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Irfan M, Majeed H, Iftikhar T, Ravi PK. A review on molecular scissoring with CRISPR/Cas9 genome editing technology. Toxicol Res (Camb) 2024; 13:tfae105. [PMID: 39006883 PMCID: PMC11240166 DOI: 10.1093/toxres/tfae105] [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: 05/14/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Genome editing is a technology to make specific changes in the DNA of a cell or an organism. It has significantly altered the landscape of life sciences, facilitating the establishment of exceedingly customized genetic modifications. Among various genome editing technologies, the CRISPR/Cas9 system, a specific endonuclease induces a double stranded DNA break and enabling modifications to the genome, has surfaced as a formidable and adaptable instrument. Its significance cannot be overstated, as it not only allows for the manipulation of genomes in model organisms but also holds great potential for revolutionary advances in medicine, particularly in treating genetic diseases. This review paper explores the remarkable journey of CRISPR/Cas9, its natural function, mechanisms, and transformative impact on genome editing and finally the use of artificial intelligence and other intelligent manufacturing tools used. The introduction provides the background on genome editing, emphasizing the emergence and significance of CRISPR/Cas9. Subsequent sections comprehensively elucidate its natural function, disease modeling, agriculture, and biotechnology, address therapeutic applications, and ongoing clinical trials while also discussing prospects and ethical implications. We summarized the key findings, indicating that CRISPR/Cas9 has empowered the creation of disease-specific animal models. This provides invaluable insights into pathogenic mechanisms and opens new avenues for drug discovery, reaffirming the transformative impact of CRISPR/Cas9 on genome editing. Finally we discussed the importance of continued research and collaboration for comprehensive utilization of the inherent capabilities of this molecular precision tool in shaping forthcoming advancements.
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Affiliation(s)
- Muskan Irfan
- Department of Biotechnology, University of Management and Technology (UMT), Lahore, Sialkot Campus, Sialkot 51310, Pakistan
| | - Hammad Majeed
- Department of Chemistry, University of Management and Technology (UMT), Lahore, Sialkot Campus, Sialkot 51310, Pakistan
| | - Tehreema Iftikhar
- Applied Botany Lab, Department of Botany, Government College University, 54000, Lahore, Pakistan
| | - Pritam Kumar Ravi
- Computer Applications Department, Ganesh Lal Agarwal College, Nilamber-Pitamber University, Jharkhand, 822101, India
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Shen G, Liu J, Yang H, Xie N, Yang Y. mRNA therapies: Pioneering a new era in rare genetic disease treatment. J Control Release 2024; 369:696-721. [PMID: 38580137 DOI: 10.1016/j.jconrel.2024.03.056] [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: 11/04/2023] [Revised: 03/16/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Rare genetic diseases, often referred to as orphan diseases due to their low prevalence and limited treatment options, have long posed significant challenges to our medical system. In recent years, Messenger RNA (mRNA) therapy has emerged as a highly promising treatment approach for various diseases caused by genetic mutations. Chemically modified mRNA is introduced into cells using carriers like lipid-based nanoparticles (LNPs), producing functional proteins that compensate for genetic deficiencies. Given the advantages of precise dosing, biocompatibility, transient expression, and minimal risk of genomic integration, mRNA therapies can safely and effectively correct genetic defects in rare diseases and improve symptoms. Currently, dozens of mRNA drugs targeting rare diseases are undergoing clinical trials. This comprehensive review summarizes the progress of mRNA therapy in treating rare genetic diseases. It introduces the development, molecular design, and delivery systems of mRNA therapy, highlighting their research progress in rare genetic diseases based on protein replacement and gene editing. The review also summarizes research progress in various rare disease models and clinical trials. Additionally, it discusses the challenges and future prospects of mRNA therapy. Researchers are encouraged to join this field and collaborate to advance the clinical translation of mRNA therapy, bringing hope to patients with rare genetic diseases.
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Affiliation(s)
- Guobo Shen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jian Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hanmei Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Na Xie
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Yang Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu 610041, China.
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Deneault E. Recent Therapeutic Gene Editing Applications to Genetic Disorders. Curr Issues Mol Biol 2024; 46:4147-4185. [PMID: 38785523 PMCID: PMC11119904 DOI: 10.3390/cimb46050255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Recent years have witnessed unprecedented progress in therapeutic gene editing, revolutionizing the approach to treating genetic disorders. In this comprehensive review, we discuss the progression of milestones leading to the emergence of the clustered regularly interspaced short palindromic repeats (CRISPR)-based technology as a powerful tool for precise and targeted modifications of the human genome. CRISPR-Cas9 nuclease, base editing, and prime editing have taken center stage, demonstrating remarkable precision and efficacy in targeted ex vivo and in vivo genomic modifications. Enhanced delivery systems, including viral vectors and nanoparticles, have further improved the efficiency and safety of therapeutic gene editing, advancing their clinical translatability. The exploration of CRISPR-Cas systems beyond the commonly used Cas9, such as the development of Cas12 and Cas13 variants, has expanded the repertoire of gene editing tools, enabling more intricate modifications and therapeutic interventions. Outstandingly, prime editing represents a significant leap forward, given its unparalleled versatility and minimization of off-target effects. These innovations have paved the way for therapeutic gene editing in a multitude of previously incurable genetic disorders, ranging from monogenic diseases to complex polygenic conditions. This review highlights the latest innovative studies in the field, emphasizing breakthrough technologies in preclinical and clinical trials, and their applications in the realm of precision medicine. However, challenges such as off-target effects and ethical considerations remain, necessitating continued research to refine safety profiles and ethical frameworks.
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Affiliation(s)
- Eric Deneault
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
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Chuecos MA, Lagor WR. Liver directed adeno-associated viral vectors to treat metabolic disease. J Inherit Metab Dis 2024; 47:22-40. [PMID: 37254440 PMCID: PMC10687323 DOI: 10.1002/jimd.12637] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/05/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
The liver is the metabolic center of the body and an ideal target for gene therapy of inherited metabolic disorders (IMDs). Adeno-associated viral (AAV) vectors can deliver transgenes to the liver with high efficiency and specificity and a favorable safety profile. Recombinant AAV vectors contain only the transgene cassette, and their payload is converted to non-integrating circular double-stranded DNA episomes, which can provide stable expression from months to years. Insights from cellular studies and preclinical animal models have provided valuable information about AAV capsid serotypes with a high liver tropism. These vectors have been applied successfully in the clinic, particularly in trials for hemophilia, resulting in the first approved liver-directed gene therapy. Lessons from ongoing clinical trials have identified key factors affecting efficacy and safety that were not readily apparent in animal models. Circumventing pre-existing neutralizing antibodies to the AAV capsid, and mitigating adaptive immune responses to transduced cells are critical to achieving therapeutic benefit. Combining the high efficiency of AAV delivery with genome editing is a promising path to achieve more precise control of gene expression. The primary safety concern for liver gene therapy with AAV continues to be the small risk of tumorigenesis from rare vector integrations. Hepatotoxicity is a key consideration in the safety of neuromuscular gene therapies which are applied at substantially higher doses. The current knowledge base and toolkit for AAV is well developed, and poised to correct some of the most severe IMDs with liver-directed gene therapy.
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Affiliation(s)
- Marcel A. Chuecos
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX USA
- Translational Biology and Molecular Medicine Program, Baylor College of Medicine, Houston, TX USA
| | - William R. Lagor
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX USA
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Gruntman AM, Xue W, Flotte TR. Approaches to Therapeutic Gene Editing in Alpha-1 Antitrypsin Deficiency. Methods Mol Biol 2024; 2750:11-17. [PMID: 38108963 DOI: 10.1007/978-1-0716-3605-3_2] [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] [Indexed: 12/19/2023]
Abstract
Five distinct gene therapy approaches have been developed for treating AATD. These approaches include knockout of the mutant (PiZ) allele by introduction of double-strand breaks (DSBs) and subsequent creation of insertions and deletions (indels) by DSB repair, homology-directed repair (HDR) targeted to the mutation site, base editing, prime editing, and alternatively targeted knock-in techniques. Each approach will be discussed and a brief summary of a standard CRISPR-Cas9 targeting method will be presented.
