1
|
Wei Y, Gao P, Pan D, Li G, Chen Y, Li S, Jiang H, Yue Y, Wu Z, Liu Z, Zhou M, Chen Y, Xu K, Wu Z, Wang X. Engineering eukaryotic transposon-encoded Fanzor2 system for genome editing in mammals. Nat Chem Biol 2025:10.1038/s41589-025-01902-7. [PMID: 40394336 DOI: 10.1038/s41589-025-01902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 04/03/2025] [Indexed: 05/22/2025]
Abstract
Eukaryotic transposon-encoded Fanzor proteins hold great promise for genome-engineering applications as a result of their compact size and mechanistic resemblance to TnpB. However, the unmodified Fanzor systems show extremely low activity in mammalian cells. Guided by the predicted structure of a Fanzor2 complex using AlphaFold3, we engineered the NlovFz2 nuclease and its cognate ωRNA to create an evolved enNlovFz2 system, with an expanded target-adjacent motif (TAM) recognition scope (5'-NMYG) and a substantially improved genome-editing efficiency, achieving an 11.1-fold increase over the wild-type NlovFz2, comparable to two previously reported IS200 or IS605 transposon-encoded TnpBs and two CRISPR-Cas12f1 nucleases. Notably, enNlovFz2 efficiently mediated gene disruption in mouse embryos and restored dystrophin expression in a humanized Duchenne muscular dystrophy mouse model with single adeno-associated virus delivery. Our findings underscore the potential of eukaryotic RNA-guided Fanzor2 nucleases as a versatile toolbox for both biological research and therapeutic applications.
Collapse
Affiliation(s)
- Yinghui Wei
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
- Hainan Institute, Northwest A&F University, Sanya, China.
| | - Pengfei Gao
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Deng Pan
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guoling Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- HuidaGene Therapeutics Co. Ltd, Shanghai, China
| | - Yufei Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shangpu Li
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Henan Jiang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yang Yue
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhenmin Wu
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zujiang Liu
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Min Zhou
- Life Science Research Core Services, Northwest A&F University, Yangling, China
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Hainan Institute, Northwest A&F University, Sanya, China
| | - Kun Xu
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
- Hainan Institute, Northwest A&F University, Sanya, China.
| | - Zhaowei Wu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
- Hainan Institute, Northwest A&F University, Sanya, China.
| |
Collapse
|
2
|
Fatehi S, Rok MJ, Marks RM, Huynh E, Kozman N, Truong HA, Chi L, Yan B, Khazeeva E, Delgado-Olguin P, Ivakine EA, Cohn RD. Template-assisted sequence knockin rescues skeletal and cardiac muscle function in a deletion model of Duchenne muscular dystrophy. Mol Ther 2025:S1525-0016(25)00375-2. [PMID: 40340246 DOI: 10.1016/j.ymthe.2025.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 04/15/2025] [Accepted: 05/02/2025] [Indexed: 05/10/2025] Open
Abstract
Duchenne muscular dystrophy (DMD) poses challenges in therapy design due to dystrophin's complex role in maintaining muscle function since the restoration of truncated protein products has failed to completely address the disease's pathophysiology in clinical trials. As ∼70% of patients harbor deletions, strategies enabling targeted DNA insertion to restore full-length dystrophin protein are essential. Here, we present template-assisted sequence knockin (TASK), a strategy that we employed to specifically correct the Dmd Δ52-54 mutation in a murine model. By co-delivering a repair template and the Cas9 nuclease using AAV9s, the splice-competent sequence for Dmd exons 52-54 was integrated into the residual intron 54 locus, resulting in the systemic restoration of full-length dystrophin at therapeutically relevant levels in the heart and across all skeletal muscles, leading to significant functional improvements. TASK demonstrates the highest efficiency of exogenous DNA knockin reported to date, achieving rescue of key dystrophic hallmarks in a deletion model of DMD.
Collapse
Affiliation(s)
- Sina Fatehi
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Matthew J Rok
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Ryan M Marks
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Emily Huynh
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Natalie Kozman
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Hong Anh Truong
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Lijun Chi
- Program in Translational Medicine, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Bei Yan
- Program in Translational Medicine, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Enzhe Khazeeva
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Paul Delgado-Olguin
- Program in Translational Medicine, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Evgueni A Ivakine
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A1, Canada.
| | - Ronald D Cohn
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada; Department of Pediatrics, The Hospital for Sick Children, Toronto, ON M5G 1E8, Canada
| |
Collapse
|
3
|
Haque US, Yokota T. Gene Editing for Duchenne Muscular Dystrophy: From Experimental Models to Emerging Therapies. Degener Neurol Neuromuscul Dis 2025; 15:17-40. [PMID: 40241992 PMCID: PMC12002074 DOI: 10.2147/dnnd.s495536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Accepted: 04/08/2025] [Indexed: 04/18/2025] Open
Abstract
The CRISPR system has emerged as a ground-breaking gene-editing tool, offering promising therapeutic potential for Duchenne muscular dystrophy (DMD), a severe genetic disorder affecting approximately 1 in 5000 male births globally. DMD is caused by mutations in the dystrophin gene, which encodes a critical membrane-associated protein essential for maintaining muscle structure, function and repair. Patients with DMD experience progressive muscle degeneration, loss of ambulation, respiratory insufficiency, and cardiac failure, with most succumbing to the disease by their third decade of life. Despite the well-characterized genetic basis of DMD, curative treatments- such as exon skipping therapies, micro-dystrophin, and steroids- remain elusive. Recent preclinical studies have demonstrated the promise of CRISPR-based approaches in restoring dystrophin expression across various models, including human cells, murine systems, and large animal models. These advancements highlight the potential of gene editing to fundamentally alter the trajectory of the disease. However, significant challenges persist, including immunogenicity, off-target effects, and limited editing efficiency, which hinder clinical translation. This review provides a comprehensive analysis of the latest developments in CRISPR-based therapeutic strategies for DMD. It emphasizes the need for further innovation in gene-editing technologies, delivery systems, and rigorous safety evaluations to overcome current barriers and harness the full potential of CRISPR/Cas as a durable and effective treatment for DMD.
Collapse
Affiliation(s)
- Umme Sabrina Haque
- Department of Neuroscience, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, T6G 2H7, Canada
| |
Collapse
|
4
|
Tang A, Yokota T. Is Duchenne gene therapy a suitable treatment despite its immunogenic class effect? Expert Opin Drug Saf 2025; 24:395-411. [PMID: 39720847 DOI: 10.1080/14740338.2024.2447072] [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: 05/21/2024] [Revised: 11/22/2024] [Accepted: 12/22/2024] [Indexed: 12/26/2024]
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD) is a severe X-linked disorder characterized by progressive muscle weakness and eventual death due to cardiomyopathy or respiratory complications. Currently, there is no cure for DMD, with standard treatments primarily focusing on symptom management. Using immunosuppressive measures and optimized vector designs allows for gene therapies to better address the genetic cause of the disease. AREAS COVERED This review evaluates the efficacy and safety of emerging DMD gene therapies as of 2024. It also discusses the potential of utrophin upregulation, gene editing, and truncated dystrophin as therapeutic strategies. It highlights safety concerns associated with these therapies, including adverse events and patient deaths. A comprehensive overview of developments covers topics such as CRISPR-Cas9 therapies, micro-dystrophin, and the potential delivery of full-length dystrophin. EXPERT OPINION The FDA's recent approval of delandistrogene moxeparvovec (Elevidys) underscores the promise of gene replacement therapies for DMD patients. Understanding the mechanisms behind the adverse effects and excluding patients with specific pathogenic variants may enhance the safety profiles of these therapies. CRISPR/Cas9 therapies, while promising, face significant regulatory and safety challenges that hinder their clinical application. Optimal DMD therapies should target both skeletal and cardiac muscles to be effective.
Collapse
Affiliation(s)
- Annie Tang
- Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Toshifumi Yokota
- Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
5
|
Padmaswari MH, Agrawal S, Nelson CE. Preclinical development of genome editing to treat Duchenne muscular dystrophy by exon skipping. J Neuromuscul Dis 2025:22143602251326993. [PMID: 40105473 DOI: 10.1177/22143602251326993] [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: 03/20/2025]
Abstract
Duchenne muscular dystrophy (DMD) is caused by loss-of-function mutations to the gene encoding dystrophin. Restoring the reading frame of dystrophin by removing internal out-of-frame exons may address symptoms of DMD. Therefore, the principle of exon skipping has been at the center stage in drug development for Duchenne muscular dystrophy (DMD) over the past two decades. Antisense oligonucleotides (AONs) have proven effective in modulating splicing sites for exon skipping, resulting in the FDA approval of several drugs using this technique in recent years. However, due to the temporary nature of AON, researchers are actively exploring genome editing as a potential long-term, single-administration treatment. The advancements in genome-editing technology over the last decade have boosted this transition. While no clinical trials for exon skipping in DMD via genome editing have been conducted as of this writing, preclinical studies show encouraging results. This review describes the preclinical landscape of genome editing for exon skipping in DMD treatment. Along with highlighting the adaptability of genome editing in exon skipping, this review also describes delivery challenges and outlines future research directions that could set a new stage for enhanced therapeutic development in DMD.
