10.1038/s41598-021-88614-9] [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] [Received: 09/18/2020] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
The natural serotypes of adeno-associated virus (AAV) or their variants, such as AAV8 and AAV5, are commonly used as vectors in the clinical programs for liver-targeted gene therapy. While AAV8 vectors are not highly efficient at targeting primary human hepatocytes, AAV3 vectors have recently demonstrated remarkable efficiency at targeting both human and non-human primate hepatocytes. However, the presence of high levels of neutralizing antibodies (NAbs) impedes transduction into hepatocytes, representing a major obstacle to the clinical application of AAV3 vectors. Herein, we engineered the viral capsid to reduce its reactivity with pre-existing NAbs, thereby enhancing the transduction efficiency. By introducing three substitutions (S472A, S587A, and N706A) on the surface loop of AAV3B capsid protein, we generated a triple mutant AAV3 (AAV.GT5) vector with less reactivity to anti-AAV capsid NAbs. While the transduction efficiency of AAV.GT5 into human hepatocellular cell lines was similar to those of parental AAV3B, it was 50-fold higher for hepatocytes derived from humanized mice compared to AAV8 vectors. Moreover, the AAV.GT5 vector yield was similar to those of the AAV2 and AAV3B vectors. Thus, high resistance to pre-existing NAbs makes AAV.GT5 a promising candidate for future liver-targeted gene therapy clinical trials.
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Affiliation(s)
- Mika Ito
- Division of Neurological Gene Therapy, Center for Open Innovation, Jichi Medical University, Tochigi, Japan
| | - Naomi Takino
- Division of Neurological Gene Therapy, Center for Open Innovation, Jichi Medical University, Tochigi, Japan
| | | | | | - Shin-Ichi Muramatsu
- Division of Neurological Gene Therapy, Center for Open Innovation, Jichi Medical University, Tochigi, Japan. .,Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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33
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Colón-Thillet R, Jerome KR, Stone D. Optimization of AAV vectors to target persistent viral reservoirs. Virol J 2021; 18:85. [PMID: 33892762 PMCID: PMC8067653 DOI: 10.1186/s12985-021-01555-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
Gene delivery of antiviral therapeutics to anatomical sites where viruses accumulate and persist is a promising approach for the next generation of antiviral therapies. Recombinant adeno-associated viruses (AAV) are one of the leading vectors for gene therapy applications that deliver gene-editing enzymes, antibodies, and RNA interference molecules to eliminate viral reservoirs that fuel persistent infections. As long-lived viral DNA within specific cellular reservoirs is responsible for persistent hepatitis B virus, Herpes simplex virus, and human immunodeficiency virus infections, the discovery of AAV vectors with strong tropism for hepatocytes, sensory neurons and T cells, respectively, is of particular interest. Identification of natural isolates from various tissues in humans and non-human primates has generated an extensive catalog of AAV vectors with diverse tropisms and transduction efficiencies, which has been further expanded through molecular genetic approaches. The AAV capsid protein, which forms the virions' outer shell, is the primary determinant of tissue tropism, transduction efficiency, and immunogenicity. Thus, over the past few decades, extensive efforts to optimize AAV vectors for gene therapy applications have focused on capsid engineering with approaches such as directed evolution and rational design. These approaches are being used to identify variants with improved transduction efficiencies, alternate tropisms, reduced sequestration in non-target organs, and reduced immunogenicity, and have produced AAV capsids that are currently under evaluation in pre-clinical and clinical trials. This review will summarize the most recent strategies to identify AAV vectors with enhanced tropism and transduction in cell types that harbor viral reservoirs.
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Affiliation(s)
- Rossana Colón-Thillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA.
