1
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Ling C, Yu C, Wang C, Yang M, Yang H, Yang K, He Y, Shen Y, Tang S, Yu X, Zhou Z, Zhou S, Zhou J, Zhu L, Li J. rAAV capsid mutants eliminate leaky expression from DNA donor template for homologous recombination. Nucleic Acids Res 2024:gkae401. [PMID: 38783157 DOI: 10.1093/nar/gkae401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 04/28/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Precise genomic editing through the combination of CRISPR/Cas systems and recombinant adeno-associated virus (rAAV)-delivered homology directed repair (HDR) donor templates represents a powerful approach. However, the challenge of effectively suppressing leaky transcription from the rAAV vector, a phenomenon associated to cytotoxicity, persists. In this study, we demonstrated substantial promoter activities of various homology arms and inverted terminal repeats (ITR). To address this issue, we identified a novel rAAV variant, Y704T, which not only yields high-vector quantities but also effectively suppresses in cis mRNA transcription driven by a robust promoter. The Y704T variant maintains normal functionality in receptor interaction, intracellular trafficking, nuclear entry, uncoating, and second-strand synthesis, while specifically exhibiting defects in transcription. Importantly, this inhibitory effect is found to be independent of ITR, promoter types, and RNA polymerases. Mechanistic studies unveiled the involvement of Valosin Containing Protein (VCP/p97) in capsid-mediated transcription repression. Remarkably, the Y704T variant delivers HDR donor templates without compromising DNA replication ability and homologous recombination efficiency. In summary, our findings enhance the understanding of capsid-regulated transcription and introduce novel avenues for the application of the rAAV-CRISPR/Cas9 system in human gene therapy.
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Affiliation(s)
- Chen Ling
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Chenghui Yu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Cong Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Ming Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Hengbin Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Keying Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yun He
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yajie Shen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai 200438, China
| | - Shiyi Tang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Xiaomin Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Zhengjun Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shaolai Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Liqing Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
- Department of Clinical Laboratory, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai 200438, China
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2
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Suchy FP, Karigane D, Nakauchi Y, Higuchi M, Zhang J, Pekrun K, Hsu I, Fan AC, Nishimura T, Charlesworth CT, Bhadury J, Nishimura T, Wilkinson AC, Kay MA, Majeti R, Nakauchi H. Genome engineering with Cas9 and AAV repair templates generates frequent concatemeric insertions of viral vectors. Nat Biotechnol 2024:10.1038/s41587-024-02171-w. [PMID: 38589662 DOI: 10.1038/s41587-024-02171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/08/2024] [Indexed: 04/10/2024]
Abstract
CRISPR-Cas9 paired with adeno-associated virus serotype 6 (AAV6) is among the most efficient tools for producing targeted gene knockins. Here, we report that this system can lead to frequent concatemeric insertions of the viral vector genome at the target site that are difficult to detect. Such errors can cause adverse and unreliable phenotypes that are antithetical to the goal of precision genome engineering. The concatemeric knockins occurred regardless of locus, vector concentration, cell line or cell type, including human pluripotent and hematopoietic stem cells. Although these highly abundant errors were found in more than half of the edited cells, they could not be readily detected by common analytical methods. We describe strategies to detect and thoroughly characterize the concatemeric viral vector insertions, and we highlight analytical pitfalls that mask their prevalence. We then describe strategies to prevent the concatemeric inserts by cutting the vector genome after transduction. This approach is compatible with established gene editing pipelines, enabling robust genetic knockins that are safer, more reliable and more reproducible.
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Affiliation(s)
- Fabian P Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Daiki Karigane
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Yusuke Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maimi Higuchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinyu Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Katja Pekrun
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ian Hsu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy C Fan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Toshinobu Nishimura
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Carsten T Charlesworth
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joydeep Bhadury
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toshiya Nishimura
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Hematology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Distinguished Professor Unit, Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
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3
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Chai S, Wakefield L, Norgard M, Li B, Enicks D, Marks DL, Grompe M. Strong ubiquitous micro-promoters for recombinant adeno-associated viral vectors. Mol Ther Methods Clin Dev 2023; 29:504-512. [PMID: 37287749 PMCID: PMC10241652 DOI: 10.1016/j.omtm.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/12/2023] [Indexed: 06/09/2023]
Abstract
Significant progress has been made in developing recombinant adeno-associated virus (rAAV) for clinical gene therapy. While rAAV is a versatile gene delivery platform, its packaging limit of 4.7 kb limits the diseases it can target. Here, we report two unusually small promoters that enable the expression of larger transgenes than standard promoters. These micro-promoters are only 84 (MP-84) and 135 bp (MP-135) in size but have activity in most cells and tissues comparable to the CAG promoter, the strongest ubiquitous promoter to date. MP-84- and MP-135-based rAAV constructs displayed robust activity in cultured cells from the three different germ-layer lineages. In addition, reporter gene expression was documented in human primary hepatocytes and pancreatic islets and in multiple mouse tissues in vivo, including brain and skeletal muscle. MP-84 and MP-135 will enable the therapeutic expression of transgenes currently too large for rAAV vectors.
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Affiliation(s)
- Sunghee Chai
- Papé Family Pediatric Research Institute, Oregon Stem Cell Center, Portland, OR, USA
| | - Leslie Wakefield
- Papé Family Pediatric Research Institute, Oregon Stem Cell Center, Portland, OR, USA
| | - Mason Norgard
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Bin Li
- Papé Family Pediatric Research Institute, Oregon Stem Cell Center, Portland, OR, USA
| | - David Enicks
- Papé Family Pediatric Research Institute, Oregon Stem Cell Center, Portland, OR, USA
| | - Daniel L. Marks
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Oregon Stem Cell Center, Portland, OR, USA
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4
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Brooks IR, Sheriff A, Moran D, Wang J, Jacków J. Challenges of Gene Editing Therapies for Genodermatoses. Int J Mol Sci 2023; 24:2298. [PMID: 36768619 PMCID: PMC9916788 DOI: 10.3390/ijms24032298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Genodermatoses encompass a wide range of inherited skin diseases, many of which are monogenic. Genodermatoses range in severity and result in early-onset cancers or life-threatening damage to the skin, and there are few curative options. As such, there is a clinical need for single-intervention treatments with curative potential. Here, we discuss the nascent field of gene editing for the treatment of genodermatoses, exploring CRISPR-Cas9 and homology-directed repair, base editing, and prime editing tools for correcting pathogenic mutations. We specifically focus on the optimisation of editing efficiency, the minimisation off-targets edits, and the tools for delivery for potential future therapies. Honing each of these factors is essential for translating gene editing therapies into the clinical setting. Therefore, the aim of this review article is to raise important considerations for investigators aiming to develop gene editing approaches for genodermatoses.
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Affiliation(s)
| | | | | | | | - Joanna Jacków
- St John’s Institute of Dermatology, King’s College London, London SE1 9RT, UK
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5
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Nieuwenhuis B, Laperrousaz E, Tribble JR, Verhaagen J, Fawcett JW, Martin KR, Williams PA, Osborne A. Improving adeno-associated viral (AAV) vector-mediated transgene expression in retinal ganglion cells: comparison of five promoters. Gene Ther 2023:10.1038/s41434-022-00380-z. [PMID: 36635457 DOI: 10.1038/s41434-022-00380-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 12/02/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023]
Abstract
Recombinant adeno-associated viral vectors (AAVs) are an effective system for gene transfer. AAV serotype 2 (AAV2) is commonly used to deliver transgenes to retinal ganglion cells (RGCs) via intravitreal injection. The AAV serotype however is not the only factor contributing to the effectiveness of gene therapies. Promoters influence the strength and cell-selectivity of transgene expression. This study compares five promoters designed to maximise AAV2 cargo space for gene delivery: chicken β-actin (CBA), cytomegalovirus (CMV), short CMV early enhancer/chicken β-actin/short β-globulin intron (sCAG), mouse phosphoglycerate kinase (PGK), and human synapsin (SYN). The promoters driving enhanced green fluorescent protein (eGFP) were examined in adult C57BL/6J mice eyes and tissues of the visual system. eGFP expression was strongest in the retina, optic nerves and brain when driven by the sCAG and SYN promoters. CBA, CMV, and PGK had moderate expression by comparison. The SYN promoter had almost exclusive transgene expression in RGCs. The PGK promoter had predominant expression in both RGCs and AII amacrine cells. The ubiquitous CBA, CMV, and sCAG promoters expressed eGFP in a variety of cell types across multiple retinal layers including Müller glia and astrocytes. We also found that these promoters could transduce human retina ex vivo, although expression was predominantly in glial cells due to low RGC viability. Taken together, this promoter comparison study contributes to optimising AAV-mediated transduction in the retina, and could be valuable for research in ocular disorders, particularly those with large or complex genetic cargos.
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Affiliation(s)
- Bart Nieuwenhuis
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Elise Laperrousaz
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - James R Tribble
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Joost Verhaagen
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands.,Centre for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - James W Fawcett
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.,Centre of Reconstructive Neuroscience, Institute of Experimental Medicine, Prague, Czech Republic
| | - Keith R Martin
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, VIC, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, VIC, Australia
| | - Pete A Williams
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Andrew Osborne
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Ikarovec Ltd, The Norwich Research Park Innovation Centre, Norwich, UK.
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6
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Pupo A, Fernández A, Low SH, François A, Suárez-Amarán L, Samulski RJ. AAV vectors: The Rubik's cube of human gene therapy. Mol Ther 2022; 30:3515-3541. [PMID: 36203359 PMCID: PMC9734031 DOI: 10.1016/j.ymthe.2022.09.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 12/12/2022] Open
Abstract
Defective genes account for ∼80% of the total of more than 7,000 diseases known to date. Gene therapy brings the promise of a one-time treatment option that will fix the errors in patient genetic coding. Recombinant viruses are highly efficient vehicles for in vivo gene delivery. Adeno-associated virus (AAV) vectors offer unique advantages, such as tissue tropism, specificity in transduction, eliciting of a relatively low immune responses, no incorporation into the host chromosome, and long-lasting delivered gene expression, making them the most popular viral gene delivery system in clinical trials, with three AAV-based gene therapy drugs already approved by the US Food and Drug Administration (FDA) or European Medicines Agency (EMA). Despite the success of AAV vectors, their usage in particular scenarios is still limited due to remaining challenges, such as poor transduction efficiency in certain tissues, low organ specificity, pre-existing humoral immunity to AAV capsids, and vector dose-dependent toxicity in patients. In the present review, we address the different approaches to improve AAV vectors for gene therapy with a focus on AAV capsid selection and engineering, strategies to overcome anti-AAV immune response, and vector genome design, ending with a glimpse at vector production methods and the current state of recombinant AAV (rAAV) at the clinical level.
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Affiliation(s)
- Amaury Pupo
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Audry Fernández
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Siew Hui Low
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Achille François
- Viralgen. Parque Tecnológico de Guipuzkoa, Edificio Kuatro, Paseo Mikeletegui, 83, 20009 San Sebastián, Spain
| | - Lester Suárez-Amarán
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA
| | - Richard Jude Samulski
- R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, Durham, NC 27709, USA,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Corresponding author: Richard Jude Samulski, R&D Department, Asklepios BioPharmaceutical, Inc. (AskBio), 20 T.W. Alexander, Suite 110 RTP, NC 27709, USA.