Collapse
Affiliation(s)
- Made Harumi Padmaswari
- Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Shilpi Agrawal
- Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Christopher E Nelson
- Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| |
Collapse
|
6
|
Severino MB, Morelli AP, Pavan ICB, Mancini MCS, Góis MM, Borges RJ, Braga RR, da Silva LGS, Quintero-Ruiz N, Costa MM, Oliveira WDL, Bezerra RMN, Ropelle ER, Simabuco FM. A CRISPR-edited isoform of the AMPK kinase LKB1 improves the response to cisplatin in A549 lung cancer cells. J Biol Chem 2025; 301:108308. [PMID: 39955067 PMCID: PMC11952844 DOI: 10.1016/j.jbc.2025.108308] [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: 04/03/2024] [Revised: 01/23/2025] [Accepted: 02/09/2025] [Indexed: 02/17/2025] Open
Abstract
Lung cancer presents the highest mortality rate in the world when compared to other cancer types and often presents chemotherapy resistance to cisplatin. The A549 nonsmall cell lung cancer line is widely used as a model for lung adenocarcinoma studies since it presents a high proliferative rate and a nonsense mutation in the STK11 gene. The LKB1 protein, encoded by the STK11 gene, is one of the major regulators of cellular metabolism through AMPK activation under nutrient deprivation. Mutation in the STK11 gene in A549 cells potentiates cancer hallmarks, such as deregulation of cellular metabolism, aside from the Warburg effect, mTOR activation, autophagy inhibition, and NRF2 and redox activation. In this study, we investigated the integration of these pathways associated with the metabolism regulation by LKB1/AMPK to improve cisplatin response in the A549 cell line. We first used the CRISPR/Cas9 system to generate cell lines with a CRISPR-edited LKB1 isoform (called Super LKB1), achieved through the introduction of a +1 adenine insertion in the first exon of the STK11 gene after NHEJ-mediated repair. This insertion led to the expression of a higher molecular weight protein containing an alternative exon described in the Peutz-Jeghers Syndrome. Through metabolic regulation by Super LKB1 expression and AMPK activation, we found an increase in autophagy flux (LC3 GFP/RFP p < 0.05), as well as a reduction in the phosphorylation of mTORC1 downstream targets (S6K2 phospho-serine 423; p < 0.05; and S6 ribosomal protein phospho-serine 240/244; p < 0.03). The NRF2 protein exhibited increased levels and more nuclear localization in A549 WT cells compared to the edited cells (p < 0.01). We also observed lower levels of H2O2 in the WT A549 cells, as a possible result of NRF2 activation, and a higher requirement of cisplatin to achieve the IC50 (WT: 10 μM; c2SL+: 5.5 μM; c3SL+: 6 μM). The data presented here suggests that the regulation of molecular pathways by the novel Super LKB1 in A549 cells related to metabolism, mTORC1, and autophagy promotes a better response of lung cancer cells to cisplatin. This NHEJ-CRISPR-based approach may be potentially used for lung cancer gene therapy.
Collapse
Affiliation(s)
- Matheus Brandemarte Severino
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Ana Paula Morelli
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Isadora Carolina Betim Pavan
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil; Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Mariana Camargo Silva Mancini
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Mariana Marcela Góis
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Rafael Junqueira Borges
- Department of Physics and Biophysics, Biosciences Institute, State University of São Paulo, Botucatu, Brazil; Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Campinas, Brazil; Center for Medicinal Chemistry (CQMED), University of Campinas, Campinas, Brazil
| | - Renata Rosseto Braga
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences, University of Campinas, Limeira, Brazil
| | | | - Nathalia Quintero-Ruiz
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Maíra Maftoum Costa
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Wesley de Lima Oliveira
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Rosângela Maria Neves Bezerra
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Eduardo Rochete Ropelle
- Laboratory of Molecular Biology of Exercise (LaBMEx), School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, Brazil; Applied Molecular Signaling Laboratory (LabSIMA), Department of Biochemistry, Federal University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
7
|
Wu YF, Chen JA, Jong YJ. Treating neuromuscular diseases: unveiling gene therapy breakthroughs and pioneering future applications. J Biomed Sci 2025; 32:30. [PMID: 39985020 PMCID: PMC11844187 DOI: 10.1186/s12929-025-01123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 01/21/2025] [Indexed: 02/23/2025] Open
Abstract
In this review, we highlight recent advancements in adeno-associated virus (AAV)-based gene therapy for genetic neuromuscular diseases (NMDs), focusing on spinal muscular atrophy (SMA) and Duchenne muscular dystrophy (DMD). We discuss the current FDA-approved gene therapies for NMDs and provide updates on preclinical studies that demonstrate the potential of various AAV-based gene therapies to reduce SMA severity and serve as effective treatments for DMD. Additionally, we explore the transformative impact of CRISPR/Cas9 technology on the future of gene therapy for NMDs. Despite these encouraging developments, further research is required to identify robust biomarkers that can guide treatment decisions and predict outcomes. Overall, these pioneering advancements in AAV-based gene therapy lay the groundwork for future efforts aimed at curing genetic NMDs and offer a roadmap for developing gene therapies for other neurodegenerative diseases.
Collapse
Affiliation(s)
- Yu-Fu Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan.
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan.
| | - Yuh-Jyh Jong
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Pediatrics, Division of Pediatric Neurology, and Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
| |
Collapse
|
8
|
Pelosse M, Marcia M. biGMamAct: efficient CRISPR/Cas9-mediated docking of large functional DNA cargoes at the ACTB locus. Synth Biol (Oxf) 2025; 10:ysaf003. [PMID: 40065842 PMCID: PMC11891445 DOI: 10.1093/synbio/ysaf003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 01/27/2025] [Accepted: 02/12/2025] [Indexed: 04/26/2025] Open
Abstract
Recent advances in molecular and cell biology and imaging have unprecedentedly enabled multiscale structure-functional studies of entire metabolic pathways from atomic to micrometer resolution and the visualization of macromolecular complexes in situ, especially if these molecules are expressed with appropriately engineered and easily detectable tags. However, genome editing in eukaryotic cells is challenging when generating stable cell lines loaded with large DNA cargoes. To address this limitation, here, we have conceived biGMamAct, a system that allows the straightforward assembly of a multitude of genetic modules and their subsequent integration in the genome at the ACTB locus with high efficacy, through standardized cloning steps. Our system comprises a set of modular plasmids for mammalian expression, which can be efficiently docked into the genome in tandem with a validated Cas9/sgRNA pair through homologous-independent targeted insertion. As a proof of concept, we have generated a stable cell line loaded with an 18.3-kilobase-long DNA cargo to express six fluorescently tagged proteins and simultaneously visualize five different subcellular compartments. Our protocol leads from the in silico design to the genetic and functional characterization of single clones within 6 weeks and can be implemented by any researcher with familiarity with molecular biology and access to mammalian cell culturing infrastructure.
Collapse
Affiliation(s)
- Martin Pelosse
- EMBL Grenoble, European Molecular Biology Laboratory, 71 avenue des Martyrs, Grenoble Cedex 9 CS 90181, 38042, France
| | - Marco Marcia
- EMBL Grenoble, European Molecular Biology Laboratory, 71 avenue des Martyrs, Grenoble Cedex 9 CS 90181, 38042, France
| |
Collapse
|
9
|
Luo X, Germer J, Burghardt T, Grau M, Lin Y, Höhn M, Lächelt U, Wagner E. Dual pH-responsive CRISPR/Cas9 ribonucleoprotein xenopeptide complexes for genome editing. Eur J Pharm Sci 2025; 205:106983. [PMID: 39647515 DOI: 10.1016/j.ejps.2024.106983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 12/02/2024] [Accepted: 12/04/2024] [Indexed: 12/10/2024]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated (Cas) protein has been proved as a powerful tool for the treatment of genetic diseases. The Cas9 protein, when combined with single-guide RNA (sgRNA), forms a Cas9/sgRNA ribonucleoprotein (RNP) capable of targeting and editing the genome. However, the limited availability of effective carriers has restricted the broader application of CRISPR/Cas9 RNP. In this study, we evaluated dual pH-responsive amphiphilic xenopeptides (XPs) for delivering CRISPR/Cas9 RNP. These artificial lipo-XPs contain apolar cationizable lipoamino fatty acid (LAF) and polar cationizable oligoaminoethylene acid units such as succinoyl-tetraethylenepentamine (Stp) in various ratios and U-shaped topologies. The carriers were screened for functional Cas9/sgRNA RNP delivery in four different reporter cell lines, including a Duchenne muscular dystrophy (DMD) exon skipping reporter cell model. Significantly enhanced cellular uptake into HeLa cells, effective endosomal disruption in HeLa gal8-mRuby3 cells, and potent genome editing by several Cas9/sgRNA RNP complexes was observed in four different cell lines in the 5 nM sgRNA range. Comparing Cas9/sgRNA RNP complexes with Cas9 mRNA/sgRNA polyplexes in the DMD reporter cell model demonstrated similar splice site editing and high exon skipping of the two different molecular Cas9 modalities. Based on these studies, analogues of two potent U1 LAF2-Stp and LAF4-Stp2 structures were deployed, tuning the amphiphilicity of the polar Stp group by replacement with the six oligoamino acids dmGtp, chGtp, dGtp, Htp, Stt, or GEIPA. The most potent LAF2-Stp analogues (containing dGtp, chGtp or GEIPA) demonstrated further enhanced gene editing efficiency with EC50 values of 1 nM in the DMD exon skipping reporter cell line. Notably, the EC50 of LAF2-dGtp reached 0.51 nM even upon serum incubation. Another carrier (LAF4-GEIPA2) complexing Cas9/sgRNA RNP and donor DNA, facilitated up to 43 % of homology-directed repair (HDR) in HeLa eGFPd2 cells visualized by the switch from green fluorescent protein (eGFP) to blue fluorescent protein (BFP). This study presents a delivery system tunable for Cas9 RNP complexes or Cas9 RNP/donor DNA polyplexes, offering an effective and easily applicable strategy for gene editing.
Collapse
Affiliation(s)
- Xianjin Luo
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Janin Germer
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Tobias Burghardt
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Melina Grau
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Yi Lin
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Miriam Höhn
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Ulrich Lächelt
- Center for Nanoscience (CeNS), LMU Munich, 80799 Munich, Germany; Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Ernst Wagner
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität Munich, Butenandtstrasse 5-13, 81377 Munich, Germany; Center for Nanoscience (CeNS), LMU Munich, 80799 Munich, Germany; CNATM - Cluster for Nucleic Acid Therapeutics Munich, Germany.
| |
Collapse
|
10
|
Bonowicz K, Jerka D, Piekarska K, Olagbaju J, Stapleton L, Shobowale M, Bartosiński A, Łapot M, Bai Y, Gagat M. CRISPR-Cas9 in Cardiovascular Medicine: Unlocking New Potential for Treatment. Cells 2025; 14:131. [PMID: 39851560 PMCID: PMC11763404 DOI: 10.3390/cells14020131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 01/12/2025] [Accepted: 01/15/2025] [Indexed: 01/26/2025] Open
Abstract
Cardiovascular diseases (CVDs) remain a significant global health challenge, with many current treatments addressing symptoms rather than the genetic roots of these conditions. The advent of CRISPR-Cas9 technology has revolutionized genome editing, offering a transformative approach to targeting disease-causing mutations directly. This article examines the potential of CRISPR-Cas9 in the treatment of various CVDs, including atherosclerosis, arrhythmias, cardiomyopathies, hypertension, and Duchenne muscular dystrophy (DMD). The technology's ability to correct single-gene mutations with high precision and efficiency positions it as a groundbreaking tool in cardiovascular therapy. Recent developments have extended the capabilities of CRISPR-Cas9 to include mitochondrial genome editing, a critical advancement for addressing mitochondrial dysfunctions often linked to cardiovascular disorders. Despite its promise, significant challenges remain, including off-target effects, ethical concerns, and limitations in delivery methods, which hinder its translation into clinical practice. This article also explores the ethical and regulatory considerations surrounding gene editing technologies, emphasizing the implications of somatic versus germline modifications. Future research efforts should aim to enhance the accuracy of CRISPR-Cas9, improve delivery systems for targeted tissues, and ensure the safety and efficacy of treatments in the long term. Overcoming these obstacles could enable CRISPR-Cas9 to not only treat but also potentially cure genetically driven cardiovascular diseases, heralding a new era in precision medicine for cardiovascular health.
