1
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Chang JC, Ryan MR, Stark MC, Liu S, Purushothaman P, Bolan F, Johnson CA, Champe M, Meng H, Lawlor MW, Halawani S, Ngaba LV, Lynch DR, Davis C, Gonzalo-Gil E, Lutz C, Urbinati F, Medicherla B, Fonck C. AAV8 gene therapy reverses cardiac pathology and prevents early mortality in a mouse model of Friedreich's ataxia. Mol Ther Methods Clin Dev 2024; 32:101193. [PMID: 38352270 PMCID: PMC10862410 DOI: 10.1016/j.omtm.2024.101193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Friedreich's ataxia (FRDA) is an autosomal-recessive disorder primarily attributed to biallelic GAA repeat expansions that reduce expression of the mitochondrial protein frataxin (FXN). FRDA is characterized by progressive neurodegeneration, with many patients developing cardiomyopathy that progresses to heart failure and death. The potential to reverse or prevent progression of the cardiac phenotype of FRDA was investigated in a mouse model of FRDA, using an adeno-associated viral vector (AAV8) containing the coding sequence of the FXN gene. The Fxnflox/null::MCK-Cre conditional knockout mouse (FXN-MCK) has an FXN gene ablation that prevents FXN expression in cardiac and skeletal muscle, leading to cardiac insufficiency, weight loss, and morbidity. FXN-MCK mice received a single intravenous injection of an AAV8 vector containing human (hFXN) or mouse (mFXN) FXN genes under the control of a phosphoglycerate kinase promoter. Compared to vehicle-treated FXN-MCK control mice, AAV-treated FXN-MCK mice displayed increases in body weight, reversal of cardiac deficits, and increases in survival without apparent toxicity in the heart or liver for up to 12 weeks postdose. FXN protein expression in heart tissue was detected in a dose-dependent manner, exhibiting wide distribution throughout the heart similar to wild type, but more speckled. These results support an AAV8-based approach to treat FRDA-associated cardiomyopathy.
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Affiliation(s)
- Joshua C. Chang
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | - Molly R. Ryan
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | - Marie C. Stark
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | - Su Liu
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | | | - Fria Bolan
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | | | - Mark Champe
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | - Hui Meng
- Diverge Translational Science Laboratory, Milwaukee, WI 53204, USA
- Medical College of Wisconsin, Department of Pathology and Laboratory Medicine, Milwaukee, WI 53226, USA
| | - Michael W. Lawlor
- Diverge Translational Science Laboratory, Milwaukee, WI 53204, USA
- Medical College of Wisconsin, Department of Pathology and Laboratory Medicine, Milwaukee, WI 53226, USA
| | - Sarah Halawani
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lucie V. Ngaba
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David R. Lynch
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | | | | | - Fabrizia Urbinati
- Formerly of Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | - Bala Medicherla
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
| | - Carlos Fonck
- Astellas Gene Therapies, Inc., South San Francisco, CA 94080, USA
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2
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Srivastava A. Rationale and strategies for the development of safe and effective optimized AAV vectors for human gene therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:949-959. [PMID: 37293185 PMCID: PMC10244667 DOI: 10.1016/j.omtn.2023.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recombinant adeno-associated virus (AAV) vectors have been, or are currently in use, in 332 phase I/II/III clinical trials in a number of human diseases, and in some cases, remarkable clinical efficacy has also been achieved. There are now three US Food and Drug Administration (FDA)-approved AAV "drugs," but it has become increasingly clear that the first generation of AAV vectors are not optimal. In addition, relatively large vector doses are needed to achieve clinical efficacy, which has been shown to provoke host immune responses culminating in serious adverse events and, more recently, in the deaths of 10 patients to date. Thus, there is an urgent need for the development of the next generation of AAV vectors that are (1) safe, (2) effective, and (3) human tropic. This review describes the strategies to potentially overcome each of the limitations of the first generation of AAV vectors and the rationale and approaches for the development of the next generation of AAV serotype vectors. These vectors promise to be efficacious at significant reduced doses, likely to achieve clinical efficacy, thereby increasing the safety as well as reducing vector production costs, ensuring translation to the clinic with higher probability of success, without the need for the use of immune suppression, for gene therapy of a wide variety of diseases in humans.