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Affiliation(s)
- Alisha M Gruntman
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Terence R Flotte
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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Ryø LB, Haslund D, Rovsing AB, Pihl R, Sanrattana W, de Maat S, Palarasah Y, Maas C, Thiel S, Mikkelsen JG. Restriction of C1-inhibitor activity in hereditary angioedema by dominant-negative effects of disease-associated SERPING1 gene variants. J Allergy Clin Immunol 2023; 152:1218-1236.e9. [PMID: 37301409 DOI: 10.1016/j.jaci.2023.04.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Patients with hereditary angioedema experience recurrent, sometimes life-threatening, attacks of edema. It is a rare genetic disorder characterized by genetic and clinical heterogenicity. Most cases are caused by genetic variants in the SERPING1 gene leading to plasma deficiency of the encoded protein C1 inhibitor (C1INH). More than 500 different hereditary angioedema-causing variants have been identified in the SERPING1 gene, but the disease mechanisms by which they result in pathologically low C1INH plasma levels remain largely unknown. OBJECTIVES The aim was to describe trans-inhibitory effects of full-length or near full-length C1INH encoded by 28 disease-associated SERPING1 variants. METHODS HeLa cells were transfected with expression constructs encoding the studied SERPING1 variants. Extensive and comparative studies of C1INH expression, secretion, functionality, and intracellular localization were carried out. RESULTS Our findings characterized functional properties of a subset of SERPING1 variants allowing the examined variants to be subdivided into 5 different clusters, each containing variants sharing specific molecular characteristics. For all variants except 2, we found that coexpression of mutant and normal C1INH negatively affected the overall capacity to target proteases. Strikingly, for a subset of variants, intracellular formation of C1INH foci was detectable only in heterozygous configurations enabling simultaneous expression of normal and mutant C1INH. CONCLUSIONS We provide a functional classification of SERPING1 gene variants suggesting that different SERPING1 variants drive the pathogenicity through different and in some cases overlapping molecular disease mechanisms. For a subset of gene variants, our data define some types of hereditary angioedema with C1INH deficiency as serpinopathies driven by dominant-negative disease mechanisms.
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Affiliation(s)
| | - Didde Haslund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Rasmus Pihl
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Wariya Sanrattana
- CDL Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Steven de Maat
- CDL Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Yaseelan Palarasah
- Department of Cancer and Inflammation Research, University of Southern Denmark, Odense, Denmark; Department of Clinical Biochemistry, Hospital of South West Jutland, Esbjerg, Denmark
| | - Coen Maas
- CDL Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Unit for Thrombosis Research, Department of Regional Health Research, University of Southern Denmark, Esbjerg, Denmark
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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Khlidj Y. What did CRISPR-Cas9 accomplish in its first 10 years? Biochem Med (Zagreb) 2023; 33:030601. [PMID: 37545694 PMCID: PMC10373057 DOI: 10.11613/bm.2023.030601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/01/2023] [Indexed: 08/08/2023] Open
Abstract
It's been 10 years now from the debut of clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) era in which gene engineering has never been so accessible, precise and efficient. This technology, like a refined surgical procedure, has offered the ability of removing different types of disease causing mutations and restoring key proteins activity with ease of outperforming the previous resembling methods: zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Additionally, CRISPR-Cas9 systems can systematically introduce genetic sequences to the specific sites in the human genome allowing to stimulate desired functions such as anti-tumoral and anti-infectious faculties. The present brief review provides an updated resume of CRISPR-Cas9's top achievements from its first appearance to the current date focusing on the breakthrough research including in vitro, in vivo and human studies. This enables the evaluation of the previous phase 'the proof-of-concept phase' and marks the beginning of the next phase which will probably bring a spate of clinical trials.
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Wang J, Wang P, Shao Y, He D. Advancing Treatment Strategies: A Comprehensive Review of Drug Delivery Innovations for Chronic Inflammatory Respiratory Diseases. Pharmaceutics 2023; 15:2151. [PMID: 37631365 PMCID: PMC10458134 DOI: 10.3390/pharmaceutics15082151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Chronic inflammatory respiratory diseases, such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis, present ongoing challenges in terms of effective treatment and management. These diseases are characterized by persistent inflammation in the airways, leading to structural changes and compromised lung function. There are several treatments available for them, such as bronchodilators, immunomodulators, and oxygen therapy. However, there are still some shortcomings in the effectiveness and side effects of drugs. To achieve optimal therapeutic outcomes while minimizing systemic side effects, targeted therapies and precise drug delivery systems are crucial to the management of these diseases. This comprehensive review focuses on the role of drug delivery systems in chronic inflammatory respiratory diseases, particularly nanoparticle-based drug delivery systems, inhaled corticosteroids (ICSs), novel biologicals, gene therapy, and personalized medicine. By examining the latest advancements and strategies in these areas, we aim to provide a thorough understanding of the current landscape and future prospects for improving treatment outcomes in these challenging conditions.
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Affiliation(s)
- Junming Wang
- Center of Emergency and Critical Care Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China; (J.W.); (P.W.); (Y.S.)
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai 201508, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai 201508, China
| | - Pengfei Wang
- Center of Emergency and Critical Care Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China; (J.W.); (P.W.); (Y.S.)
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai 201508, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai 201508, China
| | - Yiru Shao
- Center of Emergency and Critical Care Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China; (J.W.); (P.W.); (Y.S.)
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai 201508, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai 201508, China
| | - Daikun He
- Center of Emergency and Critical Care Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China; (J.W.); (P.W.); (Y.S.)
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai 201508, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai 201508, China
- Department of General Practice, Jinshan Hospital, Fudan University, Shanghai 201508, China
- Department of General Practice, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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McElvaney OF, Fraughen DD, McElvaney OJ, Carroll TP, McElvaney NG. Alpha-1 antitrypsin deficiency: current therapy and emerging targets. Expert Rev Respir Med 2023; 17:191-202. [PMID: 36896570 DOI: 10.1080/17476348.2023.2174973] [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: 03/11/2023]
Abstract
INTRODUCTION Alpha1 antitrypsin deficiency (AATD), a common hereditary disorder affecting mainly lungs, liver and skin has been the focus of some of the most exciting therapeutic approaches in medicine in the past 5 years. In this review, we discuss the therapies presently available for the different manifestations of AATD and new therapies in the pipeline. AREAS COVERED We review therapeutic options for the individual lung, liver and skin manifestations of AATD along with approaches which aim to treat all three. Along with this renewed interest in treating AATD come challenges. How is AAT best delivered to the lung? What is the desired level of AAT in the circulation and lungs which therapeutics should aim to provide? Will treating the liver disease increase the potential for lung disease? Are there treatments to target the underlying genetic defect with the potential to prevent all aspects of AATDrelated disease? EXPERT OPINION With a relatively small population able to participate in clinical studies, increased awareness and diagnosis of AATD is urgently needed. Better, more sensitive clinical parameters will assist in the generation of acceptable and robust evidence of therapeutic effect for current and emerging treatments.