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34
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Engineered AAV8 capsid acquires heparin and AVB sepharose binding capacity but has altered in vivo transduction efficiency. Gene Ther 2020; 30:236-244. [PMID: 33028973 PMCID: PMC8024426 DOI: 10.1038/s41434-020-00198-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022]
Abstract
Naturally occurring adeno-associated virus (AAV) serotypes that bind to ligands such as AVB sepharose or heparin can be purified by affinity chromatography, which is a more efficient and scalable method than gradient ultracentrifugation. Wild type AAV8 does not bind effectively to either of these molecules, which constitutes a barrier to using this vector when a high throughput design is required. Previously, AAV8 was engineered to contain a SPAKFA amino acid sequence to facilitate purification using AVB sepharose resin; however, in vivo studies were not conducted to examine whether these capsid mutations altered the transduction profile. To address this gap in knowledge, a mutant AAV8 capsid was engineered to bind to AVB sepharose and heparan sulfate (AAV8-AVB-HS), which efficiently bound to both affinity columns, resulting in elution yields of >80% of the total vector loaded compared to <5% for wild type AAV8. However, in vivo comparison by intramuscular, intravenous, and intraperitoneal vector administration demonstrated a significant decrease in AAV8-AVB-HS transduction efficiency without alteration of the transduction profile. Therefore, although it is possible to engineer AAV capsids to bind various affinity ligands, the consequences associated with mutating surface exposed residues have the potential to negatively impact other vector characteristics including in vivo potency and production yield. This study demonstrates the importance of evaluating all aspects of vector performance when engineering AAV capsids.
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Wu R, Prabhu R, Ozkan A, Sitharam M. Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis. PLoS Comput Biol 2020; 16:e1008357. [PMID: 33079933 PMCID: PMC7598928 DOI: 10.1371/journal.pcbi.1008357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/30/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Icosahedral viruses are under a micrometer in diameter, their infectious genome encapsulated by a shell assembled by a multiscale process, starting from an integer multiple of 60 viral capsid or coat protein (VP) monomers. We predict and validate inter-atomic hotspot interactions between VP monomers that are important for the assembly of 3 types of icosahedral viral capsids: Adeno Associated Virus serotype 2 (AAV2) and Minute Virus of Mice (MVM), both T = 1 single stranded DNA viruses, and Bromo Mosaic Virus (BMV), a T = 3 single stranded RNA virus. Experimental validation is by in-vitro, site-directed mutagenesis data found in literature. We combine ab-initio predictions at two scales: at the interface-scale, we predict the importance (cruciality) of an interaction for successful subassembly across each interface between symmetry-related VP monomers; and at the capsid-scale, we predict the cruciality of an interface for successful capsid assembly. At the interface-scale, we measure cruciality by changes in the capsid free-energy landscape partition function when an interaction is removed. The partition function computation uses atlases of interface subassembly landscapes, rapidly generated by a novel geometric method and curated opensource software EASAL (efficient atlasing and search of assembly landscapes). At the capsid-scale, cruciality of an interface for successful assembly of the capsid is based on combinatorial entropy. Our study goes all the way from resource-light, multiscale computational predictions of crucial hotspot inter-atomic interactions to validation using data on site-directed mutagenesis' effect on capsid assembly. By reliably and rapidly narrowing down target interactions, (no more than 1.5 hours per interface on a laptop with Intel Core i5-2500K @ 3.2 Ghz CPU and 8GB of RAM) our predictions can inform and reduce time-consuming in-vitro and in-vivo experiments, or more computationally intensive in-silico analyses.