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7
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Sui H, Xu X, Su Y, Gong Z, Yao M, Liu X, Zhang T, Jiang Z, Bai T, Wang J, Zhang J, Xu C, Luo M. Gene therapy for cystic fibrosis: Challenges and prospects. Front Pharmacol 2022; 13:1015926. [PMID: 36304167 PMCID: PMC9592762 DOI: 10.3389/fphar.2022.1015926] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Cystic fibrosis (CF) is a life-threatening autosomal-recessive disease caused by mutations in a single gene encoding cystic fibrosis transmembrane conductance regulator (CFTR). CF effects multiple organs, and lung disease is the primary cause of mortality. The median age at death from CF is in the early forties. CF was one of the first diseases to be considered for gene therapy, and efforts focused on treating CF lung disease began shortly after the CFTR gene was identified in 1989. However, despite the quickly established proof-of-concept for CFTR gene transfer in vitro and in clinical trials in 1990s, to date, 36 CF gene therapy clinical trials involving ∼600 patients with CF have yet to achieve their desired outcomes. The long journey to pursue gene therapy as a cure for CF encountered more difficulties than originally anticipated, but immense progress has been made in the past decade in the developments of next generation airway transduction viral vectors and CF animal models that reproduced human CF disease phenotypes. In this review, we look back at the history for the lessons learned from previous clinical trials and summarize the recent advances in the research for CF gene therapy, including the emerging CRISPR-based gene editing strategies. We also discuss the airway transduction vectors, large animal CF models, the complexity of CF pathogenesis and heterogeneity of CFTR expression in airway epithelium, which are the major challenges to the implementation of a successful CF gene therapy, and highlight the future opportunities and prospects.
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Affiliation(s)
- Hongshu Sui
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
- *Correspondence: Hongshu Sui, ; Changlong Xu, ; Mingjiu Luo,
| | - Xinghua Xu
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Yanping Su
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Zhaoqing Gong
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Minhua Yao
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Xiaocui Liu
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Ting Zhang
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Ziyao Jiang
- Department of Histology and Embryology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Tianhao Bai
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Junzuo Wang
- The Affiliated Tai’an City Central Hospital of Qingdao University, Tai’an, Shandong, China
| | - Jingjun Zhang
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, Shandong, China
| | - Changlong Xu
- The Reproductive Medical Center of Nanning Second People’s Hospital, Nanning, China
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, China
- *Correspondence: Hongshu Sui, ; Changlong Xu, ; Mingjiu Luo,
| | - Mingjiu Luo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- *Correspondence: Hongshu Sui, ; Changlong Xu, ; Mingjiu Luo,
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8
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Kuwayama R, Suzuki K, Nakamura J, Aizawa E, Yoshioka Y, Ikawa M, Nabatame S, Inoue KI, Shimmyo Y, Ozono K, Kinoshita T, Murakami Y. Establishment of mouse model of inherited PIGO deficiency and therapeutic potential of AAV-based gene therapy. Nat Commun 2022; 13:3107. [PMID: 35661110 PMCID: PMC9166810 DOI: 10.1038/s41467-022-30847-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
Inherited glycosylphosphatidylinositol (GPI) deficiency (IGD) is caused by mutations in GPI biosynthesis genes. The mechanisms of its systemic, especially neurological, symptoms are not clarified and fundamental therapy has not been established. Here, we report establishment of mouse models of IGD caused by PIGO mutations as well as development of effective gene therapy. As the clinical manifestations of IGD are systemic and lifelong lasting, we treated the mice with adeno-associated virus for homology-independent knock-in as well as extra-chromosomal expression of Pigo cDNA. Significant amelioration of neuronal phenotypes and growth defect was achieved, opening a new avenue for curing IGDs.
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Affiliation(s)
- Ryoko Kuwayama
- Yabumoto Department of Intractable disease research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keiichiro Suzuki
- Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan.,Graduate School of Engineering Science, Osaka University, Osaka, Japan.,Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Jun Nakamura
- Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan
| | - Emi Aizawa
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Yoshichika Yoshioka
- Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan.,Center for Information and Neural Networks, National Institute of Information and Communications Technology (NICT) and Osaka University, Osaka, Japan.,Center for Quantum Information and Quantum Biology, Osaka University, Osaka, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shin Nabatame
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ken-Ichi Inoue
- Systems Neuroscience Section, Department of Neuroscience, Primate Research Institute, Kyoto University, Kyoto, Japan
| | | | - Keiichi Ozono
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Taroh Kinoshita
- Yabumoto Department of Intractable disease research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Immunoglycobiology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yoshiko Murakami
- Yabumoto Department of Intractable disease research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
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9
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Yanda MK, Tomar V, Cebotaru CV, Guggino WB, Cebotaru L. Short-Term Steroid Treatment of Rhesus Macaque Increases Transduction. Hum Gene Ther 2022; 33:131-147. [PMID: 34806411 PMCID: PMC8885436 DOI: 10.1089/hum.2021.239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Repeat dosing poses a major hurdle for the development of an adeno-associated virus (AAV)-based gene therapy for cystic fibrosis, in part because of the potential for development of an immune reaction to the AAV1 capsid proteins. Here, to dampen the immune response to AAV1, we treated Rhesus monkeys with methylprednisolone before and after the instillation of two doses of AAV1Δ27-264-CFTR into their airways at 0 and 30 days, followed by a single dose of AAV1-GFP on day 60. Animals were euthanized on day 90, except for one monkey that was sacrificed at 1 year. No adverse events occurred, indicating that the two AAV1 vectors are safe. rAAV1-CFTR and AAV1-GFP vector genomes and mRNA transcripts were detectable in all lung sections and in the liver and pancreas at day 90 and after 1 year at levels comparable with animals necropsied at 90 days. The numbers of vector genomes for cystic fibrosis transmembrane regulator (CFTR) and green fluorescent protein (GFP) detected here were higher than those found in the monkeys infected without methylprednisolone treatment that we tested previously.1 Also, lung surface and keratin 5-positive basal cells showed higher CFTR and GFP staining than did the cells from the uninfected monkey control. Positive immunostaining, also detected in the liver and pancreas, remained stable for at least a year. All animals seroconverted for anticapsid antibodies by 90 days post-treatment. The neutralizing antibody titer declined in the animal necropsied at 1 year. Conclusion: AAV1 safely and effectively transduces monkey airway and basal cells. Both the presence of vector genomes and transduction from AAV1-CFTR and AAV1-GFP virus seen in the monkeys 4 months to 1 year after the first instillation suggest that repeat dosing with AAV1-based vectors is achievable, particularly after methylprednisolone treatment.
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Affiliation(s)
- Murali K. Yanda
- Department of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vartika Tomar
- Department of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Cristina Valeria Cebotaru
- Department of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William B. Guggino
- Department of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Liudmila Cebotaru
- Department of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Correspondence: Dr. Liudmila Cebotaru, Departments of Medicine and Physiology, Johns Hopkins University School of Medicine, Hunterian 415, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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10
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Fakhiri J, Grimm D. Best of most possible worlds: Hybrid gene therapy vectors based on parvoviruses and heterologous viruses. Mol Ther 2021; 29:3359-3382. [PMID: 33831556 PMCID: PMC8636155 DOI: 10.1016/j.ymthe.2021.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/12/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
Parvoviruses and especially the adeno-associated virus (AAV) species provide an exciting and versatile platform for the rational design or molecular evolution of human gene-therapy vectors, documented by literature from over half a century, hundreds of clinical trials, and the recent commercialization of multiple AAV gene therapeutics. For the last three decades, the power of these vectors has been further potentiated through various types of hybrid vectors created by intra- or inter-genus juxtaposition of viral DNA and protein cis elements or by synergistic complementation of parvoviral features with those of heterologous, prokaryotic, or eukaryotic viruses. Here, we provide an overview of the history and promise of this rapidly expanding field of hybrid parvoviral gene-therapy vectors, starting with early generations of chimeric particles composed of a recombinant AAV genome encapsidated in shells of synthetic AAVs or of adeno-, herpes-, baculo-, or protoparvoviruses. We then dedicate our attention to two newer, highly promising types of hybrid vectors created via (1) pseudotyping of AAV genomes with bocaviral serotypes and capsid mutants or (2) packaging of AAV DNA into, or tethering of entire vector particles to, bacteriophages. Finally, we conclude with an outlook summarizing critical requirements and improvements toward clinical translation of these original concepts.
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Affiliation(s)
- Julia Fakhiri
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Heidelberg, Germany; BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Heidelberg, Germany; BioQuant, University of Heidelberg, Heidelberg, Germany; German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany.
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11
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Hu J, Bourne RA, McGrath BC, Lin A, Pei Z, Cavener DR. Co-opting regulation bypass repair as a gene-correction strategy for monogenic diseases. Mol Ther 2021; 29:3274-3292. [PMID: 33892188 PMCID: PMC8571108 DOI: 10.1016/j.ymthe.2021.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/18/2021] [Accepted: 04/15/2021] [Indexed: 12/03/2022] Open
Abstract
With the development of CRISPR-Cas9-mediated gene-editing technologies, correction of disease-causing mutations has become possible. However, current gene-correction strategies preclude mutation repair in post-mitotic cells of human tissues, and a unique repair strategy must be designed and tested for each and every mutation that may occur in a gene. We have developed a novel gene-correction strategy, co-opting regulation bypass repair (CRBR), which can repair a spectrum of mutations in mitotic or post-mitotic cells and tissues. CRBR utilizes the non-homologous end joining (NHEJ) pathway to insert a coding sequence (CDS) and transcription/translation terminators targeted upstream of any CDS mutation and downstream of the transcriptional promoter. CRBR results in simultaneous co-option of the endogenous regulatory region and bypass of the genetic defect. We validated the CRBR strategy for human gene therapy by rescuing a mouse model of Wolcott-Rallison syndrome (WRS) with permanent neonatal diabetes caused by either a large deletion or a nonsense mutation in the PERK (EIF2AK3) gene. Additionally, we integrated a CRBR GFP-terminator cassette downstream of the human insulin promoter in cadaver pancreatic islets of Langerhans, which resulted in insulin promoter regulated expression of GFP, demonstrating the potential utility of CRBR in human tissue gene repair.
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Affiliation(s)
- Jingjie Hu
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rebecca A Bourne
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Barbara C McGrath
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alice Lin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Zifei Pei
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Douglas R Cavener
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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12
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Guggino WB, Yanda MK, Cebotaru CV, Cebotaru L. Transduction of Surface and Basal Cells in Rhesus Macaque Lung Following Repeat Dosing with AAV1CFTR. Hum Gene Ther 2021; 31:1010-1023. [PMID: 32862701 DOI: 10.1089/hum.2020.207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To test the effectiveness of repeat dosing, we sprayed two doses (1013 vg each) of AAV1Δ27-264-CFTR into airways of four rhesus monkeys at 0 and 30 days, followed by a single dose of 1013 vg of AAV1GFP on day 60. Monkeys were sacrificed on day 90. No adverse events occurred, indicating that AAV1 vectors are safe. An elevated anti-AAV1 neutralizing titer was established by the third dose. A positive ELISPOT to the adeno-associated virus (AAV) capsid but not to cystic fibrosis transmembrane conductance regulator (CFTR) occurred after the third dose in three monkeys. AAV1-CFTR and GFP vectors were detectable in all lung sections and in the heart, liver, and spleen. The CFTR protein was higher in treated monkeys than in an untreated monkey. GFP protein was detected in treated lungs. Lung surface and keratin 5-positive basal cells showed higher CFTR staining than in the uninfected monkey and were positive for GFP staining, indicating widespread gene transduction by AAV1CFTR and GFP. AAV1 safely and effectively transduces monkey airway and basal cells. Both the significant numbers of vector genomes and transduction from AAV1CFTR and GFP virus seen in the monkeys 3 months after the first instillation suggest that repeat dosing with AAV1-based vectors is achievable.