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Affiliation(s)
- Oisín F McElvaney
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Medicine, Beaumont Hospital, Dublin, Ireland
| | - Daniel D Fraughen
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Medicine, Beaumont Hospital, Dublin, Ireland
| | - Oliver J McElvaney
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Medicine, Beaumont Hospital, Dublin, Ireland
| | - Tomás P Carroll
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Medicine, Beaumont Hospital, Dublin, Ireland.,Alpha-1 Foundation Ireland, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Noel G McElvaney
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Medicine, Beaumont Hospital, Dublin, Ireland
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Li Y, Guha C, Asp P, Wang X, Tchaikovskya TL, Kim K, Mendel M, Cost GJ, Perlmutter DH, Roy-Chowdhury N, Fox IJ, Conway A, Roy-Chowdhury J. Resolution of hepatic fibrosis after ZFN-mediated gene editing in the PiZ mouse model of human α1-antitrypsin deficiency. Hepatol Commun 2023; 7:e0070. [PMID: 36848094 PMCID: PMC9974076 DOI: 10.1097/hc9.0000000000000070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/21/2022] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND α1-antitrypsin deficiency is most commonly caused by a mutation in exon-7 of SERPINA1 (SA1-ATZ), resulting in hepatocellular accumulation of a misfolded variant (ATZ). Human SA1-ATZ-transgenic (PiZ) mice exhibit hepatocellular ATZ accumulation and liver fibrosis. We hypothesized that disrupting the SA1-ATZ transgene in PiZ mice by in vivo genome editing would confer a proliferative advantage to the genome-edited hepatocytes, enabling them to repopulate the liver. METHODS To create a targeted DNA break in exon-7 of the SA1-ATZ transgene, we generated 2 recombinant adeno-associated viruses (rAAV) expressing a zinc-finger nuclease pair (rAAV-ZFN), and another rAAV for gene correction by targeted insertion (rAAV-TI). PiZ mice were injected i.v. with rAAV-TI alone or the rAAV-ZFNs at a low (7.5×1010vg/mouse, LD) or a high dose (1.5×1011vg/mouse, HD), with or without rAAV-TI. Two weeks and 6 months after treatment, livers were harvested for molecular, histological, and biochemical analyses. RESULTS Two weeks after treatment, deep sequencing of the hepatic SA1-ATZ transgene pool showed 6%±3% or 15%±4% nonhomologous end joining in mice receiving LD or HD rAAV-ZFN, respectively, which increased to 36%±12% and 36%±12%, respectively, 6 months after treatment. Two weeks postinjection of rAAV-TI with LD or HD of rAAV-ZFN, repair by targeted insertion occurred in 0.10%±0.09% and 0.25%±0.14% of SA1-ATZ transgenes, respectively, which increased to 5.2%±5.0% and 33%±13%, respectively, 6 months after treatment. Six months after rAAV-ZFN administration, there was a marked clearance of ATZ globules from hepatocytes, and resolution of liver fibrosis, along with reduction of hepatic TAZ/WWTR1, hedgehog ligands, Gli2, a TIMP, and collagen content. CONCLUSIONS ZFN-mediated SA1-ATZ transgene disruption provides a proliferative advantage to ATZ-depleted hepatocytes, enabling them to repopulate the liver and reverse hepatic fibrosis.
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Affiliation(s)
- Yanfeng Li
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Chandan Guha
- Department of Radiation Oncology, Albert Einstein College of Medicine, New York, New York, USA
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA
- Marion Bessin Liver Research Center, Albert Einstein College of Medicine, New York, New York, USA
| | - Patrik Asp
- Department of Radiation Oncology, Albert Einstein College of Medicine, New York, New York, USA
- Marion Bessin Liver Research Center, Albert Einstein College of Medicine, New York, New York, USA
| | - Xia Wang
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Tatyana L. Tchaikovskya
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
- Marion Bessin Liver Research Center, Albert Einstein College of Medicine, New York, New York, USA
| | - Kenneth Kim
- Sangamo Therapeutics, Richmond, California, USA
| | | | | | - David H. Perlmutter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Namita Roy-Chowdhury
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
- Marion Bessin Liver Research Center, Albert Einstein College of Medicine, New York, New York, USA
- Department of Genetics, Albert Einstein College of Medicine, New York, New York, USA
| | - Ira J. Fox
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Jayanta Roy-Chowdhury
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
- Marion Bessin Liver Research Center, Albert Einstein College of Medicine, New York, New York, USA
- Department of Genetics, Albert Einstein College of Medicine, New York, New York, USA
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Pires Ferreira D, Gruntman AM, Flotte TR. Gene therapy for alpha-1 antitrypsin deficiency: an update. Expert Opin Biol Ther 2023; 23:283-291. [PMID: 36825473 DOI: 10.1080/14712598.2023.2183771] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION Altering the human genetic code has been explored since the early 1990s as a definitive answer for the treatment of monogenic and acquired diseases which do not respond to conventional therapies. In Alpha-1 antitrypsin deficiency (AATD) the proper synthesis and secretion of alpha-1 antitrypsin (AAT) protein is impaired, leading to its toxic hepatic accumulation along with its pulmonary insufficiency, which is associated with parenchymal proteolytic destruction. Because AATD is caused by mutations in a single gene whose correction alone would normalize the mutant phenotype, it has become a popular target for both augmentation gene therapy and gene editing. Although gene therapy products are already a reality for the treatment of some pathologies, such as inherited retinal dystrophy and spinal muscular atrophy, AATD-related pulmonary and, especially, liver diseases still lack effective therapeutic options. AREAS COVERED Here, we review the course, challenges, and achievements of AATD gene therapy as well as update on new strategies being developed. EXPERT OPINION Reaching safe and clinically effective expression of the AAT is currently the greatest challenge for AATD gene therapy. The improvement and emergence of technologies that use gene introduction, silencing and correction hold promise for the treatment of AATD.
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Affiliation(s)
- Debora Pires Ferreira
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Alisha M Gruntman
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Terence R Flotte
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States
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12
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Çerçi B, Uzay IA, Kara MK, Dinçer P. Clinical trials and promising preclinical applications of CRISPR/Cas gene editing. Life Sci 2022; 312:121204. [PMID: 36403643 DOI: 10.1016/j.lfs.2022.121204] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/03/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Treatment of genetic disorders by genomic manipulation has been the unreachable goal of researchers for many decades. Although our understanding of the genetic basis of genetic diseases has advanced tremendously in the last few decades, the tools developed for genomic editing were not efficient and practical for their use in the clinical setting until now. The recent advancements in the research of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems offered an easy and efficient way to edit the genome and accelerated the research on their potential use in the treatment of genetic disorders. In this review, we summarize the clinical trials that evaluate the CRISPR/Cas systems for treating different genetic diseases and highlight promising preclinical research on CRISPR/Cas mediated treatment of a great diversity of genetic disorders. Ultimately, we discuss the future of CRISPR/Cas mediated genome editing in genetic diseases.
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Affiliation(s)
- Barış Çerçi
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey.
| | - Ihsan Alp Uzay
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | | | - Pervin Dinçer
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
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Zabaleta N, Torella L, Weber ND, Gonzalez‐Aseguinolaza G. mRNA and gene editing: Late breaking therapies in liver diseases. Hepatology 2022; 76:869-887. [PMID: 35243655 PMCID: PMC9546265 DOI: 10.1002/hep.32441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
The efficient delivery of RNA molecules to restore the expression of a missing or inadequately functioning protein in a target cell and the intentional specific modification of the host genome using engineered nucleases represent therapeutic concepts that are revolutionizing modern medicine. The initiation of several clinical trials using these approaches to treat metabolic liver disorders as well as the recently reported remarkable results obtained by patients with transthyretin amyloidosis highlight the advances in this field and show the potential of these therapies to treat these diseases safely and efficaciously. These advances have been possible due, firstly, to significant improvements made in RNA chemistry that increase its stability and prevent activation of the innate immune response and, secondly, to the development of very efficient liver-targeted RNA delivery systems. In parallel, the breakout of CRISPR/CRISPR-associated 9-based technology in the gene editing field has marked a turning point in in vivo modification of the cellular genome with therapeutic purposes, which can be based on gene supplementation, correction, or silencing. In the coming years we are likely to witness the therapeutic potential of these two strategies both separately and in combination. In this review we summarize the preclinical data obtained in animal models treated with mRNA as a therapeutic agent and discuss the different gene editing strategies applied to the treatment of liver diseases, highlighting both their therapeutic efficacy as well as safety concerns.
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Affiliation(s)
- Nerea Zabaleta
- Grousbeck Gene Therapy CenterSchepens Eye Research InstituteMass Eye and EarBostonMassachusettsUSA
| | - Laura Torella
- Gene Therapy and Regulation of Gene expression Program, Foundation for Applied Medical ResearchUniversity of NavarraIdisNAPamplonaSpain
| | | | - Gloria Gonzalez‐Aseguinolaza
- Gene Therapy and Regulation of Gene expression Program, Foundation for Applied Medical ResearchUniversity of NavarraIdisNAPamplonaSpain,Vivet TherapeuticsPamplonaSpain
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14
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Novel Gene-Correction-Based Therapeutic Modalities for Monogenic Liver Disorders. Bioengineering (Basel) 2022; 9:bioengineering9080392. [PMID: 36004917 PMCID: PMC9404740 DOI: 10.3390/bioengineering9080392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
The majority of monogenic liver diseases are autosomal recessive disorders, with few being sex-related or co-dominant. Although orthotopic liver transplantation (LT) is currently the sole therapeutic option for end-stage patients, such an invasive surgical approach is severely restricted by the lack of donors and post-transplant complications, mainly associated with life-long immunosuppressive regimens. Therefore, the last decade has witnessed efforts for innovative cellular or gene-based therapeutic strategies. Gene therapy is a promising approach for treatment of many hereditary disorders, such as monogenic inborn errors. The liver is an organ characterized by unique features, making it an attractive target for in vivo and ex vivo gene transfer. The current genetic approaches for hereditary liver diseases are mediated by viral or non-viral vectors, with promising results generated by gene-editing tools, such as CRISPR-Cas9 technology. Despite massive progress in experimental gene-correction technologies, limitations in validated approaches for monogenic liver disorders have encouraged researchers to refine promising gene therapy protocols. Herein, we highlighted the most common monogenetic liver disorders, followed by proposed genetic engineering approaches, offered as promising therapeutic modalities.