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Affiliation(s)
- Arun Srivastava
- Division of Cellular and Molecular Therapy, Departments of Pediatrics, Molecular Genetics and Microbiology, Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL, USA
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3
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Remembrances of Nicholas Muzyczka, PhD. Hum Gene Ther 2023; 34:247-252. [PMID: 37083260 DOI: 10.1089/hum.2023.29240.nmu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
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4
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Barnes LF, Draper BE, Kurian J, Chen YT, Shapkina T, Powers TW, Jarrold MF. Analysis of AAV-Extracted DNA by Charge Detection Mass Spectrometry Reveals Genome Truncations. Anal Chem 2023; 95:4310-4316. [PMID: 36880264 DOI: 10.1021/acs.analchem.2c04234] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Adeno-associated virus (AAV) is a widely used gene therapy vector. The intact packaged genome is a critical quality attribute and necessary for an effective therapeutic. In this work, charge detection mass spectrometry (CDMS) was used to measure the molecular weight (MW) distribution for the genome of interest (GOI) extracted from recombinant AAV (rAAV) vectors. The measured MWs were compared to sequence masses for a range of rAAV vectors with different GOIs, serotypes, and production methods (Sf9 and HEK293 cell lines). In most cases, the measured MWs were slightly larger than the sequence masses, a result attributed to counterions. However, in a few cases, the measured MWs were significantly smaller than the sequence masses. In these cases, genome truncation is the only reasonable explanation for the discrepancy. These results suggest that direct analysis of the extracted GOI by CDMS provides a rapid and powerful tool to evaluate genome integrity in gene therapy products.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Justin Kurian
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Yu-Ting Chen
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Tatiana Shapkina
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Thomas W Powers
- Analytical Research and Development, Pfizer Inc., 875 Chesterfield Pkwy. West, Chesterfield, Missouri 63017, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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5
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Shitik EM, Shalik IK, Yudkin DV. AAV- based vector improvements unrelated to capsid protein modification. Front Med (Lausanne) 2023; 10:1106085. [PMID: 36817775 PMCID: PMC9935841 DOI: 10.3389/fmed.2023.1106085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) is the leading platform for delivering genetic constructs in vivo. To date, three AAV-based gene therapeutic agents have been approved by the FDA and are used in clinical practice. Despite the distinct advantages of gene therapy development, it is clear that AAV vectors need to be improved. Enhancements in viral vectors are mainly associated with capsid protein modifications. However, there are other structures that significantly affect the AAV life cycle and transduction. The Rep proteins, in combination with inverted terminal repeats (ITRs), determine viral genome replication, encapsidation, etc. Moreover, transgene cassette expression in recombinant variants is directly related to AAV production and transduction efficiency. This review discusses the ways to improve AAV vectors by modifying ITRs, a transgene cassette, and the Rep proteins.
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6
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Zaman H, Khan A, Khan K, Toheed S, Abdullah M, Zeeshan HM, Hameed A, Umar M, Shahid M, Malik K, Afzal S. Adeno-Associated Virus-Mediated Gene Therapy. Crit Rev Eukaryot Gene Expr 2023; 33:87-100. [PMID: 37522547 DOI: 10.1615/critreveukaryotgeneexpr.2023048135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Choice of vector is the most critical step in gene therapy. Adeno-associated viruses (AAV); third generation vectors, are getting much attention of scientists to be used as vehicles due to their non-pathogenicity, excellent safety profile, low immune responses, great efficiency to transduce non-dividing cells, large capacity to transfer genetic material and long-term expression of genetic payload. AAVs have multiple serotypes and each serotype shows tropism for a specific cell. Different serotypes are used to target liver, lungs, muscles, retina, heart, CNS, kidneys, etc. Furthermore, AAV based gene therapies have tremendous marketing applications that can be perfectly incorporated in the anticipated sites of the host target genome resulting in life long expression of transgenes. Some therapeutic products use AAV vectors that are used to treat lipoprotein lipase deficiency (LPLD) and it is injected intramuscularly, to treat mutated retinal pigment epithelium RPE65 (RPE65) that is introduced to subretinal space, an intravenous infusion to treat spinal muscular atrophy and rAAV2-CFTR vector is introduced into nasal epithelial cells to treat cystic fibrosis. AAV therapies and other such interdisciplinary methodologies can create the miracles for the generation of precision gene therapies for the treatment of most serious and sometimes fatal disorders.