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Affiliation(s)
- William B Guggino
- Departments of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Murali K Yanda
- Departments of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Cristina V Cebotaru
- Departments of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Liudmila Cebotaru
- Departments of Medicine and Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Guggino WB, Cebotaru L. Gene Therapy for Cystic Fibrosis Paved the Way for the Use of Adeno-Associated Virus in Gene Therapy. Hum Gene Ther 2021; 31:538-541. [PMID: 32283956 DOI: 10.1089/hum.2020.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Shortly after the cystic fibrosis (CF) gene was identified in 1989, the race began to develop a gene therapy for this condition. Major efforts utilized full-length cystic fibrosis transmembrane conductance regulator packaged into adenovirus, adeno-associated virus (AAV), or liposomes and delivered to the airways. The drive to find a treatment for CF based on gene therapy drove the early stages of gene therapy in general, particularly those involving AAV gene therapy. Since general overviews of CF gene therapy have already been published, this review considers specifically the efforts using AAV and is focused on honoring the contributions of Dr. Barrie Carter.
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Affiliation(s)
- William B Guggino
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Liudmila Cebotaru
- Department of Physiology, Johns Hopkins University, Baltimore, Maryland, USA
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14
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von Jonquieres G, Rae CD, Housley GD. Emerging Concepts in Vector Development for Glial Gene Therapy: Implications for Leukodystrophies. Front Cell Neurosci 2021; 15:661857. [PMID: 34239416 PMCID: PMC8258421 DOI: 10.3389/fncel.2021.661857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Central Nervous System (CNS) homeostasis and function rely on intercellular synchronization of metabolic pathways. Developmental and neurochemical imbalances arising from mutations are frequently associated with devastating and often intractable neurological dysfunction. In the absence of pharmacological treatment options, but with knowledge of the genetic cause underlying the pathophysiology, gene therapy holds promise for disease control. Consideration of leukodystrophies provide a case in point; we review cell type – specific expression pattern of the disease – causing genes and reflect on genetic and cellular treatment approaches including ex vivo hematopoietic stem cell gene therapies and in vivo approaches using adeno-associated virus (AAV) vectors. We link recent advances in vectorology to glial targeting directed towards gene therapies for specific leukodystrophies and related developmental or neurometabolic disorders affecting the CNS white matter and frame strategies for therapy development in future.
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Affiliation(s)
- Georg von Jonquieres
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Caroline D Rae
- Neuroscience Research Australia, Randwick, NSW, Australia
| | - Gary D Housley
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
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15
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Dudek AM, Porteus MH. Answered and Unanswered Questions in Early-Stage Viral Vector Transduction Biology and Innate Primary Cell Toxicity for Ex-Vivo Gene Editing. Front Immunol 2021; 12:660302. [PMID: 34122418 PMCID: PMC8195279 DOI: 10.3389/fimmu.2021.660302] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/04/2021] [Indexed: 01/07/2023] Open
Abstract
Adeno-associated virus is a highly efficient DNA delivery vehicle for genome editing strategies that employ CRISPR/Cas9 and a DNA donor for homology-directed repair. Many groups have used this strategy in development of therapies for blood and immune disorders such as sickle-cell anemia and severe-combined immunodeficiency. However, recent events have called into question the immunogenicity of AAV as a gene therapy vector and the safety profile dictated by the immune response to this vector. The target cells dictating this response and the molecular mechanisms dictating cellular response to AAV are poorly understood. Here, we will investigate the current known AAV capsid and genome interactions with cellular proteins during early stage vector transduction and how these interactions may influence innate cellular responses. We will discuss the current understanding of innate immune activation and DNA damage response to AAV, and the limitations of what is currently known. In particular, we will focus on pathway differences in cell line verses primary cells, with a focus on hematopoietic stem and progenitor cells (HSPCs) in the context of ex-vivo gene editing, and what we can learn from HSPC infection by other parvoviruses. Finally, we will discuss how innate immune and DNA damage response pathway activation in these highly sensitive stem cell populations may impact long-term engraftment and clinical outcomes as these gene-editing strategies move towards the clinic, with the aim to propose pathways relevant for improved hematopoietic stem cell survival and long-term engraftment after AAV-mediated genome editing.
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Affiliation(s)
- Amanda Mary Dudek
- Department of Pediatrics, Stanford University, Stanford, CA, United States.,Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA, United States
| | - Matthew Hebden Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, United States.,Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA, United States
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16
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Pagant S, Huston MW, Moreira L, Gan L, St Martin S, Sproul S, Holmes MC, Meyer K, Wechsler T, Desnick RJ, Yasuda M. ZFN-mediated in vivo gene editing in hepatocytes leads to supraphysiologic α-Gal A activity and effective substrate reduction in Fabry mice. Mol Ther 2021; 29:3230-3242. [PMID: 33775910 PMCID: PMC8572137 DOI: 10.1016/j.ymthe.2021.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/16/2021] [Accepted: 03/22/2021] [Indexed: 12/25/2022] Open
Abstract
Fabry disease, a lysosomal storage disorder resulting from the deficient activity of α-galactosidase A (α-Gal A), is characterized by cardiac, renal, and/or cerebrovascular disease due to progressive accumulation of the enzyme’s substrates, globotriaosylceramide (Gb3) and globotriaosylsphingosine (Lyso-Gb3). We report here the preclinical evaluation of liver-targeted in vivo genome editing using zinc-finger nuclease (ZFN) technology to insert the human α-galactosidase A (hGLA) cDNA into the albumin “safe harbor” locus of Fabry mice, thereby generating an albumin-α-Gal A fusion protein. The mature α-Gal A protein is secreted into the circulation for subsequent mannose-6-phosphate receptor-mediated tissue uptake. Donor vector optimization studies showed that replacing the hGLA cDNA signal peptide sequence with that of human iduronate 2-sulfatase (IDS) achieved higher transgene expression. Intravenous adeno-associated virus (AAV) 2/8-mediated co-delivery of the IDS-hGLA donor and ZFNs targeting the albumin locus resulted in continuous, supraphysiological plasma and tissue α-Gal A activities, which essentially normalized Gb3 and Lyso-Gb3 levels in key tissues of pathology. Notably, this was achieved with <10% of hepatocytes being edited to express hGLA, occurring mostly via non-homologous end joining (NHEJ) rather than homology-directed repair (HDR). These studies indicate that ZFN-mediated in vivo genome editing has the potential to be an effective one-time therapy for Fabry disease.
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Affiliation(s)
- Silvere Pagant
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Luciana Moreira
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lin Gan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Scott Sproul
- Sangamo Therapeutics, Inc., Brisbane, CA 94005, USA
| | | | | | | | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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17
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Bulcha JT, Wang Y, Ma H, Tai PWL, Gao G. Viral vector platforms within the gene therapy landscape. Signal Transduct Target Ther 2021; 6:53. [PMID: 33558455 PMCID: PMC7868676 DOI: 10.1038/s41392-021-00487-6] [Citation(s) in RCA: 459] [Impact Index Per Article: 153.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/05/2020] [Accepted: 10/23/2020] [Indexed: 01/30/2023] Open
Abstract
Throughout its 40-year history, the field of gene therapy has been marked by many transitions. It has seen great strides in combating human disease, has given hope to patients and families with limited treatment options, but has also been subject to many setbacks. Treatment of patients with this class of investigational drugs has resulted in severe adverse effects and, even in rare cases, death. At the heart of this dichotomous field are the viral-based vectors, the delivery vehicles that have allowed researchers and clinicians to develop powerful drug platforms, and have radically changed the face of medicine. Within the past 5 years, the gene therapy field has seen a wave of drugs based on viral vectors that have gained regulatory approval that come in a variety of designs and purposes. These modalities range from vector-based cancer therapies, to treating monogenic diseases with life-altering outcomes. At present, the three key vector strategies are based on adenoviruses, adeno-associated viruses, and lentiviruses. They have led the way in preclinical and clinical successes in the past two decades. However, despite these successes, many challenges still limit these approaches from attaining their full potential. To review the viral vector-based gene therapy landscape, we focus on these three highly regarded vector platforms and describe mechanisms of action and their roles in treating human disease.
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Affiliation(s)
- Jote T Bulcha
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic medical sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Hong Ma
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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18
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Massip-Copiz MM, Valdivieso ÁG, Clauzure M, Mori C, Asensio CJA, Aguilar MÁ, Santa-Coloma TA. Epidermal growth factor receptor activity upregulates lactate dehydrogenase A expression, lactate dehydrogenase activity, and lactate secretion in cultured IB3-1 cystic fibrosis lung epithelial cells. Biochem Cell Biol 2021; 99:476-487. [PMID: 33481676 DOI: 10.1139/bcb-2020-0522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It has been postulated that reduced HCO3- transport through CFTR may lead to a decreased airway surface liquid pH. In contrast, others have reported no changes in the extracellular pH (pHe). We have recently reported that in carcinoma Caco-2/pRS26 cells (transfected with short hairpin RNA for CFTR) or CF lung epithelial IB3-1 cells, the mutation in CFTR decreased mitochondrial complex I activity and increased lactic acid production, owing to an autocrine IL-1β loop. The secreted lactate accounted for the reduced pHe, because oxamate fully restored the pHe. These effects were attributed to the IL-1β autocrine loop and the downstream signaling kinases c-Src and JNK. Here we show that the pHe of IB3-1 cells can be restored to normal values (∼7.4) by incubation with the epidermal growth factor receptor (EGFR, HER1, ErbB1) inhibitors AG1478 and PD168393. PD168393 fully restored the pHe values of IB3-1 cells, suggesting that the reduced pHe is mainly due to increased EGFR activity and lactate. Also, in IB3-1 cells, lactate dehydrogenase A mRNA, protein expression, and activity are downregulated when EGFR is inhibited. Thus, a constitutive EGFR activation seems to be responsible for the reduced pHe in IB3-1 cells.
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Affiliation(s)
- María Macarena Massip-Copiz
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Ángel G Valdivieso
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Mariángeles Clauzure
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Consuelo Mori
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Cristian J A Asensio
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - María Á Aguilar
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Tomás A Santa-Coloma
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
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19
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Ou L, Przybilla MJ, Ahlat O, Kim S, Overn P, Jarnes J, O'Sullivan MG, Whitley CB. A Highly Efficacious PS Gene Editing System Corrects Metabolic and Neurological Complications of Mucopolysaccharidosis Type I. Mol Ther 2020; 28:1442-1454. [PMID: 32278382 PMCID: PMC7264433 DOI: 10.1016/j.ymthe.2020.03.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/06/2020] [Accepted: 03/31/2020] [Indexed: 12/19/2022] Open
Abstract
Our previous study delivered zinc finger nucleases to treat mice with mucopolysaccharidosis type I (MPS I), resulting in a phase I/II clinical trial (ClinicalTrials.gov: NCT02702115). However, in the clinical trial, the efficacy needs to be improved due to the low transgene expression level. To this end, we designed a proprietary system (PS) gene editing approach with CRISPR to insert a promoterless α-l-iduronidase (IDUA) cDNA sequence into the albumin locus of hepatocytes. In this study, adeno-associated virus 8 (AAV8) vectors delivering the PS gene editing system were injected into neonatal and adult MPS I mice. IDUA enzyme activity in the brain significantly increased, while storage levels were normalized. Neurobehavioral tests showed that treated mice had better memory and learning ability. Also, histological analysis showed efficacy reflected by the absence of foam cells in the liver and vacuolation in neuronal cells. No vector-associated toxicity or increased tumorigenesis risk was observed. Moreover, no off-target effects were detected through the unbiased genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) analysis. In summary, these results showed the safety and efficacy of the PS in treating MPS I and paved the way for clinical studies. Additionally, as a therapeutic platform, the PS has the potential to treat other lysosomal diseases.