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15
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Davis JR, Wang X, Witte IP, Huang TP, Levy JM, Raguram A, Banskota S, Seidah NG, Musunuru K, Liu DR. Efficient in vivo base editing via single adeno-associated viruses with size-optimized genomes encoding compact adenine base editors. Nat Biomed Eng 2022; 6:1272-1283. [PMID: 35902773 DOI: 10.1038/s41551-022-00911-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/19/2022] [Indexed: 12/26/2022]
Abstract
The viral delivery of base editors has been complicated by their size and by the limited packaging capacity of adeno-associated viruses (AAVs). Typically, dual-AAV approaches based on trans-splicing inteins have been used. Here we show that, compared with dual-AAV systems, AAVs with size-optimized genomes incorporating compact adenine base editors (ABEs) enable efficient editing in mice at similar or lower doses. Single-AAV-encoded ABEs retro-orbitally injected in mice led to editing efficiencies in liver (66%), heart (33%) and muscle (22%) tissues that were up to 2.5-fold those of dual-AAV ABE8e, and to a 93% knockdown (on average) of human PCSK9 and of mouse Pcsk9 and Angptl3 in circulation, concomitant with substantial reductions of plasma cholesterol and triglycerides. Moreover, three size-minimized ABE8e variants, each compatible with single-AAV delivery, collectively offer compatibility with protospacer-adjacent motifs for editing approximately 82% of the adenines in the human genome. ABEs encoded within single AAVs will facilitate research and therapeutic applications of base editing by simplifying AAV production and characterization, and by reducing the dose required for the desired level of editing.
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Affiliation(s)
- Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Isaac P Witte
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jonathan M Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Nabil G Seidah
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), University of Montreal, Montreal, Quebec, Canada
| | - Kiran Musunuru
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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16
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Shin JH, Lee J, Jung YK, Kim KS, Jeong J, Choi D. Therapeutic applications of gene editing in chronic liver diseases: an update. BMB Rep 2022. [PMID: 35651324 PMCID: PMC9252892 DOI: 10.5483/bmbrep.2022.55.6.033] [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] [Indexed: 11/23/2022] Open
Abstract
Innovative genome editing techniques developed in recent decades have revolutionized the biomedical research field. Liver is the most favored target organ for genome editing owing to its ability to regenerate. The regenerative capacity of the liver enables ex vivo gene editing in which the mutated gene in hepatocytes isolated from the animal model of genetic disease is repaired. The edited hepatocytes are injected back into the animal to mitigate the disease. Furthermore, the liver is considered as the easiest target organ for gene editing as it absorbs almost all foreign molecules. The mRNA vaccines, which have been developed to manage the COVID-19 pandemic, have provided a novel gene editing strategy using Cas mRNA. A single injection of gene editing components with Cas mRNA is reported to be efficient in the treatment of patients with genetic liver diseases. In this review, we first discuss previously reported gene editing tools and cases managed using them, as well as liver diseases caused by genetic mutations. Next, we summarize the recent successes of ex vivo and in vivo gene editing approaches in ameliorating liver diseases in animals and humans.
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Affiliation(s)
- Ji Hyun Shin
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Jinho Lee
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Yun Kyung Jung
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Kyeong Sik Kim
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
- Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Korea
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17
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Packer MS, Chowdhary V, Lung G, Cheng LI, Aratyn-Schaus Y, Leboeuf D, Smith S, Shah A, Chen D, Zieger M, Cafferty BJ, Yan B, Ciaramella G, Gregoire FM, Mueller C. Evaluation of cytosine base editing and adenine base editing as a potential treatment for alpha-1 antitrypsin deficiency. Mol Ther 2022; 30:1396-1406. [PMID: 35121111 PMCID: PMC9077367 DOI: 10.1016/j.ymthe.2022.01.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/06/2021] [Accepted: 01/28/2022] [Indexed: 11/16/2022] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is a rare autosomal codominant disease caused by mutations within the SERPINA1 gene. The most prevalent variant in patients is PiZ SERPINA1, containing a single G > A transition mutation. PiZ alpha-1 antitrypsin (AAT) is prone to misfolding, leading to the accumulation of toxic aggregates within hepatocytes. In addition, the abnormally low level of AAT secreted into circulation provides insufficient inhibition of neutrophil elastase within the lungs, eventually causing emphysema. Cytosine and adenine base editors enable the programmable conversion of C⋅G to T⋅A and A⋅T to G⋅C base pairs, respectively. In this study, two different base editing approaches were developed: use of a cytosine base editor to install a compensatory mutation (p.Met374Ile) and use of an adenine base editor to mediate the correction of the pathogenic PiZ mutation. After treatment with lipid nanoparticles formulated with base editing reagents, PiZ-transgenic mice exhibited durable editing of SERPINA1 in the liver, increased serum AAT, and improved liver histology. These results indicate that base editing has the potential to address both lung and liver disease in AATD.
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Affiliation(s)
| | - Vivek Chowdhary
- Gene Therapy Department, UMass Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Genesis Lung
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Lo-I Cheng
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | | | | | - Sarah Smith
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Aalok Shah
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Delai Chen
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Marina Zieger
- Gene Therapy Department, UMass Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | | | - Bo Yan
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | | | | | - Christian Mueller
- Gene Therapy Department, UMass Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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18
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White BM, Morrisey EE, Peranteau WH. In Utero Gene Editing for Inherited Lung Diseases. CURRENT STEM CELL REPORTS 2022. [DOI: 10.1007/s40778-021-00205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Stevanovic M, Piotter E, McClements ME, MacLaren RE. CRISPR Systems Suitable for Single AAV Vector Delivery. Curr Gene Ther 2021; 22:1-14. [PMID: 34620062 DOI: 10.2174/1566523221666211006120355] [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: 05/19/2021] [Revised: 07/30/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas gene editing is a revolutionary technology that can enable the correction of genetic mutations in vivo, providing great promise as a therapeutic intervention for inherited diseases. Adeno-associated viral (AAV) vectors are a potential vehicle for delivering CRISPR/Cas. However, they are restricted by their limited packaging capacity. Identifying smaller Cas orthologs that can be packaged, along with the required guide RNA elements, into a single AAV would be an important optimization for CRISPR/Cas gene editing. Expanding the options of Cas proteins that can be delivered by a single AAV not only increases translational application but also expands the genetic sites that can be targeted for editing. This review considers the benefits and current scope of small Cas protein orthologs that are suitable for gene editing approaches using single AAV vector delivery.
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Affiliation(s)
- Marta Stevanovic
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford. United Kingdom
| | - Elena Piotter
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford. United Kingdom
| | - Michelle E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford. United Kingdom
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford. United Kingdom
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20
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Patel D, Teckman J. Liver disease with unknown etiology - have you ruled out alpha-1 antitrypsin deficiency? Ther Adv Chronic Dis 2021; 12_suppl:2040622321995684. [PMID: 34408828 PMCID: PMC8367207 DOI: 10.1177/2040622321995684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/12/2021] [Indexed: 01/13/2023] Open
Abstract
Although a less well-known consequence of alpha-1 antitrypsin deficiency (AATD) liver disease is the second leading cause of death among patients with the condition. The alpha-1 antitrypsin (AAT) protein is produced by hepatocytes within the liver, which retain pathological variants of AAT instead of secreting the proteinase inhibitor into the systemic circulation. This intracellular retention is caused by inefficient folding and polymerization of mutant AAT and the accumulation of these AAT aggregates leads to diverse manifestations of liver disease, which can present differently in both children and adults. The progression from hepatocyte apoptosis to liver inflammation, fibrosis and cirrhosis, and liver failure is still not fully understood, but in older patients, liver disease can surpass lung disease as the principal cause of death. Liver function tests (LFTs) can measure plasma levels of liver enzymes to assess liver function but require careful interpretation. Non-invasive tests are being developed that can detect early liver disease, but liver biopsy is still the gold standard for assessing liver fibrosis once abnormal LFTs have been detected in a patient. Currently, there is no licensed treatment for AATD-related liver disease (intravenous AAT therapy is not indicated for this purpose), but liver transplantation is associated with positive outcomes and may even slow emphysema progression. Therefore, new strategies are being developed to address treatment of AATD-related liver disease, such as accelerating degradation of mutant AAT and assisting hepatocytes in the folding and secretion of mutant AAT, but these approaches remain at early stages of development.