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Affiliation(s)
- Ruijin Wu
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Rahul Prabhu
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Aysegul Ozkan
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Meera Sitharam
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, United States of America
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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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Davidsson M, Wang G, Aldrin-Kirk P, Cardoso T, Nolbrant S, Hartnor M, Mudannayake J, Parmar M, Björklund T. A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism. Proc Natl Acad Sci U S A 2019; 116:27053-27062. [PMID: 31818949 PMCID: PMC6936499 DOI: 10.1073/pnas.1910061116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Adeno-associated virus (AAV) capsid modification enables the generation of recombinant vectors with tailored properties and tropism. Most approaches to date depend on random screening, enrichment, and serendipity. The approach explored here, called BRAVE (barcoded rational AAV vector evolution), enables efficient selection of engineered capsid structures on a large scale using only a single screening round in vivo. The approach stands in contrast to previous methods that require multiple generations of enrichment. With the BRAVE approach, each virus particle displays a peptide, derived from a protein, of known function on the AAV capsid surface, and a unique molecular barcode in the packaged genome. The sequencing of RNA-expressed barcodes from a single-generation in vivo screen allows the mapping of putative binding sequences from hundreds of proteins simultaneously. Using the BRAVE approach and hidden Markov model-based clustering, we present 25 synthetic capsid variants with refined properties, such as retrograde axonal transport in specific subtypes of neurons, as shown for both rodent and human dopaminergic neurons.
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Affiliation(s)
- Marcus Davidsson
- Molecular Neuromodulation, Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
| | - Gang Wang
- Molecular Neuromodulation, Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
| | - Patrick Aldrin-Kirk
- Molecular Neuromodulation, Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
| | - Tiago Cardoso
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Sara Nolbrant
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Morgan Hartnor
- Molecular Neuromodulation, Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
| | - Janitha Mudannayake
- Molecular Neuromodulation, Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Tomas Björklund
- Molecular Neuromodulation, Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden
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Zdechlik AC, He Y, Aird EJ, Gordon WR, Schmidt D. Programmable Assembly of Adeno-Associated Virus-Antibody Composites for Receptor-Mediated Gene Delivery. Bioconjug Chem 2019; 31:1093-1106. [PMID: 31809024 DOI: 10.1021/acs.bioconjchem.9b00790] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Adeno-associated virus (AAV) has emerged as a viral gene delivery vector that is safe in humans, able to infect both dividing and arrested cells and drive long-term expression (>6 months). Unfortunately, the naturally evolved properties of many AAV serotypes-including low cell type specificity and largely overlapping tropism-are mismatched to applications that require cell type-specific infection, such as neural circuit mapping or precision gene therapy. A variety of approaches to redirect AAV tropism exist, but there is still the need for a universal solution for directing AAV tropism toward user-defined cellular receptors that does not require extensive case-by-case optimization and works with readily available components. Here, we report AAV engineering approaches that enable programmable receptor-mediated gene delivery. First, we genetically encode small targeting scaffolds into a variable region of an AAV capsid and show that this redirects tropism toward the receptor recognized by these targeting scaffolds and also renders this AAV variant resistant to neutralizing antibodies present in nonhuman primate serum. We then simplify retargeting of tropism by engineering the same variable loop to encode a HUH tag, which forms a covalent bond to single-stranded DNA oligos conjugated to store-bought antibodies. We demonstrate that retargeting this HUH-AAVs toward different receptors is as simple as "arming" a premade noninfective AAV template with a different antibody in a conjugation process that uses widely available reagents and requires no optimization or extensive purification. Composite antibody-AAV nanoparticles structurally separate tropism and payload encapsulation, allowing each to be engineered independently.
