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Drouyer M, Chu TH, Labit E, Haase F, Navarro RG, Nazareth D, Rosin N, Merjane J, Scott S, Cabanes-Creus M, Westhaus A, Zhu E, Midha R, Alexander IE, Biernaskie J, Ginn SL, Lisowski L. Novel AAV variants with improved tropism for human Schwann cells. Mol Ther Methods Clin Dev 2024; 32:101234. [PMID: 38558569 PMCID: PMC10978538 DOI: 10.1016/j.omtm.2024.101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Gene therapies and associated technologies are transforming biomedical research and enabling novel therapeutic options for patients living with debilitating and incurable genetic disorders. The vector system based on recombinant adeno-associated viral vectors (AAVs) has shown great promise in recent clinical trials for genetic diseases of multiple organs, such as the liver and the nervous system. Despite recent successes toward the development of novel bioengineered AAV variants for improved transduction of primary human tissues and cells, vectors that can efficiently transduce human Schwann cells (hSCs) have yet to be identified. Here, we report the application of the functional transduction-RNA selection method in primary hSCs for the development of AAV variants for specific and efficient transgene delivery to hSCs. The two identified capsid variants, Pep2hSC1 and Pep2hSC2, show conserved potency for delivery across various in vitro, in vivo, and ex vivo models of hSCs. These novel AAV capsids will serve as valuable research tools, forming the basis for therapeutic solutions for both SC-related disorders or peripheral nervous system injury.
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Affiliation(s)
- Matthieu Drouyer
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Tak-Ho Chu
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Elodie Labit
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Florencia Haase
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Deborah Nazareth
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Nicole Rosin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jessica Merjane
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Suzanne Scott
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Rajiv Midha
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ian E. Alexander
- Gene Therapy Research Unit, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jeff Biernaskie
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samantha L. Ginn
- Gene Therapy Research Unit, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Australian Genome Therapeutics Centre, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Westmead, NSW, Australia
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland
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2
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Lopez-Gordo E, Chamberlain K, Riyad JM, Kohlbrenner E, Weber T. Natural Adeno-Associated Virus Serotypes and Engineered Adeno-Associated Virus Capsid Variants: Tropism Differences and Mechanistic Insights. Viruses 2024; 16:442. [PMID: 38543807 PMCID: PMC10975205 DOI: 10.3390/v16030442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
Today, adeno-associated virus (AAV)-based vectors are arguably the most promising in vivo gene delivery vehicles for durable therapeutic gene expression. Advances in molecular engineering, high-throughput screening platforms, and computational techniques have resulted in a toolbox of capsid variants with enhanced performance over parental serotypes. Despite their considerable promise and emerging clinical success, there are still obstacles hindering their broader use, including limited transduction capabilities, tissue/cell type-specific tropism and penetration into tissues through anatomical barriers, off-target tissue biodistribution, intracellular degradation, immune recognition, and a lack of translatability from preclinical models to clinical settings. Here, we first describe the transduction mechanisms of natural AAV serotypes and explore the current understanding of the systemic and cellular hurdles to efficient transduction. We then outline progress in developing designer AAV capsid variants, highlighting the seminal discoveries of variants which can transduce the central nervous system upon systemic administration, and, to a lesser extent, discuss the targeting of the peripheral nervous system, eye, ear, lung, liver, heart, and skeletal muscle, emphasizing their tissue and cell specificity and translational promise. In particular, we dive deeper into the molecular mechanisms behind their enhanced properties, with a focus on their engagement with host cell receptors previously inaccessible to natural AAV serotypes. Finally, we summarize the main findings of our review and discuss future directions.
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3
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McDonald A, Wijnholds J. Retinal Ciliopathies and Potential Gene Therapies: A Focus on Human iPSC-Derived Organoid Models. Int J Mol Sci 2024; 25:2887. [PMID: 38474133 DOI: 10.3390/ijms25052887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The human photoreceptor function is dependent on a highly specialised cilium. Perturbation of cilial function can often lead to death of the photoreceptor and loss of vision. Retinal ciliopathies are a genetically diverse range of inherited retinal disorders affecting aspects of the photoreceptor cilium. Despite advances in the understanding of retinal ciliopathies utilising animal disease models, they can often lack the ability to accurately mimic the observed patient phenotype, possibly due to structural and functional deviations from the human retina. Human-induced pluripotent stem cells (hiPSCs) can be utilised to generate an alternative disease model, the 3D retinal organoid, which contains all major retinal cell types including photoreceptors complete with cilial structures. These retinal organoids facilitate the study of disease mechanisms and potential therapies in a human-derived system. Three-dimensional retinal organoids are still a developing technology, and despite impressive progress, several limitations remain. This review will discuss the state of hiPSC-derived retinal organoid technology for accurately modelling prominent retinal ciliopathies related to genes, including RPGR, CEP290, MYO7A, and USH2A. Additionally, we will discuss the development of novel gene therapy approaches targeting retinal ciliopathies, including the delivery of large genes and gene-editing techniques.