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Affiliation(s)
- Dhiren Patel
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, St Louis University School of Medicine, St Louis, MO, USA
| | - Jeffrey Teckman
- Department of Pediatrics and Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, MO, USA
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21
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Rahaghi FF. Alpha-1 antitrypsin deficiency research and emerging treatment strategies: what's down the road? Ther Adv Chronic Dis 2021; 12_suppl:20406223211014025. [PMID: 34408832 PMCID: PMC8367209 DOI: 10.1177/20406223211014025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/08/2021] [Indexed: 01/29/2023] Open
Abstract
Intravenous infusion of alpha-1 antitrypsin (AAT) was approved by the United States Food and Drug Administration (FDA) to treat emphysema associated with AAT deficiency (AATD) in 1987 and there are now several FDA-approved therapy products on the market, all of which are derived from pooled human plasma. Intravenous AAT therapy has proven clinical efficacy in slowing the decline of lung function associated with AATD progression; however, it is only recommended for individuals with the most severe forms of AATD as there is a lack of evidence that this treatment is effective in treating wild-type heterozygotes (e.g., PI*MS and PI*MZ genotypes), for which the prevalence may be much higher than previously thought. There are large numbers of individuals that are currently left untreated despite displaying symptoms of AATD. Furthermore, not all countries offer AAT augmentation therapy due to its expense and inconvenience for patients. More cost-effective treatments are now being sought that show efficacy for less severe forms of AATD and many new therapeutic technologies are being investigated, such as gene repair and other interference strategies, as well as the use of chemical chaperones. New sources of AAT are also being investigated to ensure there are enough supplies to meet future demand, and new methods of assessing response to treatment are being evaluated. There is currently extensive research into AATD and its treatment, and this chapter aims to highlight important emerging treatment strategies that aim to improve the lives of patients with AATD.
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Affiliation(s)
- Franck F Rahaghi
- Advanced Lung Disease Clinic, Cleveland Clinic Florida, 2950 Cleveland Clinic Boulevard, Weston, FL 33331, USA
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22
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Werder RB, Kaserman JE, Packer MS, Lindstrom-Vautrin J, Villacorta-Martin C, Young LE, Aratyn-Schaus Y, Gregoire F, Wilson AA. Adenine Base Editing Reduces Misfolded Protein Accumulation and Toxicity in Alpha-1 Antitrypsin Deficient Patient iPSC-Hepatocytes. Mol Ther 2021; 29:3219-3229. [PMID: 34217893 PMCID: PMC8571173 DOI: 10.1016/j.ymthe.2021.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/10/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is most commonly caused by the Z mutation, a single-base substitution that leads to AAT protein misfolding and associated liver and lung disease. In this study, we apply adenine base editors to correct the Z mutation in patient induced pluripotent stem cells (iPSCs) and iPSC-derived hepatocytes (iHeps). We demonstrate that correction of the Z mutation in patient iPSCs reduces aberrant AAT accumulation and increases its secretion. Adenine base editing (ABE) of differentiated iHeps decreases ER stress in edited cells, as demonstrated by single-cell RNA sequencing. We find ABE to be highly efficient in iPSCs and do not identify off-target genomic mutations by whole-genome sequencing. These results reveal the feasibility and utility of base editing to correct the Z mutation in AATD patient cells.
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Affiliation(s)
- Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Joseph E Kaserman
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | | | | | | | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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23
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Franciosi AN, Fraughen D, Carroll TP, McElvaney NG. Alpha-1 antitrypsin deficiency: clarifying the role of the putative protective threshold. Eur Respir J 2021; 59:13993003.01410-2021. [PMID: 34172471 DOI: 10.1183/13993003.01410-2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/16/2021] [Indexed: 11/05/2022]
Abstract
AATD is the only readily identifiable monogenic cause of COPD. To date the only condition-specific treatment for AATD-associated COPD is weekly administration of intravenous purified pooled human AAT (IV-AAT). Uncertainties regarding which AATD genotypes should benefit from IV-AAT persist. IV-AAT is costly and involves weekly administration of a plasma product. Much of the risk stratification has been centred around the long-accepted hypothesis of a "putative protective threshold" of 11 µM (0.57 g·L-1) in serum. This hypothesis has become central to the paradigm of AATD care, though its derivation and accuracy for defining risk of disease remain unclear.We review the literature and examine the association between the 11 µM threshold and clinical outcomes to provide context and insight into the issues surrounding this topic.We found no data which demonstrates an increased risk of COPD dependent on the 11 µM threshold. Moreover, an abundance of recent clinical data examining this threshold refutes the hypothesis. Conversely, the use of 11 µM as a treatment target in appropriate ZZ individuals is supported by clinical evidence, although more refined dosing regimens are being explored.Continued use of the 11 µM threshold as a determinant of clinical risk is questionable, perpetuates inappropriate AAT-augmentation practices, may drive increased healthcare expenditure and should not be used as an indicator for commencing treatment.Genotype represents a more proven indicator of risk, with ZZ and rare ZZ-equivalent genotypes independently associated with COPD. New and better risk assessment models are needed to provide individuals diagnosed with AATD with reliable risk estimation and optimised treatment goals.
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Affiliation(s)
- Alessandro N Franciosi
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,University of British Columbia, Vancouver, BC, Canada.,Share first authorship.,Performed the literature review and jointly prepared the manuscript
| | - Daniel Fraughen
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Medicine, Beaumont Hospital, Dublin, Ireland.,Share first authorship.,Performed the literature review and jointly prepared the manuscript
| | - Tomás P Carroll
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland .,Alpha-1 Foundation Ireland, Royal College of Surgeons in Ireland, Dublin, Ireland.,Provided data from the Irish National Targeted Detection Programme, edited the manuscript, and is the corresponding author
| | - Noel G McElvaney
- Irish Centre for Genetic Lung Disease, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Medicine, Beaumont Hospital, Dublin, Ireland.,Senior author and edited the final manuscript
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24
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McNulty MJ, Silberstein DZ, Kuhn BT, Padgett HS, Nandi S, McDonald KA, Cross CE. Alpha-1 antitrypsin deficiency and recombinant protein sources with focus on plant sources: Updates, challenges and perspectives. Free Radic Biol Med 2021; 163:10-30. [PMID: 33279618 DOI: 10.1016/j.freeradbiomed.2020.11.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022]
Abstract
Alpha-1 antitrypsin deficiency (A1ATD) is an autosomal recessive disease characterized by low plasma levels of A1AT, a serine protease inhibitor representing the most abundant circulating antiprotease normally present at plasma levels of 1-2 g/L. The dominant clinical manifestations include predispositions to early onset emphysema due to protease/antiprotease imbalance in distal lung parenchyma and liver disease largely due to unsecreted polymerized accumulations of misfolded mutant A1AT within the endoplasmic reticulum of hepatocytes. Since 1987, the only FDA licensed specific therapy for the emphysema component has been infusions of A1AT purified from pooled human plasma at the 2020 cost of up to US $200,000/year with the risk of intermittent shortages. In the past three decades various, potentially less expensive, recombinant forms of human A1AT have reached early stages of development, one of which is just reaching the stage of human clinical trials. The focus of this review is to update strategies for the treatment of the pulmonary component of A1ATD with some focus on perspectives for therapeutic production and regulatory approval of a recombinant product from plants. We review other competitive technologies for treating the lung disease manifestations of A1ATD, highlight strategies for the generation of data potentially helpful for securing FDA Investigational New Drug (IND) approval and present challenges in the selection of clinical trial strategies required for FDA licensing of a New Drug Approval (NDA) for this disease.
