1
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Lu Y, Ling C, Shoti J, Yang H, Nath A, Keeler GD, Qing K, Srivastava A. Enhanced transgene expression from single-stranded AAV vectors in human cells in vitro and in murine hepatocytes in vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102196. [PMID: 38766527 PMCID: PMC11101737 DOI: 10.1016/j.omtn.2024.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
We identified that distal 10 nucleotides in the D-sequence in AAV2 inverted terminal repeat (ITR) share partial sequence homology to 1/2 binding site of glucocorticoid receptor-binding element (GRE). Here, we describe that (1) purified GR binds to AAV2 D-sequence, and the D-sequence competes with GR binding to its cognate binding site; (2) dexamethasone-mediated activation of GR pathway significantly increases the transduction efficiency of AAV2 vectors in human cells; (3) human osteosarcoma cells, U2OS, which lack expression of GR, are poorly transduced by AAV2 vectors, but stable transfection with a GR expression plasmid restores vector-mediated transgene expression; (4) replacement of the distal 10 nucleotides in the D-sequence of the AAV2 ITR with a full-length GRE consensus sequence significantly enhances transgene expression in human cells in vitro and in murine hepatocytes in vivo; and (5) none of the ITRs in AAV1, AAV3, AAV4, AAV5, and AAV6 genomes contains the GRE 1/2 binding site, and insertion of a full-length GRE consensus sequence in the AAV6-ITR also significantly enhances transgene expression from AAV6 vectors, both in vitro and in vivo. These novel vectors, termed generation Y AAV vectors, which are serotype, transgene, or promoter agnostic, should be useful in human gene therapy.
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Affiliation(s)
- Yuan Lu
- Full Circle Therapeutics, Shanghai, China
| | - Chen Ling
- Department of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jakob Shoti
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Hua Yang
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Aneesha Nath
- Department of Pharmacotherapy & Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - Geoffrey D. Keeler
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Keyun Qing
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Arun Srivastava
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
- Powell Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL, USA
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2
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Henderson ML, Zieba JK, Li X, Campbell DB, Williams MR, Vogt DL, Bupp CP, Edgerly YM, Rajasekaran S, Hartog NL, Prokop JW, Krueger JM. Gene Therapy for Genetic Syndromes: Understanding the Current State to Guide Future Care. BIOTECH 2024; 13:1. [PMID: 38247731 PMCID: PMC10801589 DOI: 10.3390/biotech13010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability to change the course of genetic syndromes. However, this excitement risks over-expansion into areas of genetic disease that may not fit the current state of gene therapy. While in situ (targeted to an area) and ex vivo (removal of cells, delivery, and administration of cells) approaches show promise, they have a limited target ability. Broader in vivo gene therapy trials have shown various continued challenges, including immune response, use of immune suppressants correlating to secondary infections, unknown outcomes of overexpression, and challenges in driving tissue-specific corrections. Viral delivery systems can be associated with adverse outcomes such as hepatotoxicity and lethality if uncontrolled. In some cases, these risks are far outweighed by the potentially lethal syndromes for which these systems are being developed. Therefore, it is critical to evaluate the field of genetic diseases to perform cost-benefit analyses for gene therapy. In this work, we present the current state while setting forth tools and resources to guide informed directions to avoid foreseeable issues in gene therapy that could prevent the field from continued success.
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Affiliation(s)
- Marian L. Henderson
- The Department of Biology, Calvin University, Grand Rapids, MI 49546, USA;
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Jacob K. Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Daniel B. Campbell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Michael R. Williams
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Daniel L. Vogt
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Medical Genetics, Corewell Health, Grand Rapids, MI 49503, USA
| | | | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA;
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Corewell Health, Grand Rapids, MI 49503, USA
| | - Nicholas L. Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Allergy & Immunology, Corewell Health, Grand Rapids, MI 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA;
| | - Jena M. Krueger
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Department of Neurology, Helen DeVos Children’s Hospital, Corewell Health, Grand Rapids, MI 49503, USA
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3
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Gonzalez TJ, Mitchell-Dick A, Blondel LO, Fanous MM, Hull JA, Oh DK, Moller-Tank S, Castellanos Rivera RM, Piedrahita JA, Asokan A. Structure-guided AAV capsid evolution strategies for enhanced CNS gene delivery. Nat Protoc 2023; 18:3413-3459. [PMID: 37735235 DOI: 10.1038/s41596-023-00875-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 06/13/2023] [Indexed: 09/23/2023]
Abstract
Over the past 5 years, our laboratory has systematically developed a structure-guided library approach to evolve new adeno-associated virus (AAV) capsids with altered tissue tropism, higher transduction efficiency and the ability to evade pre-existing humoral immunity. Here, we provide a detailed protocol describing two distinct evolution strategies using structurally divergent AAV serotypes as templates, exemplified by improving CNS gene transfer efficiency in vivo. We outline four major components of our strategy: (i) structure-guided design of AAV capsid libraries, (ii) AAV library production, (iii) library cycling in single versus multiple animal models, followed by (iv) evaluation of lead AAV vector candidates in vivo. The protocol spans ~95 d, excluding gene expression analysis in vivo, and can vary depending on user experience, resources and experimental design. A distinguishing attribute of the current protocol is the focus on providing biomedical researchers with 3D structural information to guide evolution of precise 'hotspots' on AAV capsids. Furthermore, the protocol outlines two distinct methods for AAV library evolution consisting of adenovirus-enabled infectious cycling in a single species and noninfectious cycling in a cross-species manner. Notably, our workflow can be seamlessly merged with other RNA transcript-based library strategies and tailored for tissue-specific capsid selection. Overall, the procedures outlined herein can be adapted to expand the AAV vector toolkit for genetic manipulation of animal models and development of human gene therapies.
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Affiliation(s)
- Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Leo O Blondel
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Marco M Fanous
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Joshua A Hull
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Daniel K Oh
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Sven Moller-Tank
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jorge A Piedrahita
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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4
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Sahel DK, Vora LK, Saraswat A, Sharma S, Monpara J, D'Souza AA, Mishra D, Tryphena KP, Kawakita S, Khan S, Azhar M, Khatri DK, Patel K, Singh Thakur RR. CRISPR/Cas9 Genome Editing for Tissue-Specific In Vivo Targeting: Nanomaterials and Translational Perspective. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207512. [PMID: 37166046 PMCID: PMC10323670 DOI: 10.1002/advs.202207512] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/15/2023] [Indexed: 05/12/2023]
Abstract
Clustered randomly interspaced short palindromic repeats (CRISPRs) and its associated endonuclease protein, i.e., Cas9, have been discovered as an immune system in bacteria and archaea; nevertheless, they are now being adopted as mainstream biotechnological/molecular scissors that can modulate ample genetic and nongenetic diseases via insertion/deletion, epigenome editing, messenger RNA editing, CRISPR interference, etc. Many Food and Drug Administration-approved and ongoing clinical trials on CRISPR adopt ex vivo strategies, wherein the gene editing is performed ex vivo, followed by reimplantation to the patients. However, the in vivo delivery of the CRISPR components is still under preclinical surveillance. This review has summarized the nonviral nanodelivery strategies for gene editing using CRISPR/Cas9 and its recent advancements, strategic points of view, challenges, and future aspects for tissue-specific in vivo delivery of CRISPR/Cas9 components using nanomaterials.
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Affiliation(s)
- Deepak Kumar Sahel
- Department of PharmacyBirla Institute of Technology and Science‐PilaniBITS‐Pilani, Vidya ViharPilaniRajasthan333031India
| | - Lalitkumar K. Vora
- School of PharmacyQueen's University Belfast97 Lisburn RoadBelfastBT9 7BLUK
| | - Aishwarya Saraswat
- College of Pharmacy & Health SciencesSt. John's UniversityQueensNY11439USA
| | - Saurabh Sharma
- Terasaki Institute for Biomedical InnovationLos AngelesCA90064USA
| | - Jasmin Monpara
- Department of Pharmaceutical SciencesUniversity of SciencesPhiladelphiaPA19104USA
| | - Anisha A. D'Souza
- Graduate School of Pharmaceutical Sciences and School of PharmacyDuquesne UniversityPittsburghPA15282USA
| | - Deepakkumar Mishra
- School of PharmacyQueen's University Belfast97 Lisburn RoadBelfastBT9 7BLUK
| | - Kamatham Pushpa Tryphena
- Molecular and Cellular Neuroscience LabDepartment of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)‐HyderabadTelangana500037India
| | - Satoru Kawakita
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
| | - Shahid Khan
- Terasaki Institute for Biomedical InnovationLos AngelesCA90064USA
| | - Mohd Azhar
- Research and Development Tata Medical and Diagnostics LimitedMumbaiMaharashtra400001India
| | - Dharmendra Kumar Khatri
- Molecular and Cellular Neuroscience LabDepartment of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)‐HyderabadTelangana500037India
| | - Ketan Patel
- College of Pharmacy & Health SciencesSt. John's UniversityQueensNY11439USA
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5
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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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6
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Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA editing: Expanding the potential of RNA therapeutics. Mol Ther 2023; 31:1533-1549. [PMID: 36620962 PMCID: PMC9824937 DOI: 10.1016/j.ymthe.2023.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
RNA therapeutics have had a tremendous impact on medicine, recently exemplified by the rapid development and deployment of mRNA vaccines to combat the COVID-19 pandemic. In addition, RNA-targeting drugs have been developed for diseases with significant unmet medical needs through selective mRNA knockdown or modulation of pre-mRNA splicing. Recently, RNA editing, particularly antisense RNA-guided adenosine deaminase acting on RNA (ADAR)-based programmable A-to-I editing, has emerged as a powerful tool to manipulate RNA to enable correction of disease-causing mutations and modulate gene expression and protein function. Beyond correcting pathogenic mutations, the technology is particularly well suited for therapeutic applications that require a transient pharmacodynamic effect, such as the treatment of acute pain, obesity, viral infection, and inflammation, where it would be undesirable to introduce permanent alterations to the genome. Furthermore, transient modulation of protein function, such as altering the active sites of enzymes or the interface of protein-protein interactions, opens the door to therapeutic avenues ranging from regenerative medicine to oncology. These emerging RNA-editing-based toolsets are poised to broadly impact biotechnology and therapeutic applications. Here, we review the emerging field of therapeutic RNA editing, highlight recent laboratory advancements, and discuss the key challenges on the path to clinical development.