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Affiliation(s)
- Andrew McDonald
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands
- Netherlands Institute of Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands
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Nemoto T, Ocari T, Planul A, Tekinsoy M, Zin EA, Dalkara D, Ferrari U. ACIDES: on-line monitoring of forward genetic screens for protein engineering. Nat Commun 2023; 14:8504. [PMID: 38148337 PMCID: PMC10751290 DOI: 10.1038/s41467-023-43967-9] [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: 04/07/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
Forward genetic screens of mutated variants are a versatile strategy for protein engineering and investigation, which has been successfully applied to various studies like directed evolution (DE) and deep mutational scanning (DMS). While next-generation sequencing can track millions of variants during the screening rounds, the vast and noisy nature of the sequencing data impedes the estimation of the performance of individual variants. Here, we propose ACIDES that combines statistical inference and in-silico simulations to improve performance estimation in the library selection process by attributing accurate statistical scores to individual variants. We tested ACIDES first on a random-peptide-insertion experiment and then on multiple public datasets from DE and DMS studies. ACIDES allows experimentalists to reliably estimate variant performance on the fly and can aid protein engineering and research pipelines in a range of applications, including gene therapy.
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Affiliation(s)
- Takahiro Nemoto
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France.
- Graduate School of Informatics, Kyoto University, Yoshida Hon-machi, Sakyo-ku, Kyoto, 606-8501, Japan.
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Tommaso Ocari
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Arthur Planul
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Muge Tekinsoy
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Emilia A Zin
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France
| | - Deniz Dalkara
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France.
| | - Ulisse Ferrari
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 17 rue Moreau, 75012, Paris, France.
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Westhaus A, Eamegdool SS, Fernando M, Fuller-Carter P, Brunet AA, Miller AL, Rashwan R, Knight M, Daniszewski M, Lidgerwood GE, Pébay A, Hewitt A, Santilli G, Thrasher AJ, Carvalho LS, Gonzalez-Cordero A, Jamieson RV, Lisowski L. AAV capsid bioengineering in primary human retina models. Sci Rep 2023; 13:21946. [PMID: 38081924 PMCID: PMC10713676 DOI: 10.1038/s41598-023-49112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Adeno-associated viral (AAV) vector-mediated retinal gene therapy is an active field of both pre-clinical as well as clinical research. As with other gene therapy clinical targets, novel bioengineered AAV variants developed by directed evolution or rational design to possess unique desirable properties, are entering retinal gene therapy translational programs. However, it is becoming increasingly evident that predictive preclinical models are required to develop and functionally validate these novel AAVs prior to clinical studies. To investigate if, and to what extent, primary retinal explant culture could be used for AAV capsid development, this study performed a large high-throughput screen of 51 existing AAV capsids in primary human retina explants and other models of the human retina. Furthermore, we applied transgene expression-based directed evolution to develop novel capsids for more efficient transduction of primary human retina cells and compared the top variants to the strongest existing benchmarks identified in the screening described above. A direct side-by-side comparison of the newly developed capsids in four different in vitro and ex vivo model systems of the human retina allowed us to identify novel AAV variants capable of high transgene expression in primary human retina cells.
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Affiliation(s)
- Adrian Westhaus
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Genethon, Evry, France
| | - Steven S Eamegdool
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | | | - Alicia A Brunet
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Annie L Miller
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | | | - Maddison Knight
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Alex Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Livia S Carvalho
- Lions Eye Institute, Nedlands, Australia
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Stem Cell Medicine Group, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.
- Australian Genome Therapeutics Centre, Children's Medical Research Institute and Sydney Children's Hospitals Network, Westmead, NSW, 2145, Australia.
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland.
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6
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Kellish PC, Marsic D, Crosson SM, Choudhury S, Scalabrino ML, Strang CE, Hill J, McCullough KT, Peterson JJ, Fajardo D, Gupte S, Makal V, Kondratov O, Kondratova L, Iyer S, Witherspoon CD, Gamlin PD, Zolotukhin S, Boye SL, Boye SE. Intravitreal injection of a rationally designed AAV capsid library in non-human primate identifies variants with enhanced retinal transduction and neutralizing antibody evasion. Mol Ther 2023; 31:3441-3456. [PMID: 37814449 PMCID: PMC10727955 DOI: 10.1016/j.ymthe.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/11/2023] Open
Abstract
Adeno-associated virus (AAV) continues to be the gold standard vector for therapeutic gene delivery and has proven especially useful for treating ocular disease. Intravitreal injection (IVtI) is a promising delivery route because it increases accessibility of gene therapies to larger patient populations. However, data from clinical and non-human primate (NHP) studies utilizing currently available capsids indicate that anatomical barriers to AAV and pre-existing neutralizing antibodies can restrict gene expression to levels that are "sub-therapeutic" in a substantial proportion of patients. Here, we performed a combination of directed evolution in NHPs of an AAV2-based capsid library with simultaneous mutations across six surface-exposed variable regions and rational design to identify novel capsid variants with improved retinal transduction following IVtI. Following two rounds of screening in NHP, enriched variants were characterized in intravitreally injected mice and NHPs and shown to have increased transduction relative to AAV2. Lead capsid variant, P2-V1, demonstrated an increased ability to evade neutralizing antibodies in human vitreous samples relative to AAV2 and AAV2.7m8. Taken together, this study further contributed to our understanding of the selective pressures associated with retinal transduction via the vitreous and identified promising novel AAV capsid variants for clinical consideration.