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Affiliation(s)
- Li Ou
- Gene Therapy Center, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Michael J Przybilla
- Gene Therapy Center, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ozan Ahlat
- Comparative Pathology Shared Resource, University of Minnesota Masonic Cancer Center, Saint Paul, MN 55108, USA
| | - Sarah Kim
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paula Overn
- Comparative Pathology Shared Resource, University of Minnesota Masonic Cancer Center, Saint Paul, MN 55108, USA
| | - Jeanine Jarnes
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - M Gerard O'Sullivan
- Comparative Pathology Shared Resource, University of Minnesota Masonic Cancer Center, Saint Paul, MN 55108, USA
| | - Chester B Whitley
- Gene Therapy Center, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
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20
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Chen HM, Resendes R, Ghodssi A, Sookiasian D, Tian M, Dollive S, Adamson-Small L, Avila N, Tazearslan C, Thompson JF, Ellsworth JL, Francone O, Seymour A, Wright JB. Molecular characterization of precise in vivo targeted gene integration in human cells using AAVHSC15. PLoS One 2020; 15:e0233373. [PMID: 32453743 PMCID: PMC7250422 DOI: 10.1371/journal.pone.0233373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/04/2020] [Indexed: 02/08/2023] Open
Abstract
Targeted gene integration via precise homologous recombination (HR)-based gene editing has the potential to correct genetic diseases. AAV (adeno-associated virus) can mediate nuclease-free gene integration at a disease-causing locus. Therapeutic application of AAV gene integration requires quantitative molecular characterization of the edited sequence that overcome technical obstacles such as excess episomal vector genomes and lengthy homology arms. Here we describe a novel molecular methodology that utilizes quantitative next-generation sequencing to characterize AAV-mediated targeted insertion and detects the presence of unintended mutations. The methods described here quantify targeted insertion and query the entirety of the target locus for the presence of insertions, deletions, single nucleotide variants (SNVs) and integration of viral components such as inverted terminal repeats (ITR). Using a humanized liver murine model, we demonstrate that hematopoietic stem-cell derived AAVHSC15 mediates in vivo targeted gene integration into human chromosome 12 at the PAH (phenylalanine hydroxylase) locus at 6% frequency, with no sign of co-incident random mutations at or above a lower limit of detection of 0.5% and no ITR sequences at the integration sites. Furthermore, analysis of heterozygous variants across the targeted locus using the methods described shows a pattern of strand cross-over, supportive of an HR mechanism of gene integration with similar efficiencies across two different haplotypes. Rapid advances in the application of AAV-mediated nuclease-free target integration, or gene editing, as a new therapeutic modality requires precise understanding of the efficiency and the nature of the changes being introduced to the target genome at the molecular level. This work provides a framework to be applied to homologous recombination gene editing platforms for assessment of introduced and natural sequence variation across a target site.
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Affiliation(s)
- Huei-Mei Chen
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Rachel Resendes
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Azita Ghodssi
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | | | - Michael Tian
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Serena Dollive
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | | | - Nancy Avila
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Cagdas Tazearslan
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - John F. Thompson
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Jeff L. Ellsworth
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Omar Francone
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Albert Seymour
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
| | - Jason B. Wright
- Homology Medicines Inc., Bedford, Massachusetts, United States of America
- * E-mail:
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21
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Tang Y, Yan Z, Engelhardt JF. Viral Vectors, Animal Models, and Cellular Targets for Gene Therapy of Cystic Fibrosis Lung Disease. Hum Gene Ther 2020; 31:524-537. [PMID: 32138545 PMCID: PMC7232698 DOI: 10.1089/hum.2020.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/05/2020] [Indexed: 12/14/2022] Open
Abstract
After more than two decades since clinical trials tested the first use of recombinant adeno-associated virus (rAAV) to treat cystic fibrosis (CF) lung disease, gene therapy for this disorder has undergone a tremendous resurgence. Fueling this enthusiasm has been an enhanced understanding of rAAV transduction biology and cellular processes that limit transduction of airway epithelia, the development of new rAAV serotypes and other vector systems with high-level tropism for airway epithelial cells, an improved understanding of CF lung pathogenesis and the cellular targets for gene therapy, and the development of new animal models that reproduce the human CF disease phenotype. These advances have created a preclinical path for both assessing the efficacy of gene therapies in the CF lung and interrogating the target cell types in the lung required for complementation of the CF disease state. Lessons learned from early gene therapy attempts with rAAV in the CF lung have guided thinking for the testing of next-generation vector systems. Although unknown questions still remain regarding the cellular targets in the lung that are required or sufficient to complement CF lung disease, the field is now well positioned to tackle these challenges. This review will highlight the role that next-generation CF animal models are playing in the preclinical development of gene therapies for CF lung disease and the knowledge gaps in disease pathophysiology that these models are attempting to fill.
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Affiliation(s)
- Yinghua Tang
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ziying Yan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - John F. Engelhardt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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22
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Nair RR, Blankvoort S, Lagartos MJ, Kentros C. Enhancer-Driven Gene Expression (EDGE) Enables the Generation of Viral Vectors Specific to Neuronal Subtypes. iScience 2020; 23:100888. [PMID: 32087575 PMCID: PMC7033522 DOI: 10.1016/j.isci.2020.100888] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/03/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Although a variety of remarkable molecular tools for studying neural circuits have recently been developed, the ability to deploy them in particular neuronal subtypes is limited by the fact that native promoters are almost never specific enough. We recently showed that one can generate transgenic mice with anatomical specificity surpassing that of native promoters by combining enhancers uniquely active in particular brain regions with a heterologous minimal promoter, an approach we call EDGE (Enhancer-Driven Gene Expression). Here we extend this strategy to the generation of viral (rAAV) vectors, showing that some EDGE rAAVs can recapitulate the specificity of the corresponding transgenic lines in wild-type animals, even of another species. This approach thus holds the promise of enabling circuit-specific manipulations in wild-type animals, not only enhancing our understanding of brain function, but perhaps one day even providing novel therapeutic avenues to approach disorders of the brain. rAAVs with enhancers unique to a brain region specify cell types of that brain region This requires viral constructs optimized to express only with enhancers One rAAV distinguishes distinct subtypes of excitatory neurons in a cortical layer The same specificity is seen in wild-type animals of at least two species
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Affiliation(s)
| | - Stefan Blankvoort
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway
| | - Maria Jose Lagartos
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway
| | - Cliff Kentros
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway; Institute of Neuroscience, University of Oregon, Eugene OR, USA.
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23
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Affiliation(s)
- Phillip W.L. Tai
- Horae Gene Therapy Center and the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
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24
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Tornabene P, Trapani I. Can Adeno-Associated Viral Vectors Deliver Effectively Large Genes? Hum Gene Ther 2020; 31:47-56. [DOI: 10.1089/hum.2019.220] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Patrizia Tornabene
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Medical Genetics, Department of Translational Medicine, Federico II University, Naples, Italy
| | - Ivana Trapani
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Medical Genetics, Department of Translational Medicine, Federico II University, Naples, Italy
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25
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Yang Q, Soltis AR, Sukumar G, Zhang X, Caohuy H, Freedy J, Dalgard CL, Wilkerson MD, Pollard HB, Pollard BS. Gene therapy-emulating small molecule treatments in cystic fibrosis airway epithelial cells and patients. Respir Res 2019; 20:290. [PMID: 31864360 PMCID: PMC6925517 DOI: 10.1186/s12931-019-1214-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
Background Several small molecule corrector and potentiator drugs have recently been licensed for Cystic Fibrosis (CF) therapy. However, other aspects of the disease, especially inflammation, are less effectively treated by these drugs. We hypothesized that small molecule drugs could function either alone or as an adjuvant to licensed therapies to treat these aspects of the disease, perhaps emulating the effects of gene therapy in CF cells. The cardiac glycoside digitoxin, which has been shown to inhibit TNFα/NFκB signaling in CF lung epithelial cells, may serve as such a therapy. Methods IB3–1 CF lung epithelial cells were treated with different Vertex (VX) drugs, digitoxin, and various drug mixtures, and ELISA assays were used to assess suppression of baseline and TNFα-activated secretion of cytokines and chemokines. Transcriptional responses to these drugs were assessed by RNA-seq and compared with gene expression in AAV-[wildtype]CFTR-treated IB3–1 (S9) cells. We also compared in vitro gene expression signatures with in vivo data from biopsied nasal epithelial cells from digitoxin-treated CF patients. Results CF cells exposed to digitoxin exhibited significant suppression of both TNFα/NFκB signaling and downstream secretion of IL-8, IL-6 and GM-CSF, with or without co-treatment with VX drugs. No evidence of drug-drug interference was observed. RNA-seq analysis showed that gene therapy-treated CF lung cells induced changes in 3134 genes. Among these, 32.6% were altered by digitoxin treatment in the same direction. Shared functional gene ontology themes for genes suppressed by both digitoxin and gene therapy included inflammation (84 gene signature), and cell-cell interactions and fibrosis (49 gene signature), while genes elevated by both were enriched for epithelial differentiation (82 gene signature). A new analysis of mRNA data from digitoxin-treated CF patients showed consistent trends in expression for genes in these signatures. Conclusions Adjuvant gene therapy-emulating activities of digitoxin may contribute to enhancing the efficacy of currently licensed correctors and potentiators in CF patients.
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Affiliation(s)
- Q Yang
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - A R Soltis
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - G Sukumar
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - X Zhang
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - H Caohuy
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - J Freedy
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - C L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA.,Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - M D Wilkerson
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA.,Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - H B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA. .,Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA.
| | - B S Pollard
- Silver Pharmaceuticals, Rockville, MD, 20854, USA.
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26
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Wykes AD, Ma S, Bathgate RAD, Gundlach AL. Targeted viral vector transduction of relaxin-3 neurons in the rat nucleus incertus using a novel cell-type specific promoter. IBRO Rep 2019; 8:1-10. [PMID: 31890981 PMCID: PMC6928288 DOI: 10.1016/j.ibror.2019.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive, ascending relaxin-3-containing neural networks are present throughout the rat forebrain. Relaxin-3 signalling modulates complex behaviours and cognitive processes including feeding, anxiety and memory. We tested a 1736 bp promoter sequence for specific transgene expression in relaxin-3 neurons of rat nucleus incertus (NI). This promoter restricted m-Cherry marker expression to NI relaxin-3 neurons with 98% specificity. This targeted transgene delivery offers a versatile method for ongoing preclinical studies of relaxin-3 circuitry.
Modern neuroscience utilizes transgenic techniques extensively to study the activity and function of brain neural networks. A key feature of this approach is its compatibility with molecular methods for selective transgene expression in neuronal circuits of interest. Until now, such targeted transgenic approaches have not been applied to the extensive circuitry involving the neuropeptide, relaxin-3. Pharmacological and gene knock-out studies have revealed relaxin-3 signalling modulates interrelated behaviours and cognitive processes, including stress and anxiety, food and alcohol consumption, and spatial and social memory, highlighting the potential of this system as a therapeutic target. In the present study, we aimed to identify a promoter sequence capable of regulating cell-type specific transgene expression from an adeno-associated viral (AAV) vector in relaxin-3 neurons of the rat nucleus incertus (NI). In parallel to relaxin-3 promoter sequences, we also tested an AAV vector containing promoter elements for the tropomyosin receptor kinase A (TrkA) gene, as TrkA is co-expressed with relaxin-3 in rat NI neurons. Stereotaxic injection of an mCherry-expressing AAV vector revealed widespread non-specific TrkA promoter (880 bp) activity in and adjacent to the NI at 8 weeks post-treatment. In contrast, mCherry expression was successfully restricted to relaxin-3 NI neurons with 98% specificity using a 1736 bp relaxin-3 promoter. In addition to detailed anatomical mapping of NI relaxin-3 networks, illustrated here in association with GABAergic medial septum neurons, this method for targeted transgene delivery offers a versatile tool for ongoing preclinical studies of relaxin-3 circuitry.