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Affiliation(s)
- Hassan Zaman
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aakif Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Khalid Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shazma Toheed
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Abdullah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Abdul Hameed
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Umar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shahid
- Division of Molecular Virology and Infectious Diseases, Center of Excellence in Molecular Biology (CEMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Kausar Malik
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Center of Excellence in Molecular Biology (CEMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
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7
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Pan X, Yue Y, Boftsi M, Wasala LP, Tran NT, Zhang K, Pintel DJ, Tai PWL, Duan D. Rational engineering of a functional CpG-free ITR for AAV gene therapy. Gene Ther 2022; 29:333-345. [PMID: 34611321 PMCID: PMC8983793 DOI: 10.1038/s41434-021-00296-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022]
Abstract
Inverted terminal repeats (ITRs) are the only wild-type components retained in the genome of adeno-associated virus (AAV) vectors. To determine whether ITR modification is a viable approach for AAV vector engineering, we rationally deleted all CpG motifs in the ITR and examined whether CpG elimination compromises AAV-vector production and transduction. Modified ITRs were stable in the plasmid and maintained the CpG-free nature in purified vectors. Replacing the wild-type ITR with the CpG-free ITR did not affect vector genome encapsidation. However, the vector yield was decreased by approximately 3-fold due to reduced vector genome replication. To study the biological potency, we made micro-dystrophin (μDys) AAV vectors carrying either the wild-type ITR or the CpG-free ITR. We delivered the CpG-free μDys vector to one side of the tibialis anterior muscle of dystrophin-null mdx mice and the wild-type μDys vector to the contralateral side. Evaluation at four months after injection showed no difference in the vector genome copy number, microdystrophin expression, and muscle histology and force. Our results suggest that the complete elimination of the CpG motif in the ITR does not affect the biological activity of the AAV vector. CpG-free ITRs could be useful in engineering therapeutic AAV vectors.
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Affiliation(s)
- Xiufang Pan
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
| | - Yongping Yue
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
| | - Maria Boftsi
- Pathobiology Area Graduate Program, University of Missouri, Columbia, MO, 65212, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65212, USA
| | - Lakmini P Wasala
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
- Pathobiology Area Graduate Program, University of Missouri, Columbia, MO, 65212, USA
| | - Ngoc Tam Tran
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Keqing Zhang
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
| | - David J Pintel
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65212, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Dongsheng Duan
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65212, USA.
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
- Department of Biomedical, Biological & Chemical Engineering, College of Engineering, University of Missouri, Columbia, MO, 65212, USA.
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8
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Barnes LF, Draper BE, Chen YT, Powers TW, Jarrold MF. Quantitative analysis of genome packaging in recombinant AAV vectors by charge detection mass spectrometry. Mol Ther Methods Clin Dev 2021; 23:87-97. [PMID: 34631929 PMCID: PMC8476707 DOI: 10.1016/j.omtm.2021.08.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
Recombinant adeno-associated virus (rAAV) has emerged as an important gene therapy vector with many clinical trials currently in progress. Analytical characterization and quantitation of particle content remain challenges in both the development and production of rAAV vectors. In this study, charge detection mass spectrometry (CDMS) and gel electrophoresis are used to characterize the DNA content of recombinant AAV8 (rAAV8) vectors with a wide range of target genome sizes. We show that the differences between the masses of empty particles and particles with the genome of interest (GOI) are correlated with the expected genome mass. A small systematic deviation (around 2%) is attributed to the packaging of counterions along with the DNA. In addition to the GOI, a broad distribution of heterogeneous DNA is packaged. The distribution peaks are close to the packaging capacity of the rAAV8 vectors. There is also evidence for the co-packaging of small DNA fragments along with the GOI. Finally, we present evidence that incubation at an elevated temperature can reduce the heterogeneity of the packaged DNA. Taken together, these results show that CDMS is a viable tool for characterization of the packaged genome.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Benjamin E Draper
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Yu-Ting Chen
- Pfizer, Inc., BioTherapeutics Pharmaceutical Sciences, Analytical R&D, 875 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Thomas W Powers
- Pfizer, Inc., BioTherapeutics Pharmaceutical Sciences, Analytical R&D, 875 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
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9
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Shoti J, Qing K, Srivastava A. Reply to "D" matters in recombinant AAV packaging. Mol Ther 2021; 29:2628-2630. [PMID: 34437839 DOI: 10.1016/j.ymthe.2021.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jakob Shoti
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL 32611, USA
| | - Keyun Qing
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL 32611, USA
| | - Arun Srivastava
- Division of Cellular and Molecular Therapy, Department of Pediatrics, Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL 32611, USA.
