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Kachanov A, Kostyusheva A, Brezgin S, Karandashov I, Ponomareva N, Tikhonov A, Lukashev A, Pokrovsky V, Zamyatnin AA, Parodi A, Chulanov V, Kostyushev D. The menace of severe adverse events and deaths associated with viral gene therapy and its potential solution. Med Res Rev 2024; 44:2112-2193. [PMID: 38549260 DOI: 10.1002/med.22036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 08/09/2024]
Abstract
Over the past decade, in vivo gene replacement therapy has significantly advanced, resulting in market approval of numerous therapeutics predominantly relying on adeno-associated viral vectors (AAV). While viral vectors have undeniably addressed several critical healthcare challenges, their clinical application has unveiled a range of limitations and safety concerns. This review highlights the emerging challenges in the field of gene therapy. At first, we discuss both the role of biological barriers in viral gene therapy with a focus on AAVs, and review current landscape of in vivo human gene therapy. We delineate advantages and disadvantages of AAVs as gene delivery vehicles, mostly from the safety perspective (hepatotoxicity, cardiotoxicity, neurotoxicity, inflammatory responses etc.), and outline the mechanisms of adverse events in response to AAV. Contribution of every aspect of AAV vectors (genomic structure, capsid proteins) and host responses to injected AAV is considered and substantiated by basic, translational and clinical studies. The updated evaluation of recent AAV clinical trials and current medical experience clearly shows the risks of AAVs that sometimes overshadow the hopes for curing a hereditary disease. At last, a set of established and new molecular and nanotechnology tools and approaches are provided as potential solutions for mitigating or eliminating side effects. The increasing number of severe adverse reactions and, sadly deaths, demands decisive actions to resolve the issue of immune responses and extremely high doses of viral vectors used for gene therapy. In response to these challenges, various strategies are under development, including approaches aimed at augmenting characteristics of viral vectors and others focused on creating secure and efficacious non-viral vectors. This comprehensive review offers an overarching perspective on the present state of gene therapy utilizing both viral and non-viral vectors.
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Affiliation(s)
- Artyom Kachanov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Anastasiya Kostyusheva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Sergey Brezgin
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Ivan Karandashov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Natalia Ponomareva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Andrey Tikhonov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Alexander Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Vadim Pokrovsky
- Laboratory of Biochemical Fundamentals of Pharmacology and Cancer Models, Blokhin Cancer Research Center, Moscow, Russia
- Department of Biochemistry, People's Friendship University, Russia (RUDN University), Moscow, Russia
| | - Andrey A Zamyatnin
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Research, Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alessandro Parodi
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Vladimir Chulanov
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Infectious Diseases, Sechenov University, Moscow, Russia
| | - Dmitry Kostyushev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
- Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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Deuker D, Asilonu E, Bracewell DG, Frank S. Adeno-Associated Virus 5 Protein Particles Produced by E. coli Cell-Free Protein Synthesis. ACS Synth Biol 2024. [PMID: 39178386 DOI: 10.1021/acssynbio.4c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2024]
Abstract
Recombinant adeno-associated viruses (rAAVs) have emerged as important tools for gene therapy and, more recently, vaccine development. Nonetheless, manufacturing can be costly and time-consuming, emphasizing the importance of alternative production platforms. We investigate the potential of E. coli-based cell-free protein synthesis (CFPS) to produce recombinant AAV5 virus-like particles (VLPs). AAV5 virus protein 3 (VP3) constructs, both with and without Strep-tag II, were expressed with CFPS. Lower reaction temperatures resulted in increased solubility, with the untagged variant containing nearly 90% more soluble VLP VP3 protein at 18 °C than at 37 °C. Affinity chromatography of N-terminally Strep(II)-tagged VP3 enabled successful isolation with minimal processing. DLS and TEM confirmed the presence of ∼20 nm particles. Furthermore, the N-terminally tagged AAV5 VP3 VLPs were biologically active, successfully internalizing into HeLa cells. This study describes an innovative approach to AAV VLP production using E. coli-based CFPS, demonstrating its potential for rapid and biologically active AAV VLP synthesis.
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Affiliation(s)
- Danielle Deuker
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Ernest Asilonu
- Cytiva Europe Limited, 5 Harbourgate Business Park, Southampton Road, Portsmouth, Hampshire PO6 4BQ, United Kingdom
| | - Daniel G Bracewell
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, United Kingdom
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3
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Matsuzaka Y, Yashiro R. Therapeutic Application and Structural Features of Adeno-Associated Virus Vector. Curr Issues Mol Biol 2024; 46:8464-8498. [PMID: 39194716 DOI: 10.3390/cimb46080499] [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: 06/10/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024] Open
Abstract
Adeno-associated virus (AAV) is characterized by non-pathogenicity, long-term infection, and broad tropism and is actively developed as a vector virus for gene therapy products. AAV is classified into more than 100 serotypes based on differences in the amino acid sequence of the capsid protein. Endocytosis involves the uptake of viral particles by AAV and accessory receptors during AAV infection. After entry into the cell, they are transported to the nucleus through the nuclear pore complex. AAVs mainly use proteoglycans as receptors to enter cells, but the types of sugar chains in proteoglycans that have binding ability are different. Therefore, it is necessary to properly evaluate the primary structure of receptor proteins, such as amino acid sequences and post-translational modifications, including glycosylation, and the higher-order structure of proteins, such as the folding of the entire capsid structure and the three-dimensional (3D) structure of functional domains, to ensure the efficacy and safety of biopharmaceuticals. To further enhance safety, it is necessary to further improve the efficiency of gene transfer into target cells, reduce the amount of vector administered, and prevent infection of non-target cells.