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Affiliation(s)
- Alexander D Wykes
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.,Florey Department of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia
| | - Sherie Ma
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.,Florey Department of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.,Florey Department of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Victoria, Australia
| | - Andrew L Gundlach
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.,Florey Department of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia
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27
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Wilmott P, Lisowski L, Alexander IE, Logan GJ. A User's Guide to the Inverted Terminal Repeats of Adeno-Associated Virus. Hum Gene Ther Methods 2019; 30:206-213. [DOI: 10.1089/hgtb.2019.276] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Patrick Wilmott
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
- Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, Puławy, Poland
- Vector and Genome Engineering Facility; Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Ian E. Alexander
- Discipline of Child and Adolescent Health, University of Sydney, Westmead, Australia
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Westmead, Australia
| | - Grant J. Logan
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Westmead, Australia
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28
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Keeler AM, Flotte TR. Recombinant Adeno-Associated Virus Gene Therapy in Light of Luxturna (and Zolgensma and Glybera): Where Are We, and How Did We Get Here? Annu Rev Virol 2019; 6:601-621. [PMID: 31283441 DOI: 10.1146/annurev-virology-092818-015530] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The recent market approvals of recombinant adeno-associated virus (rAAV) gene therapies in Europe and the United States are landmark achievements in the history of modern science. These approvals are also anticipated to herald the emergence of a new class of therapies for monogenic disorders, which had hitherto been considered untreatable. These events can be viewed as stemming from the convergence of several important historical trends: the study of basic virology, the development of genomic technologies, the imperative for translational impact of National Institutes of Health-funded research, and the development of economic models for commercialization of rare disease therapies. In this review, these historical trends are described and the key developments that have enabled clinical rAAV gene therapies are discussed, along with an overview of the current state of the field and future directions.
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Affiliation(s)
- Allison M Keeler
- Horae Gene Therapy Center and Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA;
| | - Terence R Flotte
- Horae Gene Therapy Center and Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA;
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29
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Valdivieso ÁG, Clauzure M, Massip-Copiz MM, Cancio CE, Asensio CJA, Mori C, Santa-Coloma TA. Impairment of CFTR activity in cultured epithelial cells upregulates the expression and activity of LDH resulting in lactic acid hypersecretion. Cell Mol Life Sci 2019; 76:1579-1593. [PMID: 30599064 PMCID: PMC11105536 DOI: 10.1007/s00018-018-3001-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/23/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022]
Abstract
Mutations in the gene encoding the CFTR chloride channel produce cystic fibrosis (CF). CF patients are more susceptible to bacterial infections in lungs. The most accepted hypothesis sustains that a reduction in the airway surface liquid (ASL) volume favor infections. Alternatively, it was postulated that a reduced HCO3- transport through CFTR leads to a decreased ASL pH, favoring bacterial colonization. The issue is controversial, since recent data from cultured primary cells and CF children showed normal pH values in the ASL. We have reported previously a decreased mitochondrial Complex I (mCx-I) activity in cultured cells with impaired CFTR activity. Thus, we hypothesized that the reduced mCx-I activity could lead to increased lactic acid production (Warburg-like effect) and reduced extracellular pH (pHe). In agreement with this idea, we report here that cells with impaired CFTR function (intestinal Caco-2/pRS26, transfected with an shRNA-CFTR, and lung IB3-1 CF cells) have a decreased pHe. These cells showed increased lactate dehydrogenase (LDH) activity, LDH-A expression, and lactate secretion. Similar effects were reproduced in control cells stimulated with recombinant IL-1β. The c-Src and JNK inhibitors PP2 and SP600125 were able to increase the pHe, although the differences between control and CFTR-impaired cells were not fully compensated. Noteworthy, the LDH inhibitor oxamate completely restored the pHe of the intestinal Caco-2/pRS26 cells and have a significant effect in lung IB3-1 cells; therefore, an increased lactic acid secretion seems to be the key factor that determine a reduced pHe in these epithelial cells.
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Affiliation(s)
- Ángel G Valdivieso
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), and The National Scientific and Technical Research Council of Argentina (CONICET), Alicia Moreau de Justo 1600, 1107, Buenos Aires, Argentina.
| | - Mariángeles Clauzure
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), and The National Scientific and Technical Research Council of Argentina (CONICET), Alicia Moreau de Justo 1600, 1107, Buenos Aires, Argentina
| | - María M Massip-Copiz
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), and The National Scientific and Technical Research Council of Argentina (CONICET), Alicia Moreau de Justo 1600, 1107, Buenos Aires, Argentina
| | - Carla E Cancio
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), and The National Scientific and Technical Research Council of Argentina (CONICET), Alicia Moreau de Justo 1600, 1107, Buenos Aires, Argentina
| | - Cristian J A Asensio
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), and The National Scientific and Technical Research Council of Argentina (CONICET), Alicia Moreau de Justo 1600, 1107, Buenos Aires, Argentina
| | - Consuelo Mori
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), and The National Scientific and Technical Research Council of Argentina (CONICET), Alicia Moreau de Justo 1600, 1107, Buenos Aires, Argentina
| | - Tomás A Santa-Coloma
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical Sciences, Pontifical Catholic University of Argentina (UCA), and The National Scientific and Technical Research Council of Argentina (CONICET), Alicia Moreau de Justo 1600, 1107, Buenos Aires, Argentina.
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30
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Abstract
Adeno-associated viral (AAV) gene therapy is becoming an important therapeutic modality, especially for ocular diseases, due to its efficiency of gene delivery and relative lack of pathogenicity. However, AAV sometimes can cause inflammation and toxicity. We explored such effects using injections into the mouse eye. We found a strong correlation of toxicity and inflammation with the use of promoters that were broadly active, or specifically active in the retinal pigment epithelium. AAVs with photoreceptor-specific promoters were found to be nontoxic at all doses tested. These studies reveal that safer vectors can be designed if assays for relevant and specific cell types are developed and tested with a range of vectors with different genomic elements. Adeno-associated viral vectors (AAVs) have become popular for gene therapy, given their many advantages, including their reduced inflammatory profile compared with that of other viruses. However, even in areas of immune privilege such as the eye, AAV vectors are capable of eliciting host-cell responses. To investigate the effects of such responses on several ocular cell types, we tested multiple AAV genome structures and capsid types using subretinal injections in mice. Assays of morphology, inflammation, and physiology were performed. Pathological effects on photoreceptors and the retinal pigment epithelium (RPE) were observed. Müller glia and microglia were activated, and the proinflammatory cytokines TNF-α and IL-1β were up-regulated. There was a strong correlation between cis-regulatory sequences and toxicity. AAVs with any one of three broadly active promoters, or an RPE-specific promoter, were toxic, while AAVs with four different photoreceptor-specific promoters were not toxic at the highest doses tested. There was little correlation between toxicity and transgene, capsid type, preparation method, or cellular contaminants within a preparation. The toxic effect was dose-dependent, with the RPE being more sensitive than photoreceptors. Our results suggest that ocular AAV toxicity is associated with certain AAV cis-regulatory sequences and/or their activity and that retinal damage occurs due to responses by the RPE and/or microglia. By applying multiple, sensitive assays of toxicity, AAV vectors can be designed so that they can be used safely at high dose, potentially providing greater therapeutic efficacy.
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31
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Chew J, Cook C, Gendron TF, Jansen-West K, Del Rosso G, Daughrity LM, Castanedes-Casey M, Kurti A, Stankowski JN, Disney MD, Rothstein JD, Dickson DW, Fryer JD, Zhang YJ, Petrucelli L. Aberrant deposition of stress granule-resident proteins linked to C9orf72-associated TDP-43 proteinopathy. Mol Neurodegener 2019; 14:9. [PMID: 30767771 PMCID: PMC6377782 DOI: 10.1186/s13024-019-0310-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/08/2019] [Indexed: 12/14/2022] Open
Abstract
Background A G4C2 hexanucleotide repeat expansion in the noncoding region of C9orf72 is the major genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis (c9FTD/ALS). Putative disease mechanisms underlying c9FTD/ALS include toxicity from sense G4C2 and antisense G2C4 repeat-containing RNA, and from dipeptide repeat (DPR) proteins unconventionally translated from these RNA products. Methods Intracerebroventricular injections with adeno-associated virus (AAV) encoding 2 or 149 G4C2 repeats were performed on postnatal day 0, followed by assessment of behavioral and neuropathological phenotypes. Results Relative to control mice, gliosis and neurodegeneration accompanied by cognitive and motor deficits were observed in (G4C2)149 mice by 6 months of age. Recapitulating key pathological hallmarks, we also demonstrate that sense and antisense RNA foci, inclusions of poly(GA), poly(GP), poly(GR), poly(PR), and poly(PA) DPR proteins, and inclusions of endogenous phosphorylated TDP-43 (pTDP-43) developed in (G4C2)149 mice but not control (G4C2)2 mice. Notably, proteins that play a role in the regulation of stress granules – RNA-protein assemblies that form in response to translational inhibition and that have been implicated in c9FTD/ALS pathogenesis – were mislocalized in (G4C2)149 mice as early as 3 months of age. Specifically, we observed the abnormal deposition of stress granule components within inclusions immunopositive for poly(GR) and pTDP-43, as well as evidence of nucleocytoplasmic transport defects. Conclusions Our in vivo model of c9FTD/ALS is the first to robustly recapitulate hallmark features derived from both sense and antisense C9orf72 repeat-associated transcripts complete with neurodegeneration and behavioral impairments. More importantly, the early appearance of persistent pathological stress granules prior to significant pTDP-43 deposition implicates an aberrant stress granule response as a key disease mechanism driving TDP-43 proteinopathy in c9FTD/ALS. Electronic supplementary material The online version of this article (10.1186/s13024-019-0310-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeannie Chew
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA
| | - Casey Cook
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA.,Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Rd, Jacksonville, Florida, 32224, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA.,Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Rd, Jacksonville, Florida, 32224, USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA
| | - Giulia Del Rosso
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA
| | - Lillian M Daughrity
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA
| | - Monica Castanedes-Casey
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA
| | - Aishe Kurti
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA
| | - Jeannette N Stankowski
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida, 33458, USA
| | - Jeffrey D Rothstein
- Department of Neurology, Brain Science Institute, Johns Hopkins University, 855 N Wolfe St, Baltimore, MD, 21205, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA.,Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Rd, Jacksonville, Florida, 32224, USA
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA.,Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Rd, Jacksonville, Florida, 32224, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA. .,Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Rd, Jacksonville, Florida, 32224, USA.
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA. .,Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Rd, Jacksonville, Florida, 32224, USA.