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Affiliation(s)
- Matthew J McNulty
- Department of Chemical Engineering, University of California, Davis, CA, USA
| | - David Z Silberstein
- Department of Chemical Engineering, University of California, Davis, CA, USA
| | - Brooks T Kuhn
- Department of Internal Medicine, University of California, Davis, CA, USA; University of California, Davis, Alpha-1 Deficiency Clinic, Sacramento, CA, USA
| | | | - Somen Nandi
- Department of Chemical Engineering, University of California, Davis, CA, USA; Global HealthShare Initiative®, University of California, Davis, CA, USA
| | - Karen A McDonald
- Department of Chemical Engineering, University of California, Davis, CA, USA; Global HealthShare Initiative®, University of California, Davis, CA, USA
| | - Carroll E Cross
- Department of Internal Medicine, University of California, Davis, CA, USA; University of California, Davis, Alpha-1 Deficiency Clinic, Sacramento, CA, USA; Department of Physiology and Membrane Biology, University of California, Davis, CA, USA.
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25
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Delivery of genome-editing biomacromolecules for treatment of lung genetic disorders. Adv Drug Deliv Rev 2021; 168:196-216. [PMID: 32416111 DOI: 10.1016/j.addr.2020.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 02/06/2023]
Abstract
Genome-editing systems based on clustered, regularly interspaced, short palindromic repeat (CRISPR)/associated protein (CRISPR/Cas), are emerging as a revolutionary technology for the treatment of various genetic diseases. To date, the delivery of genome-editing biomacromolecules by viral or non-viral vectors have been proposed as new therapeutic options for lung genetic disorders, such as cystic fibrosis (CF) and α-1 antitrypsin deficiency (AATD), and it has been accepted that these delivery vectors can introduce CRISPR/Cas9 machineries into target cells or tissues in vitro, ex vivo and in vivo. However, the efficient local or systemic delivery of CRISPR/Cas9 elements to the lung, enabled by either viral or by non-viral carriers, still remains elusive. Herein, we first introduce lung genetic disorders and their current treatment options, and then summarize CRISPR/Cas9-based strategies for the therapeutic genome editing of these disorders. We further summarize the pros and cons of different routes of administration for lung genetic disorders. In particular, the potentials of aerosol delivery for therapeutic CRISPR/Cas9 biomacromolecules for lung genome editing are discussed and highlighted. Finally, current challenges and future outlooks in this emerging area are briefly discussed.
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Abstract
AAT (alpha-1 antitrypsin) deficiency (AATD), characterized by low levels of circulating serine protease inhibitor AAT, results in emphysematous destruction of the lung. Inherited serum deficiency disorders, such as hemophilia and AATD, have been considered ideal candidates for gene therapy. Although viral vector-meditated transduction of the liver has demonstrated utility in hemophilia, similar success has not been achieved for AATD. The challenge for AAT gene therapy is achieving protective levels of AAT locally in the lung and mitigating potential liver toxicities linked to systemically administered viral vectors. Current strategies with ongoing clinical trials involve different routes of adeno-associated virus administrations, such as intramuscular and intrapleural injections, to provide consistent therapeutic levels from nonhepatic organ sites. Nevertheless, exploration of alternative methods of nonhepatic sourcing of AAT has been of great interest in the field. In this regard, pulmonary endothelium-targeted adenovirus vector could be a key technical mandate to achieve local augmentation of AAT within the lower respiratory tract, with the potential benefit of circumventing liver toxicities. In addition, incorporation of the CRISPR/Cas9 (CRISPR-associated protein 9) nuclease system into gene-delivery technologies has provided adjunctive technologies that could fully realize a one-time treatment for sustained, lifelong expression of AAT in patients with AATD. This review will focus on the adeno-associated virus- and adenoviral vector-mediated gene therapy strategies for the pulmonary manifestations of AATD and show that endeavoring to use genome-editing techniques will advance the current strategy to one fully compatible with direct human translation.
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Affiliation(s)
- Reka Lorincz
- Department of Radiation Oncology, Biologic Therapeutics Center, School of Medicine, Washington University, St. Louis, Missouri
| | - David T Curiel
- Department of Radiation Oncology, Biologic Therapeutics Center, School of Medicine, Washington University, St. Louis, Missouri
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27
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Piccolo P, Rossi A, Brunetti-Pierri N. Liver-directed gene-based therapies for inborn errors of metabolism. Expert Opin Biol Ther 2020; 21:229-240. [PMID: 32880494 DOI: 10.1080/14712598.2020.1817375] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Inborn errors of metabolism include several genetic disorders due to disruption of cellular biochemical reactions. Although individually rare, collectively they are a large and heterogenous group of diseases affecting a significant proportion of patients. Available treatments are often unsatisfactory. Liver-directed gene therapy has potential for treatment of several inborn errors of metabolism. While lentiviral vectors and lipid nanoparticle-mRNA have shown attractive features in preclinical studies and still have to be investigated in humans, adeno-associated virus (AAV) vectors have shown clinical success in both preclinical and clinical trials for in vivo liver-directed gene therapy. AREAS COVERED In this review, we discussed the most relevant clinical applications and the challenges of liver-directed gene-based approaches for therapy of inborn errors of metabolism. EXPERT OPINION Challenges and prospects of clinical gene therapy trials and preclinical studies that are believed to have the greatest potential for clinical translation are presented.
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Affiliation(s)
- Pasquale Piccolo
- Telethon Institute of Genetics and Medicine , Pozzuoli, Italy.,Department of Translational Medicine, Federico II University of Naples , Naples, Italy
| | - Alessandro Rossi
- Department of Translational Medicine, Federico II University of Naples , Naples, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine , Pozzuoli, Italy.,Department of Translational Medicine, Federico II University of Naples , Naples, Italy
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28
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Vu A, McCray PB. New Directions in Pulmonary Gene Therapy. Hum Gene Ther 2020; 31:921-939. [PMID: 32814451 PMCID: PMC7495918 DOI: 10.1089/hum.2020.166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
The lung has long been a target for gene therapy, yet efficient delivery and phenotypic disease correction has remained challenging. Although there have been significant advancements in gene therapies of other organs, including the development of several ex vivo therapies, in vivo therapeutics of the lung have been slower to transition to the clinic. Within the past few years, the field has witnessed an explosion in the development of new gene addition and gene editing strategies for the treatment of monogenic disorders. In this review, we will summarize current developments in gene therapy for cystic fibrosis, alpha-1 antitrypsin deficiency, and surfactant protein deficiencies. We will explore the different gene addition and gene editing strategies under investigation and review the challenges of delivery to the lung.
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Affiliation(s)
- Amber Vu
- Stead Family Department of Pediatrics, Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
| | - Paul B. McCray
- Stead Family Department of Pediatrics, Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
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29
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Hirakawa M, Krishnakumar R, Timlin J, Carney J, Butler K. Gene editing and CRISPR in the clinic: current and future perspectives. Biosci Rep 2020; 40:BSR20200127. [PMID: 32207531 PMCID: PMC7146048 DOI: 10.1042/bsr20200127] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.
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Affiliation(s)
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, Livermore, CA 94551, U.S.A
| | - Jerilyn A. Timlin
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - James P. Carney
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - Kimberly S. Butler
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
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30
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Trevisan M, Masi G, Palù G. Genome editing technologies to treat rare liver diseases. Transl Gastroenterol Hepatol 2020; 5:23. [PMID: 32258527 DOI: 10.21037/tgh.2019.10.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Liver has a central role in protein and lipid metabolism, and diseases involving hepatocytes have often repercussions on multiple organs and systems. Hepatic disorders are frequently characterized by production of defective or non-functional proteins, and traditional gene therapy approaches have been attempted for years to restore adequate protein levels through delivery of transgenes. Recently, many different genome editing platforms have been developed aimed at correcting at DNA level the defects underlying the diseases. In this Review we discuss the latest applications of these tools applied to develop therapeutic strategies for rare liver disorders, in particular updating the literature with the most recent strategies relying on base editors technology.