Collapse
Affiliation(s)
- Klaudia Bonowicz
- Department of Histology and Embryology and Vascular Biology Student Research Club, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092 Bydgoszcz, Poland; (K.B.); (D.J.); (K.P.); (J.O.); (L.S.); (M.S.)
- Faculty of Medicine, Collegium Medicum, Mazovian Academy in Płock, 09-402 Płock, Poland; (A.B.); (M.Ł.)
| | - Dominika Jerka
- Department of Histology and Embryology and Vascular Biology Student Research Club, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092 Bydgoszcz, Poland; (K.B.); (D.J.); (K.P.); (J.O.); (L.S.); (M.S.)
| | - Klaudia Piekarska
- Department of Histology and Embryology and Vascular Biology Student Research Club, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092 Bydgoszcz, Poland; (K.B.); (D.J.); (K.P.); (J.O.); (L.S.); (M.S.)
| | - Janet Olagbaju
- Department of Histology and Embryology and Vascular Biology Student Research Club, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092 Bydgoszcz, Poland; (K.B.); (D.J.); (K.P.); (J.O.); (L.S.); (M.S.)
| | - Laura Stapleton
- Department of Histology and Embryology and Vascular Biology Student Research Club, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092 Bydgoszcz, Poland; (K.B.); (D.J.); (K.P.); (J.O.); (L.S.); (M.S.)
| | - Munirat Shobowale
- Department of Histology and Embryology and Vascular Biology Student Research Club, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092 Bydgoszcz, Poland; (K.B.); (D.J.); (K.P.); (J.O.); (L.S.); (M.S.)
| | - Andrzej Bartosiński
- Faculty of Medicine, Collegium Medicum, Mazovian Academy in Płock, 09-402 Płock, Poland; (A.B.); (M.Ł.)
| | - Magdalena Łapot
- Faculty of Medicine, Collegium Medicum, Mazovian Academy in Płock, 09-402 Płock, Poland; (A.B.); (M.Ł.)
| | - Yidong Bai
- Department of Cell Systems and Anatomy, UT Health, Long School of Medicine, San Antonio, TX 78229, USA;
| | - Maciej Gagat
- Department of Histology and Embryology and Vascular Biology Student Research Club, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092 Bydgoszcz, Poland; (K.B.); (D.J.); (K.P.); (J.O.); (L.S.); (M.S.)
- Faculty of Medicine, Collegium Medicum, Mazovian Academy in Płock, 09-402 Płock, Poland; (A.B.); (M.Ł.)
| |
Collapse
|
11
|
Agrawal A, Clayton EL, Cavazos CL, Clayton BA, Rodney GG. Histone deacetylase 6 inhibition promotes microtubule acetylation and facilitates autophagosome-lysosome fusion in dystrophin-deficient mdx mice. Acta Physiol (Oxf) 2025; 241:e14243. [PMID: 39422111 DOI: 10.1111/apha.14243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 08/23/2024] [Accepted: 09/23/2024] [Indexed: 10/19/2024]
Abstract
AIM Duchenne muscular dystrophy is a progressive muscle-wasting disease caused by mutations in the dystrophin gene. Despite progress in dystrophin-targeted gene therapies, it is still a fatal disease requiring novel therapeutics that can be used synergistically or alternatively to emerging gene therapy. Defective autophagy and disorganized microtubule networks contribute to dystrophic pathogenesis, yet the mechanisms by which microtubule alterations regulate autophagy remain elusive. The present study was designed to uncover possible mechanisms underpinning the role of microtubules in regulating autophagy in dystrophic mice. METHODS Mdx mice were also supplemented with Tubastatin A, a pharmacological inhibitor of histone deacetylase 6, and pathophysiology was assessed. Mdx mice with a genetic deletion of the Nox-2 scaffolding subunit p47phox were used to assess redox dependence on tubulin acetylation. RESULTS Our data show decreased acetylation of α-tubulin with enhanced histone deacetylase 6 expression. Tubastatin A increases tubulin acetylation and Q-SNARE complex formation but does not alter microtubule organization or density, indicating improved autophagosome-lysosome fusion. Tubastatin A increases the acetylation of peroxiredoxin and protects it from hyper-oxidation, hence modulating intracellular redox status in mdx mice. Tubastatin A reduces muscle damage and enhances force production. Genetic down regulation of Nox2 activity in the mdx mice promotes autophagosome maturation but not autolysosome formation. CONCLUSION Our data highlight that autophagy is differentially regulated by redox and acetylation in mdx mice. By improving autophagy through promoting tubulin acetylation, Tubastatin A decreases the dystrophic phenotype and improves muscle function, suggesting a great potential for clinical translation and treating dystrophic patients.
Collapse
Affiliation(s)
- Akanksha Agrawal
- Department of Integrative Physiology, Baylor College of Medicine, Houston, Texas, USA
| | - Erin L Clayton
- Department of Integrative Physiology, Baylor College of Medicine, Houston, Texas, USA
| | - Courtney L Cavazos
- Department of Integrative Physiology, Baylor College of Medicine, Houston, Texas, USA
| | - Benjamin A Clayton
- Department of Integrative Physiology, Baylor College of Medicine, Houston, Texas, USA
| | - George G Rodney
- Department of Integrative Physiology, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
12
|
Huang CY, Tsai YH, Cheng YF, Wu PY, Chuang YC, Huang PY, Liu JS, Wu CC, Cheng YF. CRISPR/Cas9-mediated exon skipping to restore premature translation termination in a DFNB4 mouse model. Gene Ther 2024; 31:531-540. [PMID: 39232211 DOI: 10.1038/s41434-024-00483-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024]
Abstract
SLC26A4 encodes pendrin, a crucial anion exchanger essential for maintaining hearing function. Mutations in SLC26A4, including the prevalent c.919-2 A > G splice-site mutation among East Asian individuals, can disrupt inner ear electrolyte balance, leading to syndromic and non-syndromic hearing loss, such as Pendred syndrome and DFNB4. To explore potential therapeutic strategies, we utilized CRISPR/Cas9-mediated exon skipping to create a Slc26a4∆E8+E9/∆E8+E9 mouse model. We assessed pendrin expression in the inner ear and evaluated vestibular and auditory functions. The Slc26a4∆E8+E9/∆E8+E9 mice demonstrated reframed pendrin in the inner ear and normal vestibular functions, contrasting with severely abnormal vestibular functions observed in the Slc26a4 c.919-2 A > G splicing mutation mouse model. However, despite these molecular achievements, hearing function did not show the expected improvement, consistent with observed pathology, including cochlear hair cell loss and elevated hearing thresholds. Consequently, our findings highlight the necessity for alternative genetic editing strategies to address hearing loss caused by the SLC26A4 c.919-2 A > G mutation.
Collapse
Affiliation(s)
- Chun-Ying Huang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Hsiu Tsai
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Fen Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Peng-Yu Wu
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Chi Chuang
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Po-Yuan Huang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jai-Shin Liu
- Department of Biotechnology and Pharmaceutical Technology, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan.
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu City, Taiwan.
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.
| |
Collapse
|
13
|
Lin J, Jin M, Yang D, Li Z, Zhang Y, Xiao Q, Wang Y, Yu Y, Zhang X, Shao Z, Shi L, Zhang S, Chen WJ, Wang N, Wu S, Yang H, Xu C, Li G. Adenine base editing-mediated exon skipping restores dystrophin in humanized Duchenne mouse model. Nat Commun 2024; 15:5927. [PMID: 39009678 PMCID: PMC11251194 DOI: 10.1038/s41467-024-50340-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
Duchenne muscular dystrophy (DMD) affecting 1 in 3500-5000 live male newborns is the frequently fatal genetic disease resulted from various mutations in DMD gene encoding dystrophin protein. About 70% of DMD-causing mutations are exon deletion leading to frameshift of open reading frame and dystrophin deficiency. To facilitate translating human DMD-targeting CRISPR therapeutics into patients, we herein establish a genetically humanized mouse model of DMD by replacing exon 50 and 51 of mouse Dmd gene with human exon 50 sequence. This humanized mouse model recapitulats patient's DMD phenotypes of dystrophin deficiency and muscle dysfunction. Furthermore, we target splicing sites in human exon 50 with adenine base editor to induce exon skipping and robustly restored dystrophin expression in heart, tibialis anterior and diaphragm muscles. Importantly, systemic delivery of base editor via adeno-associated virus in the humanized male mouse model improves the muscle function of DMD mice to the similar level of wildtype ones, indicating the therapeutic efficacy of base editing strategy in treating most of DMD types with exon deletion or point mutations via exon-skipping induction.