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Affiliation(s)
- Patrick C Kellish
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Damien Marsic
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Sean M Crosson
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Shreyasi Choudhury
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Miranda L Scalabrino
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Christianne E Strang
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham AL 35294, USA
| | - Julie Hill
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham AL 35294, USA
| | - K Tyler McCullough
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - James J Peterson
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Diego Fajardo
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Siddhant Gupte
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Victoria Makal
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Oleksandr Kondratov
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Liudmyla Kondratova
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Siva Iyer
- Department of Ophthalmology, University of Florida, Gainesville, FL 32610, USA
| | - C Douglas Witherspoon
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham AL 35294, USA
| | - Paul D Gamlin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham AL 35294, USA
| | - Sergei Zolotukhin
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA
| | - Sanford L Boye
- Powell Gene Therapy Center, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - Shannon E Boye
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida, Gainesville, FL 32610, USA.
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7
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Schultz A, Cheng SY, Kirchner E, Costello S, Miettinen H, Chaverra M, King C, George L, Zhao X, Narasimhan J, Weetall M, Slaugenhaupt S, Morini E, Punzo C, Lefcort F. Reduction of retinal ganglion cell death in mouse models of familial dysautonomia using AAV-mediated gene therapy and splicing modulators. Sci Rep 2023; 13:18600. [PMID: 37903840 PMCID: PMC10616160 DOI: 10.1038/s41598-023-45376-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Familial dysautonomia (FD) is a rare neurodevelopmental and neurodegenerative disease caused by a splicing mutation in the Elongator Acetyltransferase Complex Subunit 1 (ELP1) gene. The reduction in ELP1 mRNA and protein leads to the death of retinal ganglion cells (RGCs) and visual impairment in all FD patients. Currently patient symptoms are managed, but there is no treatment for the disease. We sought to test the hypothesis that restoring levels of Elp1 would thwart the death of RGCs in FD. To this end, we tested the effectiveness of two therapeutic strategies for rescuing RGCs. Here we provide proof-of-concept data that gene replacement therapy and small molecule splicing modifiers effectively reduce the death of RGCs in mouse models for FD and provide pre-clinical foundational data for translation to FD patients.
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Affiliation(s)
- Anastasia Schultz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Shun-Yun Cheng
- Department of Ophthalmology, Neurobiology and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Emily Kirchner
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Stephanann Costello
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Heini Miettinen
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Marta Chaverra
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Colin King
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Lynn George
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
- Department of Biological and Physical Science, Montana State University Billings, Billings, MT, USA
| | - Xin Zhao
- PTC Therapeutics, Inc., South Plainfield, NJ, 07080, USA
| | | | - Marla Weetall
- PTC Therapeutics, Inc., South Plainfield, NJ, 07080, USA
| | - Susan Slaugenhaupt
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Elisabetta Morini
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Claudio Punzo
- Department of Ophthalmology, Neurobiology and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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8
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Takahashi K, Kwok JC, Sato Y, Aguirre GD, Miyadera K. Extended functional rescue following AAV gene therapy in a canine model of LRIT3-congenital stationary night blindness. Vision Res 2023; 209:108260. [PMID: 37220680 PMCID: PMC10524691 DOI: 10.1016/j.visres.2023.108260] [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: 12/19/2022] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
Congenital stationary night blindness (CSNB) is a group of inherited retinal diseases in which either rod-to-ON-bipolar cell (ON-BC) signaling, or rod function is affected leading to impaired vision under low light conditions. One type of CSNB is associated with defects in genes (NYX, GRM6, TRPM1, GPR179, and LRIT3) involved in the mGluR6 signaling cascade at the ON-BC dendritic tips. We have previously characterized a canine model of LRIT3-CSNB and demonstrated short-term safety and efficacy of an ON-BC targeting AAV-LRIT3 (AAVK9#4-shGRM6-cLRIT3-WPRE) gene therapy. Herein, we demonstrate long-term functional recovery and molecular restoration following subretinal injection of the ON-BC targeting AAV-LRIT3 vector in all eight treated eyes for up to 32 months. Following subretinal administration of the therapeutic vector, expression of the LRIT3 transgene, as well as restoration of mGluR6 signaling cascade member TRPM1, were confirmed in the outer plexiform layer (OPL) of the treated area. However, further investigation of the transgene LRIT3 transcript expression by RNA in situ hybridization (RNA-ISH) revealed off-target expression in non-BCs including the photoreceptors, inner nuclear, and ganglion cell layers, despite the use of a mutant AAVK9#4 capsid and an improved mGluR6 promoter designed to specifically transduce and promote expression in ON-BCs. While the long-term therapeutic potential of AAVK9#4-shGRM6-cLRIT3-WPRE is promising, we highlight the necessity for further optimization of AAV-LRIT3 therapy in the canine CSNB model prior to its clinical application.