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10
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Deutsch M, Günther A, Lerchundi R, Rose CR, Balfanz S, Baumann A. AAV-Mediated CRISPRi and RNAi Based Gene Silencing in Mouse Hippocampal Neurons. Cells 2021; 10:324. [PMID: 33557342 PMCID: PMC7915209 DOI: 10.3390/cells10020324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/12/2022] Open
Abstract
Uncovering the physiological role of individual proteins that are part of the intricate process of cellular signaling is often a complex and challenging task. A straightforward strategy of studying a protein's function is by manipulating the expression rate of its gene. In recent years, the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9-based technology was established as a powerful gene-editing tool for generating sequence specific changes in proliferating cells. However, obtaining homogeneous populations of transgenic post-mitotic neurons by CRISPR/Cas9 turned out to be challenging. These constraints can be partially overcome by CRISPR interference (CRISPRi), which mediates the inhibition of gene expression by competing with the transcription machinery for promoter binding and, thus, transcription initiation. Notably, CRISPR/Cas is only one of several described approaches for the manipulation of gene expression. Here, we targeted neurons with recombinant Adeno-associated viruses to induce either CRISPRi or RNA interference (RNAi), a well-established method for impairing de novo protein biosynthesis by using cellular regulatory mechanisms that induce the degradation of pre-existing mRNA. We specifically targeted hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels, which are widely expressed in neuronal tissues and play essential physiological roles in maintaining biophysical characteristics in neurons. Both of the strategies reduced the expression levels of three HCN isoforms (HCN1, 2, and 4) with high specificity. Furthermore, detailed analysis revealed that the knock-down of just a single HCN isoform (HCN4) in hippocampal neurons did not affect basic electrical parameters of transduced neurons, whereas substantial changes emerged in HCN-current specific properties.
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Affiliation(s)
- Matthias Deutsch
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-1, Leo-Brandt-Straße, 52428 Jülich, Germany; (M.D.); (S.B.)
- Department of Biology, University of California, San Diego, La Jolla, CA 92083, USA
| | - Anne Günther
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany;
| | - Rodrigo Lerchundi
- Institute of Neurobiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (R.L.); (C.R.R.)
| | - Christine R. Rose
- Institute of Neurobiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (R.L.); (C.R.R.)
| | - Sabine Balfanz
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-1, Leo-Brandt-Straße, 52428 Jülich, Germany; (M.D.); (S.B.)
| | - Arnd Baumann
- Forschungszentrum Jülich, Institute of Biological Information Processing, IBI-1, Leo-Brandt-Straße, 52428 Jülich, Germany; (M.D.); (S.B.)