Collapse
Affiliation(s)
- Jiajia Lin
- Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ming Jin
- Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Dong Yang
- HuidaGene Therapeutics Inc., Shanghai, China
| | | | - Yu Zhang
- HuidaGene Therapeutics Inc., Shanghai, China
| | | | - Yin Wang
- HuidaGene Therapeutics Inc., Shanghai, China
| | - Yuyang Yu
- HuidaGene Therapeutics Inc., Shanghai, China
| | | | - Zhurui Shao
- HuidaGene Therapeutics Inc., Shanghai, China
| | - Linyu Shi
- HuidaGene Therapeutics Inc., Shanghai, China
| | - Shu Zhang
- Department of Neurology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Wan-Jin Chen
- Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ning Wang
- Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Shiwen Wu
- Department of Neurology, First Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Hui Yang
- HuidaGene Therapeutics Inc., Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China.
| | - Chunlong Xu
- Lingang Laboratory, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China.
| | - Guoling Li
- Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
- HuidaGene Therapeutics Inc., Shanghai, China.
| |
Collapse
|
14
|
Jin M, Lin J, Li H, Li Z, Yang D, Wang Y, Yu Y, Shao Z, Chen L, Wang Z, Zhang Y, Zhang X, Wang N, Xu C, Yang H, Chen WJ, Li G. Correction of human nonsense mutation via adenine base editing for Duchenne muscular dystrophy treatment in mouse. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102165. [PMID: 38571746 PMCID: PMC10988125 DOI: 10.1016/j.omtn.2024.102165] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Duchenne muscular dystrophy (DMD) is the most prevalent herediatry disease in men, characterized by dystrophin deficiency, progressive muscle wasting, cardiac insufficiency, and premature mortality, with no effective therapeutic options. Here, we investigated whether adenine base editing can correct pathological nonsense point mutations leading to premature stop codons in the dystrophin gene. We identified 27 causative nonsense mutations in our DMD patient cohort. Treatment with adenine base editor (ABE) could restore dystrophin expression by direct A-to-G editing of pathological nonsense mutations in cardiomyocytes generated from DMD patient-derived induced pluripotent stem cells. We also generated two humanized mouse models of DMD expressing mutation-bearing exons 23 or 30 of human dystrophin gene. Intramuscular administration of ABE, driven by ubiquitous or muscle-specific promoters could correct these nonsense mutations in vivo, albeit with higher efficiency in exon 30, restoring dystrophin expression in skeletal fibers of humanized DMD mice. Moreover, a single systemic delivery of ABE with human single guide RNA (sgRNA) could induce body-wide dystrophin expression and improve muscle function in rotarod tests of humanized DMD mice. These findings demonstrate that ABE with human sgRNAs can confer therapeutic alleviation of DMD in mice, providing a basis for development of adenine base editing therapies in monogenic diseases.
Collapse
Affiliation(s)
- Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Jiajia Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Haisen Li
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
- School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Zhifang Li
- Lingang Laboratory, Shanghai 200031, China
| | - Dong Yang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Yin Wang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Yuyang Yu
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Zhurui Shao
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Long Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Zhiqiang Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Yu Zhang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Xiumei Zhang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Chunlong Xu
- Lingang Laboratory, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Hui Yang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| |
Collapse
|
15
|
Dhoke NR, Kim H, Azzag K, Crist SB, Kiley J, Perlingeiro RCR. A Novel CRISPR-Cas9 Strategy to Target DYSTROPHIN Mutations Downstream of Exon 44 in Patient-Specific DMD iPSCs. Cells 2024; 13:972. [PMID: 38891104 PMCID: PMC11171783 DOI: 10.3390/cells13110972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/25/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Mutations in the DMD gene cause fatal Duchenne Muscular Dystrophy (DMD). An attractive therapeutic approach is autologous cell transplantation utilizing myogenic progenitors derived from induced pluripotent stem cells (iPSCs). Given that a significant number of DMD mutations occur between exons 45 and 55, we developed a gene knock-in approach to correct any mutations downstream of exon 44. We applied this approach to two DMD patient-specific iPSC lines carrying mutations in exons 45 and 51 and confirmed mini-DYSTROPHIN (mini-DYS) protein expression in corrected myotubes by western blot and immunofluorescence staining. Transplantation of gene-edited DMD iPSC-derived myogenic progenitors into NSG/mdx4Cv mice produced donor-derived myofibers, as shown by the dual expression of human DYSTROPHIN and LAMIN A/C. These findings further provide proof-of-concept for the use of programmable nucleases for the development of autologous iPSC-based therapy for muscular dystrophies.
Collapse
Affiliation(s)
- Neha R. Dhoke
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (N.R.D.); (H.K.); (K.A.); (S.B.C.); (J.K.)
| | - Hyunkee Kim
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (N.R.D.); (H.K.); (K.A.); (S.B.C.); (J.K.)
| | - Karim Azzag
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (N.R.D.); (H.K.); (K.A.); (S.B.C.); (J.K.)
| | - Sarah B. Crist
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (N.R.D.); (H.K.); (K.A.); (S.B.C.); (J.K.)
| | - James Kiley
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (N.R.D.); (H.K.); (K.A.); (S.B.C.); (J.K.)
| | - Rita C. R. Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (N.R.D.); (H.K.); (K.A.); (S.B.C.); (J.K.)
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
16
|
Laurent M, Geoffroy M, Pavani G, Guiraud S. CRISPR-Based Gene Therapies: From Preclinical to Clinical Treatments. Cells 2024; 13:800. [PMID: 38786024 PMCID: PMC11119143 DOI: 10.3390/cells13100800] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
In recent years, clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) protein have emerged as a revolutionary gene editing tool to treat inherited disorders affecting different organ systems, such as blood and muscles. Both hematological and neuromuscular genetic disorders benefit from genome editing approaches but face different challenges in their clinical translation. The ability of CRISPR/Cas9 technologies to modify hematopoietic stem cells ex vivo has greatly accelerated the development of genetic therapies for blood disorders. In the last decade, many clinical trials were initiated and are now delivering encouraging results. The recent FDA approval of Casgevy, the first CRISPR/Cas9-based drug for severe sickle cell disease and transfusion-dependent β-thalassemia, represents a significant milestone in the field and highlights the great potential of this technology. Similar preclinical efforts are currently expanding CRISPR therapies to other hematologic disorders such as primary immunodeficiencies. In the neuromuscular field, the versatility of CRISPR/Cas9 has been instrumental for the generation of new cellular and animal models of Duchenne muscular dystrophy (DMD), offering innovative platforms to speed up preclinical development of therapeutic solutions. Several corrective interventions have been proposed to genetically restore dystrophin production using the CRISPR toolbox and have demonstrated promising results in different DMD animal models. Although these advances represent a significant step forward to the clinical translation of CRISPR/Cas9 therapies to DMD, there are still many hurdles to overcome, such as in vivo delivery methods associated with high viral vector doses, together with safety and immunological concerns. Collectively, the results obtained in the hematological and neuromuscular fields emphasize the transformative impact of CRISPR/Cas9 for patients affected by these debilitating conditions. As each field suffers from different and specific challenges, the clinical translation of CRISPR therapies may progress differentially depending on the genetic disorder. Ongoing investigations and clinical trials will address risks and limitations of these therapies, including long-term efficacy, potential genotoxicity, and adverse immune reactions. This review provides insights into the diverse applications of CRISPR-based technologies in both preclinical and clinical settings for monogenic blood disorders and muscular dystrophy and compare advances in both fields while highlighting current trends, difficulties, and challenges to overcome.
Collapse
Affiliation(s)
- Marine Laurent
- INTEGRARE, UMR_S951, Genethon, Inserm, Univ Evry, Université Paris-Saclay, 91190 Evry, France
| | | | - Giulia Pavani
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Simon Guiraud
- SQY Therapeutics, 78180 Montigny-le-Bretonneux, France
| |
Collapse
|
17
|
Alizadeh F, Abraghan YJ, Farrokhi S, Yousefi Y, Mirahmadi Y, Eslahi A, Mojarrad M. Production of Duchenne muscular dystrophy cellular model using CRISPR-Cas9 exon deletion strategy. Mol Cell Biochem 2024; 479:1027-1040. [PMID: 37289342 DOI: 10.1007/s11010-023-04759-3] [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: 03/24/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023]
Abstract
Duchenne Muscular Dystrophy (DMD) is a progressive muscle wasting disorder caused by loss-of-function mutations in the dystrophin gene. Although the search for a definitive cure has failed to date, extensive efforts have been made to introduce effective therapeutic strategies. Gene editing technology is a great revolution in biology, having an immediate application in the generation of research models. DMD muscle cell lines are reliable sources to evaluate and optimize therapeutic strategies, in-depth study of DMD pathology, and screening the effective drugs. However, only a few immortalized muscle cell lines with DMD mutations are available. In addition, obtaining muscle cells from patients also requires an invasive muscle biopsy. Mostly DMD variants are rare, making it challenging to identify a patient with a particular mutation for a muscle biopsy. To overcome these challenges and generate myoblast cultures, we optimized a CRISPR/Cas9 gene editing approach to model the most common DMD mutations that include approximately 28.2% of patients. GAP-PCR and sequencing results show the ability of the CRISPR-Cas9 system to efficient deletion of mentioned exons. We showed producing truncated transcript due to the targeted deletion by RT-PCR and sequencing. Finally, mutation-induced disruption of dystrophin protein expression was confirmed by western blotting. All together, we successfully created four immortalized DMD muscle cell lines and showed the efficacy of the CRISPR-Cas9 system for the generation of immortalized DMD cell models with the targeted deletions.
Collapse
Affiliation(s)
- Farzaneh Alizadeh
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yousef Jafari Abraghan
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Farrokhi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yasamin Yousefi
- Department of Biochemistry, Mashhad University of Ferdowsi, Mashhad, Iran
| | - Yeganeh Mirahmadi
- Department of Biochemistry, Genetics and Molecular Biology, Islamic Azad University, Mashhad, Iran
| | - Atieh Eslahi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Genetic Center of Khorasan Razavi, Mashhad, Iran.
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
18
|
Zhang ML, Li HB, Jin Y. Application and perspective of CRISPR/Cas9 genome editing technology in human diseases modeling and gene therapy. Front Genet 2024; 15:1364742. [PMID: 38666293 PMCID: PMC11043577 DOI: 10.3389/fgene.2024.1364742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) mediated Cas9 nuclease system has been extensively used for genome editing and gene modification in eukaryotic cells. CRISPR/Cas9 technology holds great potential for various applications, including the correction of genetic defects or mutations within the human genome. The application of CRISPR/Cas9 genome editing system in human disease research is anticipated to solve a multitude of intricate molecular biology challenges encountered in life science research. Here, we review the fundamental principles underlying CRISPR/Cas9 technology and its recent application in neurodegenerative diseases, cardiovascular diseases, autoimmune related diseases, and cancer, focusing on the disease modeling and gene therapy potential of CRISPR/Cas9 in these diseases. Finally, we provide an overview of the limitations and future prospects associated with employing CRISPR/Cas9 technology for diseases study and treatment.