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Affiliation(s)
- Kei Takahashi
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer C Kwok
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yu Sato
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gustavo D Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keiko Miyadera
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Park H, Jo SH, Lee RH, Macks CP, Ku T, Park J, Lee CW, Hur JK, Sohn CH. Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206939. [PMID: 37026425 PMCID: PMC10238226 DOI: 10.1002/advs.202206939] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/10/2023] [Indexed: 06/04/2023]
Abstract
Spatial transcriptomics is a newly emerging field that enables high-throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems. By transitioning from conventional biological studies to "in situ" biology, spatial transcriptomics can provide transcriptome-scale spatial information. Currently, the ability to simultaneously characterize gene expression profiles of cells and relevant cellular environment is a paradigm shift for biological studies. In this review, recent progress in spatial transcriptomics and its applications in neuroscience and cancer studies are highlighted. Technical aspects of existing technologies and future directions of new developments (as of March 2023), computational analysis of spatial transcriptome data, application notes in neuroscience and cancer studies, and discussions regarding future directions of spatial multi-omics and their expanding roles in biomedical applications are emphasized.
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Affiliation(s)
- Han‐Eol Park
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
- School of Biological SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Song Hyun Jo
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Rosalind H. Lee
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Christian P. Macks
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Jihwan Park
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Chung Whan Lee
- Department of ChemistryGachon UniversitySeongnamGyeonggi‐do13120Republic of Korea
| | - Junho K. Hur
- Department of GeneticsCollege of MedicineHanyang UniversitySeoul04763Republic of Korea
| | - Chang Ho Sohn
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
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10
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Schultz A, Cheng SY, Kirchner E, Costello S, Miettinen H, Chaverra M, King C, George L, Zhao X, Narasimhan J, Weetall M, Slaugenhaupt S, Morini E, Punzo C, Lefcort F. Reduction of retinal ganglion cell death in mouse models of familial dysautonomia using AAV-mediated gene therapy and splicing modulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541535. [PMID: 37293016 PMCID: PMC10245894 DOI: 10.1101/2023.05.22.541535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Familial dysautonomia (FD) is a rare neurodevelopmental and neurodegenerative disease caused by a splicing mutation in the Elongator Acetyltransferase Complex Subunit 1 ( ELP1 ) gene. The reduction in ELP1 mRNA and protein leads to the death of retinal ganglion cells (RGCs) and visual impairment in all FD patients. Currently, patient symptoms are managed, but there is no treatment for the disease. We sought to test the hypothesis that restoring levels of Elp1 would thwart the death of RGCs in FD. To this end, we tested the effectiveness of two therapeutic strategies for rescuing RGCs. Here we provide proof-of-concept data that gene replacement therapy and small molecule splicing modifiers effectively reduce the death of RGCs in mouse models for FD and provide pre-clinical data foundation for translation to FD patients.
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11
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Zin EA, Ozturk BE, Dalkara D, Byrne LC. Developing New Vectors for Retinal Gene Therapy. Cold Spring Harb Perspect Med 2023; 13:a041291. [PMID: 36987583 PMCID: PMC10691475 DOI: 10.1101/cshperspect.a041291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Since their discovery over 55 years ago, adeno-associated virus (AAV) vectors have become powerful tools for experimental and therapeutic in vivo gene delivery, particularly in the retina. Increasing knowledge of AAV structure and biology has propelled forward the development of engineered AAV vectors with improved abilities for gene delivery. However, major obstacles to safe and efficient therapeutic gene delivery remain, including tropism, inefficient and untargeted gene delivery, and limited carrying capacity. Additional improvements to AAV vectors will be required to achieve therapeutic benefit while avoiding safety issues. In this review, we provide an overview of recent methods for engineering-enhanced AAV capsids, as well as remaining challenges that must be overcome to achieve optimized therapeutic gene delivery in the eye.
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Affiliation(s)
- Emilia A Zin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Bilge E Ozturk
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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12
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Szumska J, Grimm D. Boosters for adeno-associated virus (AAV) vector (r)evolution. Cytotherapy 2023; 25:254-260. [PMID: 35999132 DOI: 10.1016/j.jcyt.2022.07.005] [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: 03/30/2022] [Revised: 07/06/2022] [Accepted: 07/16/2022] [Indexed: 02/07/2023]
Abstract
Adeno-associated virus (AAV) is one of the most exciting and most versatile templates for engineering of gene-delivery vectors for use in human gene therapy, owing to the existence of numerous naturally occurring capsid variants and their amenability to directed molecular evolution. As a result, the field has witnessed an explosion of novel "designer" AAV capsids and ensuing vectors over the last two decades, which have been isolated from comprehensive capsid libraries generated through technologies such as DNA shuffling or peptide display, and stratified under stringent positive and/or negative selection pressures. Here, we briefly highlight a panel of recent, innovative and transformative methodologies that we consider to have exceptional potential to advance directed AAV capsid evolution and to thereby accelerate AAV vector revolution. These avenues comprise original technologies for (i) barcoding and high-throughput screening of individual AAV variants or entire capsid libraries, (ii) selection of transduction-competent AAV vectors on the DNA level, (iii) enrichment of expression-competent AAV variants on the RNA level, as well as (iv) high-resolution stratification of focused AAV capsid libraries on the single-cell level. Together with other emerging AAV engineering stratagems, such as rational design or machine learning, these pioneering techniques promise to provide an urgently needed booster for AAV (r)evolution.