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32
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Fakhiri J, Schneider MA, Puschhof J, Stanifer M, Schildgen V, Holderbach S, Voss Y, El Andari J, Schildgen O, Boulant S, Meister M, Clevers H, Yan Z, Qiu J, Grimm D. Novel Chimeric Gene Therapy Vectors Based on Adeno-Associated Virus and Four Different Mammalian Bocaviruses. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 12:202-222. [PMID: 30766894 PMCID: PMC6360332 DOI: 10.1016/j.omtm.2019.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/11/2019] [Indexed: 02/06/2023]
Abstract
Parvoviruses are highly attractive templates for the engineering of safe, efficient, and specific gene therapy vectors, as best exemplified by adeno-associated virus (AAV). Another candidate that currently garners increasing attention is human bocavirus 1 (HBoV1). Notably, HBoV1 capsids can cross-package recombinant (r)AAV2 genomes, yielding rAAV2/HBoV1 chimeras that specifically transduce polarized human airway epithelia (pHAEs). Here, we largely expanded the repertoire of rAAV/BoV chimeras, by assembling packaging plasmids encoding the capsid genes of four additional primate bocaviruses, HBoV2–4 and GBoV (Gorilla BoV). Capsid protein expression and efficient rAAV cross-packaging were validated by immunoblotting and qPCR, respectively. Interestingly, not only HBoV1 but also HBoV4 and GBoV transduced pHAEs as well as primary human lung organoids. Flow cytometry analysis of pHAEs revealed distinct cellular specificities between the BoV isolates, with HBoV1 targeting ciliated, club, and KRT5+ basal cells, whereas HBoV4 showed a preference for KRT5+ basal cells. Surprisingly, primary human hepatocytes, skeletal muscle cells, and T cells were also highly amenable to rAAV/BoV transduction. Finally, we adapted our pipeline for AAV capsid gene shuffling to all five BoV isolates. Collectively, our chimeric rAAV/BoV vectors and bocaviral capsid library represent valuable new resources to dissect BoV biology and to breed unique gene therapy vectors.
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Affiliation(s)
- Julia Fakhiri
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,German Center for Lung Research (DZL), Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
| | - Jens Puschhof
- Hubrecht Institute and Oncode Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Megan Stanifer
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,Research Group "Cellular Polarity of Viral Infection", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Verena Schildgen
- Institute for Pathology, Kliniken der Stadt Köln gGmbH, Hospital of the Private University Witten/Herdecke, Cologne, Germany
| | - Stefan Holderbach
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Yannik Voss
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Jihad El Andari
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Oliver Schildgen
- Institute for Pathology, Kliniken der Stadt Köln gGmbH, Hospital of the Private University Witten/Herdecke, Cologne, Germany
| | - Steeve Boulant
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,Research Group "Cellular Polarity of Viral Infection", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,German Center for Lung Research (DZL), Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
| | - Hans Clevers
- Hubrecht Institute and Oncode Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.,University Medical Center (UMC) Utrecht, Utrecht, the Netherlands.,Princess Máxima Centre, Utrecht, the Netherlands
| | - Ziying Yan
- Department of Anatomy and Cell Biology, Center for Gene Therapy, The University of Iowa, Iowa City, IA, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
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33
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Noninvasive optical activation of Flp recombinase for genetic manipulation in deep mouse brain regions. Nat Commun 2019; 10:314. [PMID: 30659191 PMCID: PMC6338782 DOI: 10.1038/s41467-018-08282-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/22/2018] [Indexed: 01/04/2023] Open
Abstract
Spatiotemporal control of gene expression or labeling is a valuable strategy for identifying functions of genes within complex neural circuits. Here, we develop a highly light-sensitive and efficient photoactivatable Flp recombinase (PA-Flp) that is suitable for genetic manipulation in vivo. The highly light-sensitive property of PA-Flp is ideal for activation in deep mouse brain regions by illumination with a noninvasive light-emitting diode. In addition, PA-Flp can be extended to the Cre-lox system through a viral vector as Flp-dependent Cre expression platform, thereby activating both Flp and Cre. Finally, we demonstrate that PA-Flp–dependent, Cre-mediated Cav3.1 silencing in the medial septum increases object-exploration behavior in mice. Thus, PA-Flp is a noninvasive, highly efficient, and easy-to-use optogenetic module that offers a side-effect-free and expandable genetic manipulation tool for neuroscience research. Most approaches to control gene expression in vivo require generation of knock-in mouse lines and often lack spatiotemporal control. Here the authors develop a photo-activatable Flp recombinase system and demonstrate its use by controlling object-exploration behavior in mice through Cav3.1 silencing.
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34
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Zou W, Xiong M, Deng X, Engelhardt JF, Yan Z, Qiu J. A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium. Viruses 2019; 11:v11010033. [PMID: 30621044 PMCID: PMC6357044 DOI: 10.3390/v11010033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/30/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023] Open
Abstract
Human bocavirus 1 (HBoV1) infects well-differentiated (polarized) human airway epithelium (HAE) cultured at an air-liquid interface (ALI). In the present study, we applied next-generation RNA sequencing to investigate the genome-wide transcription profile of HBoV1, including viral mRNA and small RNA transcripts, in HBoV1-infected HAE cells. We identified novel transcription start and termination sites and confirmed the previously identified splicing events. Importantly, an additional proximal polyadenylation site (pA)p2 and a new distal polyadenylation site (pA)dREH lying on the right-hand hairpin (REH) of the HBoV1 genome were identified in processing viral pre-mRNA. Of note, all viral nonstructural proteins-encoding mRNA transcripts use both the proximal polyadenylation sites [(pA)p1 and (pA)p2] and distal polyadenylation sites [(pA)d1 and (pA)dREH] for termination. However, capsid proteins-encoding transcripts only use the distal polyadenylation sites. While the (pA)p1 and (pA)p2 sites were utilized at roughly equal efficiency for proximal polyadenylation of HBoV1 mRNA transcripts, the (pA)d1 site was more preferred for distal polyadenylation. Additionally, small RNA-seq analysis confirmed there is only one viral noncoding RNA (BocaSR) transcribed from nt 5199⁻5340 of the HBoV1 genome. Thus, our study provides a systematic and unbiased transcription profile, including both mRNA and small RNA transcripts, of HBoV1 in HBoV1-infected HAE-ALI cultures.
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Affiliation(s)
- Wei Zou
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Min Xiong
- The Children's Mercy Hospital, School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA.
| | - Xuefeng Deng
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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35
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Scharf C, Eymann C, Emicke P, Bernhardt J, Wilhelm M, Görries F, Winter J, von Woedtke T, Darm K, Daeschlein G, Steil L, Hosemann W, Beule A. Improved Wound Healing of Airway Epithelial Cells Is Mediated by Cold Atmospheric Plasma: A Time Course-Related Proteome Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:7071536. [PMID: 31223425 PMCID: PMC6541959 DOI: 10.1155/2019/7071536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/28/2019] [Indexed: 01/08/2023]
Abstract
The promising potential of cold atmospheric plasma (CAP) treatment as a new therapeutic option in the field of medicine, particularly in Otorhinolaryngology and Respiratory medicine, demands primarily the assessment of potential risks and the prevention of any direct and future cell damages. Consequently, the application of a special intensity of CAP that is well tolerated by cells and tissues is of particular interest. Although improvement of wound healing by CAP treatment has been described, the underlying mechanisms and the molecular influences on human tissues are so far only partially characterized. In this study, human S9 bronchial epithelial cells were treated with cold plasma of atmospheric pressure plasma jet that was previously proven to accelerate the wound healing in a clinically relevant extent. We studied the detailed cellular adaptation reactions for a specified plasma intensity by time-resolved comparative proteome analyses of plasma treated vs. nontreated cells to elucidate the mechanisms of the observed improved wound healing and to define potential biomarkers and networks for the evaluation of plasma effects on human epithelial cells. K-means cluster analysis and time-related analysis of fold-change factors indicated concordantly clear differences between the short-term (up to 1 h) and long-term (24-72 h) adaptation reactions. Thus, the induction of Nrf2-mediated oxidative and endoplasmic reticulum stress response, PPAR-alpha/RXR activation as well as production of peroxisomes, and prevention of apoptosis already during the first hour after CAP treatment are important cell strategies to overcome oxidative stress and to protect and maintain cell integrity and especially microtubule dynamics. After resolving of stress, when stress adaptation was accomplished, the cells seem to start again with proliferation and cellular assembly and organization. The observed strategies and identification of marker proteins might explain the accelerated wound healing induced by CAP, and these indicators might be subsequently used for risk assessment and quality management of application of nonthermal plasma sources in clinical settings.
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Affiliation(s)
- Christian Scharf
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Christine Eymann
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Philipp Emicke
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Jörg Bernhardt
- 2Institute for Microbiology, University of Greifswald, Germany
| | - Martin Wilhelm
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Fabian Görries
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Jörn Winter
- 3Leibniz Institute for Plasma Science and Technology (INP), Greifswald, Germany
| | - Thomas von Woedtke
- 3Leibniz Institute for Plasma Science and Technology (INP), Greifswald, Germany
- 4Department of Hygiene and Environmental Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Katrin Darm
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Georg Daeschlein
- 5Department of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- 6Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Germany
| | - Werner Hosemann
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
| | - Achim Beule
- 1Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Germany
- 7Department of Otorhinolaryngology, University Hospital Münster, Münster, Germany
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36
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McClements ME, Barnard AR, Singh MS, Charbel Issa P, Jiang Z, Radu RA, MacLaren RE. An AAV Dual Vector Strategy Ameliorates the Stargardt Phenotype in Adult Abca4-/- Mice. Hum Gene Ther 2018; 30:590-600. [PMID: 30381971 DOI: 10.1089/hum.2018.156] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The recent approval in the United States of the first adeno-associated viral (AAV) vector for the treatment of an inherited retinal degeneration validates this approach for the treatment of many other diseases. A major limiting factor continues to be the size restriction of the AAV transgene at under 5 kb. Stargardt disease is the most prevalent form of recessively inherited blindness and is caused by mutations in ABCA4, the gene that codes for ATP-binding cassette transporter protein family member 4, which has a coding sequence length of 6.8 kb. Dual vector approaches increase the capacity of AAV gene therapy, but at the cost of substantially reduced levels of target protein, which may be insufficient to achieve a therapeutic effect. Here we show that the efficacy of recombination of dual vectors is dependent on the length of DNA overlap between two transgenes. With optimized recombination, full-length ABCA4 protein is expressed in the photoreceptor outer segments of Abca4-/- mice at levels sufficient to reduce bisretinoid formation and correct the autofluorescent phenotype. These observations support a dual vector approach in future clinical trials using AAV gene therapy to treat Stargardt disease.
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Affiliation(s)
- Michelle E McClements
- 1 Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Alun R Barnard
- 1 Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | | | - Peter Charbel Issa
- 1 Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.,3 Oxford Eye Hospital, Oxford, United Kingdom
| | - Zhichun Jiang
- 4 Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Roxana A Radu
- 4 Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Robert E MacLaren
- 1 Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.,3 Oxford Eye Hospital, Oxford, United Kingdom
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37
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Cooney AL, McCray PB, Sinn PL. Cystic Fibrosis Gene Therapy: Looking Back, Looking Forward. Genes (Basel) 2018; 9:genes9110538. [PMID: 30405068 PMCID: PMC6266271 DOI: 10.3390/genes9110538] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 01/02/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that encodes a cAMP-regulated anion channel. Although CF is a multi-organ system disease, most people with CF die of progressive lung disease that begins early in childhood and is characterized by chronic bacterial infection and inflammation. Nearly 90% of people with CF have at least one copy of the ΔF508 mutation, but there are hundreds of CFTR mutations that result in a range of disease severities. A CFTR gene replacement approach would be efficacious regardless of the disease-causing mutation. After the discovery of the CFTR gene in 1989, the in vitro proof-of-concept for gene therapy for CF was quickly established in 1990. In 1993, the first of many gene therapy clinical trials attempted to rescue the CF defect in airway epithelia. Despite the initial enthusiasm, there is still no FDA-approved gene therapy for CF. Here we discuss the history of CF gene therapy, from the discovery of the CFTR gene to current state-of-the-art gene delivery vector designs. While implementation of CF gene therapy has proven more challenging than initially envisioned; thanks to continued innovation, it may yet become a reality.