Collapse
Affiliation(s)
- Man-Ling Zhang
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Hong-Bin Li
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yong Jin
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| |
Collapse
|
19
|
Chrzanowski S, Batra R. CRISPR-Based Gene Editing Techniques in Pediatric Neurological Disorders. Pediatr Neurol 2024; 153:166-174. [PMID: 38394831 DOI: 10.1016/j.pediatrneurol.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
The emergence of gene editing technologies offers a unique opportunity to develop mutation-specific treatments for pediatric neurological disorders. Gene editing systems can potentially alter disease trajectory by correcting dysfunctional mutations or therapeutically altering gene expression. Clustered regularly interspaced short palindromic repeats (CRISPR)-based approaches are attractive gene therapy platforms to personalize treatments because of their specificity, ease of design, versatility, and cost. However, many such approaches remain in the early stages of development, with ongoing efforts to optimize editing efficiency, minimize unintended off-target effects, and mitigate pathologic immune responses. Given the rapid evolution of CRISPR-based therapies, it is prudent for the clinically based child neurologist to have a conceptual understanding of what such therapies may entail, including both benefits and risks and how such therapies may be clinically applied. In this review, we describe the fundamentals of CRISPR-based therapies, discuss the opportunities and challenges that have arisen, and highlight preclinical work in several pediatric neurological diseases.
Collapse
Affiliation(s)
- Stephen Chrzanowski
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts.
| | | |
Collapse
|
20
|
Swiderski K, Chan AS, Herold MJ, Kueh AJ, Chung JD, Hardee JP, Trieu J, Chee A, Naim T, Gregorevic P, Lynch GS. The BALB/c.mdx62 mouse exhibits a dystrophic muscle pathology and is a model of Duchenne muscular dystrophy. Dis Model Mech 2024; 17:dmm050502. [PMID: 38602028 PMCID: PMC11095634 DOI: 10.1242/dmm.050502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
Duchenne muscular dystrophy (DMD) is a devastating monogenic skeletal muscle-wasting disorder. Although many pharmacological and genetic interventions have been reported in preclinical studies, few have progressed to clinical trials with meaningful benefit. Identifying therapeutic potential can be limited by availability of suitable preclinical mouse models. More rigorous testing across models with varied background strains and mutations can identify treatments for clinical success. Here, we report the generation of a DMD mouse model with a CRISPR-induced deletion within exon 62 of the dystrophin gene (Dmd) and the first generated in BALB/c mice. Analysis of mice at 3, 6 and 12 months of age confirmed loss of expression of the dystrophin protein isoform Dp427 and resultant dystrophic pathology in limb muscles and the diaphragm, with evidence of centrally nucleated fibers, increased inflammatory markers and fibrosis, progressive decline in muscle function, and compromised trabecular bone development. The BALB/c.mdx62 mouse is a novel model of DMD with associated variations in the immune response and muscle phenotype, compared with those of existing models. It represents an important addition to the preclinical model toolbox for developing therapeutic strategies.
Collapse
Affiliation(s)
- Kristy Swiderski
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Audrey S. Chan
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marco J. Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3052, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - Andrew J. Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3052, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - Jin D. Chung
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Justin P. Hardee
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jennifer Trieu
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Annabel Chee
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Timur Naim
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Paul Gregorevic
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gordon S. Lynch
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| |
Collapse
|
21
|
Elasbali AM, Al-Soud WA, Anwar S, Alhassan HH, Adnan M, Hassan MI. A review on mechanistic insights into structure and function of dystrophin protein in pathophysiology and therapeutic targeting of Duchenne muscular dystrophy. Int J Biol Macromol 2024; 264:130544. [PMID: 38428778 DOI: 10.1016/j.ijbiomac.2024.130544] [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: 01/11/2024] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive genetic disorder characterized by progressive and severe muscle weakening and degeneration. Among the various forms of muscular dystrophy, it stands out as one of the most common and impactful, predominantly affecting boys. The condition arises due to mutations in the dystrophin gene, a key player in maintaining the structure and function of muscle fibers. The manuscript explores the structural features of dystrophin protein and their pivotal roles in DMD. We present an in-depth analysis of promising therapeutic approaches targeting dystrophin and their implications for the therapeutic management of DMD. Several therapies aiming to restore dystrophin protein or address secondary pathology have obtained regulatory approval, and many others are ongoing clinical development. Notably, recent advancements in genetic approaches have demonstrated the potential to restore partially functional dystrophin forms. The review also provides a comprehensive overview of the status of clinical trials for major therapeutic genetic approaches for DMD. In addition, we have summarized the ongoing therapeutic approaches and advanced mechanisms of action for dystrophin restoration and the challenges associated with DMD therapeutics.
Collapse
Affiliation(s)
- Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Science, College of Applied Sciences-Sakaka, Jouf University, Sakaka, Saudi Arabia; Molekylärbiologi, Klinisk Mikrobiologi och vårdhygien, Region Skåne, Sölvegatan 23B, 221 85 Lund, Sweden
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Hassan H Alhassan
- Department of Clinical Laboratory Science, College of Applied Sciences-Sakaka, Jouf University, Sakaka, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| |
Collapse
|
22
|
Jin M, Lin J, Zhang Y, Xiao Q, Kong X, Zhang X, Shao Z, Wang Y, Yu Y, Li J, Chen WJ, Li G, Yang H, Wang N. enOsCas12f1-mediated exon skipping for Duchenne muscular dystrophy therapy in humanized mouse model. J Genet Genomics 2024; 51:256-259. [PMID: 38103683 DOI: 10.1016/j.jgg.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Affiliation(s)
- Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian 350004, China
| | - Jiajia Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian 350004, China
| | - Yu Zhang
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China
| | - Qingquan Xiao
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China
| | - Xiangfeng Kong
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China
| | - Xiumei Zhang
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China
| | - Zhurui Shao
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China
| | - Yin Wang
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China
| | - Yuyang Yu
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China
| | - Jinjing Li
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian 350004, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian 350004, China
| | - Guoling Li
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China.
| | - Hui Yang
- HUIDAGENE Therapeutics Co., Ltd., Shanghai 200131, China Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian 350004, China.
| |
Collapse
|
23
|
Wang J, Zhang X, Chen H, Ren H, Zhou M, Zhao Y. Engineered stem cells by emerging biomedical stratagems. Sci Bull (Beijing) 2024; 69:248-279. [PMID: 38101962 DOI: 10.1016/j.scib.2023.12.006] [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: 07/10/2023] [Revised: 09/24/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023]
Abstract
Stem cell therapy holds immense potential as a viable treatment for a widespread range of intractable disorders. As the safety of stem cell transplantation having been demonstrated in numerous clinical trials, various kinds of stem cells are currently utilized in medical applications. Despite the achievements, the therapeutic benefits of stem cells for diseases are limited, and the data of clinical researches are unstable. To optimize tthe effectiveness of stem cells, engineering approaches have been developed to enhance their inherent abilities and impart them with new functionalities, paving the way for the next generation of stem cell therapies. This review offers a detailed analysis of engineered stem cells, including their clinical applications and potential for future development. We begin by briefly introducing the recent advances in the production of stem cells (induced pluripotent stem cells (iPSCs), embryonic stem cells (ESCs), mesenchymal stem cells (MSCs) and hematopoietic stem cells (HSCs)). Furthermore, we present the latest developments of engineered strategies in stem cells, including engineered methods in molecular biology and biomaterial fields, and their application in biomedical research. Finally, we summarize the current obstacles and suggest future prospects for engineered stem cells in clinical translations and biomedical applications.
Collapse
Affiliation(s)
- Jinglin Wang
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaoxuan Zhang
- Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hanxu Chen
- Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Haozhen Ren
- Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Min Zhou
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
| | - Yuanjin Zhao
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Shenzhen Research Institute, Southeast University, Shenzhen 518038, China.
| |
Collapse
|
24
|
Levchenko O, Panchuk I, Kochergin-Nikitsky K, Petrova I, Nagieva S, Pilkin M, Yakovlev I, Smirnikhina S, Deev R, Lavrov A. Unexpected extra exon skipping in the DYSF gene during restoring the reading frame by CRISPR/Cas9. Biosystems 2024; 235:105072. [PMID: 37944631 DOI: 10.1016/j.biosystems.2023.105072] [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: 08/15/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The DYSF gene encoding dysferlin protein is one of the largest and has many transcripts. Pathogenic variants in the gene can lead to various types of myopathies, which makes it a good object for studying the events occurring in it during genome editing by the CRISPR/Cas method. In this study, we evaluated the possibility of permanent skipping of exons 3-4, and 26-27 which deletion does not violate the reading frame and allows to eliminate truncated variants within exons. Editing was performed with simultaneous transfection of two sgRNA- and sa/spCas9-containing plasmids on HEK293T cell cultures and healthy donor myoblasts. Skipping of exons 3-4 was performed by destroying the splicing acceptor sites, and exons 26-27 by cuts in the flanking exons with the corresponding deletion in the DNA. Some unexpected results were obtained, when exons 26-27 were skipped, exon 30 was also absent in the transcript, although it is not alternatively spliced and is normally present in all transcripts. This event indicates that DNA changes near splicing sites can affect adjacent exons and the whole gene. However, this fact requires further study.
Collapse
Affiliation(s)
- Olga Levchenko
- Research Centre for Medical Genetics, 115522, Moscow, Russia.
| | - Irina Panchuk
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | | | - Irina Petrova
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | - Sabina Nagieva
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | - Maxim Pilkin
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | | | | | - Roman Deev
- North-Western State Medical University named after I.I. Mechnikov, 191015, St. Petersburg, Russia
| | | |
Collapse
|
25
|
Lin M, Wang X. Natural Biopolymer-Based Delivery of CRISPR/Cas9 for Cancer Treatment. Pharmaceutics 2023; 16:62. [PMID: 38258073 PMCID: PMC10819213 DOI: 10.3390/pharmaceutics16010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Over the last decade, the clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become the most promising gene editing tool and is broadly utilized to manipulate the gene for disease treatment, especially for cancer, which involves multiple genetic alterations. Typically, CRISPR/Cas9 machinery is delivered in one of three forms: DNA, mRNA, or ribonucleoprotein. However, the lack of efficient delivery systems for these macromolecules confined the clinical breakthrough of this technique. Therefore, a variety of nanomaterials have been fabricated to improve the stability and delivery efficiency of the CRISPR/Cas9 system. In this context, the natural biopolymer-based carrier is a particularly promising platform for CRISPR/Cas9 delivery due to its great stability, low toxicity, excellent biocompatibility, and biodegradability. Here, we focus on the advances of natural biopolymer-based materials for CRISPR/Cas9 delivery in the cancer field and discuss the challenges for their clinical translation.