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Affiliation(s)
- Joanna Szumska
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, Heidelberg, Germany; BioQuant Center and Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, Heidelberg, Germany; BioQuant Center and Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, Heidelberg, Germany; German Center for Infection Research (Deutsches Zentrum für Infektionsforschung, DZIF) and German Center for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Erkrankungen, DZHK), partner site Heidelberg, Heidelberg, Germany.
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13
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Ghauri MS, Ou L. AAV Engineering for Improving Tropism to the Central Nervous System. BIOLOGY 2023; 12:biology12020186. [PMID: 36829465 PMCID: PMC9953251 DOI: 10.3390/biology12020186] [Citation(s) in RCA: 0] [Impact Index Per Article: 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
- Correspondence:
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14
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Cabanes-Creus M, Navarro RG, Liao SH, Scott S, Carlessi R, Roca-Pinilla R, Knight M, Baltazar G, Zhu E, Jones M, Denisenko E, Forrest AR, Alexander IE, Tirnitz-Parker JE, Lisowski L. Characterization of the humanized FRG mouse model and development of an AAV-LK03 variant with improved liver lobular biodistribution. Mol Ther Methods Clin Dev 2023; 28:220-237. [PMID: 36700121 PMCID: PMC9860073 DOI: 10.1016/j.omtm.2022.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Recent clinical successes have intensified interest in using adeno-associated virus (AAV) vectors for therapeutic gene delivery. The liver is a key clinical target, given its critical physiological functions and involvement in a wide range of genetic diseases. In the present study, we first investigated the validity of a liver xenograft mouse model repopulated with primary hepatocytes using single-nucleus RNA sequencing (sn-RNA-seq) by studying the transcriptomic profile of human hepatocytes pre- and post-engraftment. Complementary immunofluorescence analyses performed in highly engrafted animals confirmed that the human hepatocytes organize and present appropriate patterns of zone-dependent enzyme expression in this model. Next, we tested a set of rationally designed HSPG de-targeted AAV-LK03 variants for relative transduction performance in human hepatocytes. We used immunofluorescence, next-generation sequencing, and single-nucleus transcriptomics data from highly engrafted FRG mice to demonstrate that the optimally HSPG de-targeted AAV-LK03 displayed a significantly improved lobular transduction profile in this model.
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Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Sophia H.Y. Liao
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Suzanne Scott
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Rodrigo Carlessi
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Ramon Roca-Pinilla
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Maddison Knight
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney, and Sydney Children’s Hospitals Network, Westmead, NSW 2145, Australia
| | - Matthew Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Alistair R.R. Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Ian E. Alexander
- Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney, and Sydney Children’s Hospitals Network, Westmead, NSW 2145, Australia,Discipline of Child and Adolescent Health, The University of Sydney, Sydney Medical School, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Janina E.E. Tirnitz-Parker
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia,UWA Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia,Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland,Corresponding author: Dr. Leszek Lisowski, Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.
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15
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Gene augmentation prevents retinal degeneration in a CRISPR/Cas9-based mouse model of PRPF31 retinitis pigmentosa. Nat Commun 2022; 13:7695. [PMID: 36509783 PMCID: PMC9744804 DOI: 10.1038/s41467-022-35361-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa, an untreatable form of blindness. Gene therapy is a promising treatment for PRPF31-retinitis pigmentosa, however, there are currently no suitable animal models in which to develop AAV-mediated gene augmentation. Here we establish Prpf31 mutant mouse models using AAV-mediated CRISPR/Cas9 knockout, and characterize the resulting retinal degeneration phenotype. Mouse models with early-onset morphological and functional impairments like those in patients were established, providing new platforms in which to investigate pathogenetic mechanisms and develop therapeutic methods. AAV-mediated PRPF31 gene augmentation restored the retinal structure and function in a rapidly degenerating mouse model, demonstrating the first in vivo proof-of-concept for AAV-mediated gene therapy to treat PRPF31-retinitis pigmentosa. AAV-CRISPR/Cas9-PRPF31 knockout constructs also mediated efficient PRPF31 knockout in human and non-human primate retinal explants, laying a foundation for establishing non-human primate models using the method developed here.
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16
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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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17
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Wang X, Chan V, Corridon PR. Acellular Tissue-Engineered Vascular Grafts from Polymers: Methods, Achievements, Characterization, and Challenges. Polymers (Basel) 2022; 14:polym14224825. [PMID: 36432950 PMCID: PMC9695055 DOI: 10.3390/polym14224825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Extensive and permanent damage to the vasculature leading to different pathogenesis calls for developing innovative therapeutics, including drugs, medical devices, and cell therapies. Innovative strategies to engineer bioartificial/biomimetic vessels have been extensively exploited as an effective replacement for vessels that have seriously malfunctioned. However, further studies in polymer chemistry, additive manufacturing, and rapid prototyping are required to generate highly engineered vascular segments that can be effectively integrated into the existing vasculature of patients. One recently developed approach involves designing and fabricating acellular vessel equivalents from novel polymeric materials. This review aims to assess the design criteria, engineering factors, and innovative approaches for the fabrication and characterization of biomimetic macro- and micro-scale vessels. At the same time, the engineering correlation between the physical properties of the polymer and biological functionalities of multiscale acellular vascular segments are thoroughly elucidated. Moreover, several emerging characterization techniques for probing the mechanical properties of tissue-engineered vascular grafts are revealed. Finally, significant challenges to the clinical transformation of the highly promising engineered vessels derived from polymers are identified, and unique perspectives on future research directions are presented.