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Affiliation(s)
| | - Sami Nourreddine
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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7
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Farraha M, Rao R, Igoor S, Le TYL, Barry MA, Davey C, Kok C, Chong JJ, Kizana E. Recombinant Adeno-Associated Viral Vector-Mediated Gene Transfer of hTBX18 Generates Pacemaker Cells from Ventricular Cardiomyocytes. Int J Mol Sci 2022; 23:ijms23169230. [PMID: 36012498 PMCID: PMC9408910 DOI: 10.3390/ijms23169230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
Sinoatrial node dysfunction can manifest as bradycardia, leading to symptoms of syncope and sudden cardiac death. Electronic pacemakers are the current standard of care but are limited due to a lack of biological chronotropic control, cost of revision surgeries, and risk of lead- and device-related complications. We therefore aimed to develop a biological alternative to electronic devices by using a clinically relevant gene therapy vector to demonstrate conversion of cardiomyocytes into sinoatrial node-like cells in an in vitro context. Neonatal rat ventricular myocytes were transduced with recombinant adeno-associated virus vector 6 encoding either hTBX18 or green fluorescent protein and maintained for 3 weeks. At the endpoint, qPCR, Western blot analysis and immunocytochemistry were used to assess for reprogramming into pacemaker cells. Cell morphology and Arclight action potentials were imaged via confocal microscopy. Compared to GFP, hTBX18-transduced cells showed that hTBX18, HCN4 and Cx45 were upregulated. Cx43 was significantly downregulated, while sarcomeric α-actinin remained unchanged. Cardiomyocytes transduced with hTBX18 acquired the tapering morphology of native pacemaker cells, as compared to the block-like, striated appearance of ventricular cardiomyocytes. Analysis of the action potentials showed phase 4 depolarization and a significant decrease in the APD50 of the hTBX18-transduced cells. We have demonstrated that rAAV-hTBX18 gene transfer to ventricular myocytes results in morphological, molecular, physiological, and functional changes, recapitulating the pacemaker phenotype in an in vitro setting. The generation of these induced pacemaker-like cells using a clinically relevant vector opens new prospects for biological pacemaker development.
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Affiliation(s)
- Melad Farraha
- Sydney Medical School, the University of Sydney, Sydney 2006, Australia
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
| | - Renuka Rao
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
| | - Sindhu Igoor
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
| | - Thi Y. L. Le
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
| | - Michael A. Barry
- Department of Cardiology, Westmead Hospital, Sydney 2145, Australia
| | - Christopher Davey
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
- School of Physics, the University of Sydney, Sydney 2006, Australia
| | - Cindy Kok
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
| | - James J.H. Chong
- Sydney Medical School, the University of Sydney, Sydney 2006, Australia
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
- Department of Cardiology, Westmead Hospital, Sydney 2145, Australia
| | - Eddy Kizana
- Sydney Medical School, the University of Sydney, Sydney 2006, Australia
- Centre for Heart Research, the Westmead Institute for Medical Research, Sydney 2145, Australia
- Department of Cardiology, Westmead Hospital, Sydney 2145, Australia
- Correspondence:
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8
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Wang S, Atkinson GRS, Hayes WB. SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment. NPJ Syst Biol Appl 2022; 8:25. [PMID: 35859153 PMCID: PMC9300714 DOI: 10.1038/s41540-022-00232-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/20/2022] [Indexed: 12/31/2022] Open
Abstract
Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them. The topological alignment of two protein–protein interaction (PPI) networks should thus expose protein pairs with similar interaction partners allowing, for example, the prediction of common Gene Ontology (GO) terms. Unfortunately, no network alignment algorithm based on topology alone has been able to achieve this aim, though those that include sequence similarity have seen some success. We argue that this failure of topology alone is due to the sparsity and incompleteness of the PPI network data of almost all species, which provides the network topology with a small signal-to-noise ratio that is effectively swamped when sequence information is added to the mix. Here we show that the weak signal can be detected using multiple stochastic samples of “good” topological network alignments, which allows us to observe regions of the two networks that are robustly aligned across multiple samples. The resulting network alignment frequency (NAF) strongly correlates with GO-based Resnik semantic similarity and enables the first successful cross-species predictions of GO terms based on topology-only network alignments. Our best predictions have an AUPR of about 0.4, which is competitive with state-of-the-art algorithms, even when there is no observable sequence similarity and no known homology relationship. While our results provide only a “proof of concept” on existing network data, we hypothesize that predicting GO terms from topology-only network alignments will become increasingly practical as the volume and quality of PPI network data increase.
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Affiliation(s)
- Siyue Wang
- Department of Computer Science, University of California, Irvine, CA, 92697-3435, USA
| | - Giles R S Atkinson
- Department of Computer Science, University of California, Irvine, CA, 92697-3435, USA
| | - Wayne B Hayes
- Department of Computer Science, University of California, Irvine, CA, 92697-3435, USA.
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9
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Brimble MA, Cheng PH, Winston SM, Reeves IL, Souquette A, Spence Y, Zhou J, Wang YD, Morton CL, Valentine M, Thomas PG, Nathwani AC, Gray JT, Davidoff AM. Preventing packaging of translatable P5-associated DNA contaminants in recombinant AAV vector preps. Mol Ther Methods Clin Dev 2022; 24:280-291. [PMID: 35211640 PMCID: PMC8829444 DOI: 10.1016/j.omtm.2022.01.008] [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: 08/16/2021] [Accepted: 01/16/2022] [Indexed: 11/25/2022]
Abstract
Recombinant adeno-associated virus (rAAV) vectors are increasingly being used for clinical gene transfer and have shown great potential for the treatment of several monogenic disorders. However, contaminant DNA from producer plasmids can be packaged into rAAV alongside the intended expression cassette-containing vector genome. The consequences of this are unknown. Our analysis of rAAV preps revealed abundant contaminant sequences upstream of the AAV replication (Rep) protein driving promoter, P5, on the Rep-Cap producer plasmid. Characterization of P5-associated contaminants after infection showed transfer, persistence, and transcriptional activity in AAV-transduced murine hepatocytes, in addition to in vitro evidence suggestive of integration. These contaminants can also be efficiently translated and immunogenic, revealing previously unrecognized side effects of rAAV-mediated gene transfer. P5-associated contaminant packaging and activity were independent of an inverted terminal repeat (ITR)-flanked vector genome. To prevent incorporation of these potentially harmful sequences, we constructed a modified P5-promoter (P5-HS), inserting a DNA spacer between an Rep binding site and an Rep nicking site in P5. This prevented upstream DNA contamination regardless of transgene or AAV serotype, while maintaining vector yield. Thus, we have constructed an rAAV production plasmid that improves vector purity and can be implemented across clinical rAAV applications. These findings represent new vector safety and production considerations for rAAV gene therapy.
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Affiliation(s)
- Mark A. Brimble
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK
| | - Pei-Hsin Cheng
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Stephen M. Winston
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Isaiah L. Reeves
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yunyu Spence
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junfang Zhou
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher L. Morton
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amit C. Nathwani
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK
- Katharine Dormandy Haemophilia and Thrombosis Centre, Royal Free Hospital, London NW3 2QG, UK
| | - John T. Gray
- Vertex Cell and Genetic Therapies, Vertex Pharmaceuticals, Boston, MA 02210, USA
| | - Andrew M. Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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10
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Tissue and cell-type-specific transduction using rAAV vectors in lung diseases. J Mol Med (Berl) 2021; 99:1057-1071. [PMID: 34021360 DOI: 10.1007/s00109-021-02086-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Gene therapy of genetically determined diseases, including some pathologies of the respiratory system, requires an efficient method for transgene delivery. Recombinant adeno-associated viral (rAAV) vectors are well studied and employed in gene therapy, as they are relatively simple and low immunogenic and able to efficiently transduce eukaryotic cells. To date, many natural and artificial (with modified capsids) AAV serotypes have been isolated, demonstrating preferential tropism toward different tissues and cells in accordance with the prevalent receptors on the cell surface. However, rAAV-mediated delivery is not strictly specific due to wide tropism of some viral serotypes. Thus, the development of the methods allowing modulating specificity of these vectors could be beneficial in some cases. This review describes various approaches for retargeting rAAV to respiratory cells, for example, using different types of capsid modifications and regulation of a transgene expression by tissue-specific promoters. Part of the review is devoted to the issues of transduction of stem and progenitor lung cells using AAV, which is a complicated task today.
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11
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Chen OG, Mather SE, Brommel CM, Hamilton BA, Ehler A, Villacreses R, Girgis RE, Abou Alaiwa M, Stoltz DA, Zabner J, Li X. Transduction of Pig Small Airway Epithelial Cells and Distal Lung Progenitor Cells by AAV4. Cells 2021; 10:cells10051014. [PMID: 33923029 PMCID: PMC8145967 DOI: 10.3390/cells10051014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) is caused by genetic mutations of the CF transmembrane conductance regulator (CFTR), leading to disrupted transport of Cl− and bicarbonate and CF lung disease featuring bacterial colonization and chronic infection in conducting airways. CF pigs engineered by mutating CFTR develop lung disease that mimics human CF, and are well-suited for investigating CF lung disease therapeutics. Clinical data suggest small airways play a key role in the early pathogenesis of CF lung disease, but few preclinical studies have focused on small airways. Efficient targeted delivery of CFTR cDNA to small airway epithelium may correct the CFTR defect and prevent lung infections. Adeno-associated virus 4 (AAV4) is a natural AAV serotype and a safe vector with lower immunogenicity than other gene therapy vectors such as adenovirus. Our analysis of AAV natural serotypes using cultured primary pig airway epithelia showed that AAV4 has high tropism for airway epithelia and higher transduction efficiency for small airways compared with large airways. AAV4 mediated the delivery of CFTR, and corrected Cl− transport in cultured primary small airway epithelia from CF pigs. Moreover, AAV4 was superior to all other natural AAV serotypes in transducing ITGα6β4+ pig distal lung progenitor cells. In addition, AAV4 encoding eGFP can infect pig distal lung epithelia in vivo. This study demonstrates AAV4 tropism in small airway progenitor cells, which it efficiently transduces. AAV4 offers a novel tool for mechanistical study of the role of small airway in CF lung pathogenesis in a preclinical large animal model.