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11
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Maurer AC, Weitzman MD. Adeno-Associated Virus Genome Interactions Important for Vector Production and Transduction. Hum Gene Ther 2020; 31:499-511. [PMID: 32303138 PMCID: PMC7232694 DOI: 10.1089/hum.2020.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Recombinant adeno-associated virus has emerged as one of the most promising gene therapy delivery vectors. Development of these vectors took advantage of key features of the wild-type adeno-associated virus (AAV), enabled by basic studies of the underlying biology and requirements for transcription, replication, and packaging of the viral genome. Each step in generating and utilizing viral vectors involves numerous molecular interactions that together determine the efficiency of vector production and gene delivery. Once delivered into the cell, interactions with host proteins will determine the fate of the viral genome, and these will impact the intended goal of gene delivery. Here, we provide an overview of known interactions of the AAV genome with viral and cellular proteins involved in its amplification, packaging, and expression. Further appreciation of how the AAV genome interacts with host factors will enhance how this simple virus can be harnessed for an array of vector purposes that benefit human health.
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Affiliation(s)
- Anna C. Maurer
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Matthew D. Weitzman
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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12
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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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13
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Savy A, Dickx Y, Nauwynck L, Bonnin D, Merten OW, Galibert L. Impact of Inverted Terminal Repeat Integrity on rAAV8 Production Using the Baculovirus/Sf9 Cells System. Hum Gene Ther Methods 2018; 28:277-289. [PMID: 28967288 PMCID: PMC5655423 DOI: 10.1089/hgtb.2016.133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adeno-associated virus (AAV) inverted terminal repeats (ITRs) are key elements of AAV. These guanine-cytosine-rich structures are involved in the replication and encapsidation of the AAV genome, along with its integration in and excision from the host genome. These sequences are the only AAV-derived DNA sequences conserved in recombinant AAV (rAAV), as they allow its replication, encapsidation, and long-term maintenance and expression in target cells. Due to the original vector design, plasmids containing the gene of interest flanked by ITRs and used for rAAV production often present incomplete, truncated, or imperfect ITR sequences. For example, pSUB201 and its derivatives harbor a truncated (14 nt missing on the external part of the ITR), flop-orientated ITR plus 46 bp of non-ITR viral DNA at each end of the rAAV genome. It has been shown that rAAV genomes can be replicated, even with incomplete, truncated, or imperfect ITR sequences, leading to the production of rAAV vectors in transfection experiments. Nonetheless, it was hypothesized that unmodified wild-type (WT) ITR sequences could lead to a higher yield of rAAV, with less non-rAAV encapsidated DNA originating from the production cells and/or baculovirus shuttle vector genomes. This work studied the impact of imperfect ITRs on the level of encapsidated rAAV genomes and baculovirus-derived DNA sequences using the baculovirus/Sf9 cells production system. Replacement of truncated ITRs with WT and additional wtAAV2 sequences has an impact on the two major features of rAAV production: (1) a rise from 10% to 40% of full capsids obtained, and (2) up to a 10-fold reduction in non-rAAV encapsidated DNA. Furthermore, this study considered the impact on these major parameters of additional ITR elements and ITRs coupled with various regulatory elements of different origins. Implementation of the use of complete ITRs in the frame of the baculovirus-based rAAV expression system is one step that will be required to optimize the quality of rAAV-based gene therapy drugs.
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Affiliation(s)
- Adrien Savy
- 1 Research and Development , Généthon, Evry, France .,2 Université d'Evry Val-d'Essonne , Evry, France
| | - Yohann Dickx
- 1 Research and Development , Généthon, Evry, France
| | | | | | | | - Lionel Galibert
- 1 Research and Development , Généthon, Evry, France .,3 Rare Diseases Research Unit, Pfizer, London, United Kingdom
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Aponte-Ubillus JJ, Barajas D, Peltier J, Bardliving C, Shamlou P, Gold D. Molecular design for recombinant adeno-associated virus (rAAV) vector production. Appl Microbiol Biotechnol 2017; 102:1045-1054. [PMID: 29204900 PMCID: PMC5778157 DOI: 10.1007/s00253-017-8670-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/17/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022]
Abstract
Recombinant adeno-associated virus (rAAV) vectors are increasingly popular tools for gene therapy applications. Their non-pathogenic status, low inflammatory potential, availability of viral serotypes with different tissue tropisms, and prospective long-lasting gene expression are important attributes that make rAAVs safe and efficient therapeutic options. Over the last three decades, several groups have engineered recombinant AAV-producing platforms, yielding high titers of transducing vector particles. Current specific productivity yields from different platforms range from 103 to 105 vector genomes (vg) per cell, and there is an ongoing effort to improve vector yields in order to satisfy high product demands required for clinical trials and future commercialization. Crucial aspects of vector production include the molecular design of the rAAV-producing host cell line along with the design of AAV genes, promoters, and regulatory elements. Appropriately, configuring and balancing the expression of these elements not only contributes toward high productivity, it also improves process robustness and product quality. In this mini-review, the rational design of rAAV-producing expression systems is discussed, with special attention to molecular strategies that contribute to high-yielding, biomanufacturing-amenable rAAV production processes. Details on molecular optimization from four rAAV expression systems are covered: adenovirus, herpesvirus, and baculovirus complementation systems, as well as a recently explored yeast expression system.