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Affiliation(s)
- Xinyu Wang
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Vincent Chan
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence: (V.C.); (P.R.C.)
| | - Peter R. Corridon
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence: (V.C.); (P.R.C.)
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18
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Intranasal application of adeno-associated viruses: a systematic review. Transl Res 2022; 248:87-110. [PMID: 35597541 DOI: 10.1016/j.trsl.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 01/13/2023]
Abstract
Adeno-associated viruses (AAVs) represent some of the most commonly employed vectors for targeted gene delivery and their extensive study has resulted in the approval of multiple gene therapies to treat human diseases. The intranasal route of vector application in gene therapy offers several advantages over traditional ways of administration. In addition to targeting local tissue like the olfactory epithelium, it provides minimally invasive access to various organ systems, including the central nervous system and the respiratory tract. Through a systematic literature review, a total of 53 articles that investigated the intranasal application of AAVs were identified, included, and summarized in this manuscript. Within these studies, AAV-based gene therapy was mainly investigated for its application in various infectious, pulmonary, or neurologic and/or psychiatric diseases. This review gives a comprehensive overview of the current technological state of the art regarding the intranasal application of AAVs for gene transfer and discusses remaining hurdles, which still have to be resolved before this approach can effectively be implemented in the routine clinical setting.
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19
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Corridon PR, Wang X, Shakeel A, Chan V. Digital Technologies: Advancing Individualized Treatments through Gene and Cell Therapies, Pharmacogenetics, and Disease Detection and Diagnostics. Biomedicines 2022; 10:biomedicines10102445. [PMID: 36289707 PMCID: PMC9599083 DOI: 10.3390/biomedicines10102445] [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: 09/02/2022] [Accepted: 09/25/2022] [Indexed: 11/28/2022] Open
Abstract
Digital technologies are shifting the paradigm of medicine in a way that will transform the healthcare industry. Conventional medical approaches focus on treating symptoms and ailments for large groups of people. These approaches can elicit differences in treatment responses and adverse reactions based on population variations, and are often incapable of treating the inherent pathophysiology of the medical conditions. Advances in genetics and engineering are improving healthcare via individualized treatments that include gene and cell therapies, pharmacogenetics, disease detection, and diagnostics. This paper highlights ways that artificial intelligence can help usher in an age of personalized medicine.
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Affiliation(s)
- Peter R. Corridon
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence:
| | - Xinyu Wang
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Adeeba Shakeel
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Vincent Chan
- Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
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20
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Targeting the lung epithelium after intravenous delivery by directed evolution of underexplored sites on the AAV capsid. Mol Ther Methods Clin Dev 2022; 26:331-342. [PMID: 35990749 PMCID: PMC9372736 DOI: 10.1016/j.omtm.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022]
Abstract
Advances in adeno-associated virus (AAV) engineering have provided exciting new tools for research and potential solutions for gene therapy. However, the lung has not received the same tailored engineering as other major targets of debilitating genetic disorders. To address this, here we engineered the surface-exposed residues AA452-458 of AAV9 capsid proteins at the three-fold axis of symmetry and employed a Cre-transgenic-based screening platform to identify AAV capsids targeted to the lung after intravenous delivery in mice. Using a custom image processing pipeline to quantify transgene expression across whole tissue images, we found that one engineered variant, AAV9.452sub.LUNG1, displays dramatically improved transgene expression in lung tissue after systemic delivery in mice. This improved transduction extends to alveolar epithelial type II cells, expanding the toolbox for gene therapy research for diseases specific to the lung.
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21
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Keng CT, Guo K, Liu YC, Shen KY, Lim DS, Lovatt M, Ang HP, Mehta JS, Chew WL. Multiplex viral tropism assay in complex cell populations with single-cell resolution. Gene Ther 2022; 29:555-565. [PMID: 35999303 PMCID: PMC9482877 DOI: 10.1038/s41434-022-00360-3] [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: 02/11/2022] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022]
Abstract
Gene therapy constitutes one of the most promising mode of disease treatments. Two key properties for therapeutic delivery vectors are its transduction efficiency (how well the vector delivers therapeutic cargo to desired target cells) and specificity (how well it avoids off-target delivery into unintended cells within the body). Here we developed an integrated bioinformatics and experimental pipeline that enables multiplex measurement of transduction efficiency and specificity, particularly by measuring how libraries of delivery vectors transduce libraries of diverse cell types. We demonstrated that pairing high-throughput measurement of AAV identity with high-resolution single-cell RNA transcriptomic sequencing maps how natural and engineered AAV variants transduce individual cells within human cerebral and ocular organoids. We further demonstrate that efficient AAV transduction observed in organoids is recapitulated in vivo in non-human primates. This library-on-library technology will be important for determining the safety and efficacy of therapeutic delivery vectors.