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Affiliation(s)
- Oliver G Chen
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Steven E Mather
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christian M Brommel
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Bradley A Hamilton
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Annie Ehler
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Raul Villacreses
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Reda E Girgis
- Pulmonary Medicine, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Mahmoud Abou Alaiwa
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - David A Stoltz
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Joseph Zabner
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Xiaopeng Li
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI 49503, USA
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12
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Carneiro A, Lee H, Lin L, van Haasteren J, Schaffer DV. Novel Lung Tropic Adeno-Associated Virus Capsids for Therapeutic Gene Delivery. Hum Gene Ther 2020; 31:996-1009. [PMID: 32799685 DOI: 10.1089/hum.2020.169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Efforts to identify mutations that underlie inherited genetic diseases combined with strides in the development of gene therapy vectors over the last three decades have culminated in the approval of several adeno-associated virus (AAV)-based gene therapies. Genetic diseases that manifest in the lung such as cystic fibrosis (CF) and surfactant deficiencies, however, have so far proven to be elusive targets. Early clinical trials in CF using AAV serotype 2 (AAV2) achieved safety, but not efficacy endpoints; however, importantly, these studies provided critical information on barriers that need to be surmounted to translate AAV lung gene therapy toward clinical success. Bolstered with an improved understanding of AAV biology and more clinically relevant lung models, next-generation molecular biology and bioinformatics approaches have given rise to novel AAV capsid variants that offer improvements in transduction efficiency, immunological profile, and the ability to circumvent physical barriers in the lung such as mucus. This review discusses the principal limiting barriers to clinical success in lung gene therapy and focuses on novel engineered AAV capsid variants that have been developed to overcome those challenges.
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Affiliation(s)
- Ana Carneiro
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Hyuncheol Lee
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA
| | - Li Lin
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Joost van Haasteren
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA
| | - David V Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA.,Department of Bioengineering, University of California, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.,Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA.,Innovative Genomics Institute (IGI), University of California, Berkeley, California, USA
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13
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King NE, Suzuki S, Barillà C, Hawkins FJ, Randell SH, Reynolds SD, Stripp BR, Davis BR. Correction of Airway Stem Cells: Genome Editing Approaches for the Treatment of Cystic Fibrosis. Hum Gene Ther 2020; 31:956-972. [PMID: 32741223 PMCID: PMC7495916 DOI: 10.1089/hum.2020.160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by variations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although CF affects multiple organs, the primary cause of mortality is respiratory failure resulting from poor clearance of hyperviscous secretions and subsequent airway infection. Recently developed CFTR modulators provide significant therapeutic benefit to the majority of CF individuals. However, treatments directed at the underlying cause are needed for the ∼7% of CF patients who are not expected to be responsive to these modulators. Genome editing can restore the native CFTR genetic sequence and function to mutant cells, representing an approach to establish durable physiologic CFTR correction. Although editing the CFTR gene in various airway cell types may transiently restore CFTR activity, effort is focused on editing airway basal stem/progenitor cells, since their correction would allow appropriate and durable expression of CFTR in stem cell-derived epithelial cell types. Substantial progress has been made to directly correct airway basal cells in vitro, theoretically enabling transplantation of autologous corrected cells to regenerate an airway with CFTR functional cells. Another approach to create autologous, gene-edited airway basal cells is derivation of CF donor-specific induced pluripotent stem cells, correction of the CFTR gene, and subsequent directed differentiation to airway basal cells. Further work is needed to translate these advances by developing effective transplantation methods. Alternatively, gene editing in vivo may enable CFTR correction. However, this approach will require robust delivery methods ensuring that basal cells are efficiently targeted and corrected. Recent advances in gene editing-based therapies provide hope that the genetic underpinning of CF can be durably corrected in airway epithelial stem cells, thereby preventing or treating lung disease in all people with CF.
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Affiliation(s)
- Nicholas E. King
- Center for Stem Cell and Regenerative Medicine, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Shingo Suzuki
- Center for Stem Cell and Regenerative Medicine, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Cristina Barillà
- Center for Stem Cell and Regenerative Medicine, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Finn J. Hawkins
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Scott H. Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Susan D. Reynolds
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Barry R. Stripp
- Lung and Regenerative Medicine Institutes, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Brian R. Davis
- Center for Stem Cell and Regenerative Medicine, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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14
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Tay LS, Palmer N, Panwala R, Chew WL, Mali P. Translating CRISPR-Cas Therapeutics: Approaches and Challenges. CRISPR J 2020; 3:253-275. [PMID: 32833535 PMCID: PMC7469700 DOI: 10.1089/crispr.2020.0025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
CRISPR-Cas clinical trials have begun, offering a first glimpse at how DNA and RNA targeting could enable therapies for many genetic and epigenetic human diseases. The speedy progress of CRISPR-Cas from discovery and adoption to clinical use is built on decades of traditional gene therapy research and belies the multiple challenges that could derail the successful translation of these new modalities. Here, we review how CRISPR-Cas therapeutics are translated from technological systems to therapeutic modalities, paying particular attention to the therapeutic cascade from cargo to delivery vector, manufacturing, administration, pipelines, safety, and therapeutic target profiles. We also explore potential solutions to some of the obstacles facing successful CRISPR-Cas translation. We hope to illuminate how CRISPR-Cas is brought from the academic bench toward use in the clinic.
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Affiliation(s)
- Lavina Sierra Tay
- Laboratory of Synthetic Biology and Genome Editing Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Nathan Palmer
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Wei Leong Chew
- Laboratory of Synthetic Biology and Genome Editing Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
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15
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Tse LV, Meganck RM, Graham RL, Baric RS. The Current and Future State of Vaccines, Antivirals and Gene Therapies Against Emerging Coronaviruses. Front Microbiol 2020; 11:658. [PMID: 32390971 PMCID: PMC7193113 DOI: 10.3389/fmicb.2020.00658] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
Emerging coronaviruses (CoV) are constant global public health threats to society. Multiple ongoing clinical trials for vaccines and antivirals against CoVs showcase the availability of medical interventions to both prevent and treat the future emergence of highly pathogenic CoVs in human. However, given the diverse nature of CoVs and our close interactions with wild, domestic and companion animals, the next epidemic zoonotic CoV could resist the existing vaccines and antivirals developed, which are primarily focused on Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS CoV). In late 2019, the novel CoV (SARS-CoV-2) emerged in Wuhan, China, causing global public health concern. In this review, we will summarize the key advancements of current vaccines and antivirals against SARS-CoV and MERS-CoV as well as discuss the challenge and opportunity in the current SARS-CoV-2 crisis. At the end, we advocate the development of a "plug-and-play" platform technologies that could allow quick manufacturing and administration of broad-spectrum countermeasures in an outbreak setting. We will discuss the potential of AAV-based gene therapy technology for in vivo therapeutic antibody delivery to combat SARS-CoV-2 outbreak and the future emergence of severe CoVs.
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Affiliation(s)
- Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rita M. Meganck
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rachel L. Graham
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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16
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Wang D, Tai PWL, Gao G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat Rev Drug Discov 2019; 18:358-378. [PMID: 30710128 DOI: 10.1038/s41573-019-0012-9] [Citation(s) in RCA: 1163] [Impact Index Per Article: 232.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Adeno-associated virus (AAV) vectors are the leading platform for gene delivery for the treatment of a variety of human diseases. Recent advances in developing clinically desirable AAV capsids, optimizing genome designs and harnessing revolutionary biotechnologies have contributed substantially to the growth of the gene therapy field. Preclinical and clinical successes in AAV-mediated gene replacement, gene silencing and gene editing have helped AAV gain popularity as the ideal therapeutic vector, with two AAV-based therapeutics gaining regulatory approval in Europe or the United States. Continued study of AAV biology and increased understanding of the associated therapeutic challenges and limitations will build the foundation for future clinical success.
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Affiliation(s)
- Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA. .,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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17
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Xu M, Li J, Xie J, He R, Su Q, Gao G, Tai PW. High-Throughput Quantification of In Vivo Adeno-Associated Virus Transduction with Barcoded Non-Coding RNAs. Hum Gene Ther 2019; 30:946-956. [PMID: 31072208 PMCID: PMC6703241 DOI: 10.1089/hum.2018.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) have become favorable gene delivery vehicles for expressing therapeutic transgenes. Capsid engineering efforts to produce novel AAVs with improved transduction efficiencies, unique tissue specificities, and reduced host immunities are a direct response to the high demand for treatment needs that preexisting rAAVs cannot currently fulfill. New AAV capsids discovered by directed evolution methods, in silico design, or from natural proviral sequences ultimately require extensive characterization in relevant in vivo models. Consequently, quantitative screening of candidate capsid libraries now requires reliable high-throughput sequencing approaches. In this study, we have developed a vector/transgene tracking system that employs the indexing of a non-coding RNA. Specifically, a barcoded Tough Decoy (bcTuD) that express highly stable RNA transcripts that can be used as readouts for transduction efficiency. The pseudo-hairpin structure of the bcTuD contains a variable region that is amenable to barcode insertion, which can be detected by target amplicon sequencing. The described approach, named AAV-bcTuD screening, offers a new alternative for in vivo assessment of rAAV that can accurately quantify vector genomes and transcript abundances in tissues, as exampled by the demonstration in liver and brain infections. Proof-of-concept is provided to show that vector genome and transcript detection in tissues with this method is accurate and consistent for a vector dose range of upwards to four logs in a mixed vector injection, showing that this technique is robust, sensitive, and applicable for multiplexed screening of capsid performance in vivo.