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Affiliation(s)
- Ashley L Cooney
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Paul B McCray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Patrick L Sinn
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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38
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Analysis of Staphylococcus aureus proteins secreted inside infected human epithelial cells. Int J Med Microbiol 2018; 308:664-674. [DOI: 10.1016/j.ijmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 05/24/2018] [Accepted: 06/16/2018] [Indexed: 11/22/2022] Open
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39
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Shao W, Earley LF, Chai Z, Chen X, Sun J, He T, Deng M, Hirsch ML, Ting J, Samulski RJ, Li C. Double-stranded RNA innate immune response activation from long-term adeno-associated virus vector transduction. JCI Insight 2018; 3:120474. [PMID: 29925692 DOI: 10.1172/jci.insight.120474] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/17/2018] [Indexed: 12/16/2022] Open
Abstract
Data from clinical trials for hemophilia B using adeno-associated virus (AAV) vectors have demonstrated decreased transgenic coagulation factor IX (hFIX) expression 6-10 weeks after administration of a high vector dose. While it is likely that capsid-specific cytotoxic T lymphocytes eliminate vector-transduced hepatocytes, thereby resulting in decreased hFIX, this observation is not intuitively consistent with restored hFIX levels following prednisone application. Although the innate immune response is immediately activated following AAV vector infection via TLR pathways, no studies exist regarding the role of the innate immune response at later time points after AAV vector transduction. Herein, activation of the innate immune response in cell lines, primary human hepatocytes, and hepatocytes in a human chimeric mouse model was observed at later time points following AAV vector transduction. Mechanistic analysis demonstrated that the double-stranded RNA (dsRNA) sensor MDA5 was necessary for innate immune response activation and that transient knockdown of MDA5, or MAVS, decreased IFN-β expression while increasing transgene production in AAV-transduced cells. These results both highlight the role of the dsRNA-triggered innate immune response in therapeutic transgene expression at later time points following AAV transduction and facilitate the execution of effective strategies to block the dsRNA innate immune response in future clinical trials.
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Affiliation(s)
| | | | | | | | - Junjiang Sun
- Gene Therapy Center.,Division of Pharmacoengineering and Molecular Pharmaceutics, School of Pharmacy
| | | | - Meng Deng
- Lineberger Comprehensive Cancer Center
| | | | | | | | - Chengwen Li
- Gene Therapy Center.,Department of Pediatrics, School of Medicine, and.,Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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40
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Song CQ, Wang D, Jiang T, O'Connor K, Tang Q, Cai L, Li X, Weng Z, Yin H, Gao G, Mueller C, Flotte TR, Xue W. In Vivo Genome Editing Partially Restores Alpha1-Antitrypsin in a Murine Model of AAT Deficiency. Hum Gene Ther 2018; 29:853-860. [PMID: 29597895 DOI: 10.1089/hum.2017.225] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) genome editing holds promise in the treatment of genetic diseases that currently lack effective long-term therapies. Patients with alpha-1 antitrypsin (AAT) deficiency develop progressive lung disease due to the loss of AAT's antiprotease function and liver disease due to a toxic gain of function of the common mutant allele. However, it remains unknown whether CRISPR-mediated AAT correction in the liver, where AAT is primarily expressed, can correct either or both defects. Here we show that AAV delivery of CRISPR can effectively correct Z-AAT mutation in the liver of a transgenic mouse model. Specifically, we co-injected two AAVs: one expressing Cas9 and another encoding an AAT guide RNA and homology-directed repair template. In both neonatal and adult mice, this treatment partially restored M-AAT in the serum. Furthermore, deep sequencing confirmed both indel mutations and precise gene correction in the liver, permitting careful analysis of gene editing events in vivo. This study demonstrates a proof of concept for the application of CRISPR-Cas9 technology to correct AAT mutations in vivo and validates continued exploration of this approach for the treatment of patients with AAT deficiency.
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Affiliation(s)
- Chun-Qing Song
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Dan Wang
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Tingting Jiang
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kevin O'Connor
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Qiushi Tang
- 3 Departments of Pediatrics and Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Lingling Cai
- 4 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xiangrui Li
- 4 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Zhiping Weng
- 4 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China .,5 Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Hao Yin
- 6 Medical Research Institute, Wuhan University , Wuhan, China
| | - Guangping Gao
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Christian Mueller
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Terence R Flotte
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts.,3 Departments of Pediatrics and Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Wen Xue
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,7 Program in Molecular Medicine and Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
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41
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Ziesemer S, Eiffler I, Schönberg A, Müller C, Hochgräfe F, Beule AG, Hildebrandt JP. Staphylococcus aureusα-Toxin Induces Actin Filament Remodeling in Human Airway Epithelial Model Cells. Am J Respir Cell Mol Biol 2018; 58:482-491. [DOI: 10.1165/rcmb.2016-0207oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Sabine Ziesemer
- Animal Physiology and Biochemistry, Zoological Institute, and
| | - Ina Eiffler
- Animal Physiology and Biochemistry, Zoological Institute, and
| | | | | | - Falko Hochgräfe
- Junior Research Group Pathoproteomics, Competence Center Functional Genomics, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Achim G. Beule
- Department of Otorhinolaryngology, Head and Neck Surgery, Greifswald University Hospital, Greifswald, Germany; and
- Department of Otorhinolaryngology, University Hospital, Münster, Germany
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42
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Brown N, Song L, Kollu NR, Hirsch ML. Adeno-Associated Virus Vectors and Stem Cells: Friends or Foes? Hum Gene Ther 2018; 28:450-463. [PMID: 28490211 DOI: 10.1089/hum.2017.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The infusion of healthy stem cells into a patient-termed "stem-cell therapy"-has shown great promise for the treatment of genetic and non-genetic diseases, including mucopolysaccharidosis type 1, Parkinson's disease, multiple sclerosis, numerous immunodeficiency disorders, and aplastic anemia. Stem cells for cell therapy can be collected from the patient (autologous) or collected from another "healthy" individual (allogeneic). The use of allogenic stem cells is accompanied with the potentially fatal risk that the transplanted donor T cells will reject the patient's cells-a process termed "graft-versus-host disease." Therefore, the use of autologous stem cells is preferred, at least from the immunological perspective. However, an obvious drawback is that inherently as "self," they contain the disease mutation. As such, autologous cells for use in cell therapies often require genetic "correction" (i.e., gene addition or editing) prior to cell infusion and therefore the requirement for some form of nucleic acid delivery, which sets the stage for the AAV controversy discussed herein. Despite being the most clinically applied gene delivery context to date, unlike other more concerning integrating and non-integrating vectors such as retroviruses and adenovirus, those based on adeno-associated virus (AAV) have not been employed in the clinic. Furthermore, published data regarding AAV vector transduction of stem cells are inconsistent in regards to vector transduction efficiency, while the pendulum swings far in the other direction with demonstrations of AAV vector-induced toxicity in undifferentiated cells. The variation present in the literature examining the transduction efficiency of AAV vectors in stem cells may be due to numerous factors, including inconsistencies in stem-cell collection, cell culture, vector preparation, and/or transduction conditions. This review summarizes the controversy surrounding AAV vector transduction of stem cells, hopefully setting the stage for future elucidation and eventual therapeutic applications.
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Affiliation(s)
- Nolan Brown
- 1 Gene Therapy Center, University of North Carolina at Chapel Hill , North Carolina.,2 Department of Ophthalmology, University of North Carolina at Chapel Hill , North Carolina
| | - Liujiang Song
- 1 Gene Therapy Center, University of North Carolina at Chapel Hill , North Carolina.,2 Department of Ophthalmology, University of North Carolina at Chapel Hill , North Carolina
| | - Nageswara R Kollu
- 1 Gene Therapy Center, University of North Carolina at Chapel Hill , North Carolina.,2 Department of Ophthalmology, University of North Carolina at Chapel Hill , North Carolina
| | - Matthew L Hirsch
- 1 Gene Therapy Center, University of North Carolina at Chapel Hill , North Carolina.,2 Department of Ophthalmology, University of North Carolina at Chapel Hill , North Carolina
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43
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Julien L, Chassagne J, Peccate C, Lorain S, Piétri-Rouxel F, Danos O, Benkhelifa-Ziyyat S. RFX1 and RFX3 Transcription Factors Interact with the D Sequence of Adeno-Associated Virus Inverted Terminal Repeat and Regulate AAV Transduction. Sci Rep 2018; 8:210. [PMID: 29317724 PMCID: PMC5760533 DOI: 10.1038/s41598-017-18604-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/13/2017] [Indexed: 12/31/2022] Open
Abstract
Adeno-associated virus (AAV) transduction efficiency depends on the way in which cellular proteins process viral genomes in the nucleus. In this study, we have investigated the binding of nuclear proteins to the double stranded D (dsD) sequence of the AAV inverted terminal repeat (ITRs) by electromobility shift assay. We present here several lines of evidence that transcription factors belonging to the RFX protein family bind specifically and selectively to AAV2 and AAV1 dsD sequences. Using supershift experiments, we characterize complexes containing RFX1 homodimers and RFX1/RFX3 heterodimers. Following transduction of HEK-293 cells, the AAV genome can be pulled-down by RFX1 and RFX3 antibodies. Moreover, our data suggest that RFX proteins which interact with transcriptional enhancers of several mammalian DNA viruses, can act as regulators of AAV mediated transgene expression.
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Affiliation(s)
- Laura Julien
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Julie Chassagne
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Cécile Peccate
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Stéphanie Lorain
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - France Piétri-Rouxel
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Olivier Danos
- REGENXBIO, 9600 Blackwell Rd, Rockville, MD, 20850, USA
| | - Sofia Benkhelifa-Ziyyat
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France.
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44
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Maddalena A, Tornabene P, Tiberi P, Minopoli R, Manfredi A, Mutarelli M, Rossi S, Simonelli F, Naggert JK, Cacchiarelli D, Auricchio A. Triple Vectors Expand AAV Transfer Capacity in the Retina. Mol Ther 2017; 26:524-541. [PMID: 29292161 PMCID: PMC5835116 DOI: 10.1016/j.ymthe.2017.11.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 11/23/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023] Open
Abstract
Retinal gene transfer with adeno-associated viral (AAV) vectors holds great promise for the treatment of inherited retinal degenerations (IRDs). One limit of AAV is its transfer capacity of about 5 kb, which can be expanded to about 9 kb, using dual AAV vectors. This strategy would still not suffice for treatment of IRDs such as Usher syndrome type 1D or Alström syndrome type I (ALMS) due to mutations in CDH23 or ALMS1, respectively. To overcome this limitation, we generated triple AAV vectors, with a maximal transfer capacity of about 14 kb. Transcriptomic analysis following triple AAV transduction showed the expected full-length products along a number of aberrant transcripts. However, only the full-length transcripts are efficiently translated in vivo. We additionally showed that approximately 4% of mouse photoreceptors are transduced by triple AAV vectors and showed correct localization of recombinant ALMS1. The low-photoreceptor transduction levels might justify the modest and transient improvement we observe in the retina of a mouse model of ALMS. However, the levels of transduction mediated by triple AAV vectors in pig retina reached 40% of those observed with single vectors, and this bodes well for further improving the efficiency of triple AAV vectors in the retina.