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Affiliation(s)
- Yasunari Matsuzaka
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
| | - Ryu Yashiro
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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4
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Zhou X, Liu J, Xiao S, Liang X, Li Y, Mo F, Xin X, Yang Y, Gao C. Adeno-Associated Virus Engineering and Load Strategy for Tropism Modification, Immune Evasion and Enhanced Transgene Expression. Int J Nanomedicine 2024; 19:7691-7708. [PMID: 39099791 PMCID: PMC11296317 DOI: 10.2147/ijn.s459905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/21/2024] [Indexed: 08/06/2024] Open
Abstract
Gene therapy aims to add, replace or turn off genes to help treat disease. To date, the US Food and Drug Administration (FDA) has approved 14 gene therapy products. With the increasing interest in gene therapy, feasible gene delivery vectors are necessary for inserting new genes into cells. There are different kinds of gene delivery vectors including viral vectors like lentivirus, adenovirus, retrovirus, adeno-associated virus et al, and non-viral vectors like naked DNA, lipid vectors, polymer nanoparticles, exosomes et al, with viruses being the most commonly used. Among them, the most concerned vector is adeno-associated virus (AAV) because of its safety, natural ability to efficiently deliver gene into cells and sustained transgene expression in multiple tissues. In addition, the AAV genome can be engineered to generate recombinant AAV (rAAV) containing transgene sequences of interest and has been proven to be a safe gene vector. Recently, rAAV vectors have been approved for the treatment of various rare diseases. Despite these approvals, some major limitations of rAAV remain, namely nonspecific tissue targeting and host immune response. Additional problems include neutralizing antibodies that block transgene delivery, a finite transgene packaging capacity, high viral titer used for per dose and high cost. To deal with these challenges, several techniques have been developed. Based on differences in engineering methods, this review proposes three strategies: gene engineering-based capsid modification (capsid modification), capsid surface tethering through chemical conjugation (surface tethering), and other formulations loaded with AAV (virus load). In addition, the major advantages and limitations encountered in rAAV engineering strategies are summarized.
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Affiliation(s)
- Xun Zhou
- School of Pharmacy, Henan University, Kaifeng, People’s Republic of China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Jingzhou Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Shuang Xiao
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
- School of Pharmacy, Guangxi Medical University, Nanning, People’s Republic of China
| | - Xiaoqing Liang
- School of Pharmacy, Henan University, Kaifeng, People’s Republic of China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Yi Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Fengzhen Mo
- School of Pharmacy, Guangxi Medical University, Nanning, People’s Republic of China
| | - Xin Xin
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Yang Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Chunsheng Gao
- School of Pharmacy, Henan University, Kaifeng, People’s Republic of China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
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Battista M, Carelli V, Bottazzi L, Bandello F, Cascavilla ML, Barboni P. Gene therapy for Leber hereditary optic neuropathy. Expert Opin Biol Ther 2024; 24:521-528. [PMID: 38939999 DOI: 10.1080/14712598.2024.2359015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/20/2024] [Indexed: 06/29/2024]
Abstract
INTRODUCTION Leber hereditary optic neuropathy (LHON) is among the most frequent inherited mitochondrial disease, causing a severe visual impairment, mostly in young-adult males. The causative mtDNA variants (the three common are m.11778 G>A/MT-ND4, m.3460 G>A/MT-ND1, and m.14484T>C/MT-ND6) by affecting complex I impair oxidative phosphorylation in retinal ganglion cells, ultimately leading to irreversible cell death and consequent functional loss. The gene therapy based on allotopic expression of a wild-type transgene carried by adeno-associated viral vectors (AVV-based) appears a promising approach in mitochondrial disease and its efficacy has been explored in several large clinical trials. AREAS COVERED The review work employed basic concepts in mitochondrial diseases, LHON, and gene therapy procedures. Reports from completed trials in LHON (i.e. RESCUE) were reviewed and critically compared. EXPERT OPINION New challenges, as the improvement of the contralateral untreated eye or the apparently better outcome in patients treated in later stages (6-12 months), were highlighted by the latest gene therapy trials. A better understanding of the pathogenetic mechanisms of the disease together with combined therapy (medical and gene therapy) and optimization in genetic correction approaches could improve the visual outcome of treated eyes.
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Affiliation(s)
- Marco Battista
- Department of Ophthalmology, University Vita-Salute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- Programma di Neurogenetica, IRCCS Istituto di Scienze Neurologiche di Bologna, Bologna, Italy
| | - Leonardo Bottazzi
- Department of Ophthalmology, University Vita-Salute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesco Bandello
- Department of Ophthalmology, University Vita-Salute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Maria Lucia Cascavilla
- Department of Ophthalmology, University Vita-Salute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Piero Barboni
- Department of Ophthalmology, University Vita-Salute, IRCCS Ospedale San Raffaele, Milan, Italy
- Studio Oculistico d'Azeglio, Bologna, Italy
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Coplan L, Zhang Z, Ragone N, Reeves J, Rodriguez A, Shevade A, Bak H, Tustian AD. High-yield recombinant adeno-associated viral vector production by multivariate optimization of bioprocess and transfection conditions. Biotechnol Prog 2024; 40:e3445. [PMID: 38450973 DOI: 10.1002/btpr.3445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Recombinant adeno-associated viral vectors (rAAVs) are one of the most used vehicles for gene therapy, with five rAAV therapeutics commercially approved by the FDA. To improve product yield, we optimized the suspension production process of rAAV8 vectors carrying a proprietary transgene using a commercially available transfection reagent, FectoVIR-AAV. Using a miniaturized automated 250 mL scale bioreactor system, we generated models of vector genome (vg) titer, capsid (cp) titer, and Vg:Cp percentage from two multivariate design of experiment studies, one centered around bioreactor operating parameters, and another based on the transfection conditions. Using the optimized process returned from these models, the vector genome titer from the bioreactor was improved to beyond 1 × 1012 vg/mL. Five critical parameters were identified that had large effects on the pre-purification vector quantity-the transfection pH, production pH, complexation time, viable cell density at transfection, and transfection reagent to DNA ratio. The optimized process was further assessed for its performance extending to six AAV serotypes, namely AAV1, AAV2, AAV5, AAV6, AAV8, and AAV9 carrying a transgene encoding for green fluorescent protein (GFP). Five of the six serotypes returned higher vector genome titers than the control condition. These data suggest that the choice of transfection reagent is a major factor in improving vector yield. The multivariate design of experiment approach is a powerful way to optimize production processes, and the optimized process from one AAV vector can to some extent be generalized to other serotypes and transgenes to accelerate development timelines of new programs.