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Affiliation(s)
- Meiyu Xu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Ran He
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
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18
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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: 195] [Impact Index Per Article: 39.0] [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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19
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Zhou ZP, Yang LL, Cao H, Chen ZR, Zhang Y, Wen XY, Hu J. In Vitro Validation of a CRISPR-Mediated CFTR Correction Strategy for Preclinical Translation in Pigs. Hum Gene Ther 2019; 30:1101-1116. [PMID: 31099266 DOI: 10.1089/hum.2019.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Early efforts in cystic fibrosis (CF) gene therapy faced major challenges in delivery efficiency and sustained therapeutic gene expression. Recent advancements in engineered site-specific endonucleases such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 make permanent CF transmembrane conductance regulator (CFTR) gene correction possible. However, because of safety concerns of the CRISPR/Cas9 system and challenges in in vivo delivery to inflamed CF airway, CRISPR-based gene correction strategies need to be tested in proper animal models. In this study, we aimed at creating vectors for testing CFTR gene correction in pig models. We constructed helper-dependent adenoviral (HD-Ad) vectors to deliver CRISPR/Cas9 and a donor template (a 6 kb LacZ or 8.7 kb human CFTR expression cassette) into cultured pig cells. We demonstrated precise integration of each donor into the GGTA1 safe harbor through Cas9-induced homology directed repair with 3 kb homology arms. In addition, we showed that both LacZ and hCFTR were persistently expressed in transduced cells. Furthermore, we created a CFTR-deficient cell line for testing CFTR correction. We detected hCFTR mRNA and protein expression in cells transduced with the hCFTR vector. We also demonstrated CFTR function in the CF cells transduced with the HD-Ad delivering the CRISPR-Cas9 system and hCFTR donor at late cellular passages using the membrane potential sensitive dye-based assay (FLIPR®). Combined with our previous report on gene delivery to pig airway basal cells, these data provide the feasibility of testing CRISPR/Cas9-mediated permanent human CFTR correction through HD-Ad vector delivery in pigs.
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Affiliation(s)
- Zhichang Peter Zhou
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada.,Zebrafish Centre for Advanced Drug Discovery and Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada
| | - Liang Leo Yang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Huibi Cao
- Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Ziyan Rachel Chen
- Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Yiqian Zhang
- Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Xiao-Yan Wen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Zebrafish Centre for Advanced Drug Discovery and Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Canada.,Department of Medicine, Physiology and Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Jim Hu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Program of Translational Medicine, The Hospital for Sick Children, Toronto, Canada
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20
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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: 76] [Impact Index Per Article: 12.7] [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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21
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Farraha M, Kumar S, Chong J, Cho HC, Kizana E. Gene Therapy Approaches to Biological Pacemakers. J Cardiovasc Dev Dis 2018; 5:jcdd5040050. [PMID: 30347716 PMCID: PMC6306875 DOI: 10.3390/jcdd5040050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 01/01/2023] Open
Abstract
Bradycardia arising from pacemaker dysfunction can be debilitating and life threatening. Electronic pacemakers serve as effective treatment options for pacemaker dysfunction. They however present their own limitations and complications. This has motivated research into discovering more effective and innovative ways to treat pacemaker dysfunction. Gene therapy is being explored for its potential to treat various cardiac conditions including cardiac arrhythmias. Gene transfer vectors with increasing transduction efficiency and biosafety have been developed and trialed for cardiovascular disease treatment. With an improved understanding of the molecular mechanisms driving pacemaker development, several gene therapy targets have been identified to generate the phenotypic changes required to correct pacemaker dysfunction. This review will discuss the gene therapy vectors in use today along with methods for their delivery. Furthermore, it will evaluate several gene therapy strategies attempting to restore biological pacing, having the potential to emerge as viable therapies for pacemaker dysfunction.
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Affiliation(s)
- Melad Farraha
- Centre for Heart Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Saurabh Kumar
- Department of Cardiology, Westmead Hospital, Westmead, NSW 2145, Australia.
| | - James Chong
- Centre for Heart Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
- Department of Cardiology, Westmead Hospital, Westmead, NSW 2145, Australia.
| | - Hee Cheol Cho
- Departments of Pediatrics and Biomedical Engineering, Emory University, Atlanta, GA 30322, USA.
| | - Eddy Kizana
- Centre for Heart Research, the Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
- Department of Cardiology, Westmead Hospital, Westmead, NSW 2145, Australia.
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22
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van Haasteren J, Hyde SC, Gill DR. Lessons learned from lung and liver in-vivo gene therapy: implications for the future. Expert Opin Biol Ther 2018; 18:959-972. [PMID: 30067117 PMCID: PMC6134476 DOI: 10.1080/14712598.2018.1506761] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/27/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Ex-vivo gene therapy has had significant clinical impact over the last couple of years and in-vivo gene therapy products are being approved for clinical use. Gene therapy and gene editing approaches have huge potential to treat genetic disease and chronic illness. AREAS COVERED This article provides a review of in-vivo approaches for gene therapy in the lung and liver, exploiting non-viral and viral vectors with varying serotypes and pseudotypes to target-specific cells. Antibody responses inhibiting viral vectors continue to constrain effective repeat administration. Lessons learned from ex-vivo gene therapy and genome editing are also discussed. EXPERT OPINION The fields of lung and liver in-vivo gene therapy are thriving and a comparison highlights obstacles and opportunities for both. Overcoming immunological issues associated with repeated administration of viral vectors remains a key challenge. The addition of targeted small molecules in combination with viral vectors may offer one solution. A substantial bottleneck to the widespread adoption of in-vivo gene therapy is how to ensure sufficient capacity for clinical-grade vector production. In the future, the exploitation of gene editing approaches for in-vivo disease treatment may facilitate the resurgence of non-viral gene transfer approaches, which tend to be eclipsed by more efficient viral vectors.
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Affiliation(s)
- Joost van Haasteren
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Science, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen C. Hyde
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Science, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Deborah R. Gill
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Science, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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23
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Steines B, Dickey DD, Bergen J, Excoffon KJ, Weinstein JR, Li X, Yan Z, Abou Alaiwa MH, Shah VS, Bouzek DC, Powers LS, Gansemer ND, Ostedgaard LS, Engelhardt JF, Stoltz DA, Welsh MJ, Sinn PL, Schaffer DV, Zabner J. CFTR gene transfer with AAV improves early cystic fibrosis pig phenotypes. JCI Insight 2016; 1:e88728. [PMID: 27699238 DOI: 10.1172/jci.insight.88728] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The physiological components that contribute to cystic fibrosis (CF) lung disease are steadily being elucidated. Gene therapy could potentially correct these defects. CFTR-null pigs provide a relevant model to test gene therapy vectors. Using an in vivo selection strategy that amplifies successful capsids by replicating their genomes with helper adenovirus coinfection, we selected an adeno-associated virus (AAV) with tropism for pig airway epithelia. The evolved capsid, termed AAV2H22, is based on AAV2 with 5 point mutations that result in a 240-fold increased infection efficiency. In contrast to AAV2, AAV2H22 binds specifically to pig airway epithelia and is less reliant on heparan sulfate for transduction. We administer AAV2H22-CFTR expressing the CF transmembrane conductance regulator (CFTR) cDNA to the airways of CF pigs. The transduced airways expressed CFTR on ciliated and nonciliated cells, induced anion transport, and improved the airway surface liquid pH and bacterial killing. Most gene therapy studies to date focus solely on Cl- transport as the primary metric of phenotypic correction. Here, we describe a gene therapy experiment where we not only correct defective anion transport, but also restore bacterial killing in CFTR-null pig airways.
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Affiliation(s)
- Benjamin Steines
- Department of Internal Medicine.,Molecular and Cellular Biology Program, and.,Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - David D Dickey
- Department of Internal Medicine.,Molecular and Cellular Biology Program, and
| | - Jamie Bergen
- Departments of Chemical and Biomolecular Engineering, Bioengineering, The Helen Wills Neuroscience Institute, Molecular and Cellular Biology, University of California, Berkeley, California, USA
| | | | - John R Weinstein
- Departments of Chemical and Biomolecular Engineering, Bioengineering, The Helen Wills Neuroscience Institute, Molecular and Cellular Biology, University of California, Berkeley, California, USA
| | - Xiaopeng Li
- Department of Internal Medicine.,Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | | | - Mahmoud H Abou Alaiwa
- Department of Internal Medicine.,Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Viral S Shah
- Department of Internal Medicine.,Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | | | | | | | - Lynda S Ostedgaard
- Department of Internal Medicine.,Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | | | - David A Stoltz
- Department of Internal Medicine.,Molecular and Cellular Biology Program, and.,Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Michael J Welsh
- Department of Internal Medicine.,Molecular and Cellular Biology Program, and.,Molecular Physiology and Biophysics
| | - Patrick L Sinn
- Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA.,Howard Hughes Medical Institute, and
| | - David V Schaffer
- Departments of Chemical and Biomolecular Engineering, Bioengineering, The Helen Wills Neuroscience Institute, Molecular and Cellular Biology, University of California, Berkeley, California, USA
| | - Joseph Zabner
- Department of Internal Medicine.,Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
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24
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Kim N, Duncan GA, Hanes J, Suk JS. Barriers to inhaled gene therapy of obstructive lung diseases: A review. J Control Release 2016; 240:465-488. [PMID: 27196742 DOI: 10.1016/j.jconrel.2016.05.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022]
Abstract
Knowledge of genetic origins of obstructive lung diseases has made inhaled gene therapy an attractive alternative to the current standards of care that are limited to managing disease symptoms. Initial lung gene therapy clinical trials occurred in the early 1990s following the discovery of the genetic defect responsible for cystic fibrosis (CF), a monogenic disorder. However, despite over two decades of intensive effort, gene therapy has yet to help patients with CF or any other obstructive lung disease. The slow progress is due in part to poor understanding of the biological barriers to inhaled gene therapy. Encouragingly, clinical trials have shown that inhaled gene therapy with various viral vectors and non-viral gene vectors is well tolerated by patients, and continued research has provided valuable lessons and resources that may lead to future success of this therapeutic strategy. In this review, we first introduce representative obstructive lung diseases and examine limitations of currently available therapeutic options. We then review key components for successful execution of inhaled gene therapy, including gene delivery systems, primary physiological barriers and strategies to overcome them, and advances in preclinical disease models with which the most promising systems may be identified for human clinical trials.