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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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40
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Le DT, Radukic MT, Müller KM. Adeno-associated virus capsid protein expression in Escherichia coli and chemically defined capsid assembly. Sci Rep 2019; 9:18631. [PMID: 31819093 PMCID: PMC6901487 DOI: 10.1038/s41598-019-54928-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/20/2019] [Indexed: 01/17/2023] Open
Abstract
Research and clinical applications of recombinant adeno-associated virus (rAAV) significantly increased in recent years alongside regulatory approvals of rAAV gene therapy products. To date, all rAAV vectors as well as AAV empty capsids are produced in eukaryotic cells. We explored a new route to generate AAV capsids with the aim to analyze capsid assembly in a chemically defined setting and pave the way for new production methods and applications based on AAV virus-like particles (VLPs). We generated these empty capsids by bacterial expression and subsequent concomitant protein refolding and VLP formation. AAV serotype 2 structural protein VP3 was expressed in Escherichia coli. VLPs formed as demonstrated by dynamic light scattering, atomic force microscopy, and ELISA. Furthermore, VLPs internalized into human HeLa cells. To extend the application range of the VLPs, we tested peptide insertions, at the genetic level, in a surface loop (amino acid position 587) or at the C-terminus of VP3 and these variants also formed VLPs. VLPs developed without assembly-activating protein (AAP), but adding purified recombinant AAP to the refolding process increased capsid yield. Our findings offer a new route to understand AAV assembly biology and open a toolbox for AAV production strategies that might enable capsid display for vaccination and matching of capsids with cargoes at large scale and low cost.
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Affiliation(s)
- Dinh To Le
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Marco T Radukic
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
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41
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Maurer AC, Pacouret S, Cepeda Diaz AK, Blake J, Andres-Mateos E, Vandenberghe LH. The Assembly-Activating Protein Promotes Stability and Interactions between AAV's Viral Proteins to Nucleate Capsid Assembly. Cell Rep 2019; 23:1817-1830. [PMID: 29742436 DOI: 10.1016/j.celrep.2018.04.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/31/2017] [Accepted: 04/04/2018] [Indexed: 11/30/2022] Open
Abstract
The adeno-associated virus (AAV) vector is a preferred delivery platform for in vivo gene therapy. Natural and engineered variations of the AAV capsid affect a plurality of phenotypes relevant to gene therapy, including vector production and host tropism. Fundamental to these aspects is the mechanism of AAV capsid assembly. Here, the role of the viral co-factor assembly-activating protein (AAP) was evaluated in 12 naturally occurring AAVs and 9 putative ancestral capsid intermediates. The results demonstrate increased capsid protein stability and VP-VP interactions in the presence of AAP. The capsid's dependence on AAP can be partly overcome by strengthening interactions between monomers within the assembly, as illustrated by the transfer of a minimal motif defined by a phenotype-to-phylogeny mapping method. These findings suggest that the emergence of AAP within the Dependovirus genus relaxes structural constraints on AAV assembly in favor of increasing the degrees of freedom for the capsid to evolve.
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Affiliation(s)
- Anna C Maurer
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA 02114, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Simon Pacouret
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA 02114, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Ana Karla Cepeda Diaz
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA 02114, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Jessica Blake
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA 02114, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Eva Andres-Mateos
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA 02114, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA 02114, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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42
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Keeler AM, Flotte TR. Recombinant Adeno-Associated Virus Gene Therapy in Light of Luxturna (and Zolgensma and Glybera): Where Are We, and How Did We Get Here? Annu Rev Virol 2019; 6:601-621. [PMID: 31283441 PMCID: PMC7123914 DOI: 10.1146/annurev-virology-092818-015530] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The recent market approvals of recombinant adeno-associated virus (rAAV) gene therapies in Europe and the United States are landmark achievements in the history of modern science. These approvals are also anticipated to herald the emergence of a new class of therapies for monogenic disorders, which had hitherto been considered untreatable. These events can be viewed as stemming from the convergence of several important historical trends: the study of basic virology, the development of genomic technologies, the imperative for translational impact of National Institutes of Health-funded research, and the development of economic models for commercialization of rare disease therapies. In this review, these historical trends are described and the key developments that have enabled clinical rAAV gene therapies are discussed, along with an overview of the current state of the field and future directions.