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Affiliation(s)
- Louis Coplan
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
- Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland, USA
| | - Zhe Zhang
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Nicole Ragone
- Research Operations, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - John Reeves
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Audrey Rodriguez
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Aishwarya Shevade
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Hanne Bak
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Andrew D Tustian
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
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7
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Xie Y, Butler M. N-glycomic profiling of capsid proteins from Adeno-Associated Virus serotypes. Glycobiology 2024; 34:cwad074. [PMID: 37774344 PMCID: PMC10950483 DOI: 10.1093/glycob/cwad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023] Open
Abstract
Adeno-associated virus (AAV) vector has become the leading platform for gene delivery. Each serotype exhibits a different tissue tropism, immunogenicity, and in vivo transduction performance. Therefore, selecting the most suitable AAV serotype is critical for efficient gene delivery to target cells or tissues. Genome divergence among different serotypes is due mainly to the hypervariable regions of the AAV capsid proteins. However, the heterogeneity of capsid glycosylation is largely unexplored. In the present study, the N-glycosylation profiles of capsid proteins of AAV serotypes 1 to 9 have been systemically characterized and compared using a previously developed high-throughput and high-sensitivity N-glycan profiling platform. The results showed that all 9 investigated AAV serotypes were glycosylated, with comparable profiles. The most conspicuous feature was the high abundance mannosylated N-glycans, including FM3, M5, M6, M7, M8, and M9, that dominated the chromatograms within a range of 74 to 83%. Another feature was the relatively lower abundance of fucosylated and sialylated N-glycan structures, in the range of 23%-40% and 10%-17%, respectively. However, the exact N-glycan composition differed. These differences may be utilized to identify potential structural relationships between the 9 AAV serotypes. The current research lays the foundation for gaining better understanding of the importance of N-glycans on the AAV capsid surface that may play a significant role in tissue tropism, interaction with cell surface receptors, cellular uptake, and intracellular processing.
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Affiliation(s)
- Yongjing Xie
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Michael Butler
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin (UCD), Belfield, Dublin 4, D04 V1W8, Ireland
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8
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Hadi M, Qutaiba B Allela O, Jabari M, Jasoor AM, Naderloo O, Yasamineh S, Gholizadeh O, Kalantari L. Recent advances in various adeno-associated viruses (AAVs) as gene therapy agents in hepatocellular carcinoma. Virol J 2024; 21:17. [PMID: 38216938 PMCID: PMC10785434 DOI: 10.1186/s12985-024-02286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
Primary liver cancer, which is scientifically referred to as hepatocellular carcinoma (HCC), is a significant concern in the field of global health. It has been demonstrated that conventional chemotherapy, chemo-hormonal therapy, and conformal radiotherapy are ineffective against HCC. New therapeutic approaches are thus urgently required. Identifying single or multiple mutations in genes associated with invasion, metastasis, apoptosis, and growth regulation has resulted in a more comprehensive comprehension of the molecular genetic underpinnings of malignant transformation, tumor advancement, and host interaction. This enhanced comprehension has notably propelled the development of novel therapeutic agents. Therefore, gene therapy (GT) holds great promise for addressing the urgent need for innovative treatments in HCC. However, the complexity of HCC demands precise and effective therapeutic approaches. The adeno-associated virus (AAV) distinctive life cycle and ability to persistently infect dividing and nondividing cells have rendered it an alluring vector. Another appealing characteristic of the wild-type virus is its evident absence of pathogenicity. As a result, AAV, a vector that lacks an envelope and can be modified to transport DNA to specific cells, has garnered considerable interest in the scientific community, particularly in experimental therapeutic strategies that are still in the clinical stage. AAV vectors emerge as promising tools for HCC therapy due to their non-immunogenic nature, efficient cell entry, and prolonged gene expression. While AAV-mediated GT demonstrates promise across diverse diseases, the current absence of ongoing clinical trials targeting HCC underscores untapped potential in this context. Furthermore, gene transfer through hepatic AAV vectors is frequently facilitated by GT research, which has been propelled by several congenital anomalies affecting the liver. Notwithstanding the enthusiasm associated with this notion, recent discoveries that expose the integration of the AAV vector genome at double-strand breaks give rise to apprehensions regarding their enduring safety and effectiveness. This review explores the potential of AAV vectors as versatile tools for targeted GT in HCC. In summation, we encapsulate the multifaceted exploration of AAV vectors in HCC GT, underlining their transformative potential within the landscape of oncology and human health.
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Affiliation(s)
- Meead Hadi
- Department of Microbiology, Faculty of Basic Science, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | | | - Mansoureh Jabari
- Medical Campus, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Asna Mahyazadeh Jasoor
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Omid Naderloo
- Department of Laboratory Sciences, Faculty of Medicine, Islamic Azad University of Gorgan Breanch, Gorgan, Iran
| | | | | | - Leila Kalantari
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
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Fu X, Suo H, Zhang J, Chen D. Machine-learning-guided Directed Evolution for AAV Capsid Engineering. Curr Pharm Des 2024; 30:811-824. [PMID: 38445704 DOI: 10.2174/0113816128286593240226060318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Target gene delivery is crucial to gene therapy. Adeno-associated virus (AAV) has emerged as a primary gene therapy vector due to its broad host range, long-term expression, and low pathogenicity. However, AAV vectors have some limitations, such as immunogenicity and insufficient targeting. Designing or modifying capsids is a potential method of improving the efficacy of gene delivery, but hindered by weak biological basis of AAV, complexity of the capsids, and limitations of current screening methods. Artificial intelligence (AI), especially machine learning (ML), has great potential to accelerate and improve the optimization of capsid properties as well as decrease their development time and manufacturing costs. This review introduces the traditional methods of designing AAV capsids and the general steps of building a sequence-function ML model, highlights the applications of ML in the development workflow, and summarizes its advantages and challenges.
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Affiliation(s)
- Xianrong Fu
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Hairui Suo
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jiachen Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Dongmei Chen
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
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10
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Dogbey DM, Torres VES, Fajemisin E, Mpondo L, Ngwenya T, Akinrinmade OA, Perriman AW, Barth S. Technological advances in the use of viral and non-viral vectors for delivering genetic and non-genetic cargos for cancer therapy. Drug Deliv Transl Res 2023; 13:2719-2738. [PMID: 37301780 PMCID: PMC10257536 DOI: 10.1007/s13346-023-01362-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2023] [Indexed: 06/12/2023]
Abstract
The burden of cancer is increasing globally. Several challenges facing its mainstream treatment approaches have formed the basis for the development of targeted delivery systems to carry and distribute anti-cancer payloads to their defined targets. This site-specific delivery of drug molecules and gene payloads to selectively target druggable biomarkers aimed at inducing cell death while sparing normal cells is the principal goal for cancer therapy. An important advantage of a delivery vector either viral or non-viral is the cumulative ability to penetrate the haphazardly arranged and immunosuppressive tumour microenvironment of solid tumours and or withstand antibody-mediated immune response. Biotechnological approaches incorporating rational protein engineering for the development of targeted delivery systems which may serve as vehicles for packaging and distribution of anti-cancer agents to selectively target and kill cancer cells are highly desired. Over the years, these chemically and genetically modified delivery systems have aimed at distribution and selective accumulation of drug molecules at receptor sites resulting in constant maintenance of high drug bioavailability for effective anti-tumour activity. In this review, we highlighted the state-of-the art viral and non-viral drug and gene delivery systems and those under developments focusing on cancer therapy.