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Affiliation(s)
- Namho Kim
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregg A Duncan
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Justin Hanes
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Environmental and Health Sciences, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neurosurgery, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jung Soo Suk
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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25
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Pulmonary Targeting of Adeno-associated Viral Vectors by Next-generation Sequencing-guided Screening of Random Capsid Displayed Peptide Libraries. Mol Ther 2016; 24:1050-1061. [PMID: 27018516 DOI: 10.1038/mt.2016.62] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 03/16/2016] [Indexed: 12/31/2022] Open
Abstract
Vectors mediating strong, durable, and tissue-specific transgene expression are mandatory for safe and effective gene therapy. In settings requiring systemic vector administration, the availability of suited vectors is extremely limited. Here, we present a strategy to select vectors with true specificity for a target tissue from random peptide libraries displayed on adeno-associated virus (AAV) by screening the library under circulation conditions in a murine model. Guiding the in vivo screening by next-generation sequencing, we were able to monitor the selection kinetics and to determine the right time point to discontinue the screening process. The establishment of different rating scores enabled us to identify the most specifically enriched AAV capsid candidates. As proof of concept, a capsid variant was selected that specifically and very efficiently delivers genes to the endothelium of the pulmonary vasculature after intravenous administration. This technical approach of selecting target-specific vectors in vivo is applicable to any given tissue of interest and therefore has broad implications in translational research and medicine.
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Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene was identified in 1989. This opened the door for the development of cystic fibrosis (CF) gene therapy, which has been actively pursued for the last 20 years. Although 26 clinical trials involving approximately 450 patients have been carried out, the vast majority of these trials were short and included small numbers of patients; they were not designed to assess clinical benefit, but to establish safety and proof-of-concept for gene transfer using molecular end points such as the detection of recombinant mRNA or correction of the ion transport defect. The only currently published trial designed and powered to assess clinical efficacy (defined as improvement in lung function) administered AAV2-CFTR to the lungs of patients with CF. The U.K. Cystic Fibrosis Gene Therapy Consortium completed, in the autumn of 2014, the first nonviral gene therapy trial designed to answer whether repeated nonviral gene transfer (12 doses over 12 months) can lead to clinical benefit. The demonstration that the molecular defect in CFTR can be corrected with small-molecule drugs, and the success of gene therapy in other monogenic diseases, is boosting interest in CF gene therapy. Developments are discussed here.
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Affiliation(s)
- Uta Griesenbach
- Department of Gene Therapy and the U.K. Cystic Fibrosis Gene Therapy Consortium, Imperial College, London SW3 6LR, United Kingdom
| | - Kamila M Pytel
- Department of Gene Therapy and the U.K. Cystic Fibrosis Gene Therapy Consortium, Imperial College, London SW3 6LR, United Kingdom
| | - Eric W F W Alton
- Department of Gene Therapy and the U.K. Cystic Fibrosis Gene Therapy Consortium, Imperial College, London SW3 6LR, United Kingdom
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27
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Li C, Wu S, Albright B, Hirsch M, Li W, Tseng YS, Agbandje-McKenna M, McPhee S, Asokan A, Samulski RJ. Development of Patient-specific AAV Vectors After Neutralizing Antibody Selection for Enhanced Muscle Gene Transfer. Mol Ther 2016; 24:53-65. [PMID: 26220272 PMCID: PMC4754536 DOI: 10.1038/mt.2015.134] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/18/2015] [Indexed: 01/07/2023] Open
Abstract
A major hindrance in gene therapy trials with adeno-associated virus (AAV) vectors is the presence of neutralizing antibodies (NAbs) that inhibit AAV transduction. In this study, we used directed evolution techniques in vitro and in mouse muscle to select novel NAb escape AAV chimeric capsid mutants in the presence of individual patient serum. AAV mutants isolated in vitro escaped broad patient-specific NAb activity but had poor transduction ability in vivo. AAV mutants isolated in vivo had enhanced NAb evasion from cognate serum and had high muscle transduction ability. More importantly, structural modeling identified a 100 amino acid motif from AAV6 in variable region (VR) III that confers this enhanced muscle tropism. In addition, a predominantly AAV8 capsid beta barrel template with a specific preference for AAV1/AAV9 in VR VII located at threefold symmetry axis facilitates NAb escape. Our data strongly support that chimeric AAV capsids composed of modular and nonoverlapping domains from various serotypes are capable of evading patient-specific NAbs and have enhanced muscle transduction.
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Affiliation(s)
- Chengwen Li
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shuqing Wu
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- China National Academy of Nanotechnology & Engineering, Tianjin, China
| | - Blake Albright
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew Hirsch
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wuping Li
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu-Shan Tseng
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Scott McPhee
- Asklepios BioPharmaceutical Inc., Chapel Hill, North Carolina, USA
| | - Aravind Asokan
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - R Jude Samulski
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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28
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GDNF and AADC Gene Therapy for Parkinson’s Disease. Transl Neurosci 2016. [DOI: 10.1007/978-1-4899-7654-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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29
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Castle MJ, Turunen HT, Vandenberghe LH, Wolfe JH. Controlling AAV Tropism in the Nervous System with Natural and Engineered Capsids. Methods Mol Biol 2016; 1382:133-49. [PMID: 26611584 PMCID: PMC4993104 DOI: 10.1007/978-1-4939-3271-9_10] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
More than one hundred naturally occurring variants of adeno-associated virus (AAV) have been identified, and this library has been further expanded by an array of techniques for modification of the viral capsid. AAV capsid variants possess unique antigenic profiles and demonstrate distinct cellular tropisms driven by differences in receptor binding. AAV capsids can be chemically modified to alter tropism, can be produced as hybrid vectors that combine the properties of multiple serotypes, and can carry peptide insertions that introduce novel receptor-binding activity. Furthermore, directed evolution of shuffled genome libraries can identify engineered variants with unique properties, and rational modification of the viral capsid can alter tropism, reduce blockage by neutralizing antibodies, or enhance transduction efficiency. This large number of AAV variants and engineered capsids provides a varied toolkit for gene delivery to the CNS and retina, with specialized vectors available for many applications, but selecting a capsid variant from the array of available vectors can be difficult. This chapter describes the unique properties of a range of AAV variants and engineered capsids, and provides a guide for selecting the appropriate vector for specific applications in the CNS and retina.
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Affiliation(s)
- Michael J Castle
- Research Institute of the Children's Hospital of Philadelphia, 502-G Abramson Pediatric Research Building, 3615 Civic Center Boulevard, Philadelphia, PA, 19104, USA
- Department of Neurosciences, University of California-San Diego, La Jolla, CA, 92093, USA
| | - Heikki T Turunen
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Luk H Vandenberghe
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - John H Wolfe
- Research Institute of the Children's Hospital of Philadelphia, 502-G Abramson Pediatric Research Building, 3615 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- W.F. Goodman Center for Comparative Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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30
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Hastie E, Samulski RJ. Adeno-associated virus at 50: a golden anniversary of discovery, research, and gene therapy success--a personal perspective. Hum Gene Ther 2015; 26:257-65. [PMID: 25807962 DOI: 10.1089/hum.2015.025] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Fifty years after the discovery of adeno-associated virus (AAV) and more than 30 years after the first gene transfer experiment was conducted, dozens of gene therapy clinical trials are in progress, one vector is approved for use in Europe, and breakthroughs in virus modification and disease modeling are paving the way for a revolution in the treatment of rare diseases, cancer, as well as HIV. This review will provide a historical perspective on the progression of AAV for gene therapy from discovery to the clinic, focusing on contributions from the Samulski lab regarding basic science and cloning of AAV, optimized large-scale production of vectors, preclinical large animal studies and safety data, vector modifications for improved efficacy, and successful clinical applications.
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Affiliation(s)
- Eric Hastie
- 1Gene Therapy Center, University of North Carolina, Chapel Hill, NC 27599-7352
| | - R Jude Samulski
- 1Gene Therapy Center, University of North Carolina, Chapel Hill, NC 27599-7352.,2Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599-7352
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31
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Yan Z, Sun X, Feng Z, Li G, Fisher JT, Stewart ZA, Engelhardt JF. Optimization of Recombinant Adeno-Associated Virus-Mediated Expression for Large Transgenes, Using a Synthetic Promoter and Tandem Array Enhancers. Hum Gene Ther 2015; 26:334-46. [PMID: 25763813 DOI: 10.1089/hum.2015.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The packaging capacity of recombinant adeno-associated viral (rAAV) vectors limits the size of the promoter that can be used to express the 4.43-kb cystic fibrosis transmembrane conductance regulator (CFTR) cDNA. To circumvent this limitation, we screened a set of 100-mer synthetic enhancer elements, composed of ten 10-bp repeats, for their ability to augment CFTR transgene expression from a short 83-bp synthetic promoter in the context of an rAAV vector designed for use in the cystic fibrosis (CF) ferret model. Our initial studies assessing transcriptional activity in monolayer (nonpolarized) cultures of human airway cell lines and primary ferret airway cells revealed that three of these synthetic enhancers (F1, F5, and F10) significantly promoted transcription of a luciferase transgene in the context of plasmid transfection. Further analysis in polarized cultures of human and ferret airway epithelia at an air-liquid interface (ALI), as well as in the ferret airway in vivo, demonstrated that the F5 enhancer produced the highest level of transgene expression in the context of an AAV vector. Furthermore, we demonstrated that increasing the size of the viral genome from 4.94 to 5.04 kb did not significantly affect particle yield of the vectors, but dramatically reduced the functionality of rAAV-CFTR vectors because of small terminal deletions that extended into the CFTR expression cassette of the 5.04-kb oversized genome. Because rAAV-CFTR vectors greater than 5 kb in size are dramatically impaired with respect to vector efficacy, we used a shortened ferret CFTR minigene with a 159-bp deletion in the R domain to construct an rAAV vector (AV2/2.F5tg83-fCFTRΔR). This vector yielded an ∼17-fold increase in expression of CFTR and significantly improved Cl(-) currents in CF ALI cultures. Our study has identified a small enhancer/promoter combination that may have broad usefulness for rAAV-mediated CF gene therapy to the airway.