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Affiliation(s)
- Allison M Keeler
- Horae Gene Therapy Center and Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA;
| | - Terence R Flotte
- Horae Gene Therapy Center and Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA;
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43
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Khan N, Bammidi S, Jayandharan GR. A CD33 Antigen-Targeted AAV6 Vector Expressing an Inducible Caspase-9 Suicide Gene Is Therapeutic in a Xenotransplantation Model of Acute Myeloid Leukemia. Bioconjug Chem 2019; 30:2404-2416. [PMID: 31436412 DOI: 10.1021/acs.bioconjchem.9b00511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Current chemotherapeutic regimens for acute myeloid leukemia (AML) have been modestly effective in patients and are associated with poor long-term survival (<30% at 5 years). Viral vector-based suicide gene therapy is an attractive option, if these vectors can target the AML cells with high specificity and efficiency. In this study, we have developed a receptor-specific adeno-associated virus (AAV) based vector to target the CD33 antigen which is overexpressed in leukemic cells. A targeting peptide was rationally designed from the antigen-binding regions of a CD33 monoclonal antibody. This peptide was further expressed on the capsid of the AAV6 vector, since this serotype was most efficient among AAV1-rh10 vectors to infect the pro-monocytic, human myeloid leukemia cells (U937). AAV6-CD33 vectors expressing a suicide gene, the inducible caspase 9 (iCasp9), and its prodrug AP20187 significantly reduced (∼59%) the viability of U937 cells. To further test its efficacy and specificity in vivo, AAV6-CD33 vectors were administered into a xenotransplantation model of AML in zebrafish through systemic delivery. We observed a significant antileukemic effect with AAV6-CD33 vectors, with a markedly higher survival (100% for AAV6-CD33 vectors vs 15% for mock-treated) and a higher number of TUNEL positive apoptotic cells after systemic vector delivery. Taken together, our work demonstrates the efficacy and translational potential of CD33-targeted AAV6 vectors for cytotoxic gene therapy in AML.
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Affiliation(s)
- Nusrat Khan
- Department of Biological Sciences and Bioengineering , Indian Institute of Technology , Kanpur , 208016 , Uttar Pradesh , India
| | - Sridhar Bammidi
- Department of Biological Sciences and Bioengineering , Indian Institute of Technology , Kanpur , 208016 , Uttar Pradesh , India
| | - Giridhara R Jayandharan
- Department of Biological Sciences and Bioengineering , Indian Institute of Technology , Kanpur , 208016 , Uttar Pradesh , India
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44
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Tordo J, O'Leary C, Antunes ASLM, Palomar N, Aldrin-Kirk P, Basche M, Bennett A, D'Souza Z, Gleitz H, Godwin A, Holley RJ, Parker H, Liao AY, Rouse P, Youshani AS, Dridi L, Martins C, Levade T, Stacey KB, Davis DM, Dyer A, Clément N, Björklund T, Ali RR, Agbandje-McKenna M, Rahim AA, Pshezhetsky A, Waddington SN, Linden RM, Bigger BW, Henckaerts E. A novel adeno-associated virus capsid with enhanced neurotropism corrects a lysosomal transmembrane enzyme deficiency. Brain 2019; 141:2014-2031. [PMID: 29788236 PMCID: PMC6037107 DOI: 10.1093/brain/awy126] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Recombinant adeno-associated viruses (AAVs) are popular in vivo gene transfer vehicles. However, vector doses needed to achieve therapeutic effect are high and some target tissues in the central nervous system remain difficult to transduce. Gene therapy trials using AAV for the treatment of neurological disorders have seldom led to demonstrated clinical efficacy. Important contributing factors are low transduction rates and inefficient distribution of the vector. To overcome these hurdles, a variety of capsid engineering methods have been utilized to generate capsids with improved transduction properties. Here we describe an alternative approach to capsid engineering, which draws on the natural evolution of the virus and aims to yield capsids that are better suited to infect human tissues. We generated an AAV capsid to include amino acids that are conserved among natural AAV2 isolates and tested its biodistribution properties in mice and rats. Intriguingly, this novel variant, AAV-TT, demonstrates strong neurotropism in rodents and displays significantly improved distribution throughout the central nervous system as compared to AAV2. Additionally, sub-retinal injections in mice revealed markedly enhanced transduction of photoreceptor cells when compared to AAV2. Importantly, AAV-TT exceeds the distribution abilities of benchmark neurotropic serotypes AAV9 and AAVrh10 in the central nervous system of mice, and is the only virus, when administered at low dose, that is able to correct the neurological phenotype in a mouse model of mucopolysaccharidosis IIIC, a transmembrane enzyme lysosomal storage disease, which requires delivery to every cell for biochemical correction. These data represent unprecedented correction of a lysosomal transmembrane enzyme deficiency in mice and suggest that AAV-TT-based gene therapies may be suitable for treatment of human neurological diseases such as mucopolysaccharidosis IIIC, which is characterized by global neuropathology.