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Affiliation(s)
- Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
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31
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Dai W, Wu J, Wang D, Wang J. Cancer gene therapy by NF-κB-activated cancer cell-specific expression of CRISPR/Cas9 targeting telomeres. Gene Ther 2020; 27:266-280. [DOI: 10.1038/s41434-020-0128-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023]
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32
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Identification of Protein Expression Changes in Hepatocellular Carcinoma through iTRAQ. DISEASE MARKERS 2020; 2020:2632716. [PMID: 32076459 PMCID: PMC7008262 DOI: 10.1155/2020/2632716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/28/2019] [Accepted: 01/03/2020] [Indexed: 12/21/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is a malignant tumor associated with a poor prognosis. Serum biomarkers of HCC have the potential to improve the diagnosis, provide a means to monitor the tumors, and predict their malignancy. Proteins that are expressed differentially between HCC patients and normal controls have the potential to be biomarkers. Method Serum samples from 10 confirmed HCC patients and 10 controls were collected. The differentially expressed proteins in the serum were identified using an isobaric tags for relative and absolute quantitation- (iTRAQ-) based method. Potential serum biomarkers were validated by ELISA in another 20 HCC patients and 20 controls. Their expression data in HCC were extracted from The Cancer Genome Atlas (TCGA) dataset. Results A total of 260 proteins were measured in the serum of HCC patients and compared to those in sex- and age-matched normal controls. Forty-one proteins displayed significant changes, with 26 being downregulated and 15 being upregulated. Upregulated proteins included alpha-1-antitrypsin (A1AT) and peroxiredoxin 2 (PRDX2), and downregulated proteins included paraoxonase 1 (PON1) and C-reactive protein (CRP). We then used ELISA to measure serum levels of A1AT, PRDX2, PON1, and CRP in another 20 patients with HCC and found that only PON1 levels were consistent with the iTRAQ result. In TCGA dataset, PON1 expression was downregulated in HCC tissues (P < 0.001) and low expression of PON1 was associated with poor survival in HCC patients (P < 0.001) and low expression of PON1 was associated with poor survival in HCC patients ( Conclusions PON1 could act as a biomarker for HCC to assist in the diagnosis of HCC.
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Wang C, Zhao P, Sun S, Teckman J, Balch WE. Leveraging Population Genomics for Individualized Correction of the Hallmarks of Alpha-1 Antitrypsin Deficiency. CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2020; 7:224-246. [PMID: 32726074 DOI: 10.15326/jcopdf.7.3.2019.0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deep medicine is rapidly moving towards a high-definition approach for therapeutic management of the patient as an individual given the rapid progress of genome sequencing technologies and machine learning algorithms. While considered a monogenic disease, alpha-1 antitrypsin (AAT) deficiency (AATD) patients present with complex and variable phenotypes we refer to as the "hallmarks of AATD" that involve distinct molecular mechanisms in the liver, plasma and lung tissues, likely due to both coding and non-coding variation as well as genetic and environmental modifiers in different individuals. Herein, we briefly review the current therapeutic strategies for the management of AATD. To embrace genetic diversity in the management of AATD, we provide an overview of the disease phenotypes of AATD patients harboring different AAT variants. Linking genotypic diversity to phenotypic diversity illustrates the potential for sequence-specific regions of AAT protein fold design to play very different roles during nascent synthesis in the liver and/or function in post-liver plasma and lung environments. We illustrate how to manage diversity with recently developed machine learning (ML) approaches that bridge sequence-to-function-to-structure knowledge gaps based on the principle of spatial covariance (SCV). SCV relationships provide a deep understanding of the genotype to phenotype transformation initiated by AAT variation in the population to address the role of genetic and environmental modifiers in the individual. Embracing the complexity of AATD in the population is critical for risk management and therapeutic intervention to generate a high definition medicine approach for the patient.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Jeffrey Teckman
- Pediatrics and Biochemistry, Saint Louis University, and Cardinal Glennon Children's Medical Center, St. Louis, Missouri
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, California
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34
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CRISPR Diagnosis and Therapeutics with Single Base Pair Precision. Trends Mol Med 2019; 26:337-350. [PMID: 31791730 DOI: 10.1016/j.molmed.2019.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Clustered regularly interspaced short palindromic repeats, or CRISPR, has been widely accepted as a versatile genome editing tool with significant potential for medical application. Reliable allele specificity is one of the most critical elements for successful application of this technology to develop high-precision therapeutics and diagnostics. CRISPR-based genome editing tools achieve high-fidelity distinction of single-base differences in target genomic loci by structural identification of CRISPR-associated (Cas) proteins and sequences of the guide RNAs. In this review, we describe the structural features of ribonucleoprotein complex formation by CRISPR proteins and guide RNAs that eventually recognize target DNA sequences. This structural understanding provides the basis for the recent applications of enhanced single-base precision genome editing technologies for effective distinction of specific alleles.
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35
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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: 1181] [Impact Index Per Article: 236.2] [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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36
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Zabaleta N, Hommel M, Salas D, Gonzalez-Aseguinolaza G. Genetic-Based Approaches to Inherited Metabolic Liver Diseases. Hum Gene Ther 2019; 30:1190-1203. [DOI: 10.1089/hum.2019.140] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Nerea Zabaleta
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona, Spain
| | - Mirja Hommel
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona, Spain
| | - David Salas
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona, Spain
| | - Gloria Gonzalez-Aseguinolaza
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona, Spain
- Vivet Therapeutics, Pamplona, Spain
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37
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Ubags N, Platé M, Almendros I, Bartel S. Why ERS Early Career Members should attend the International Congress 2019 in Madrid. Breathe (Sheff) 2019; 15:128-130. [PMID: 31191724 PMCID: PMC6544792 DOI: 10.1183/20734735.0018-2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The European Respiratory Society (ERS) International Congress will take place from September 28 to October 2, 2019, in Madrid, Spain, and as every year, the rich and diverse programme will be full of opportunities for ERS Early Career Members (ECMs). Alongside all the outstanding scientific sessions, which are aimed at physicians, physician-researchers and basic researchers in all fields related to pulmonary medicine, the Early Career Member Committee (ECMC) also organises several sessions dedicated to the professional development of ECMs. The #ERSCongress is the largest respiratory conference worldwide. This article points out why
@ERSTalk Early Career Members can especially benefit from attending this huge event and gives upcoming fellowship deadlines.http://ow.ly/3GQ530o8Ezh
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Affiliation(s)
- Niki Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, CHUV, Epalinges, Switzerland.,These authors contributed equally
| | - Manuela Platé
- Centre for Inflammation and Tissue Repair, UCL Respiratory, Rayne Building, University College London, London, UK.,These authors contributed equally
| | - Isaac Almendros
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Sabine Bartel
- University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, GRIAC Research Institute, Groningen, The Netherlands
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38
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Campbell LA, Richie CT, Maggirwar NS, Harvey BK. Cas9 Ribonucleoprotein Complex Delivery: Methods and Applications for Neuroinflammation. J Neuroimmune Pharmacol 2019; 14:565-577. [PMID: 31172397 DOI: 10.1007/s11481-019-09856-z] [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: 02/14/2019] [Accepted: 05/02/2019] [Indexed: 12/20/2022]
Abstract
The CRISPR/Cas9 system is a revolutionary gene editing technology that combines simplicity of use and efficiency of mutagenesis. As this technology progresses toward human therapies, valid concerns including off-target mutations and immunogenicity must be addressed. One approach to address these issues is to minimize the presence of the CRISPR/Cas9 components by maintaining a tighter temporal control of Cas9 endonuclease and reducing the time period of activity. This has been achieved to some degree by delivering the CRISPR/Cas9 system via pre-formed Cas9 + gRNA ribonucleoprotein (RNP) complexes. In this review, we first discuss the molecular modifications that can be made using CRISPR/Cas9 and provide an overview of current methods for delivering Cas9 RNP complexes both in vitro and in vivo. We conclude with examples of how Cas9 RNP delivery may be used to target neuroinflammatory processes, namely in regard to viral infections of the central nervous system and neurodegenerative diseases. We propose that Cas9 RNP delivery is a viable approach when considering the CRISPR/Cas9 system for both experimentation and the treatment of disease. Graphical Abstract.
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Affiliation(s)
- Lee A Campbell
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA.
| | - Christopher T Richie
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Nishad S Maggirwar
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Brandon K Harvey
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA.