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Affiliation(s)
- Ziying Yan
- 1 Department of Anatomy and Cell Biology, University of Iowa School of Medicine , Iowa City, IA 52242.,2 Center for Gene Therapy, University of Iowa School of Medicine , Iowa City, IA 52242
| | - Xingshen Sun
- 1 Department of Anatomy and Cell Biology, University of Iowa School of Medicine , Iowa City, IA 52242
| | - Zehua Feng
- 1 Department of Anatomy and Cell Biology, University of Iowa School of Medicine , Iowa City, IA 52242
| | - Guiying Li
- 3 Department of Surgery, University of Iowa School of Medicine , Iowa City, IA 52242
| | - John T Fisher
- 1 Department of Anatomy and Cell Biology, University of Iowa School of Medicine , Iowa City, IA 52242
| | - Zoe A Stewart
- 3 Department of Surgery, University of Iowa School of Medicine , Iowa City, IA 52242
| | - John F Engelhardt
- 1 Department of Anatomy and Cell Biology, University of Iowa School of Medicine , Iowa City, IA 52242.,2 Center for Gene Therapy, University of Iowa School of Medicine , Iowa City, IA 52242.,4 Department of Internal Medicine, University of Iowa School of Medicine , Iowa City, IA 52242
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32
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Sen D. Improving clinical efficacy of adeno associated vectors by rational capsid bioengineering. J Biomed Sci 2014; 21:103. [PMID: 25425174 PMCID: PMC4251935 DOI: 10.1186/s12929-014-0103-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/10/2014] [Indexed: 11/13/2022] Open
Abstract
Adeno associated vectors (AAV) have shown considerable promise to treat various genetic disorders in both preclinical and clinical settings mainly because of its safety profile. However, efficient use of AAV to deliver genes in immune-competent sites like muscles and liver requires very high doses which are associated with concomitant cellular immune response against the viral capsids leading to destruction of the transduced cells. Coupled with that, there are enough evidences that at high doses, AAV particles are subjected to increased cellular phosphorylation/uniquitination leading to proteasome mediated degradation and loss of the viral particles. The presence of preexisting immunity against AAV further adds on to the problem which is acting as a major roadblock to efficiently use it as a gene therapy vector in the clinics. To overcome this, rational bioengineering of AAV capsid becomes a prime tool by which specific amino acid residue(s) can be suitably modified/replaced by compatible residue(s) to create vectors having lower host immune response and higher intracellular trafficking rate. This article reviews the various aspects of rationally designing AAV capsids like by site-directed mutagenesis, directed evolution and combinatorial libraries which can create vectors having not only immune evasive property but also enhanced gene expression and transduction capability. One or more combinations of these strategies have strong potential to create novel vectors which will have suitable clinical efficiency even at a low dose.
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Affiliation(s)
- Dwaipayan Sen
- School of Biosciences and Technology, Vellore Institute of Technology (VIT) University, Vellore, 632014, Tamil Nadu, India.
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33
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Manzano-Szalai K, Thell K, Willensdorfer A, Weghofer M, Pfanzagl B, Singer J, Ritter M, Stremnitzer C, Flaschberger I, Michaelis U, Jensen-Jarolim E. Adeno-associated virus-like particles as new carriers for B-cell vaccines: testing immunogenicity and safety in BALB/c mice. Viral Immunol 2014; 27:438-48. [PMID: 25247267 DOI: 10.1089/vim.2014.0059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Adeno-associated viruses (AAVs) are established vectors for gene therapy of different human diseases. AAVs are assembled of 60 capsomers, which can be genetically modified, allowing high-density display of short peptide sequences at their surface. The aim of our study was to evaluate the immunogenicity and safety of an adeno-associated virus-like particle (AAVLP)-displayed B-cell peptide epitope taking ovalbumin (OVA) as a model antigen or allergen from egg, respectively. An OVA-derived B-cell epitope was expressed as fusion protein with the AAV-2 capsid protein of VP3 (AAVLP-OVA) and for control, with the nonrelated peptide TP18 (AAVLP-TP18). Cellular internalization studies revealed an impaired uptake of AAVLP-OVA by mouse BMDC, macrophages, and human HeLa cells. Nevertheless, BALB/c mice immunized subcutaneously with AAVLP-OVA formed similarly high titers of OVA-specific IgG1 compared to mice immunized with the native OVA. The extent of the immune response was independent whether aluminum hydroxide or water in oil emulsion was used as adjuvant. Furthermore, in mice immunized with native OVA, high OVA-specific IgE levels were observed, which permitted OVA-specific mast-cell degranulation in a β-hexosaminidase release assay, whereas immunizations with AAVLP-OVA rendered background IgE levels only. Accordingly, OVA-immunized mice, but not AAVLP-OVA immunized mice, displayed an anaphylactic reaction with a significant drop of body temperature upon intravenous OVA challenge. From this mouse model, we conclude that AAVLPs that display B-cell epitope peptides on their surface are suitable vaccine candidates, especially in the field of allergy.
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Affiliation(s)
- Krisztina Manzano-Szalai
- 1 Comparative Medicine, Messerli Research Institute, University of Veterinary Medicine Vienna , Medical University of Vienna and University of Vienna, Vienna, Austria
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34
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Abstract
Gene therapy has been considered as the most ideal medical intervention for genetic diseases because it is intended to target the cause of diseases instead of disease symptoms. Availability of techniques for identification of genetic mutations and for in vitro manipulation of genes makes it practical and attractive. After the initial hype in 1990s and later disappointments in clinical trials for more than a decade, light has finally come into the tunnel in recent years, especially in the field of eye gene therapy where it has taken big strides. Clinical trials in gene therapy for retinal degenerative diseases such as Leber's congenital amaurosis (LCA) and choroideremia demonstrated clear therapeutic efficacies without apparent side effects. Although these successful examples are still rare and sporadic in the field, they provide the proof of concept for harnessing the power of gene therapy to treat genetic diseases and to modernize our medication. In addition, those success stories illuminate the path for the development of gene therapy treating other genetic diseases. Because of the differences in target organs and cells, distinct barriers to gene delivery exist in gene therapy for each genetic disease. It is not feasible for authors to review the current development in the entire field. Thus, in this article, we will focus on what we can learn from the current success in gene therapy for retinal degenerative diseases to speed up the gene therapy development for lung diseases, such as cystic fibrosis.
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35
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Drouin LM, Agbandje-McKenna M. Adeno-associated virus structural biology as a tool in vector development. Future Virol 2013; 8:1183-1199. [PMID: 24533032 PMCID: PMC3921901 DOI: 10.2217/fvl.13.112] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adeno-associated viruses (AAVs) have become important therapeutic gene delivery vectors in recent years. However, there are challenges, including intractable tissues/cell types and pre-existing immune responses, which need to be overcome for full realization of this system. This review addresses strategies aimed at improving AAV efficacy in the clinic through the creation of hybrid vectors that display altered or more targeted specific tissue tropisms, while also escaping recognition from host-derived neutralizing antibodies. Characterization of these viruses with respect to serotypes contributing to their capsid, using available 3D structures, enables the identification of regions critical for particular tropism and antigenic phenotypes. Structural information also allows for rational design of vectors with specific targeted tropisms for improved therapeutic efficacy.
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Affiliation(s)
- Lauren M Drouin
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, 1600 SW Archer Road, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, 1600 SW Archer Road, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
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A novel chimeric adenoassociated virus 2/human bocavirus 1 parvovirus vector efficiently transduces human airway epithelia. Mol Ther 2013; 21:2181-94. [PMID: 23896725 DOI: 10.1038/mt.2013.92] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/11/2013] [Indexed: 12/30/2022] Open
Abstract
Human bocavirus virus-1 (HBoV1), a newly discovered autonomous parvovirus with a 5,500 nt genome, efficiently infects human-polarized airway epithelia (HAE) from the apical membrane. We hypothesized that the larger genome and high airway tropism of HBoV1 would be ideal for creating a viral vector for lung gene therapy. To this end, we successfully generated recombinant HBoV1 (rHBoV1) from an open reading frames-disrupted rHBoV1 genome that efficiently transduces HAE from the apical surface. We next evaluated whether HBoV1 capsids could package oversized rAAV2 genomes. These studies created a rAAV2/HBoV1 chimeric virus (5.5 kb genome) capable of apically transducing HAE at 5.6- and 70-fold greater efficiency than rAAV1 or rAAV2 (4.7-kb genomes), respectively. Molecular studies demonstrated that viral uptake from the apical surface was significantly greater for rAAV2/HBoV1 than for rAAV2 or rAAV1, and that polarization of airway epithelial cells was required for HBoV1 capsid-mediated gene transfer. Furthermore, rAAV2/HBoV1-CFTR virus containing the full-length cystic fibrosis transmembrane conductance regulator (CFTR) gene coding sequence and the strong CBA promoter efficiently corrected CFTR-dependent chloride transport in cystic fibrosis (CF) HAE. In summary, using the combined advantages of AAV and HBoV1, we have developed a novel and promising viral vector for CF lung gene therapy and also potentially HBoV1 vaccine development.