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Affiliation(s)
- Julie Tordo
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Claire O'Leary
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - André S L M Antunes
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Nuria Palomar
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Patrick Aldrin-Kirk
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Mark Basche
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zelpha D'Souza
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Hélène Gleitz
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Annie Godwin
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Rebecca J Holley
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Helen Parker
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Ai Yin Liao
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Rouse
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Amir Saam Youshani
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Larbi Dridi
- CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - Carla Martins
- CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - Thierry Levade
- Centre Hospitalo-Universitaire de Toulouse, Institut Fédératif de Biologie, Laboratoire de Biochimie Métabolique, and Unité Mixte de Recherche (UMR) 1037 Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Cancérologie de Toulouse, Toulouse, France
| | - Kevin B Stacey
- Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Daniel M Davis
- Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Adam Dyer
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Nathalie Clément
- Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL, USA
| | - Tomas Björklund
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Robin R Ali
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| | - 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
| | - Ahad A Rahim
- Department of Pharmacology, UCL School of Pharmacy, University College London, London, UK
| | | | - Simon N Waddington
- Gene Transfer Technology Group, Institute for Women's Health, University College London, London, UK.,Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R Michael Linden
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Brian W Bigger
- Stem Cell and Neurotherapies, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Els Henckaerts
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
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45
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Yang YS, Xie J, Wang D, Kim JM, Tai PWL, Gravallese E, Gao G, Shim JH. Bone-targeting AAV-mediated silencing of Schnurri-3 prevents bone loss in osteoporosis. Nat Commun 2019; 10:2958. [PMID: 31273195 PMCID: PMC6609711 DOI: 10.1038/s41467-019-10809-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
RNAi-based bone anabolic gene therapy has demonstrated initial success, but many practical challenges are still unmet. Here, we demonstrate that a recombinant adeno-associated virus 9 (rAAV9) is highly effective for transducing osteoblast lineage cells in the bone. The adaptor protein Schnurri-3 (SHN3) is a promising therapeutic target for osteoporosis, as deletion of shn3 prevents bone loss in osteoporotic mice and short-term inhibition of shn3 in adult mice increases bone mass. Accordingly, systemic and direct joint administration of an rAAV9 vector carrying an artificial-microRNA that targets shn3 (rAAV9-amiR-shn3) in mice markedly enhanced bone formation via augmented osteoblast activity. Additionally, systemic delivery of rAAV9-amiR-shn3 in osteoporotic mice counteracted bone loss and enhanced bone mechanical properties. Finally, we rationally designed a capsid that exhibits improved specificity to bone by grafting the bone-targeting peptide motif (AspSerSer)6 onto the AAV9-VP2 capsid protein. Collectively, our results identify a bone-targeting rAAV-mediated gene therapy for osteoporosis.