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Nikolić MZ, Garrido-Martin EM, Greiffo FR, Fabre A, Heijink IH, Boots A, Greene CM, Hiemstra PS, Bartel S. From the pathophysiology of the human lung alveolus to epigenetic editing: Congress 2018 highlights from ERS Assembly 3 "Basic and Translational Science.". ERJ Open Res 2019; 5:00194-2018. [PMID: 31111040 PMCID: PMC6513036 DOI: 10.1183/23120541.00194-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/23/2019] [Indexed: 12/16/2022] Open
Abstract
The European Respiratory Society (ERS) International Congress is the largest respiratory congress and brings together leading experts in all fields of respiratory medicine and research. ERS Assembly 3 shapes the basic and translational science aspects of this congress, aiming to combine cutting-edge novel developments in basic research with novel clinical findings. In this article, we summarise a selection of the scientific highlights from the perspective of the three groups within Assembly 3. In particular, we discuss new insights into the pathophysiology of the human alveolus, novel tools in organoid development and (epi)genome editing, as well as insights from the presented abstracts on novel therapeutic targets being identified for idiopathic pulmonary fibrosis. The amount of basic and translational science presented at #ERSCongress is steadily increasing, showing novel cutting-edge technologies and models.http://bit.ly/2GgXIJi
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Affiliation(s)
- Marko Z Nikolić
- University College London, Division of Medicine, London, UK.,These contributed equally to this work
| | - Eva M Garrido-Martin
- H12O-CNIO Lung Cancer Clinical Research Unit, Research Institute Hospital 12 Octubre - Spanish National Cancer Research Centre (CNIO), and Biomedical Research Networking Centre Consortium of Cancer (CIBERONC), Madrid, Spain.,These contributed equally to this work
| | - Flavia R Greiffo
- Comprehensive Pneumology Center, Ludwig-Maximilians University (LMU), University Hospital Grosshadern, and Helmholtz Zentrum München; Member of the German Center for Lung Research (DZL), Munich, Germany.,These contributed equally to this work
| | - Aurélie Fabre
- University College Dublin, St Vincent's University Hospital, Elm Park, Dublin, Ireland
| | - Irene H Heijink
- University of Groningen, University Medical Center Groningen, Depts of Pathology and Medical Biology and Pulmonology, GRIAC Research Institute, Groningen, The Netherlands
| | - Agnes Boots
- Dept of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Catherine M Greene
- Lung Biology Group, Dept of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Pieter S Hiemstra
- Dept of Pulmonology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Sabine Bartel
- Early Life Origins of Chronic Lung Disease, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
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40
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In vitro and in vivo translational models for rare liver diseases. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1003-1018. [DOI: 10.1016/j.bbadis.2018.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 02/07/2023]
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41
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McCullough KT, Boye SL, Fajardo D, Calabro K, Peterson JJ, Strang CE, Chakraborty D, Gloskowski S, Haskett S, Samuelsson S, Jiang H, Witherspoon CD, Gamlin PD, Maeder ML, Boye SE. Somatic Gene Editing of GUCY2D by AAV-CRISPR/Cas9 Alters Retinal Structure and Function in Mouse and Macaque. Hum Gene Ther 2019; 30:571-589. [PMID: 30358434 PMCID: PMC6534089 DOI: 10.1089/hum.2018.193] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/23/2018] [Indexed: 12/15/2022] Open
Abstract
Mutations in GUCY2D, the gene encoding retinal guanylate cyclase-1 (retGC1), are the leading cause of autosomal dominant cone-rod dystrophy (CORD6). Significant progress toward clinical application of gene replacement therapy for Leber congenital amaurosis (LCA) due to recessive mutations in GUCY2D (LCA1) has been made, but a different approach is needed to treat CORD6 where gain of function mutations cause dysfunction and dystrophy. The CRISPR/Cas9 gene editing system efficiently disrupts genes at desired loci, enabling complete gene knockout or homology directed repair. Here, adeno-associated virus (AAV)-delivered CRISPR/Cas9 was used specifically to edit/disrupt this gene's early coding sequence in mouse and macaque photoreceptors in vivo, thereby knocking out retGC1 expression and demonstrably altering retinal function and structure. Neither preexisting nor induced Cas9-specific T-cell responses resulted in ocular inflammation in macaques, nor did it limit GUCY2D editing. The results show, for the first time, the ability to perform somatic gene editing in primates using AAV-CRISPR/Cas9 and demonstrate the viability this approach for treating inherited retinal diseases in general and CORD6 in particular.
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Affiliation(s)
| | - Sanford L. Boye
- Department of Ophthalmology, University of Florida, Gainesville, Florida
| | - Diego Fajardo
- Department of Ophthalmology, University of Florida, Gainesville, Florida
| | - Kaitlyn Calabro
- Department of Ophthalmology, University of Florida, Gainesville, Florida
| | - James J. Peterson
- Department of Ophthalmology, University of Florida, Gainesville, Florida
| | - Christianne E. Strang
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Dibyendu Chakraborty
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | | | | | | | - Paul D. Gamlin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Shannon E. Boye
- Department of Ophthalmology, University of Florida, Gainesville, Florida
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Abstract
CRISPR, a revolutionizing technology allowing researchers to navigate in and edit the genome, is moving on the fast track toward clinical use for ex vivo correction of disease-causing mutations in stem cells. As we await the first trials utilizing ex vivo CRISPR editing, implementation of CRISPR-based gene editing as an in vivo treatment directly in patients still remains an ultimate challenge. However, quickly accumulating evidence has provided proof-of-concept for efficacious editing in vivo. Attempts to edit genes directly in animals have largely relied on classical vector systems based on virus-based delivery of gene cassettes encoding the Cas9 endonuclease and single guide RNA, the key components of the CRISPR system. However, whereas persistent gene expression has been the primary goal of gene therapy for decades, things may be different in the case of CRISPR delivery. Is short-term presence of the CRISPR components perhaps sufficient for efficacy and ideal for safety?-and are strategies needed for restricting immune recognition of the bacteria-derived editing tool? Here, while answers to these questions still blow in the wind, we review prominent examples of genome editing with focus on targeting of genes with CRISPR in liver, muscles, and eyes of the mouse.
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Song CQ, Wang D, Jiang T, O'Connor K, Tang Q, Cai L, Li X, Weng Z, Yin H, Gao G, Mueller C, Flotte TR, Xue W. In Vivo Genome Editing Partially Restores Alpha1-Antitrypsin in a Murine Model of AAT Deficiency. Hum Gene Ther 2018; 29:853-860. [PMID: 29597895 DOI: 10.1089/hum.2017.225] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) genome editing holds promise in the treatment of genetic diseases that currently lack effective long-term therapies. Patients with alpha-1 antitrypsin (AAT) deficiency develop progressive lung disease due to the loss of AAT's antiprotease function and liver disease due to a toxic gain of function of the common mutant allele. However, it remains unknown whether CRISPR-mediated AAT correction in the liver, where AAT is primarily expressed, can correct either or both defects. Here we show that AAV delivery of CRISPR can effectively correct Z-AAT mutation in the liver of a transgenic mouse model. Specifically, we co-injected two AAVs: one expressing Cas9 and another encoding an AAT guide RNA and homology-directed repair template. In both neonatal and adult mice, this treatment partially restored M-AAT in the serum. Furthermore, deep sequencing confirmed both indel mutations and precise gene correction in the liver, permitting careful analysis of gene editing events in vivo. This study demonstrates a proof of concept for the application of CRISPR-Cas9 technology to correct AAT mutations in vivo and validates continued exploration of this approach for the treatment of patients with AAT deficiency.
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Affiliation(s)
- Chun-Qing Song
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Dan Wang
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Tingting Jiang
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kevin O'Connor
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Qiushi Tang
- 3 Departments of Pediatrics and Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Lingling Cai
- 4 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xiangrui Li
- 4 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Zhiping Weng
- 4 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China .,5 Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Hao Yin
- 6 Medical Research Institute, Wuhan University , Wuhan, China
| | - Guangping Gao
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Christian Mueller
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Terence R Flotte
- 2 Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts.,3 Departments of Pediatrics and Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Wen Xue
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.,7 Program in Molecular Medicine and Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
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