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Affiliation(s)
- Dennis Makafui Dogbey
- South African Research Chair in Cancer Biotechnology, Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Emmanuel Fajemisin
- South African Research Chair in Cancer Biotechnology, Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Liyabona Mpondo
- South African Research Chair in Cancer Biotechnology, Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Takunda Ngwenya
- South African Research Chair in Cancer Biotechnology, Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Olusiji Alex Akinrinmade
- South African Research Chair in Cancer Biotechnology, Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Adam W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, Bristol, UK
| | - Stefan Barth
- South African Research Chair in Cancer Biotechnology, Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
- Medical Biotechnology and Immunotherapy Research Unit, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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11
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Tur-Planells V, García-Sastre A, Cuadrado-Castano S, Nistal-Villan E. Engineering Non-Human RNA Viruses for Cancer Therapy. Vaccines (Basel) 2023; 11:1617. [PMID: 37897020 PMCID: PMC10611381 DOI: 10.3390/vaccines11101617] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Alongside the development and progress in cancer immunotherapy, research in oncolytic viruses (OVs) continues advancing novel treatment strategies to the clinic. With almost 50 clinical trials carried out over the last decade, the opportunities for intervention using OVs are expanding beyond the old-fashioned concept of "lytic killers", with promising breakthrough therapeutic strategies focused on leveraging the immunostimulatory potential of different viral platforms. This review presents an overview of non-human-adapted RNA viruses engineered for cancer therapy. Moreover, we describe the diverse strategies employed to manipulate the genomes of these viruses to optimize their therapeutic capabilities. By focusing on different aspects of this particular group of viruses, we describe the insights into the promising advancements in the field of virotherapy and its potential to revolutionize cancer treatment.
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Affiliation(s)
- Vicent Tur-Planells
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Cuadrado-Castano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute (IGI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Estanislao Nistal-Villan
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
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12
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Hiemenz C, Pacios-Michelena A, Helbig C, Vezočnik V, Strebl M, Nikels F, Hawe A, Garidel P, Menzen T. Characterization of Virus Particles and Submicron-Sized Particulate Impurities in Recombinant Adeno-Associated Virus Drug Product. J Pharm Sci 2023; 112:2190-2202. [PMID: 37211315 DOI: 10.1016/j.xphs.2023.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/23/2023]
Abstract
Characterization of particulate impurities such as aggregates is necessary to develop safe and efficacious adeno-associated virus (AAV) drug products. Although aggregation of AAVs can reduce the bioavailability of the virus, only a limited number of studies focus on the analysis of aggregates. We explored three technologies for their capability to characterize AAV monomers and aggregates in the submicron (<1 µm) size range: (i) mass photometry (MP), (ii) asymmetric flow field flow fractionation coupled to a UV-detector (AF4-UV/Vis) and (iii) microfluidic resistive pulse sensing (MRPS). Although low counts for aggregates impeded a quantitative analysis, MP was affirmed as an accurate and rapid method for quantifying the genome content of empty/filled/double-filled capsids, consistent with sedimentation velocity analytical ultracentrifugation results. MRPS and AF4-UV/Vis enabled the detection and quantification of aggregate content. The developed AF4-UV/Vis method separated AAV monomers from smaller aggregates, thereby enabling a quantification of aggregates <200 nm. MRPS was experienced as a straightforward method to determine the particle concentration and size distribution between 250-2000 nm, provided that the samples do not block the microfluidic cartridge. Overall, within this study we explored the benefits and limitations of the complementary technologies for assessing aggregate content in AAV samples.
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Affiliation(s)
| | | | | | | | - Michael Strebl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany
| | - Felix Nikels
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany.
| | - Andrea Hawe
- Coriolis Pharma Research GmbH, Martinsried, Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Martinsried, Germany.
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13
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Kadian M, Kok CY, Ravindran D, Passam F, Pasalic L, Kizana E. Focal Anticoagulation by Somatic Gene Transfer: Towards Preventing Cardioembolic Stroke. Heart Lung Circ 2023:S1443-9506(23)00509-7. [PMID: 37316436 DOI: 10.1016/j.hlc.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023]
Abstract
Cardioembolic stroke (CS) has emerged as a leading cause of ischaemic stroke (IS); distinguished by thrombi embolising to the brain from cardiac origins; most often from the left atrial appendage (LAA). Contemporary therapeutic options are largely dependent on systemic anticoagulation as a blanket preventative strategy, yet this does not represent a nuanced or personalised solution. Contraindications to systemic anticoagulation create significant unmedicated and high-risk cohorts, leaving these patients at risk of significant morbidity and mortality. Atrial appendage occlusion devices are increasingly used to mitigate stroke risk from thrombi emerging from the LAA in patients ineligible for oral anticoagulants (OACs). Their use, however, is not without risk or significant cost, and does not address the underlying aetiology of thrombosis and CS. Viral vector-based gene therapy has emerged as a novel strategy to target a spectrum of haemostatic disorders, achieving success through the adeno-associated virus (AAV) based therapy of haemophilia. Yet, thrombotic disorders, such as CS, have had limited exploration within the realm of AAV gene therapy approaches-presenting a gap in the literature and an opportunity for further research. Gene therapy has the potential to directly address the cause of CS by localised targeting of the molecular remodelling that serves to promote thrombosis.
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Affiliation(s)
- Megha Kadian
- The Centre for Heart Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine, The University of Queensland, St Lucia, Qld, Australia
| | - Cindy Y Kok
- The Centre for Heart Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
| | - Dhanya Ravindran
- The Centre for Heart Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
| | - Freda Passam
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; The Heart Research Institute, Charles Perkins Centre, Sydney, NSW, Australia
| | - Leonardo Pasalic
- Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia; Department of Haematology, Institute of Clinical Pathology and Medical Research (ICPMR), Sydney Centres for Thrombosis and Haemostasis, Westmead Hospital, Sydney, NSW, Australia
| | - Eddy Kizana
- The Centre for Heart Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia; Department of Cardiology, Westmead Hospital, Sydney, NSW, Australia.