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Affiliation(s)
- Andrea Maddalena
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy
| | - Patrizia Tornabene
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy
| | - Paola Tiberi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy
| | - Renato Minopoli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy; Armenise/Harvard Laboratory of Integrative Genomics, TIGEM, Pozzuoli 80078, Italy
| | | | - Settimio Rossi
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples 80121, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples 80121, Italy
| | | | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy; Armenise/Harvard Laboratory of Integrative Genomics, TIGEM, Pozzuoli 80078, Italy
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy; Medical Genetics, Department of Advanced Biomedicine, Federico II University, Naples 80131, Italy.
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45
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Guggino WB, Benson J, Seagrave J, Yan Z, Engelhardt J, Gao G, Conlon TJ, Cebotaru L. A Preclinical Study in Rhesus Macaques for Cystic Fibrosis to Assess Gene Transfer and Transduction by AAV1 and AAV5 with a Dual-Luciferase Reporter System. HUM GENE THER CL DEV 2017; 28:145-156. [PMID: 28726496 DOI: 10.1089/humc.2017.067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease that is potentially treatable by gene therapy. Since the identification of the gene encoding CF transmembrane conductance regulator, a number of preclinical and clinical trials have been conducted using the first generation of adeno-associated virus, AAV2. All these studies showed that AAV gene therapy for CF is safe, but clinical benefit was not clearly demonstrated. Thus, a new generation of AAV vectors based on other serotypes is needed to move the field forward. This study tested two AAV serotypes (AAV1 and AAV5) using a dual-luciferase reporter system with firefly and Renilla luciferase genes packaged into AAV1 or AAV5, respectively. Two male and two female Rhesus macaques were each instilled in their lungs with both serotypes using a Penn-Century microsprayer. Both AAV1 and AAV5 vector genomes were detected in all the lung samples when measured at the time of necropsy, 45 days after instillation. However, the vector genome number for AAV1 was at least 10-fold higher than for AAV5. Likewise, luciferase activity was also detected in the same samples at 45 days. AAV1-derived activity was not statistically greater than that derived from AAV5. These data suggest that gene transfer is greater for AAV1 than for AAV5 in macaque lungs. Serum neutralizing antibodies were increased dramatically against both serotypes but were less abundant with AAV1 than with AAV5. No adverse events were noted, again indicating that AAV gene therapy is safe. These results suggest that with more lung-tropic serotypes such as AAV1, new clinical studies of gene therapy using AAV are warranted.
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Affiliation(s)
- William B Guggino
- 1 Department of Physiology, Johns Hopkins University , Baltimore, Maryland
| | - Janet Benson
- 2 Lovelace Respiratory Research Institute , Albuquerque, New Mexico
| | | | - Ziying Yan
- 3 Department of Anatomy and Cell Biology, University of Iowa , Iowa City, Iowa
| | - John Engelhardt
- 3 Department of Anatomy and Cell Biology, University of Iowa , Iowa City, Iowa
| | - Guangping Gao
- 4 Department of Microbiology & Physiological Systems, University of Massachusetts , Worcester, Massachusetts
| | - Thomas J Conlon
- 5 Department of Pediatrics, University of Florida , Gainesville, Florida
| | - Liudmila Cebotaru
- 6 Department of Medicine, Johns Hopkins University , Baltimore, Maryland
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46
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Guggino WB, Cebotaru L. Adeno-Associated Virus (AAV) gene therapy for cystic fibrosis: current barriers and recent developments. Expert Opin Biol Ther 2017; 17:1265-1273. [PMID: 28657358 DOI: 10.1080/14712598.2017.1347630] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Since the cystic fibrosis (CF) gene was discovered in 1989, researchers have worked to develop a gene therapy. One of the most promising and enduring vectors is the AAV, which has been shown to be safe. In particular, several clinical trials have been conducted with AAV serotype 2. All of them detected viral genomes, but identification of mRNA transduction was not consistent; clinical outcomes in Phase II studies were also inconsistent. The lack of a positive outcome has been attributed to a less-than-efficient viral infection by AAV2, a weak transgene promoter and the host immune response to the vector. Areas covered: Herein, the authors focus on AAV gene therapy for CF, evaluating past experience with this approach and identifying ways forward, based on the progress that has already been made in identifying and overcoming the limitations of AAV gene therapy. Expert opinion: Such progress makes it clear that this is an opportune time to push forward toward the development of a gene therapy for CF. Drugs to treat the basic defect in CF represent a remarkable advance but cannot treat a significant cohort of patients with rare mutations. Thus, there is a critical need to develop a gene therapy for those individuals.
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Affiliation(s)
- William B Guggino
- a Departments of Medicine and Physiology , Johns Hopkins University , Baltimore , MD , USA
| | - Liudmila Cebotaru
- a Departments of Medicine and Physiology , Johns Hopkins University , Baltimore , MD , USA
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47
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Logan GJ, Dane AP, Hallwirth CV, Smyth CM, Wilkie EE, Amaya AK, Zhu E, Khandekar N, Ginn SL, Liao SHY, Cunningham SC, Sasaki N, Cabanes-Creus M, Tam PPL, Russell DW, Lisowski L, Alexander IE. Identification of liver-specific enhancer-promoter activity in the 3' untranslated region of the wild-type AAV2 genome. Nat Genet 2017. [PMID: 28628105 DOI: 10.1038/ng.3893] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Vectors based on adeno-associated virus type 2 (AAV2) are powerful tools for gene transfer and genome editing applications. The level of interest in this system has recently surged in response to reports of therapeutic efficacy in human clinical trials, most notably for those in patients with hemophilia B (ref. 3). Understandably, a recent report drawing an association between AAV2 integration events and human hepatocellular carcinoma (HCC) has generated controversy about the causal or incidental nature of this association and the implications for AAV vector safety. Here we describe and functionally characterize a previously unknown liver-specific enhancer-promoter element in the wild-type AAV2 genome that is found between the stop codon of the cap gene, which encodes proteins that form the capsid, and the right-hand inverted terminal repeat. This 124-nt sequence is within the 163-nt common insertion region of the AAV genome, which has been implicated in the dysregulation of known HCC driver genes and thus offers added insight into the possible link between AAV integration events and the multifactorial pathogenesis of HCC.
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Affiliation(s)
- Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Allison P Dane
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Christine M Smyth
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Emilie E Wilkie
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Embryology Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Neeta Khandekar
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Sophia H Y Liao
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C Cunningham
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Natsuki Sasaki
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia
| | - Martí Cabanes-Creus
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Molecular Immunology Unit, Centre for Immunodeficiency, Institute of Child Health, University College London, London, UK
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - David W Russell
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Leszek Lisowski
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, University of Sydney, Sydney, New South Wales, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Westmead, New South Wales, Australia
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48
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Abstract
AAV has been studied for 55 years and has been developed as a vector for about 35 years. By now, there is a fairly good idea of the dimensions of what would be useful to know to employ AAV optimally as a vector, but there are still many unanswered questions within the system. As with all biological systems, each good experiment raises further questions to answer. This article provides an overview of those areas in which unknown information can be identified and of those questions that have not yet been recognized. Some of these are touched on in the six review articles in this issue of Human Gene Therapy.
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Affiliation(s)
- Kenneth I Berns
- Guest Co-Editors, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine , Gainesville, Florida
| | - Nicholas Muzyczka
- Guest Co-Editors, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine , Gainesville, Florida
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49
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Jackson KL, Dayton RD, Deverman BE, Klein RL. Better Targeting, Better Efficiency for Wide-Scale Neuronal Transduction with the Synapsin Promoter and AAV-PHP.B. Front Mol Neurosci 2016; 9:116. [PMID: 27867348 PMCID: PMC5095393 DOI: 10.3389/fnmol.2016.00116] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/19/2016] [Indexed: 11/13/2022] Open
Abstract
Widespread genetic modification of cells in the central nervous system (CNS) with a viral vector has become possible and increasingly more efficient. We previously applied an AAV9 vector with the cytomegalovirus/chicken beta-actin (CBA) hybrid promoter and achieved wide-scale CNS transduction in neonatal and adult rats. However, this method transduces a variety of tissues in addition to the CNS. Thus we studied intravenous AAV9 gene transfer with a synapsin promoter to better target the neurons. We noted in systematic comparisons that the synapsin promoter drives lower level expression than does the CBA promoter. The engineered adeno-associated virus (AAV)-PHP.B serotype was compared with AAV9, and AAV-PHP.B did enhance the efficiency of expression. Combining the synapsin promoter with AAV-PHP.B could therefore be advantageous in terms of combining two refinements of targeting and efficiency. Wide-scale expression was used to model a disease with widespread pathology. Vectors encoding the amyotrophic lateral sclerosis (ALS)-related protein transactive response DNA-binding protein, 43 kDa (TDP-43) with the synapsin promoter and AAV-PHP.B were used for efficient CNS-targeted TDP-43 expression. Intracerebroventricular injections were also explored to limit TDP-43 expression to the CNS. The neuron-selective promoter and the AAV-PHP.B enhanced gene transfer and ALS disease modeling in adult rats.
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Affiliation(s)
- Kasey L Jackson
- Department of Pharmacology, Toxicology, and Neuroscience, Louisiana State University Health Sciences Center Shreveport, LA, USA
| | - Robert D Dayton
- Department of Pharmacology, Toxicology, and Neuroscience, Louisiana State University Health Sciences Center Shreveport, LA, USA
| | - Benjamin E Deverman
- Division of Biology and Biological Engineering, California Institute of Technology Pasadena, CA, USA
| | - Ronald L Klein
- Department of Pharmacology, Toxicology, and Neuroscience, Louisiana State University Health Sciences Center Shreveport, LA, USA
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50
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Stutika C, Mietzsch M, Gogol-Döring A, Weger S, Sohn M, Chen W, Heilbronn R. Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation. PLoS One 2016; 11:e0161454. [PMID: 27611072 PMCID: PMC5017669 DOI: 10.1371/journal.pone.0161454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/05/2016] [Indexed: 01/10/2023] Open
Abstract
Most DNA viruses express small regulatory RNAs, which interfere with viral or cellular gene expression. For adeno-associated virus (AAV), a small ssDNA virus with a complex biphasic life cycle miRNAs or other small regulatory RNAs have not yet been described. This is the first comprehensive Illumina-based RNA-Seq analysis of small RNAs expressed by AAV alone or upon co-infection with helper adenovirus or HSV. Several hotspots of AAV-specific small RNAs were detected mostly close to or within the AAV-ITR and apparently transcribed from the newly identified anti-p5 promoter. An additional small RNA hotspot was located downstream of the p40 promoter, from where transcription of non-coding RNAs associated with the inhibition of adenovirus replication were recently described. Parallel detection of known Ad and HSV miRNAs indirectly validated the newly identified small AAV RNA species. The predominant small RNAs were analyzed on Northern blots and by human argonaute protein-mediated co-immunoprecipitation. None of the small AAV RNAs showed characteristics of bona fide miRNAs, but characteristics of alternative RNA processing indicative of differentially regulated AAV promoter-associated small RNAs. Furthermore, the AAV-induced regulation of cellular miRNA levels was analyzed at different time points post infection. In contrast to other virus groups AAV infection had virtually no effect on the expression of cellular miRNA, which underscores the long-established concept that wild-type AAV infection is apathogenic.
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Affiliation(s)
- Catrin Stutika
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
| | - Mario Mietzsch
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
| | | | - Stefan Weger
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
| | - Madlen Sohn
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin Institute for Medical Systems Biology, Laboratory for Functional Genomics and Systems Biology, Berlin, Germany
| | - Wei Chen
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin Institute for Medical Systems Biology, Laboratory for Functional Genomics and Systems Biology, Berlin, Germany
| | - Regine Heilbronn
- Charité Medical School, Campus Benjamin Franklin, Institute of Virology, Berlin, Germany
- * E-mail:
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