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Affiliation(s)
- Juan Jose Aponte-Ubillus
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA.
- Keck Graduate Institute of Applied Life Sciences, 535 Watson drive, Claremont, CA, 91711, USA.
| | - Daniel Barajas
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA
| | - Joseph Peltier
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA
| | - Cameron Bardliving
- Keck Graduate Institute of Applied Life Sciences, 535 Watson drive, Claremont, CA, 91711, USA
| | - Parviz Shamlou
- Keck Graduate Institute of Applied Life Sciences, 535 Watson drive, Claremont, CA, 91711, USA
| | - Daniel Gold
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA
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Nambiar B, Cornell Sookdeo C, Berthelette P, Jackson R, Piraino S, Burnham B, Nass S, Souza D, O'Riordan CR, Vincent KA, Cheng SH, Armentano D, Kyostio-Moore S. Characteristics of Minimally Oversized Adeno-Associated Virus Vectors Encoding Human Factor VIII Generated Using Producer Cell Lines and Triple Transfection. Hum Gene Ther Methods 2017; 28:23-38. [PMID: 28166648 DOI: 10.1089/hgtb.2016.124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Several ongoing clinical studies are evaluating recombinant adeno-associated virus (rAAV) vectors as gene delivery vehicles for a variety of diseases. However, the production of vectors with genomes >4.7 kb is challenging, with vector preparations frequently containing truncated genomes. To determine whether the generation of oversized rAAVs can be improved using a producer cell-line (PCL) process, HeLaS3-cell lines harboring either a 5.1 or 5.4 kb rAAV vector genome encoding codon-optimized cDNA for human B-domain deleted Factor VIII (FVIII) were isolated. High-producing "masterwells" (MWs), defined as producing >50,000 vg/cell, were identified for each oversized vector. These MWs provided stable vector production for >20 passages. The quality and potency of the AAVrh8R/FVIII-5.1 and AAVrh8R/FVIII-5.4 vectors generated by the PCL method were then compared to those prepared via transient transfection (TXN). Southern and dot blot analyses demonstrated that both production methods resulted in packaging of heterogeneously sized genomes. However, the PCL-derived rAAV vector preparations contained some genomes >4.7 kb, whereas the majority of genomes generated by the TXN method were ≤4.7 kb. The PCL process reduced packaging of non-vector DNA for both the AAVrh8R/FVIII-5.1 and the AAVrh8R/FVIII-5.4 kb vector preparations. Furthermore, more DNA-containing viral particles were obtained for the AAVrh8R/FVIII-5.1 vector. In a mouse model of hemophilia A, animals administered a PCL-derived rAAV vector exhibited twofold higher plasma FVIII activity and increased levels of vector genomes in the liver than mice treated with vector produced via TXN did. Hence, the quality of oversized vectors prepared using the PCL method is greater than that of vectors generated using the TXN process, and importantly this improvement translates to enhanced performance in vivo.