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Capsid antibodies to different adeno-associated virus serotypes bind common regions. J Virol 2013; 87:9111-24. [PMID: 23760240 DOI: 10.1128/jvi.00622-13] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Interactions between viruses and the host antibody immune response are critical in the development and control of disease, and antibodies are also known to interfere with the efficacy of viral vector-based gene delivery. The adeno-associated viruses (AAVs) being developed as vectors for corrective human gene delivery have shown promise in clinical trials, but preexisting antibodies are detrimental to successful outcomes. However, the antigenic epitopes on AAV capsids remain poorly characterized. Cryo-electron microscopy and three-dimensional image reconstruction were used to define the locations of epitopes to which monoclonal fragment antibodies (Fabs) against AAV1, AAV2, AAV5, and AAV6 bind. Pseudoatomic modeling showed that, in each serotype, Fabs bound to a limited number of sites near the protrusions surrounding the 3-fold axes of the T=1 icosahedral capsids. For the closely related AAV1 and AAV6, a common Fab exhibited substoichiometric binding, with one Fab bound, on average, between two of the three protrusions as a consequence of steric crowding. The other AAV Fabs saturated the capsid and bound to the walls of all 60 protrusions, with the footprint for the AAV5 antibody extending toward the 5-fold axis. The angle of incidence for each bound Fab on the AAVs varied and resulted in significant differences in how much of each viral capsid surface was occluded beyond the Fab footprints. The AAV-antibody interactions showed a common set of footprints that overlapped some known receptor-binding sites and transduction determinants, thus suggesting potential mechanisms for virus neutralization by the antibodies.
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38
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Griesenbach U, Alton EWFW. Expert opinion in biological therapy: update on developments in lung gene transfer. Expert Opin Biol Ther 2013; 13:345-60. [DOI: 10.1517/14712598.2013.735656] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Huang Q, Deng X, Yan Z, Cheng F, Luo Y, Shen W, Lei-Butters DCM, Chen AY, Li Y, Tang L, Söderlund-Venermo M, Engelhardt JF, Qiu J. Establishment of a reverse genetics system for studying human bocavirus in human airway epithelia. PLoS Pathog 2012; 8:e1002899. [PMID: 22956907 PMCID: PMC3431310 DOI: 10.1371/journal.ppat.1002899] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/24/2012] [Indexed: 12/21/2022] Open
Abstract
Human bocavirus 1 (HBoV1) has been identified as one of the etiological agents of wheezing in young children with acute respiratory-tract infections. In this study, we have obtained the sequence of a full-length HBoV1 genome (including both termini) using viral DNA extracted from a nasopharyngeal aspirate of an infected patient, cloned the full-length HBoV1 genome, and demonstrated DNA replication, encapsidation of the ssDNA genome, and release of the HBoV1 virions from human embryonic kidney 293 cells. The HBoV1 virions generated from this cell line-based production system exhibits a typical icosahedral structure of approximately 26 nm in diameter, and is capable of productively infecting polarized primary human airway epithelia (HAE) from the apical surface. Infected HAE showed hallmarks of lung airway-tract injury, including disruption of the tight junction barrier, loss of cilia and epithelial cell hypertrophy. Notably, polarized HAE cultured from an immortalized airway epithelial cell line, CuFi-8 (originally derived from a cystic fibrosis patient), also supported productive infection of HBoV1. Thus, we have established a reverse genetics system and generated the first cell line-based culture system for the study of HBoV1 infection, which will significantly advance the study of HBoV1 replication and pathogenesis. Human bocavirus 1 (HBoV1) has been identified as one of the etiological agents of wheezing in young children with acute respiratory-tract infections. HBoV1 productively infects polarized primary human airway epithelia. However, no cell lines permissive to HBoV1 infection have yet been established. More importantly, the sequences at both ends of the HBoV1 genome have remained unknown. We have resolved both of these issues in this study. We have sequenced a full-length HBoV1 genome and cloned it into a plasmid. We further demonstrated that this HBoV1 plasmid replicated and produced viruses in human embryonic kidney 293 cells. Infection of these HBoV1 progeny virions produced obvious cytopathogenic effects in polarized human airway epithelia, which were represented by disruption of the epithelial barrier. Moreover, we identified an airway epithelial cell line supporting HBoV1 infection, when it was polarized. This is the first study to obtain the full-length HBoV1 genome, to demonstrate pathogenesis of HBoV1 infection in human airway epithelia, and to identify the first cell line to support productive HBoV1 infection.
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Affiliation(s)
- Qinfeng Huang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Xuefeng Deng
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Ziying Yan
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Fang Cheng
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Yong Luo
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Weiran Shen
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Diana C. M. Lei-Butters
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Aaron Yun Chen
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Yi Li
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Liang Tang
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | | | - John F. Engelhardt
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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40
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Abstract
rAAV vectors have emerged as one of the leading gene transfer systems in preclinical and clinical applications. Promising intrinsic features of this vector system are nonpathogenicity, high stability and low immunogenicity. Application of the vector system has been improved by simplifying the production procedure and by expanding the vector platform using alternative serotypes and vectors with artificial capsids (mosaic, hybrid or specifically engineered). The current limitations of the vector system are addressed based on the increasing knowledge on the virus-host interaction by further optimizing the capsid as well as the vector genome.
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41
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Recombinant adeno-associated virus: clinical application and development as a gene-therapy vector. Ther Deliv 2012; 3:835-56. [DOI: 10.4155/tde.12.63] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gene therapy is gaining momentum as a method of treating human disease. Initially conceived as a strategy to complement defective genes in monogenic disorders, the scope of gene therapy has expanded to encompass a variety of applications. Likewise, the molecular tools for gene delivery have evolved and diversified to meet these various therapeutic needs. Recombinant adeno-associated virus (rAAV) has made significant strides toward clinical application with an excellent safety profile and successes in several clinical trials. This review covers the basic biology of rAAV as a gene therapy vector as well as its advantages compared with other methods of gene delivery. The status of clinical trials utilizing rAAV is also discussed in detail. In conclusion, methods of engineering the vector to overcome challenges identified from these trials are covered, with emphasis on modification of the viral capsid to increase the tissue/cell-specific targeting and transduction efficiency.
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Distinct transduction difference between adeno-associated virus type 1 and type 6 vectors in human polarized airway epithelia. Gene Ther 2012; 20:328-37. [PMID: 22695783 PMCID: PMC3443503 DOI: 10.1038/gt.2012.46] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Of the many biologically isolated AAV serotypes, AAV1 and AAV6 share the highest degree of sequence homology, with only six different capsid residues. We compared the transduction efficiencies of rAAV1 and rAAV6 in primary polarized human airway epithelia (HAE) and found significant differences in their abilities to transduce epithelia from the apical and basolateral membranes. rAAV1 transduction was ~10-fold higher than rAAV6 following apical infection, while rAAV6 transduction was ~10-fold higher than rAAV1 following basolateral infection. Furthermore, rAAV6 demonstrated significant polarity of transduction (100-fold; basolateral≫apical), while rAAV1 transduced from both membranes with equal efficiency. To evaluate capsid residues responsible for the observed serotype differences, we mutated the six divergent amino acids either alone or in combination. Results from these studies demonstrated that capsid residues 418 and 513 most significantly controlled membrane polarity differences in transduction between serotypes, with the rAAV6-D418E/K513E mutant demonstrating decreased (~10-fold) basolateral transduction and the rAAV1-E418D/E513K mutant demonstrating a transduction polarity identical to rAAV6-WT. However, none of the rAAV6 mutants obtained apical transduction efficiencies of rAAV1-WT, suggesting that all six divergent capsid residues in AAV1 act in concert to improve apical transduction of HAE.
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43
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Asokan A, Schaffer DV, Jude Samulski R. The AAV vector toolkit: poised at the clinical crossroads. Mol Ther 2012; 20:699-708. [PMID: 22273577 PMCID: PMC3321598 DOI: 10.1038/mt.2011.287] [Citation(s) in RCA: 322] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/02/2011] [Indexed: 12/14/2022] Open
Abstract
The discovery of naturally occurring adeno-associated virus (AAV) isolates in different animal species and the generation of engineered AAV strains using molecular genetics tools have yielded a versatile AAV vector toolkit. Promising results in preclinical animal models of human disease spurred the much awaited transition toward clinical application, and early successes in phase I/II clinical trials for a broad spectrum of genetic diseases have recently been reported. As the gene therapy community forges ahead with cautious optimism, both preclinical and clinical studies using first generation AAV vectors have highlighted potential challenges. These include cross-species variation in vector tissue tropism and gene transfer efficiency, pre-existing humoral immunity to AAV capsids and vector dose-dependent toxicity in patients. A battery of second generation AAV vectors, engineered through rational and combinatorial approaches to address the aforementioned concerns, are now available. This review will provide an overview of preclinical studies with the ever-expanding AAV vector portfolio in large animal models and an update on new lead AAV vector candidates poised for clinical translation.
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Affiliation(s)
- Aravind Asokan
- Gene Therapy Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David V Schaffer
- Department of Chemical Engineering, University of California, Berkeley, California, USA
- The Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - R Jude Samulski
- Gene Therapy Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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44
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Abstract
Gene therapy vectors based on adeno-associated virus (AAV) are currently in clinical trials for numerous disease targets, such as muscular dystrophy, hemophilia, Parkinson's disease, Leber's congenital amaurosis and macular degeneration. Despite its considerable promise and emerging clinical success, several challenges impede the broader implementation of AAV gene therapy, including the prevalence of neutralizing antibodies in the human population, low transduction of a number of therapeutically relevant cell and tissue types, an inability to overcome physical and cellular barriers in vivo and a relatively limited carrying capacity. These challenges arise as the demands we place on AAV vectors are often different from or even at odds with the properties nature bestowed on their parent viruses. Viral-directed evolution-the iterative generation of large, diverse libraries of viral mutants and selection for variants with specific properties of interest-offers an approach to address these problems. Here we outline progress in creating novel classes of AAV variant libraries and highlight the successful isolation of variants with novel and advantageous in vitro and in vivo gene delivery properties.