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14
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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: 31] [Impact Index Per Article: 31.0] [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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15
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Xiang YS, Hao GG. Biophysical characterization of adeno-associated virus capsid through the viral transduction life cycle. J Genet Eng Biotechnol 2023; 21:62. [PMID: 37195476 DOI: 10.1186/s43141-023-00518-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/11/2023] [Indexed: 05/18/2023]
Abstract
Adeno-associated virus (AAV) vectors have emerged as the leading delivery platforms for gene therapy. Throughout the life cycle of the virions, the capsid vector carries out diverse functions, ranging from cell surface receptor engagement, cellular entry, endosomal escape, nuclear import to new particle packaging, and assembly. Each of these steps is mediated by exquisite structure features of the viral capsid and its interaction with viral genome, Rep proteins, and cellular organelle and apparatus. In this brief review, we provide an overview of results from over a decade of extensive biophysical studies of the capsid employing various techniques. The remaining unaddressed questions and perspective are also discussed. The detailed understanding of the structure and function interplay would provide insight to the strategy for improving the efficacy and safety of the viral vectors.
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Affiliation(s)
| | - Gang Gary Hao
- Weston Biomedical Reviews, 65 Autumn Road, Weston, MA, 02493, USA.
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16
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Golm SK, Hübner W, Müller KM. Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses 2023; 15:v15051174. [PMID: 37243260 DOI: 10.3390/v15051174] [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: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.
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Affiliation(s)
- Susanne K Golm
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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17
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Escudero-Duch C, Muñoz-Moreno L, Martin-Saavedra F, Sanchez-Casanova S, Lerma-Juarez MA, Vilaboa N. Remote control of transgene expression using noninvasive near-infrared irradiation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 242:112697. [PMID: 36963296 DOI: 10.1016/j.jphotobiol.2023.112697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/26/2023]
Abstract
This study investigated whether noninvasive near-infrared (NIR) energy could be transduced into heat in deep-seated organs in which adenovirus type-5 vectors tend to accumulate, thereby activating heat shock protein (HSP) promoter-mediated transgene expression, without local administration of photothermal agents. NIR irradiation of the subdiaphragmatic and left dorsocranial part of the abdominal cavity of adult immunocompetent C3H/HeNRj mice with an 808-nm laser effectively increased the temperature of the irradiated regions of the liver and spleen, respectively, resulting in the accumulation of the heat-inducible HSP70 protein. Spatial control of transgene expression was achieved in the NIR-irradiated regions of the mice administered an adenoviral vector carrying a firefly luciferase (fLuc) coding sequence controlled by a human HSP70B promoter, as assessed by bioluminescence and immunohistochemistry analyses. Levels of reporter gene expression were modulated by controlling NIR power density. Spatial control of transgene expression through NIR-focused activation of the HSP70B promoter, as well as temporal regulation by administering rapamycin was achieved in the spleens of mice inoculated with an adenoviral vector encoding a rapamycin-dependent transactivator driven by the HSP70B promoter and an adenoviral vector carrying a fLuc coding sequence controlled by the rapamycin-activated transactivator. Mice that were administered rapamycin and exposed to NIR light expressed fLuc activity in the splenic region, whereas no activity was detected in mice that were only administered rapamycin or vehicle or only NIR-irradiated. Thus, in the absence of any exogenously supplied photothermal material, remote control of heat-induced transgene expression can be achieved in the liver and spleen by means of noninvasive NIR irradiation.
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Affiliation(s)
- Clara Escudero-Duch
- CIBER de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain; Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Laura Muñoz-Moreno
- CIBER de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain; Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Francisco Martin-Saavedra
- CIBER de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain; Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Silvia Sanchez-Casanova
- CIBER de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain; Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Miguel Angel Lerma-Juarez
- CIBER de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain; Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Nuria Vilaboa
- CIBER de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain; Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain.
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18
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Stankov S, Cuchel M. Gene editing for dyslipidemias: New tools to "cut" lipids. Atherosclerosis 2023; 368:14-24. [PMID: 36725417 PMCID: PMC10493168 DOI: 10.1016/j.atherosclerosis.2023.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/23/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
Effective lipid lowering therapies are essential for the prevention of atherosclerosis and cardiovascular disease. Available treatments have evolved in both their efficacy and their frequency of administration, and currently include monoclonal antibodies, antisense oligonucleotides and siRNA approaches. However, an unmet need remains for more effective and long-lasting therapeutics. Gene editing permanently alters endogenous gene expression and has the potential to revolutionize disease treatment. Despite the existence of several gene editing approaches, the CRISPR/Cas9 system has emerged as the preferred technology because of its high efficiency and relative simplicity. This review provides a general overview of this promising technology and an update on the progress made towards the development of treatments of dyslipidemia. The recently started phase 1b gene editing clinical trial targeting PCSK9 in patients with heterozygous familial hypercholesterolemia and cardiovascular disease highlights how gene editing may become available to treat not only patients affected by rare disorders of lipid metabolism, but also patients that are difficult-to-treat or at high risk. Other targets like ANGPTL3, LDLR, and APOC3 are on track for further pre-clinical development. The identification of novel targets using electronic health record-linked biobanks and human sequencing studies will continue to expand the potential target pool, and clinical assessment of treated patients will provide essential efficacy and safety information on current strategies. Gene editing of genes regulating lipid metabolism holds promise as an exciting new therapeutic approach. However, since gene editing permanently alters a patient's genome, its therapeutic application in humans will require careful safety assessment and ethical considerations.
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Affiliation(s)
- Sylvia Stankov
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Marina Cuchel
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, PA, USA.
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19
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Issa SS, Shaimardanova AA, Solovyeva VV, Rizvanov AA. Various AAV Serotypes and Their Applications in Gene Therapy: An Overview. Cells 2023; 12:cells12050785. [PMID: 36899921 PMCID: PMC10000783 DOI: 10.3390/cells12050785] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Despite scientific discoveries in the field of gene and cell therapy, some diseases still have no effective treatment. Advances in genetic engineering methods have enabled the development of effective gene therapy methods for various diseases based on adeno-associated viruses (AAVs). Today, many AAV-based gene therapy medications are being investigated in preclinical and clinical trials, and new ones are appearing on the market. In this article, we present a review of AAV discovery, properties, different serotypes, and tropism, and a following detailed explanation of their uses in gene therapy for disease of different organs and systems.