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Affiliation(s)
- Yeon-Suk Yang
- Department of Medicine/Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jung-Min Kim
- Department of Medicine/Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Ellen Gravallese
- Department of Medicine/Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Jae-Hyuck Shim
- Department of Medicine/Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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46
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Kurian JJ, Lakshmanan R, Chmely WM, Hull JA, Yu JC, Bennett A, McKenna R, Agbandje-McKenna M. Adeno-Associated Virus VP1u Exhibits Protease Activity. Viruses 2019; 11:E399. [PMID: 31035643 PMCID: PMC6563295 DOI: 10.3390/v11050399] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 02/05/2023] Open
Abstract
Adeno-associated viruses (AAVs) are being developed for gene delivery applications, with more than 100 ongoing clinical trials aimed at the treatment of monogenic diseases. In this study, the unique N-terminus of AAV capsid viral protein 1 (VP1u), containing a canonical group XIII PLA2 enzyme domain, was observed to also exhibit proteolytic activity. This protease activity can target casein and gelatin, two standard substrates used for testing protease function but does not self-cleave in the context of the capsid or target globular proteins, for example, bovine serum albumin (BSA). However, heated BSA is susceptible to VP1u-mediated cleavage, suggesting that disordered proteins are substrates for this protease function. The protease activity is partially inhibited by divalent cation chelators ethylenediaminetetraacetic acid (EDTA) and ethylene-bis(oxyethylenenitrilo)tetraacetic acid (EGTA), and human alpha-2-macroglobulin (A2M), a non-specific protease inhibitor. Interestingly, both the bovine pancreatic (group VIIA) and bee venom (group III) PLA2 enzymes also exhibit protease function against casein. This indicates that PLA2 groups, including VP1u, have a protease function. Amino acid substitution of the PLA2 catalytic motif (76HD/AN) in the AAV2 VP1u resulted in attenuation of protease activity, suggesting that the protease and PLA2 active sites are related. However, the amino acid substitution of histidine H38, which is not involved in PLA2 function, to alanine, also affects protease activity, suggesting that the active site/mechanism of the PLA2 and protease function are not identical.
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Affiliation(s)
- Justin J Kurian
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Renuk Lakshmanan
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - William M Chmely
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Joshua A Hull
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Jennifer C Yu
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Robert McKenna
- 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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47
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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: 108] [Impact Index Per Article: 21.6] [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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48
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Maurer AC, Cepeda Diaz AK, Vandenberghe LH. Residues on Adeno-associated Virus Capsid Lumen Dictate Interactions and Compatibility with the Assembly-Activating Protein. J Virol 2019; 93:e02013-18. [PMID: 30651367 PMCID: PMC6430561 DOI: 10.1128/jvi.02013-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/04/2019] [Indexed: 01/09/2023] Open
Abstract
The adeno-associated virus (AAV) serves as a broadly used vector system for in vivo gene delivery. The process of AAV capsid assembly remains poorly understood. The viral cofactor assembly-activating protein (AAP) is required for maximum AAV production and has multiple roles in capsid assembly, namely, trafficking of the structural proteins (VP) to the nuclear site of assembly, promoting the stability of VP against multiple degradation pathways, and facilitating stable interactions between VP monomers. The N-terminal 60 amino acids of AAP (AAPN) are essential for these functions. Presumably, AAP must physically interact with VP to execute its multiple functions, but the molecular nature of the AAP-VP interaction is not well understood. Here, we query how structurally related AAVs functionally engage AAP from AAV serotype 2 (AAP2) toward virion assembly. These studies led to the identification of key residues on the lumenal capsid surface that are important for AAP-VP and for VP-VP interactions. Replacing a cluster of glutamic acid residues with a glutamine-rich motif on the conserved VP beta-barrel structure of variants incompatible with AAP2 creates a gain-of-function mutant compatible with AAP2. Conversely, mutating positively charged residues within the hydrophobic region of AAP2 and conserved core domains within AAPN creates a gain-of-function AAP2 mutant that rescues assembly of the incompatible variant. Our results suggest a model for capsid assembly where surface charge/neutrality dictates an interaction between AAPN and the lumenal VP surface to nucleate capsid assembly.IMPORTANCE Efforts to engineer the AAV capsid to gain desirable properties for gene therapy (e.g., tropism, reduced immunogenicity, and higher potency) require that capsid modifications do not affect particle assembly. The relationship between VP and the cofactor that facilitates its assembly, AAP, is central to both assembly preservation and vector production. Understanding the requirements for this compatibility can inform manufacturing strategies to maximize production and reduce costs. Additionally, library-based approaches that simultaneously examine a large number of capsid variants would benefit from a universally functional AAP, which could hedge against overlooking variants with potentially valuable phenotypes that were lost during vector library production due to incompatibility with the cognate AAP. Studying interactions between the structural and nonstructural components of AAV enhances our fundamental knowledge of capsid assembly mechanisms and the protein-protein interactions required for productive assembly of the icosahedral capsid.