Collapse
Affiliation(s)
| | - Xueyan Wang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
26
|
Tominari T, Takatoya M, Matsubara T, Matsunobe M, Arai D, Matsumoto C, Hirata M, Yoshinouchi S, Miyaura C, Itoh Y, Komaki H, Takeda S, Aoki Y, Inada M. Establishment of a Triple Quadrupole HPLC-MS Quantitation Method for Dystrophin Protein in Mouse and Human Skeletal Muscle. Int J Mol Sci 2023; 25:303. [PMID: 38203473 PMCID: PMC10779312 DOI: 10.3390/ijms25010303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common type of neuromuscular disease caused by mutations in the DMD gene encoding dystrophin protein. To quantitively assess human dystrophin protein in muscle biopsy samples, it is imperative to consistently detect as low as 0.003% of the dystrophin protein relative to the total muscle protein content. The quantitation of dystrophin protein has traditionally been conducted using semiquantitative immunoblotting or immunohistochemistry; however, there is a growing need to establish a more precise quantitative method by employing liquid chromatography-mass spectrometry (LC-MS) to measure dystrophin protein. In this study, a novel quantification method was established using a mouse experiment platform applied to the clinical quantification of human dystrophin protein. The method using a spike-in approach with a triple quadrupole LC-MS quantitated the amount of dystrophin in wild-type and human DMD transgenic mice but not in DMD-null mice. In conclusion, we established a quantitating method of dystrophin using HPLC-LC-MS with a novel spike-in approach. These results indicate that our methodology could be applied to several LC-MS devices to enable the accurate measurement of dystrophin protein in patients with DMD.
Collapse
Affiliation(s)
- Tsukasa Tominari
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Masaru Takatoya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Toshiya Matsubara
- Life Science Research Center, Shimadzu Corporation, Nakagyo, Kyoto 604-8511, Japan
| | - Michio Matsunobe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Daichi Arai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Chiho Matsumoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Michiko Hirata
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Shosei Yoshinouchi
- Cooperative Major of Advanced Health Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Chisato Miyaura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Yoshifumi Itoh
- Inada Research Unit, Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, UK
| | - Hirofumi Komaki
- Translational Medical Center, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Shin’ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Masaki Inada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Cooperative Major of Advanced Health Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Inada Research Unit, Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| |
Collapse
|
27
|
Driver K, Vo C, Scriba CK, Saker S, Larmonier T, Malfatti E, Romero NB, Ravenscroft G, Laing NG, Taylor RL, Clayton JS. Generation of two induced pluripotent stem cell lines from a 33-year-old central core disease patient with a heterozygous dominant c.14145_14156delCTACTGGGACA (p.Asn4715_Asp4718del) deletion in the RYR1 gene. Stem Cell Res 2023; 73:103258. [PMID: 38029555 DOI: 10.1016/j.scr.2023.103258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
Central core disease (CCD) is a congenital disorder that results in hypotonia, delayed motor development, and areas of reduced oxidative activity in the muscle fibre. Two induced pluripotent stem cell (iPSC) lines were generated from the lymphoblastoid cells of a 33-year-old male with CCD, caused by a previously unreported dominant c.14145_14156delCTACTGGGACA (p.Asn4715_Asp4718del) deletion in the RYR1 gene. Both lines demonstrated typical morphology, pluripotency, trilineage differentiation, and had a normal karyotype. As the first published iPSC model of CCD caused by an RYR1 variant these lines are a potential resource for further investigation of RYR1-related myopathies in a human context.
Collapse
Affiliation(s)
- Karrison Driver
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Christina Vo
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Carolin K Scriba
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia; Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA, Australia
| | - Safaa Saker
- Genethon, DNA and Cell Bank, 91000 Evry, France
| | | | - Edoardo Malfatti
- APHP, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Henri Mondor Hospital, France; Université Paris Est, U955, INSERM, IMRB, F-94010 Créteil, France
| | - Norma B Romero
- Sorbonne Université, Myology Institute, Neuromuscular Morphology Unit, Center for Research in Myology, GH Pitié-Salpêtrière, Paris, France; Centre de Référence de Pathologie Neuromusculaire Paris-Est, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Rhonda L Taylor
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Joshua S Clayton
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia.
| |
Collapse
|
28
|
Hicks MR, Saleh KK, Clock B, Gibbs DE, Yang M, Younesi S, Gane L, Gutierrez-Garcia V, Xi H, Pyle AD. Regenerating human skeletal muscle forms an emerging niche in vivo to support PAX7 cells. Nat Cell Biol 2023; 25:1758-1773. [PMID: 37919520 PMCID: PMC10709143 DOI: 10.1038/s41556-023-01271-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 09/26/2023] [Indexed: 11/04/2023]
Abstract
Skeletal muscle stem and progenitor cells including those derived from human pluripotent stem cells (hPSCs) offer an avenue towards personalized therapies and readily fuse to form human-mouse myofibres in vivo. However, skeletal muscle progenitor cells (SMPCs) inefficiently colonize chimeric stem cell niches and instead associate with human myofibres resembling foetal niches. We hypothesized competition with mouse satellite cells (SCs) prevented SMPC engraftment into the SC niche and thus generated an SC ablation mouse compatible with human engraftment. Single-nucleus RNA sequencing of SC-ablated mice identified the absence of a transient myofibre subtype during regeneration expressing Actc1. Similarly, ACTC1+ human myofibres supporting PAX7+ SMPCs increased in SC-ablated mice, and after re-injury we found SMPCs could now repopulate into chimeric niches. To demonstrate ACTC1+ myofibres are essential to supporting PAX7 SMPCs, we generated caspase-inducible ACTC1 depletion human pluripotent stem cells, and upon SMPC engraftment we found a 90% reduction in ACTC1+ myofibres and a 100-fold decrease in PAX7 cell numbers compared with non-induced controls. We used spatial RNA sequencing to identify key factors driving emerging human niche formation between ACTC1+ myofibres and PAX7+ SMPCs in vivo. This revealed that transient regenerating human myofibres are essential for emerging niche formation in vivo to support PAX7 SMPCs.
Collapse
Affiliation(s)
- Michael R Hicks
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA.
- Physiology and Biophysics, University of California, Irvine, CA, USA.
| | - Kholoud K Saleh
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Molecular, Cellular & Integrative Physiology Program, University of California, Los Angeles, CA, USA
| | - Ben Clock
- Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Devin E Gibbs
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Mandee Yang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Shahab Younesi
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Lily Gane
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | | | - Haibin Xi
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - April D Pyle
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonnson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
| |
Collapse
|
29
|
Du X, McManus DP, French JD, Sivakumaran H, Johnston RL, Kondrashova O, Fogarty CE, Jones MK, You H. Lentiviral Transduction-based CRISPR/Cas9 Editing of Schistosoma mansoni Acetylcholinesterase. Curr Genomics 2023; 24:155-170. [PMID: 38178986 PMCID: PMC10761339 DOI: 10.2174/1389202924666230823094608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/02/2023] [Accepted: 07/17/2023] [Indexed: 01/06/2024] Open
Abstract
Background Recent studies on CRISPR/Cas9-mediated gene editing in Schistosoma mansoni have shed new light on the study and control of this parasitic helminth. However, the gene editing efficiency in this parasite is modest. Methods To improve the efficiency of CRISPR/Cas9 genome editing in schistosomes, we used lentivirus, which has been effectively used for gene editing in mammalian cells, to deliver plasmid DNA encoding Cas9 nuclease, a sgRNA targeting acetylcholinesterase (SmAChE) and a mCherry fluorescence marker into schistosomes. Results MCherry fluorescence was observed in transduced eggs, schistosomula, and adult worms, indicating that the CRISPR components had been delivered into these parasite stages by lentivirus. In addition, clearly changed phenotypes were observed in SmAChE-edited parasites, including decreased SmAChE activity, reduced hatching ability of edited eggs, and altered behavior of miracidia hatched from edited eggs. Next-generation sequencing analysis demonstrated that the lentiviral transduction-based CRISPR/Cas9 gene modifications in SmAChE-edited schistosomes were homology-directed repair predominant but with much lower efficiency than that obtained using electroporation (data previously published by our laboratory) for the delivery of CRISPR components. Conclusion Taken together, electroporation is more efficient than lentiviral transduction in the delivery of CRISPR/Cas9 into schistosomes for programmed genome editing. The exploration of tactics for enhancing CRISPR/Cas9 gene editing provides the basis for the future improvement of programmed genome editing in S. mansoni.
Collapse
Affiliation(s)
- Xiaofeng Du
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Donald P. McManus
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Juliet D. French
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Haran Sivakumaran
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rebecca L. Johnston
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Olga Kondrashova
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Conor E. Fogarty
- Centre for Bioinnovation, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia
| | - Malcolm K. Jones
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Hong You
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| |
Collapse
|
30
|
Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
Collapse
Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
| | | | | |
Collapse
|
31
|
Sparmann A, Vogel J. RNA-based medicine: from molecular mechanisms to therapy. EMBO J 2023; 42:e114760. [PMID: 37728251 PMCID: PMC10620767 DOI: 10.15252/embj.2023114760] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
RNA-based therapeutics have the potential to revolutionize the treatment and prevention of human diseases. While early research faced setbacks, it established the basis for breakthroughs in RNA-based drug design that culminated in the extraordinarily fast development of mRNA vaccines to combat the COVID-19 pandemic. We have now reached a pivotal moment where RNA medicines are poised to make a broad impact in the clinic. In this review, we present an overview of different RNA-based strategies to generate novel therapeutics, including antisense and RNAi-based mechanisms, mRNA-based approaches, and CRISPR-Cas-mediated genome editing. Using three rare genetic diseases as examples, we highlight the opportunities, but also the challenges to wide-ranging applications of this class of drugs.
Collapse
Affiliation(s)
- Anke Sparmann
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
| | - Jörg Vogel
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
- Institute of Molecular Infection Biology (IMIB)University of WürzburgWürzburgGermany
| |
Collapse
|
32
|
Madigan V, Zhang F, Dahlman JE. Drug delivery systems for CRISPR-based genome editors. Nat Rev Drug Discov 2023; 22:875-894. [PMID: 37723222 DOI: 10.1038/s41573-023-00762-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 09/20/2023]
Abstract
CRISPR-based drugs can theoretically manipulate any genetic target. In practice, however, these drugs must enter the desired cell without eliciting an unwanted immune response, so a delivery system is often required. Here, we review drug delivery systems for CRISPR-based genome editors, focusing on adeno-associated viruses and lipid nanoparticles. After describing how these systems are engineered and their subsequent characterization in preclinical animal models, we highlight data from recent clinical trials. Preclinical targeting mediated by polymers, proteins, including virus-like particles, and other vehicles that may deliver CRISPR systems in the future is also discussed.