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Affiliation(s)
- Shaza S. Issa
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alisa A. Shaimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Valeriya V. Solovyeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Albert A. Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Correspondence: ; Tel.: +7-(905)-3167599
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20
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Shitik EM, Shalik IK, Yudkin DV. AAV- based vector improvements unrelated to capsid protein modification. Front Med (Lausanne) 2023; 10:1106085. [PMID: 36817775 PMCID: PMC9935841 DOI: 10.3389/fmed.2023.1106085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) is the leading platform for delivering genetic constructs in vivo. To date, three AAV-based gene therapeutic agents have been approved by the FDA and are used in clinical practice. Despite the distinct advantages of gene therapy development, it is clear that AAV vectors need to be improved. Enhancements in viral vectors are mainly associated with capsid protein modifications. However, there are other structures that significantly affect the AAV life cycle and transduction. The Rep proteins, in combination with inverted terminal repeats (ITRs), determine viral genome replication, encapsidation, etc. Moreover, transgene cassette expression in recombinant variants is directly related to AAV production and transduction efficiency. This review discusses the ways to improve AAV vectors by modifying ITRs, a transgene cassette, and the Rep proteins.
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21
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Kolyasnikova NM, Pestov NB, Sanchez-Pimentel JP, Barlev NA, Ishmukhametov AA. Anti-cancer Virotherapy in Russia: Lessons from the Past, Current Challenges and Prospects for the Future. Curr Pharm Biotechnol 2023; 24:266-278. [PMID: 35578840 DOI: 10.2174/1389201023666220516121813] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 11/22/2022]
Abstract
The idea of using the lytic power of viruses against malignant cells has been entertained for many decades. However, oncolytic viruses gained broad attention as an emerging anti-cancer therapy only recently with the successful implementation of several oncolytic viruses to treat advanced melanoma. Here we review the history of oncolytic viruses in the Russian Federation and recent biotechnological advances in connection with the perspectives of their practical use against aggressive tumors such as glioblastoma or pancreatic cancer. A particular emphasis is made on novel applications of safe non-lytic virus-derived vectors armed with prodrug-converting enzyme transgenes. Rational improvement of oncotropism by conjugation with biopolymers and nanoformulations is also discussed.
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Affiliation(s)
- Nadezhda M Kolyasnikova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Poselok Instituta Poliomielita 8 bd 17, Poselenie Moskovskiy, Moscow, 108819, Russia
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Poselok Instituta Poliomielita 8 bd 17, Poselenie Moskovskiy, Moscow, 108819, Russia.,Moscow Institute of Physics and Technology, Phystech School of Biological and Medical Physics, Laboratory of Molecular Oncology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Group of Cross-Linking Enzymes, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Jeanne P Sanchez-Pimentel
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Poselok Instituta Poliomielita 8 bd 17, Poselenie Moskovskiy, Moscow, 108819, Russia
| | - Nikolay A Barlev
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Poselok Instituta Poliomielita 8 bd 17, Poselenie Moskovskiy, Moscow, 108819, Russia.,Moscow Institute of Physics and Technology, Phystech School of Biological and Medical Physics, Laboratory of Molecular Oncology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia.,Institute of Biomedical Chemistry, Pogodinskaya 10, Moscow, 119435, Russia
| | - Aidar A Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Poselok Instituta Poliomielita 8 bd 17, Poselenie Moskovskiy, Moscow, 108819, Russia
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22
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RNA-targeting strategies as a platform for ocular gene therapy. Prog Retin Eye Res 2023; 92:101110. [PMID: 35840489 DOI: 10.1016/j.preteyeres.2022.101110] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023]
Abstract
Genetic medicine is offering hope as new therapies are emerging for many previously untreatable diseases. The eye is at the forefront of these advances, as exemplified by the approval of Luxturna® by the United States Food and Drug Administration (US FDA) in 2017 for the treatment of one form of Leber Congenital Amaurosis (LCA), an inherited blindness. Luxturna® was also the first in vivo human gene therapy to gain US FDA approval. Numerous gene therapy clinical trials are ongoing for other eye diseases, and novel delivery systems, discovery of new drug targets and emerging technologies are currently driving the field forward. Targeting RNA, in particular, is an attractive therapeutic strategy for genetic disease that may have safety advantages over alternative approaches by avoiding permanent changes in the genome. In this regard, antisense oligonucleotides (ASO) and RNA interference (RNAi) are the currently popular strategies for developing RNA-targeted therapeutics. Enthusiasm has been further fuelled by the emergence of clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR associated (Cas) systems that allow targeted manipulation of nucleic acids. RNA-targeting CRISPR-Cas systems now provide a novel way to develop RNA-targeted therapeutics and may provide superior efficiency and specificity to existing technologies. In addition, RNA base editing technologies using CRISPR-Cas and other modalities also enable precise alteration of single nucleotides. In this review, we showcase advances made by RNA-targeting systems for ocular disease, discuss applications of ASO and RNAi technologies, highlight emerging CRISPR-Cas systems and consider the implications of RNA-targeting therapeutics in the development of future drugs to treat eye disease.
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23
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Zaman H, Khan A, Khan K, Toheed S, Abdullah M, Zeeshan HM, Hameed A, Umar M, Shahid M, Malik K, Afzal S. Adeno-Associated Virus-Mediated Gene Therapy. Crit Rev Eukaryot Gene Expr 2023; 33:87-100. [PMID: 37522547 DOI: 10.1615/critreveukaryotgeneexpr.2023048135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Choice of vector is the most critical step in gene therapy. Adeno-associated viruses (AAV); third generation vectors, are getting much attention of scientists to be used as vehicles due to their non-pathogenicity, excellent safety profile, low immune responses, great efficiency to transduce non-dividing cells, large capacity to transfer genetic material and long-term expression of genetic payload. AAVs have multiple serotypes and each serotype shows tropism for a specific cell. Different serotypes are used to target liver, lungs, muscles, retina, heart, CNS, kidneys, etc. Furthermore, AAV based gene therapies have tremendous marketing applications that can be perfectly incorporated in the anticipated sites of the host target genome resulting in life long expression of transgenes. Some therapeutic products use AAV vectors that are used to treat lipoprotein lipase deficiency (LPLD) and it is injected intramuscularly, to treat mutated retinal pigment epithelium RPE65 (RPE65) that is introduced to subretinal space, an intravenous infusion to treat spinal muscular atrophy and rAAV2-CFTR vector is introduced into nasal epithelial cells to treat cystic fibrosis. AAV therapies and other such interdisciplinary methodologies can create the miracles for the generation of precision gene therapies for the treatment of most serious and sometimes fatal disorders.