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45
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Abstract
Parvoviruses package a ssDNA genome. Both nonpathogenic and pathogenic members exist, including those that cause fetal infections, encompassing the entire spectrum of virus phenotypes. Their small genomes and simple coding strategy has enabled functional annotation of many steps in the infectious life cycle. They assemble a multifunctional capsid responsible for cell recognition and the transport of the packaged genome to the nucleus for replication and progeny virus production. It is also the target of the host immune response. Understanding how the capsid structure relates to the function of parvoviruses provides a platform for recombinant engineering of viral gene delivery vectors for the treatment of clinical diseases, and is fundamental for dissecting the viral determinants of pathogenicity. This review focuses on our current understanding of parvovirus capsid structure and function with respect to the infectious life cycle.
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Affiliation(s)
- Sujata Halder
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, 1600 SW Archer Road, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
| | - Robert Ng
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, 1600 SW Archer Road, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, 1600 SW Archer Road, PO Box 100245, University of Florida, Gainesville, FL 32610, USA
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46
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Oakland M, Sinn PL, McCray PB. Advances in cell and gene-based therapies for cystic fibrosis lung disease. Mol Ther 2012; 20:1108-15. [PMID: 22371844 DOI: 10.1038/mt.2012.32] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis (CF) is a disease characterized by airway infection, inflammation, remodeling, and obstruction that gradually destroy the lungs. Direct delivery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene to airway epithelia may offer advantages, as the tissue is accessible for topical delivery of vectors. Yet, physical and host immune barriers in the lung present challenges for successful gene transfer to the respiratory tract. Advances in gene transfer approaches, tissue engineering, and novel animal models are generating excitement within the CF research field. This review discusses current challenges and advancements in viral and nonviral vectors, cell-based therapies, and CF animal models.
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Affiliation(s)
- Mayumi Oakland
- Department of Microbiology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA
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47
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Bowles DE, McPhee SWJ, Li C, Gray SJ, Samulski JJ, Camp AS, Li J, Wang B, Monahan PE, Rabinowitz JE, Grieger JC, Govindasamy L, Agbandje-McKenna M, Xiao X, Samulski RJ. Phase 1 gene therapy for Duchenne muscular dystrophy using a translational optimized AAV vector. Mol Ther 2012; 20:443-55. [PMID: 22068425 PMCID: PMC3277234 DOI: 10.1038/mt.2011.237] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 10/06/2011] [Indexed: 12/12/2022] Open
Abstract
Efficient and widespread gene transfer is required for successful treatment of Duchenne muscular dystrophy (DMD). Here, we performed the first clinical trial using a chimeric adeno-associated virus (AAV) capsid variant (designated AAV2.5) derived from a rational design strategy. AAV2.5 was generated from the AAV2 capsid with five mutations from AAV1. The novel chimeric vector combines the improved muscle transduction capacity of AAV1 with reduced antigenic crossreactivity against both parental serotypes, while keeping the AAV2 receptor binding. In a randomized double-blind placebo-controlled phase I clinical study in DMD boys, AAV2.5 vector was injected into the bicep muscle in one arm, with saline control in the contralateral arm. A subset of patients received AAV empty capsid instead of saline in an effort to distinguish an immune response to vector versus minidystrophin transgene. Recombinant AAV genomes were detected in all patients with up to 2.56 vector copies per diploid genome. There was no cellular immune response to AAV2.5 capsid. This trial established that rationally designed AAV2.5 vector was safe and well tolerated, lays the foundation of customizing AAV vectors that best suit the clinical objective (e.g., limb infusion gene delivery) and should usher in the next generation of viral delivery systems for human gene transfer.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Capsid Proteins/chemistry
- Capsid Proteins/genetics
- Capsid Proteins/immunology
- Cell Line
- Child
- Child, Preschool
- Dependovirus/genetics
- Dependovirus/physiology
- Dystrophin/genetics
- Dystrophin/metabolism
- Genetic Therapy
- Genetic Vectors/administration & dosage
- Genetic Vectors/genetics
- Genetic Vectors/immunology
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Muscle, Skeletal/metabolism
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/immunology
- Muscular Dystrophy, Duchenne/therapy
- Protein Conformation
- Sequence Alignment
- T-Lymphocytes/immunology
- Transduction, Genetic
- Viral Tropism
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Affiliation(s)
- Dawn E Bowles
- Department of Surgery, Division of Surgical Sciences, Duke University Medical Center, Durham, North Carolina, USA
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48
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Asuri P, Bartel MA, Vazin T, Jang JH, Wong TB, Schaffer DV. Directed evolution of adeno-associated virus for enhanced gene delivery and gene targeting in human pluripotent stem cells. Mol Ther 2012; 20:329-38. [PMID: 22108859 PMCID: PMC3277219 DOI: 10.1038/mt.2011.255] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 10/27/2011] [Indexed: 12/12/2022] Open
Abstract
Efficient approaches for the precise genetic engineering of human pluripotent stem cells (hPSCs) can enhance both basic and applied stem cell research. Adeno- associated virus (AAV) vectors are of particular interest for their capacity to mediate efficient gene delivery to and gene targeting in various cells. However, natural AAV serotypes offer only modest transduction of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs), which limits their utility for efficiently manipulating the hPSC genome. Directed evolution is a powerful means to generate viral vectors with novel capabilities, and we have applied this approach to create a novel AAV variant with high gene delivery efficiencies (~50%) to hPSCs, which are importantly accompanied by a considerable increase in gene-targeting frequencies, up to 0.12%. While this level is likely sufficient for numerous applications, we also show that the gene-targeting efficiency mediated by an evolved AAV variant can be further enhanced (>1%) in the presence of targeted double- stranded breaks (DSBs) generated by the co-delivery of artificial zinc finger nucleases (ZFNs). Thus, this study demonstrates that under appropriate selective pressures, AAV vectors can be created to mediate efficient gene targeting in hPSCs, alone or in the presence of ZFN- mediated double-stranded DNA breaks.
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Affiliation(s)
- Prashanth Asuri
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1462, USA
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Looi K, Sutanto EN, Banerjee B, Garratt L, Ling KM, Foo CJ, Stick SM, Kicic A. Bronchial brushings for investigating airway inflammation and remodelling. Respirology 2011; 16:725-37. [PMID: 21624002 DOI: 10.1111/j.1440-1843.2011.02001.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Asthma is the commonest medical cause for hospital admission for children in Australia, affects more than 300 million people worldwide, and is incurable, severe in large number and refractory to treatment in many. However, there have been no new significant treatments despite intense research and billions of dollars. The advancement in our understanding in this disease has been limited due to its heterogeneity, genetic complexity and has severely been hampered particularly in children by the difficulty in obtaining relevant target organ tissue. This review attempts to provide an overview of the currently used and recently developed/adapted techniques used to obtain lung tissue with specific reference to the airway epithelium.
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Affiliation(s)
- Kevin Looi
- School of Paediatrics and Child Health, Centre for Health Research, The University of Western Australia, Nedlands, Australia
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50
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Hickey RD, Lillegard JB, Fisher JE, McKenzie TJ, Hofherr SE, Finegold MJ, Nyberg SL, Grompe M. Efficient production of Fah-null heterozygote pigs by chimeric adeno-associated virus-mediated gene knockout and somatic cell nuclear transfer. Hepatology 2011; 54:1351-9. [PMID: 21674562 PMCID: PMC3184202 DOI: 10.1002/hep.24490] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 05/25/2011] [Indexed: 12/15/2022]
Abstract
UNLABELLED Hereditary tyrosinemia type I (HT1) results in hepatic failure, cirrhosis, and hepatocellular carcinoma (HCC) early in childhood and is caused by a deficiency in the enzyme fumarylacetoacetate hydrolase (FAH). In a novel approach we used the chimeric adeno-associated virus DJ serotype (AAV-DJ) and homologous recombination to target and disrupt the porcine Fah gene. AAV-DJ is an artificial chimeric AAV vector containing hybrid capsid sequences from three naturally occurring serotypes (AAV2, 8, and 9). The AAV-DJ vector was used to deliver the knockout construct to fetal pig fibroblasts with an average knockout targeting frequency of 5.4%. Targeted Fah-null heterozygote fibroblasts were used as nuclear donors for somatic cell nuclear transfer (SCNT) to porcine oocytes and multiple viable Fah-null heterozygote pigs were generated. Fah-null heterozygotes were phenotypically normal, but had decreased Fah transcriptional and enzymatic activity compared to wildtype animals. CONCLUSION This study is the first to use a recombinant chimeric AAV vector to knockout a gene in porcine fibroblasts for the purpose of SCNT. In using the AAV-DJ vector we observed targeting frequencies that were higher than previously reported with other naturally occurring serotypes. We expect that the subsequent generation of FAH-null homozygote pigs will serve as a significant advancement for translational research in the areas of metabolic liver disease, cirrhosis, and HCC.
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Affiliation(s)
- Raymond D. Hickey
- Papé Family Pediatric Research Institute & Oregon Stem Cell Center, Oregon Health & Sciences University, Portland, Oregon 97239, USA, Department of Molecular & Medical Genetics, Oregon Health & Sciences University, Portland, Oregon 97239, USA
| | - Joseph B. Lillegard
- Department of Surgery Division of Transplant Surgery, Mayo Medical Center, 200 First St. SW, Rochester, Minnesota 55905, USA
| | - James E. Fisher
- Department of Surgery Division of Transplant Surgery, Mayo Medical Center, 200 First St. SW, Rochester, Minnesota 55905, USA
| | - Travis J. McKenzie
- Department of Surgery Division of Transplant Surgery, Mayo Medical Center, 200 First St. SW, Rochester, Minnesota 55905, USA
| | - Sean E. Hofherr
- Mayo Clinic College of Medicine, Biochemical Genetics Laboratory, 200 1st St. SW, Rochester, MN 55905, USA
| | - Milton J. Finegold
- Department of Pathology, Texas Children’s Hospital, Houston, Texas 77030, USA
| | - Scott L. Nyberg
- Department of Surgery Division of Transplant Surgery, Mayo Medical Center, 200 First St. SW, Rochester, Minnesota 55905, USA
| | - Markus Grompe
- Papé Family Pediatric Research Institute & Oregon Stem Cell Center, Oregon Health & Sciences University, Portland, Oregon 97239, USA
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