Collapse
Affiliation(s)
- Victoria Madigan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
33
|
Li L, Vasan L, Kartono B, Clifford K, Attarpour A, Sharma R, Mandrozos M, Kim A, Zhao W, Belotserkovsky A, Verkuyl C, Schmitt-Ulms G. Advances in Recombinant Adeno-Associated Virus Vectors for Neurodegenerative Diseases. Biomedicines 2023; 11:2725. [PMID: 37893099 PMCID: PMC10603849 DOI: 10.3390/biomedicines11102725] [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: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors are gene therapy delivery tools that offer a promising platform for the treatment of neurodegenerative diseases. Keeping up with developments in this fast-moving area of research is a challenge. This review was thus written with the intention to introduce this field of study to those who are new to it and direct others who are struggling to stay abreast of the literature towards notable recent studies. In ten sections, we briefly highlight early milestones within this field and its first clinical success stories. We showcase current clinical trials, which focus on gene replacement, gene augmentation, or gene suppression strategies. Next, we discuss ongoing efforts to improve the tropism of rAAV vectors for brain applications and introduce pre-clinical research directed toward harnessing rAAV vectors for gene editing applications. Subsequently, we present common genetic elements coded by the single-stranded DNA of rAAV vectors, their so-called payloads. Our focus is on recent advances that are bound to increase treatment efficacies. As needed, we included studies outside the neurodegenerative disease field that showcased improved pre-clinical designs of all-in-one rAAV vectors for gene editing applications. Finally, we discuss risks associated with off-target effects and inadvertent immunogenicity that these technologies harbor as well as the mitigation strategies available to date to make their application safer.
Collapse
Affiliation(s)
- Leyao Li
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
| | - Lakshmy Vasan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Bryan Kartono
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Kevan Clifford
- Institute of Medical Science, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Centre for Addiction and Mental Health (CAMH), 250 College St., Toronto, ON M5T 1R8, Canada
| | - Ahmadreza Attarpour
- Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Raghav Sharma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Matthew Mandrozos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ain Kim
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Wenda Zhao
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ari Belotserkovsky
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Claire Verkuyl
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
34
|
D'Ambrosio ES, Mendell JR. Evolving Therapeutic Options for the Treatment of Duchenne Muscular Dystrophy. Neurotherapeutics 2023; 20:1669-1681. [PMID: 37673849 PMCID: PMC10684843 DOI: 10.1007/s13311-023-01423-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/08/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common childhood form of muscular dystrophy. It is caused by mutations in the DMD gene, leading to reduced or absent expression of the dystrophin protein. Clinically, this results in loss of ambulation, cardiomyopathy, respiratory failure, and eventually death. In the past decades, the use of corticosteroids has slowed down the disease progression. More recently, the development of genetically mediated therapies has emerged as the most promising treatment for DMD. These strategies include exon skipping with antisense oligonucleotides, gene replacement therapy with adeno-associated virus, and gene editing with CRISPR (clustered regularly interspaced short palindromic repeats) technology. In this review, we highlight the most up-to-date therapeutic progresses in the field, with emphasis on past and recent experiences, as well as the latest clinical results of DMD micro-dystrophin gene therapy. Additionally, we discuss the lessons learned along the way and the challenges encountered, all of which have helped advance the field, with the potential to finally alleviate such a devastating disease.
Collapse
Affiliation(s)
- Eleonora S D'Ambrosio
- Center for Gene Therapy, Department of Pediatrics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Ohio State University, Columbus, OH, 43205, USA. eleonora.d'
| | - Jerry R Mendell
- Center for Gene Therapy, Department of Pediatrics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Ohio State University, Columbus, OH, 43205, USA
| |
Collapse
|
35
|
Egorova TV, Polikarpova AV, Vassilieva SG, Dzhenkova MA, Savchenko IM, Velyaev OA, Shmidt AA, Soldatov VO, Pokrovskii MV, Deykin AV, Bardina MV. CRISPR-Cas9 correction in the DMD mouse model is accompanied by upregulation of Dp71f protein. Mol Ther Methods Clin Dev 2023; 30:161-180. [PMID: 37457303 PMCID: PMC10339130 DOI: 10.1016/j.omtm.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a severe hereditary disease caused by a deficiency in the dystrophin protein. The most frequent types of disease-causing mutations in the DMD gene are frameshift deletions of one or more exons. Precision genome editing systems such as CRISPR-Cas9 have shown potential to restore open reading frames in numerous animal studies. Here, we applied an AAV-CRISPR double-cut strategy to correct a mutation in the DMD mouse model with exon 8-34 deletion, encompassing the N-terminal actin-binding domain. We report successful excision of the 100-kb genomic sequence, which includes exons 6 and 7, and partial improvement in cardiorespiratory function. While corrected mRNA was abundant in muscle tissues, only a low level of truncated dystrophin was produced, possibly because of protein instability. Furthermore, CRISPR-Cas9-mediated genome editing upregulated the Dp71f dystrophin isoform on the sarcolemma. Given the previously reported Dp71-associated muscle pathology, our results question the applicability of genome editing strategies for some DMD patients with N-terminal mutations. The safety and efficacy of CRISPR-Cas9 constructs require rigorous investigation in patient-specific animal models.
Collapse
Affiliation(s)
- Tatiana V. Egorova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
| | - Anna V. Polikarpova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
| | - Svetlana G. Vassilieva
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Marina A. Dzhenkova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Irina M. Savchenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Oleg A. Velyaev
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna A. Shmidt
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladislav O. Soldatov
- Research Institute of Living Systems Pharmacology, Belgorod National Research University, Belgorod 308007, Russia
| | - Mikhail V. Pokrovskii
- Research Institute of Living Systems Pharmacology, Belgorod National Research University, Belgorod 308007, Russia
| | - Alexey V. Deykin
- Marlin Biotech LLC, Sochi 354340, Russia
- Joint Center for Genetic Technologies, Laboratory of Genetic Technologies and Gene Editing for Biomedicine and Veterinary Medicine, Department of Pharmacology and Clinical Pharmacology, Belgorod National Research University, Belgorod 308015, Russia
| | - Maryana V. Bardina
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| |
Collapse
|
36
|
Stephenson AA, Nicolau S, Vetter TA, Dufresne GP, Frair EC, Sarff JE, Wheeler GL, Kelly BJ, White P, Flanigan KM. CRISPR-Cas9 homology-independent targeted integration of exons 1-19 restores full-length dystrophin in mice. Mol Ther Methods Clin Dev 2023; 30:486-499. [PMID: 37706184 PMCID: PMC10495553 DOI: 10.1016/j.omtm.2023.08.009] [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: 03/09/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
Duchenne muscular dystrophy is an X-linked disorder typically caused by out-of-frame mutations in the DMD gene. Most of these are deletions of one or more exons, which can theoretically be corrected through CRISPR-Cas9-mediated knockin. Homology-independent targeted integration is a mechanism for achieving such a knockin without reliance on homology-directed repair pathways, which are inactive in muscle. We designed a system based on insertion into intron 19 of a DNA fragment containing a pre-spliced mega-exon encoding DMD exons 1-19, along with the MHCK7 promoter, and delivered it via a pair of AAV9 vectors in mice carrying a Dmd exon 2 duplication. Maximal efficiency was achieved using a Cas9:donor adeno-associated virus (AAV) ratio of 1:5, with Cas9 under the control of the SPc5-12 promoter. This approach achieved editing of 1.4% of genomes in the heart, leading to 30% correction at the transcript level and restoration of 11% of normal dystrophin levels. Treatment efficacy was lower in skeletal muscles. Sequencing additionally revealed integration of fragmentary and recombined AAV genomes at the target site. These data provide proof of concept for a gene editing system that could restore full-length dystrophin in individuals carrying mutations upstream of intron 19, accounting for approximately 25% of Duchenne muscular dystrophy patients.
Collapse
Affiliation(s)
- Anthony A. Stephenson
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Stefan Nicolau
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Tatyana A. Vetter
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Gabrielle P. Dufresne
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Emma C. Frair
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Jessica E. Sarff
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Gregory L. Wheeler
- The Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Benjamin J. Kelly
- The Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Peter White
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
- The Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Kevin M. Flanigan
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
- Department of Neurology, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
37
|
Kita Y, Okuzaki Y, Naoe Y, Lee J, Bang U, Okawa N, Ichiki A, Jonouchi T, Sakurai H, Kojima Y, Hotta A. Dual CRISPR-Cas3 system for inducing multi-exon skipping in DMD patient-derived iPSCs. Stem Cell Reports 2023; 18:1753-1765. [PMID: 37625413 PMCID: PMC10545483 DOI: 10.1016/j.stemcr.2023.07.007] [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: 10/03/2022] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
To restore dystrophin protein in various mutation patterns of Duchenne muscular dystrophy (DMD), the multi-exon skipping (MES) approach has been investigated. However, only limited techniques are available to induce a large deletion to cover the target exons spread over several hundred kilobases. Here, we utilized the CRISPR-Cas3 system for MES induction and showed that dual crRNAs could induce a large deletion at the dystrophin exon 45-55 region (∼340 kb), which can be applied to various types of DMD patients. We developed a two-color SSA-based reporter system for Cas3 to enrich the genome-edited cell population and demonstrated that MES induction restored dystrophin protein in DMD-iPSCs with three distinct mutations. Whole-genome sequencing and distance analysis detected no significant off-target deletion near the putative crRNA binding sites. Altogether, dual CRISPR-Cas3 is a promising tool to induce a gigantic genomic deletion and restore dystrophin protein via MES induction.
Collapse
Affiliation(s)
- Yuto Kita
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuya Okuzaki
- Nagoya University Graduate School of Bioagricultural Sciences, Avian Bioscience Research Center, Furo-cho, Chikusa-ku, Nagoya, Aishi 464-8601, Japan
| | - Youichi Naoe
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Joseph Lee
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Uikyu Bang
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Natsumi Okawa
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akane Ichiki
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tatsuya Jonouchi
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yusuke Kojima
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa 251-8555, Japan.
| |
Collapse
|
38
|
Ebrahimi S, Khosravi MA, Raz A, Karimipoor M, Parvizi P. CRISPR-Cas Technology as a Revolutionary Genome Editing tool: Mechanisms and Biomedical Applications. IRANIAN BIOMEDICAL JOURNAL 2023; 27:219-46. [PMID: 37873636 PMCID: PMC10707817 DOI: 10.61186/ibj.27.5.219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/14/2023] [Indexed: 12/17/2023]
Abstract
Programmable nucleases are powerful genomic tools for precise genome editing. These tools precisely recognize, remove, or change DNA at a defined site, thereby, stimulating cellular DNA repair pathways that can cause mutations or accurate replacement or deletion/insertion of a sequence. CRISPR-Cas9 system is the most potent and useful genome editing technique adapted from the defense immune system of certain bacteria and archaea against viruses and phages. In the past decade, this technology made notable progress, and at present, it has largely been used in genome manipulation to make precise gene editing in plants, animals, and human cells. In this review, we aim to explain the basic principle, mechanisms of action, and applications of this system in different areas of medicine, with emphasizing on the detection and treatment of parasitic diseases.