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Affiliation(s)
- Hassan Zaman
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aakif Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Khalid Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shazma Toheed
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Abdullah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Abdul Hameed
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Umar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shahid
- Division of Molecular Virology and Infectious Diseases, Center of Excellence in Molecular Biology (CEMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Kausar Malik
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Center of Excellence in Molecular Biology (CEMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
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Li H, Zha S, Li H, Liu H, Wong KL, All AH. Polymeric Dendrimers as Nanocarrier Vectors for Neurotheranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203629. [PMID: 36084240 DOI: 10.1002/smll.202203629] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Dendrimers are polymers with well-defined 3D branched structures that are vastly utilized in various neurotheranostics and biomedical applications, particularly as nanocarrier vectors. Imaging agents can be loaded into dendrimers to improve the accuracy of diagnostic imaging processes. Likewise, combining pharmaceutical agents and anticancer drugs with dendrimers can enhance their solubility, biocompatibility, and efficiency. Practically, by modifying ligands on the surface of dendrimers, effective therapeutic and diagnostic platforms can be constructed and implemented for targeted delivery. Dendrimer-based nanocarriers also show great potential in gene delivery. Since enzymes can degrade genetic materials during their blood circulation, dendrimers exhibit promising packaging and delivery alternatives, particularly for central nervous system (CNS) treatments. The DNA and RNA encapsulated in dendrimers represented by polyamidoamine that are used for targeted brain delivery, via chemical-structural adjustments and appropriate generation, significantly improve the correlation between transfection efficiency and cytotoxicity. This article reports a comprehensive review of dendrimers' structures, synthesis processes, and biological applications. Recent progress in diagnostic imaging processes and therapeutic applications for cancers and other CNS diseases are presented. Potential challenges and future directions in the development of dendrimers, which provide the theoretical basis for their broader applications in healthcare, are also discussed.
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Affiliation(s)
- Hengde Li
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon, Hong Kong SAR, P. R. China
| | - Shuai Zha
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon, Hong Kong SAR, P. R. China
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, P. R. China
| | - Haolan Li
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon, Hong Kong SAR, P. R. China
| | - Haitao Liu
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon, Hong Kong SAR, P. R. China
| | - Ka-Leung Wong
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon, Hong Kong SAR, P. R. China
| | - Angelo H All
- Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon, Hong Kong SAR, P. R. China
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25
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Ramamurthy RM, Atala A, Porada CD, Almeida-Porada G. Organoids and microphysiological systems: Promising models for accelerating AAV gene therapy studies. Front Immunol 2022; 13:1011143. [PMID: 36225917 PMCID: PMC9549755 DOI: 10.3389/fimmu.2022.1011143] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
The FDA has predicted that at least 10-20 gene therapy products will be approved by 2025. The surge in the development of such therapies can be attributed to the advent of safe and effective gene delivery vectors such as adeno-associated virus (AAV). The enormous potential of AAV has been demonstrated by its use in over 100 clinical trials and the FDA’s approval of two AAV-based gene therapy products. Despite its demonstrated success in some clinical settings, AAV-based gene therapy is still plagued by issues related to host immunity, and recent studies have suggested that AAV vectors may actually integrate into the host cell genome, raising concerns over the potential for genotoxicity. To better understand these issues and develop means to overcome them, preclinical model systems that accurately recapitulate human physiology are needed. The objective of this review is to provide a brief overview of AAV gene therapy and its current hurdles, to discuss how 3D organoids, microphysiological systems, and body-on-a-chip platforms could serve as powerful models that could be adopted in the preclinical stage, and to provide some examples of the successful application of these models to answer critical questions regarding AAV biology and toxicity that could not have been answered using current animal models. Finally, technical considerations while adopting these models to study AAV gene therapy are also discussed.
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26
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Becker J, Fakhiri J, Grimm D. Fantastic AAV Gene Therapy Vectors and How to Find Them—Random Diversification, Rational Design and Machine Learning. Pathogens 2022; 11:pathogens11070756. [PMID: 35890005 PMCID: PMC9318892 DOI: 10.3390/pathogens11070756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Parvoviruses are a diverse family of small, non-enveloped DNA viruses that infect a wide variety of species, tissues and cell types. For over half a century, their intriguing biology and pathophysiology has fueled intensive research aimed at dissecting the underlying viral and cellular mechanisms. Concurrently, their broad host specificity (tropism) has motivated efforts to develop parvoviruses as gene delivery vectors for human cancer or gene therapy applications. While the sum of preclinical and clinical data consistently demonstrates the great potential of these vectors, these findings also illustrate the importance of enhancing and restricting in vivo transgene expression in desired cell types. To this end, major progress has been made especially with vectors based on Adeno-associated virus (AAV), whose capsid is highly amenable to bioengineering, repurposing and expansion of its natural tropism. Here, we provide an overview of the state-of-the-art approaches to create new AAV variants with higher specificity and efficiency of gene transfer in on-target cells. We first review traditional and novel directed evolution approaches, including high-throughput screening of AAV capsid libraries. Next, we discuss programmable receptor-mediated targeting with a focus on two recent technologies that utilize high-affinity binders. Finally, we highlight one of the latest stratagems for rational AAV vector characterization and optimization, namely, machine learning, which promises to facilitate and accelerate the identification of next-generation, safe and precise gene delivery vehicles.
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Affiliation(s)
- Jonas Becker
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Center for Integrative Infectious Diseases Research (CIID), BioQuant, 69120 Heidelberg, Germany;
- Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - Julia Fakhiri
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
- Correspondence: (J.F.); (D.G.); Tel.: +49-174-3486203 (J.F.); +49-6221-5451331 (D.G.)
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Center for Integrative Infectious Diseases Research (CIID), BioQuant, 69120 Heidelberg, Germany;
- German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (J.F.); (D.G.); Tel.: +49-174-3486203 (J.F.); +49-6221-5451331 (D.G.)
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27
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Hanaford AR, Cho YJ, Nakai H. AAV-vector based gene therapy for mitochondrial disease: progress and future perspectives. Orphanet J Rare Dis 2022; 17:217. [PMID: 35668433 PMCID: PMC9169410 DOI: 10.1186/s13023-022-02324-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/09/2022] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial diseases are a group of rare, heterogeneous diseases caused by gene mutations in both nuclear and mitochondrial genomes that result in defects in mitochondrial function. They are responsible for significant morbidity and mortality as they affect multiple organ systems and particularly those with high energy-utilizing tissues, such as the nervous system, skeletal muscle, and cardiac muscle. Virtually no effective treatments exist for these patients, despite the urgent need. As the majority of these conditions are monogenic and caused by mutations in nuclear genes, gene replacement is a highly attractive therapeutic strategy. Adeno-associated virus (AAV) is a well-characterized gene replacement vector, and its safety profile and ability to transduce quiescent cells nominates it as a potential gene therapy vehicle for several mitochondrial diseases. Indeed, AAV vector-based gene replacement is currently being explored in clinical trials for one mitochondrial disease (Leber hereditary optic neuropathy) and preclinical studies have been published investigating this strategy in other mitochondrial diseases. This review summarizes the preclinical findings of AAV vector-based gene replacement therapy for mitochondrial diseases including Leigh syndrome, Barth syndrome, ethylmalonic encephalopathy, and others.