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Srivastava A. Adeno-Associated Virus: The Naturally Occurring Virus Versus the Recombinant Vector. Hum Gene Ther 2016; 27:1-6. [PMID: 26784640 DOI: 10.1089/hum.2015.29017.asr] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Arun Srivastava
- Division of Cellular and Molecular Therapy, Department of Pediatrics and Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center; Genetics Institute; Shands Cancer Center; University of Florida College of Medicine , Gainesville, Florida
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Ling C, Yin Z, Li J, Zhang D, Aslanidi G, Srivastava A. Strategies to generate high-titer, high-potency recombinant AAV3 serotype vectors. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 3:16029. [PMID: 27200382 PMCID: PMC4856060 DOI: 10.1038/mtm.2016.29] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 02/08/2023]
Abstract
Although recombinant adeno-associated virus serotype 3 (AAV3) vectors were largely ignored previously, owing to their poor transduction efficiency in most cells and tissues examined, our initial observation of the selective tropism of AAV3 serotype vectors for human liver cancer cell lines and primary human hepatocytes has led to renewed interest in this serotype. AAV3 vectors and their variants have recently proven to be extremely efficient in targeting human and nonhuman primate hepatocytes in vitro as well as in vivo. In the present studies, we wished to evaluate the relative contributions of the cis-acting inverted terminal repeats (ITRs) from AAV3 (ITR3), as well as the trans-acting Rep proteins from AAV3 (Rep3) in the AAV3 vector production and transduction. To this end, we utilized two helper plasmids: pAAVr2c3, which carries rep2 and cap3 genes, and pAAVr3c3, which carries rep3 and cap3 genes. The combined use of AAV3 ITRs, AAV3 Rep proteins, and AAV3 capsids led to the production of recombinant vectors, AAV3-Rep3/ITR3, with up to approximately two to fourfold higher titers than AAV3-Rep2/ITR2 vectors produced using AAV2 ITRs, AAV2 Rep proteins, and AAV3 capsids. We also observed that the transduction efficiency of Rep3/ITR3 AAV3 vectors was approximately fourfold higher than that of Rep2/ITR2 AAV3 vectors in human hepatocellular carcinoma cell lines in vitro. The transduction efficiency of Rep3/ITR3 vectors was increased by ~10-fold, when AAV3 capsids containing mutations in two surface-exposed residues (serine 663 and threonine 492) were used to generate a S663V+T492V double-mutant AAV3 vector. The Rep3/ITR3 AAV3 vectors also transduced human liver tumors in vivo approximately twofold more efficiently than those generated with Rep2/ITR2. Our data suggest that the transduction efficiency of AAV3 vectors can be significantly improved both using homologous Rep proteins and ITRs as well as by capsid optimization. Thus, the combined use of homologous Rep proteins, ITRs, and capsids should also lead to more efficacious other AAV serotype vectors for their optimal use in human gene therapy.
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Affiliation(s)
- Chen Ling
- Division of Cellular and Molecular Therapy, Department of Pediatrics; University of Florida College of Medicine, Gainesville, Florida, USA; Powell Gene Therapy Center; University of Florida College of Medicine, Gainesville, Florida, USA; Shands Cancer Center; University of Florida College of Medicine, Gainesville, Florida, USA
| | - Zifei Yin
- Division of Cellular and Molecular Therapy, Department of Pediatrics; University of Florida College of Medicine , Gainesville, Florida, USA
| | - Jun Li
- Division of Cellular and Molecular Therapy, Department of Pediatrics; University of Florida College of Medicine , Gainesville, Florida, USA
| | - Daniel Zhang
- Division of Cellular and Molecular Therapy, Department of Pediatrics; University of Florida College of Medicine , Gainesville, Florida, USA
| | - George Aslanidi
- Division of Cellular and Molecular Therapy, Department of Pediatrics; University of Florida College of Medicine, Gainesville, Florida, USA; Powell Gene Therapy Center; University of Florida College of Medicine, Gainesville, Florida, USA
| | - Arun Srivastava
- Division of Cellular and Molecular Therapy, Department of Pediatrics; University of Florida College of Medicine, Gainesville, Florida, USA; Powell Gene Therapy Center; University of Florida College of Medicine, Gainesville, Florida, USA; Shands Cancer Center; University of Florida College of Medicine, Gainesville, Florida, USA; Genetics Institute; University of Florida College of Medicine, Gainesville, Florida, USA; Department of Molecular Genetics & Microbiology; University of Florida College of Medicine, Gainesville, Florida, USA
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