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Affiliation(s)
- Choong Tat Keng
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Ke Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Yu-Chi Liu
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and Refractive Surgery Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and External Eye Diseases, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Kimberle Yanyin Shen
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Daryl Shern Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Matthew Lovatt
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Heng Pei Ang
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Jodhbir S Mehta
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and Refractive Surgery Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and External Eye Diseases, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore. .,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
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22
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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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23
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Abstract
Cardiovascular disease remains the leading cause of morbidity and mortality in the developed world. In recent decades, extraordinary effort has been devoted to defining the molecular and pathophysiological characteristics of the diseased heart and vasculature. Mouse models have been especially powerful in illuminating the complex signaling pathways, genetic and epigenetic regulatory circuits, and multicellular interactions that underlie cardiovascular disease. The advent of CRISPR genome editing has ushered in a new era of cardiovascular research and possibilities for genetic correction of disease. Next-generation sequencing technologies have greatly accelerated the identification of disease-causing mutations, and advances in gene editing have enabled the rapid modeling of these mutations in mice and patient-derived induced pluripotent stem cells. The ability to correct the genetic drivers of cardiovascular disease through delivery of gene editing components in vivo, while still facing challenges, represents an exciting therapeutic frontier. In this review, we provide an overview of cardiovascular disease mechanisms and the potential applications of CRISPR genome editing for disease modeling and correction. We also discuss the extent to which mice can faithfully model cardiovascular disease and the opportunities and challenges that lie ahead.
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Affiliation(s)
- Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas
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24
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Xi Z, Öztürk BE, Johnson ME, Turunç S, Stauffer WR, Byrne LC. Quantitative single-cell transcriptome-based ranking of engineered AAVs in human retinal explants. Mol Ther Methods Clin Dev 2022; 25:476-489. [PMID: 35615708 PMCID: PMC9118357 DOI: 10.1016/j.omtm.2022.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/26/2022] [Indexed: 11/07/2022]
Abstract
Gene therapy is a rapidly developing field, and adeno-associated viruses (AAVs) are a leading viral-vector candidate for therapeutic gene delivery. Newly engineered AAVs with improved abilities are now entering the clinic. It has proven challenging, however, to predict the translational potential of gene therapies developed in animal models due to cross-species differences. Human retinal explants are the only available model of fully developed human retinal tissue and are thus important for the validation of candidate AAV vectors. In this study, we evaluated 18 wild-type and engineered AAV capsids in human retinal explants using a recently developed single-cell RNA sequencing (RNA-seq) AAV engineering pipeline (scAAVengr). Human retinal explants retained the same major cell types as fresh retina, with similar expression of cell-specific markers except for a photoreceptor population with altered expression of photoreceptor-specific genes. The efficiency and tropism of AAVs in human explants were quantified with single-cell resolution. The top-performing serotypes, K91, K912, and 7m8, were further validated in non-human primate and human retinal explants. Together, this study provides detailed information about the transcriptome profiles of retinal explants and quantifies the infectivity of leading AAV serotypes in human retina, accelerating the translation of retinal gene therapies to the clinic.
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Affiliation(s)
- Zhouhuan Xi
- Department of Ophthalmology, University of Pittsburgh, PA, USA.,Eye Center of Xiangya Hospital, Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, Hunan, China
| | - Bilge E Öztürk
- Department of Ophthalmology, University of Pittsburgh, PA, USA
| | - Molly E Johnson
- Department of Ophthalmology, University of Pittsburgh, PA, USA
| | - Serhan Turunç
- Department of Ophthalmology, University of Pittsburgh, PA, USA
| | | | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, PA, USA.,Department of Neurobiology, University of Pittsburgh, PA, USA.,Department of Bioengineering, University of Pittsburgh, PA, USA
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25
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Challis RC, Ravindra Kumar S, Chen X, Goertsen D, Coughlin GM, Hori AM, Chuapoco MR, Otis TS, Miles TF, Gradinaru V. Adeno-Associated Virus Toolkit to Target Diverse Brain Cells. Annu Rev Neurosci 2022; 45:447-469. [PMID: 35440143 DOI: 10.1146/annurev-neuro-111020-100834] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recombinant adeno-associated viruses (AAVs) are commonly used gene delivery vehicles for neuroscience research. They have two engineerable features: the capsid (outer protein shell) and cargo (encapsulated genome). These features can be modified to enhance cell type or tissue tropism and control transgene expression, respectively. Several engineered AAV capsids with unique tropisms have been identified, including variants with enhanced central nervous system transduction, cell type specificity, and retrograde transport in neurons. Pairing these AAVs with modern gene regulatory elements and state-of-the-art reporter, sensor, and effector cargo enables highly specific transgene expression for anatomical and functional analyses of brain cells and circuits. Here, we discuss recent advances that provide a comprehensive (capsid and cargo) AAV toolkit for genetic access to molecularly defined brain cell types. Expected final online publication date for the Annual Review of Neuroscience, Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Rosemary C Challis
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Sripriya Ravindra Kumar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - David Goertsen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Gerard M Coughlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Acacia M Hori