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Affiliation(s)
- Allison R Hanaford
- Center for Integrative Brain Research, Seattle Children's Reserach Institute, Seattle, WA, 98101, USA.
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Yoon-Jae Cho
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, 97239, USA
- Division of Pediatric Neurology, Doernbecher Children's Hospital, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Hiroyuki Nakai
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Molecular Immunology and Microbiology, Oregon Health and Science University, Portland, OR, 97239, USA
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
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28
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Kasatkina LA, Ma C, Matlashov ME, Vu T, Li M, Kaberniuk AA, Yao J, Verkhusha VV. Optogenetic manipulation and photoacoustic imaging using a near-infrared transgenic mouse model. Nat Commun 2022; 13:2813. [PMID: 35589810 PMCID: PMC9120076 DOI: 10.1038/s41467-022-30547-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/06/2022] [Indexed: 12/21/2022] Open
Abstract
Optogenetic manipulation and optical imaging in the near-infrared range allow non-invasive light-control and readout of cellular and organismal processes in deep tissues in vivo. Here, we exploit the advantages of Rhodopseudomonas palustris BphP1 bacterial phytochrome, which incorporates biliverdin chromophore and reversibly photoswitches between the ground (740-800 nm) and activated (620-680 nm) states, to generate a loxP-BphP1 transgenic mouse model. The mouse enables Cre-dependent temporal and spatial targeting of BphP1 expression in vivo. We validate the optogenetic performance of endogenous BphP1, which in the activated state binds its engineered protein partner QPAS1, to trigger gene transcription in primary cells and living mice. We demonstrate photoacoustic tomography of BphP1 expression in different organs, developing embryos, virus-infected tissues and regenerating livers, with the centimeter penetration depth. The transgenic mouse model provides opportunities for both near-infrared optogenetics and photoacoustic imaging in vivo and serves as a source of primary cells and tissues with genomically encoded BphP1.
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Affiliation(s)
- Ludmila A Kasatkina
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Mikhail E Matlashov
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Tri Vu
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Mucong Li
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Andrii A Kaberniuk
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
| | - Vladislav V Verkhusha
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland.
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29
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Beloukhova MI, Lukashev AN, Volchkov PY, Zamyatnin AA, Deviatkin AA. Robust AAV Genotyping Based on Genetic Distances in Rep Gene That Are Maintained by Ubiquitous Recombination. Viruses 2022; 14:1038. [PMID: 35632781 PMCID: PMC9143360 DOI: 10.3390/v14051038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 02/01/2023] Open
Abstract
Adeno-associated viruses (AAVs) are a convenient tool for gene therapy delivery. According to the current classification, they are divided into the species AAV A and AAV B within the genus Dependoparvovirus. Historically AAVs were also subdivided on the intraspecies level into 13 serotypes, which differ in tissue tropism and targeted gene delivery capacity. Serotype, however, is not a universal taxonomic category, and their assignment is not always robust. Cross-reactivity has been shown, indicating that classification could not rely on the results of serological tests alone. Moreover, since the isolation of AAV4, all subsequent AAVs were subdivided into serotypes based primarily on genetic differences and phylogenetic reconstructions. An increased interest in the use of AAV as a gene delivery tool justifies the need to improve the existing classification. Here, we suggest genotype-based AAV classification below the species level based on the rep gene. A robust threshold was established as 10% nt differences within the 1248 nt genome fragment, with 4 distinct AAV genotypes identified. This distinct sub-species structure is maintained by ubiquitous recombination within, but not between, rep genes of the suggested genotypes.
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Affiliation(s)
- Marina I. Beloukhova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
| | - Pavel Y. Volchkov
- Genome Engineering Lab, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia;
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Department of Immunology, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Andrei A. Deviatkin
- Genome Engineering Lab, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia;
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia
- Laboratory of Postgenomic Technologies, Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia
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30
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Stiles K, Frenk EZ, Kaminsky SM, Crystal RG. Genetic Modification of the AAV5 Capsid with Lysine Residues Results in a Lung-tropic, Liver-detargeted Gene Transfer Vector. Hum Gene Ther 2022; 33:148-154. [PMID: 35018834 DOI: 10.1089/hum.2021.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Intravenous (IV) administration of naturally occurring adeno-associated virus (AAV) vectors are liver tropic, with a significant proportion of the total vector dose mediating gene expression in liver hepatocytes. AAV capsids that are directed towards other organs such as lung may be useful for therapy of non-liver-based diseases. Based on the knowledge that the lung capillary endothelium is the first capillary bed encountered by an intravenously administered AAV vector, and that the lung endothelium glycocalyx is enriched in negatively charged sialic acid, we hypothesized that adding positively changed lysine residues to the AAV capsid would enhance AAV biodistribution to the lung following intravenous administration. Using site directed mutagenesis, two lysine residues were inserted into variable loop VIII of the AAV serotype 5 capsid vector (AAV5-PK2). Organ distribution of AAV5-PK2 was compared to AAV5, AAVrh.10, AAV2, and AAV2-7m8 4 wk after intravenous administration (1011 gc) to C57Bl/6 male mice. As predicted, following intravenous administration, AAAV5-PK2 had the highest biodistribution in the lung (p<0.02 compared to AAV5, AAVrh.10, AAV2 and AAV2-7m8). Further, biodistribution to liver of AAV5-PK2 was 2-logs decreased compared to AAV5 (p<10-4) with a ratio of AAV5-PK2 lung to liver of 62-fold compared to AAV5 of 0.2-fold (p<0.0003). The AAV5-PK2 capsid represents a lung-tropic AAV vector that is also significantly detargeted from the liver, a property that may be useful in lung directed gene therapies.
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Affiliation(s)
- Katie Stiles
- Weill Cornell Medicine, 12295, New York, New York, United States;
| | - Esther Z Frenk
- Weill Cornell Medical College, 12295, 1300 York Avenue, New York, New York, United States, 10065;
| | | | - Ronald G Crystal
- Weill Medical College of Cornell University, Department of Genetic Medicine, 1300 York Avenue, Box 96, New York, New York, United States, 10021;
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