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Affiliation(s)
- Anna C Maurer
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, Massachusetts, USA
- Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ana Karla Cepeda Diaz
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, Massachusetts, USA
- Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, Massachusetts, USA
- Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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49
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Büning H, Srivastava A. Capsid Modifications for Targeting and Improving the Efficacy of AAV Vectors. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 12:248-265. [PMID: 30815511 PMCID: PMC6378346 DOI: 10.1016/j.omtm.2019.01.008] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the past decade, recombinant vectors based on a non-pathogenic parvovirus, the adeno-associated virus (AAV), have taken center stage as a gene delivery vehicle for the potential gene therapy for a number of human diseases. To date, the safety of AAV vectors in 176 phase I, II, and III clinical trials and their efficacy in at least eight human diseases are now firmly documented. Despite these remarkable achievements, it has also become abundantly clear that the full potential of first generation AAV vectors composed of naturally occurring capsids is not likely to be realized, since the wild-type AAV did not evolve for the purpose of therapeutic gene delivery. In this article, we provide a brief historical account of the progress that has been made in the development of capsid-modified, next-generation AAV vectors to ensure both the safety and efficacy of these vectors in targeting a wide variety of human diseases.
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Affiliation(s)
- Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Arun Srivastava
- Division of Cellular and Molecular Therapy, Departments of Pediatrics and Molecular Genetics & Microbiology, Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL, USA
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50
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Alméciga-Díaz CJ, Montaño AM, Barrera LA, Tomatsu S. Tailoring the AAV2 capsid vector for bone-targeting. Pediatr Res 2018; 84:545-551. [PMID: 30323349 PMCID: PMC6266866 DOI: 10.1038/s41390-018-0095-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/01/2018] [Accepted: 05/11/2018] [Indexed: 11/08/2022]
Abstract
BACKGROUND Targeting specific tissues remains a major challenge to the promise of gene therapy. For example, several strategies have failed to target adeno-associated virus 2 (AAV2) vectors, to bone. We have evaluated in vitro and in vivo the affinity of an AAV2 vector to bone matrix, hydroxyapatite (HA) to treat Mucopolysacccharidosis IVA. METHODS To increase vector affinity to HA, an aspartic acid octapeptide (D8) was inserted immediately after the N-terminal region of the VP2 capsid protein. The modified vector had physical titers and transduction efficiencies comparable to the unmodified vector. RESULTS The bone-targeting vector had significantly higher HA affinity and vector genome copies in bone than the unmodified vector. The modified vector was also released from HA, and its enzyme activity in bone, 3 months post infusion, was 4.7-fold higher than the unmodified vector. CONCLUSION Inserting a bone-targeting peptide into the vector capsid increases gene delivery and expression in the bone without decreasing enzyme expression. This approach could be a novel strategy to treat systemic bone diseases.
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Affiliation(s)
- Carlos J Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism, Pontificia Universidad Javeriana, Bogotá, DC, Colombia.
| | - Adriana M Montaño
- Department of Pediatrics, School of Medicine, Saint Louis University, St. Louis, MO, USA.
| | - Luis A Barrera
- Institute for the Study of Inborn Errors of Metabolism, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Shunji Tomatsu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA.
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