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Miguel R Chuapoco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Thomas S Otis
- Sainsbury Wellcome Centre, University College London, London, United Kingdom
| | - Timothy F Miles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
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26
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Miyadera K, Santana E, Roszak K, Iffrig S, Visel M, Iwabe S, Boyd RF, Bartoe JT, Sato Y, Gray A, Ripolles-Garcia A, Dufour VL, Byrne LC, Flannery JG, Beltran WA, Aguirre GD. Targeting ON-bipolar cells by AAV gene therapy stably reverses LRIT3-congenital stationary night blindness. Proc Natl Acad Sci U S A 2022; 119:e2117038119. [PMID: 35316139 PMCID: PMC9060458 DOI: 10.1073/pnas.2117038119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 01/08/2023] Open
Abstract
SignificanceCanine models of inherited retinal diseases have helped advance adeno-associated virus (AAV)-based gene therapies targeting specific cells in the outer retina for treating blinding diseases in patients. However, therapeutic targeting of diseases such as congenital stationary night blindness (CSNB) that exhibit defects in ON-bipolar cells (ON-BCs) of the midretina remains underdeveloped. Using a leucine-rich repeat, immunoglobulin-like and transmembrane domain 3 (LRIT3) mutant canine model of CSNB exhibiting ON-BC dysfunction, we tested the ability of cell-specific AAV capsids and promotors to specifically target ON-BCs for gene delivery. Subretinal injection of one vector demonstrated safety and efficacy with robust and stable rescue of electroretinography signals and night vision up to 1 y, paving the way for clinical trials in patients.
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Affiliation(s)
- Keiko Miyadera
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Evelyn Santana
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Karolina Roszak
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Sommer Iffrig
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Meike Visel
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Simone Iwabe
- Ophthalmology Services, Charles River Laboratories, Mattawan, MI 49071
| | - Ryan F. Boyd
- Ophthalmology Services, Charles River Laboratories, Mattawan, MI 49071
| | - Joshua T. Bartoe
- Ophthalmology Services, Charles River Laboratories, Mattawan, MI 49071
| | - Yu Sato
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexa Gray
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ana Ripolles-Garcia
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Valérie L. Dufour
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Leah C. Byrne
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - John G. Flannery
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - William A. Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gustavo D. Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
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27
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Öztürk BE, Johnson ME, Kleyman M, Turunç S, He J, Jabalameli S, Xi Z, Visel M, Dufour VL, Iwabe S, Pompeo Marinho LFL, Aguirre GD, Sahel JA, Schaffer DV, Pfenning AR, Flannery JG, Beltran WA, Stauffer WR, Byrne LC. scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution. eLife 2021; 10:64175. [PMID: 34664552 PMCID: PMC8612735 DOI: 10.7554/elife.64175] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/11/2021] [Indexed: 12/14/2022] Open
Abstract
Background Adeno-associated virus (AAV)-mediated gene therapies are rapidly advancing to the clinic, and AAV engineering has resulted in vectors with increased ability to deliver therapeutic genes. Although the choice of vector is critical, quantitative comparison of AAVs, especially in large animals, remains challenging. Methods Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) to simultaneously quantify and rank efficiency of competing AAV vectors across all cell types in the same animal. Results To demonstrate proof-of-concept for the scAAVengr workflow, we quantified - with cell-type resolution - the abilities of naturally occurring and newly engineered AAVs to mediate gene expression in primate retina following intravitreal injection. A top performing variant identified using this pipeline, K912, was used to deliver SaCas9 and edit the rhodopsin gene in macaque retina, resulting in editing efficiency similar to infection rates detected by the scAAVengr workflow. scAAVengr was then used to identify top-performing AAV variants in mouse brain, heart, and liver following systemic injection. Conclusions These results validate scAAVengr as a powerful method for development of AAV vectors. Funding This work was supported by funding from the Ford Foundation, NEI/NIH, Research to Prevent Blindness, Foundation Fighting Blindness, UPMC Immune Transplant and Therapy Center, and the Van Sloun fund for canine genetic research.
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Affiliation(s)
- Bilge E Öztürk
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States
| | - Molly E Johnson
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States
| | - Michael Kleyman
- Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States
| | - Serhan Turunç
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States
| | - Jing He
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, United States
| | - Sara Jabalameli
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States
| | - Zhouhuan Xi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States.,Eye Center of Xiangya Hospital, Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
| | - Meike Visel
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, United States
| | - Valérie L Dufour
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Simone Iwabe
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Luis Felipe L Pompeo Marinho
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Gustavo D Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States
| | - David V Schaffer
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, United States.,Chemical Engineering, University of California, Berkeley, Berkeley, United States
| | - Andreas R Pfenning
- Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, United States.,Vision Science, Herbert Wertheim School of Optometry, University of California Berkeley, Berkeley, United States
| | - William A Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - William R Stauffer
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, United States
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, United States.,Department of Neurobiology, University of Pittsburgh, Pittsburgh, United States.,Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Bioengineering, University of Pittsburgh, Pittsburgh, United States
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