Collapse
Affiliation(s)
- Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Ali Khosravi
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
39
|
Shah MNA, Yokota T. Cardiac therapies for Duchenne muscular dystrophy. Ther Adv Neurol Disord 2023; 16:17562864231182934. [PMID: 37425427 PMCID: PMC10328182 DOI: 10.1177/17562864231182934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/11/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a devastating disease that results in life-limiting complications such as loss of skeletal muscle function as well as respiratory and cardiac complications. Advanced therapeutics in pulmonary care have significantly reduced respiratory complication-related mortality, making cardiomyopathy the main determinant factor of survival. While there are multiple therapies such as the use of anti-inflammatory drugs, physical therapy, and ventilatory assistance targeted toward delaying the disease progression in DMD, a cure remains elusive. In the last decade, several therapeutic approaches have been developed to improve patient survival. These include small molecule-based therapy, micro-dystrophin gene delivery, CRISPR-mediated gene editing, nonsense readthrough, exon skipping, and cardiosphere-derived cell therapy. Associated with the specific benefits of each of these approaches are their individual risks and limitations. The variability in the genetic aberrations leading to DMD also limits the widespread use of these therapies. While numerous approaches have been explored to treat DMD pathophysiology, only a handful have successfully advanced through the preclinical stages. In this review, we summarize the currently approved as well as the most promising therapeutics undergoing clinical trials aimed toward treating DMD with a focus on its cardiac manifestations.
Collapse
Affiliation(s)
- Md Nur Ahad Shah
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
40
|
Bez Batti Angulski A, Hosny N, Cohen H, Martin AA, Hahn D, Bauer J, Metzger JM. Duchenne muscular dystrophy: disease mechanism and therapeutic strategies. Front Physiol 2023; 14:1183101. [PMID: 37435300 PMCID: PMC10330733 DOI: 10.3389/fphys.2023.1183101] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/24/2023] [Indexed: 07/13/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe, progressive, and ultimately fatal disease of skeletal muscle wasting, respiratory insufficiency, and cardiomyopathy. The identification of the dystrophin gene as central to DMD pathogenesis has led to the understanding of the muscle membrane and the proteins involved in membrane stability as the focal point of the disease. The lessons learned from decades of research in human genetics, biochemistry, and physiology have culminated in establishing the myriad functionalities of dystrophin in striated muscle biology. Here, we review the pathophysiological basis of DMD and discuss recent progress toward the development of therapeutic strategies for DMD that are currently close to or are in human clinical trials. The first section of the review focuses on DMD and the mechanisms contributing to membrane instability, inflammation, and fibrosis. The second section discusses therapeutic strategies currently used to treat DMD. This includes a focus on outlining the strengths and limitations of approaches directed at correcting the genetic defect through dystrophin gene replacement, modification, repair, and/or a range of dystrophin-independent approaches. The final section highlights the different therapeutic strategies for DMD currently in clinical trials.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Joseph M. Metzger
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, United States
| |
Collapse
|
41
|
Chai AC, Chemello F, Li H, Nishiyama T, Chen K, Zhang Y, Sánchez-Ortiz E, Alomar A, Xu L, Liu N, Bassel-Duby R, Olson EN. Single-swap editing for the correction of common Duchenne muscular dystrophy mutations. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:522-535. [PMID: 37215149 PMCID: PMC10192335 DOI: 10.1016/j.omtn.2023.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disease of progressive muscle weakness and wasting caused by the absence of dystrophin protein. Current gene therapy approaches using antisense oligonucleotides require lifelong dosing and have limited efficacy in restoring dystrophin production. A gene editing approach could permanently correct the genome and restore dystrophin protein expression. Here, we describe single-swap editing, in which an adenine base editor edits a single base pair at a splice donor site or splice acceptor site to enable exon skipping or reframing. In human induced pluripotent stem cell-derived cardiomyocytes, we demonstrate that single-swap editing can enable beneficial exon skipping or reframing for the three most therapeutically relevant exons-DMD exons 45, 51, and 53-which could be beneficial for 30% of all DMD patients. Furthermore, an adeno-associated virus delivery method for base editing components can efficiently restore dystrophin production locally and systemically in skeletal and cardiac muscles of a DMD mouse model containing a deletion of Dmd exon 44. Our studies demonstrate single-swap editing as a potential gene editing therapy for common DMD mutations.
Collapse
Affiliation(s)
- Andreas C. Chai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Francesco Chemello
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Takahiko Nishiyama
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Efraín Sánchez-Ortiz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adeeb Alomar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
42
|
Sekine S, Mayama S, Nishijima N, Kojima T, Endo-Takahashi Y, Ishii Y, Shiono H, Akiyama S, Sakurai A, Sashida S, Hamano N, Tada R, Suzuki R, Maruyama K, Negishi Y. Development of a Gene and Nucleic Acid Delivery System for Skeletal Muscle Administration via Limb Perfusion Using Nanobubbles and Ultrasound. Pharmaceutics 2023; 15:1665. [PMID: 37376113 PMCID: PMC10302710 DOI: 10.3390/pharmaceutics15061665] [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: 04/27/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Strategies for gene and nucleic acid delivery to skeletal muscles have been extensively explored to treat Duchenne muscular dystrophy (DMD) and other neuromuscular diseases. Of these, effective intravascular delivery of naked plasmid DNA (pDNA) and nucleic acids into muscles is an attractive approach, given the high capillary density in close contact with myofibers. We developed lipid-based nanobubbles (NBs) using polyethylene-glycol-modified liposomes and an echo-contrast gas and found that these NBs could improve tissue permeability by ultrasound (US)-induced cavitation. Herein, we delivered naked pDNA or antisense phosphorodiamidate morpholino oligomers (PMOs) into the regional hindlimb muscle via limb perfusion using NBs and US exposure. pDNA encoding the luciferase gene was injected with NBs via limb perfusion into normal mice with application of US. High luciferase activity was achieved in a wide area of the limb muscle. DMD model mice were administered PMOs, designed to skip the mutated exon 23 of the dystrophin gene, with NBs via intravenous limb perfusion, followed by US exposure. The number of dystrophin-positive fibers increased in the muscles of mdx mice. Combining NBs and US exposure, which can be widely delivered to the hind limb muscles via the limb vein, could be an effective therapeutic approach for DMD and other neuromuscular disorders.
Collapse
Affiliation(s)
- Shohko Sekine
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Sayaka Mayama
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Nobuaki Nishijima
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Takuo Kojima
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Yoko Endo-Takahashi
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Yuko Ishii
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Hitomi Shiono
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Saki Akiyama
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Akane Sakurai
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Sanae Sashida
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Nobuhito Hamano
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Rui Tada
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| | - Ryo Suzuki
- Laboratory of Drug and Gene Delivery Research, Faculty of Pharma-Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan;
- Advanced Comprehensive Research Organization (ACRO), Teikyo University, Tokyo 173-8605, Japan;
| | - Kazuo Maruyama
- Advanced Comprehensive Research Organization (ACRO), Teikyo University, Tokyo 173-8605, Japan;
- Laboratory of Ultrasound Theranostics, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
| | - Yoichi Negishi
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan (Y.E.-T.); (N.H.); (R.T.)
| |
Collapse
|
43
|
Tang F, Xiao Y, Zhou C, Zhang H, Wang J, Zeng Y. NGS-based targeted sequencing identified six novel variants in patients with Duchenne/Becker muscular dystrophy from southwestern China. BMC Med Genomics 2023; 16:121. [PMID: 37254189 DOI: 10.1186/s12920-023-01556-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND At present, Multiplex ligation-dependent probe amplification (MLPA) and exome sequencing are common gene detection methods in patients with Duchenne muscular dystrophy or Becker muscular dystrophy (DMD/BMD), but they can not cover the whole-genome sequence of the DMD gene. In this study, the whole genome capture of the DMD gene and next-generation sequencing (NGS) technology were used to detect the patients with DMD/BMD in Southwest China, to clarify the application value of this technology and further study the gene variant spectrum. METHODS From 2017 to 2020, 51 unrelated patients with DMD/BMD in southwestern China were clinically diagnosed at West China Second University Hospital of Sichuan University (Chengdu, China). The whole-genome of the DMD gene was captured from the peripheral blood of all patients, and next-generation sequencing was performed. Large copy number variants (CNVs) in the exon regions of the DMD gene were verified through MLPA, and small variations (such as single nucleotide variation and < 50 bp fragment insertions/deletions) were validated using Sanger sequencing. RESULTS Among the 51 patients, 49 (96.1% [49/51]) had pathogenic or likely pathogenic variants in the DMD gene. Among the 49 positive samples, 17 patients (34.7% [17/49]) had CNVs in the exon regions and 32 patients (65.3% [32/49]) had small variations. A total of six novel variants were identified: c.10916_10917del, c.1790T>A, c.1842del, c.5015del, c.5791_5792insCA, and exons 38-50 duplication. CONCLUSIONS Pathogenic or likely pathogenic variants of the DMD gene were detected in 49 patients (96.1% [49/51]), of which 6 variants (12.2% [6/49]) had not been previously reported. This study confirmed the value of NGS-based targeted sequencing for the DMD gene expanding the spectrum of variants in DMD, which may provide effective genetic counseling and prenatal diagnosis for families.
Collapse
Affiliation(s)
- Feng Tang
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yuanyuan Xiao
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Cong Zhou
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Haixia Zhang
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yang Zeng
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
| |
Collapse
|
44
|
Moore OM, Ho KS, Copeland JS, Parthasarathy V, Wehrens XHT. Genome Editing and Cardiac Arrhythmias. Cells 2023; 12:1363. [PMID: 37408197 PMCID: PMC10216508 DOI: 10.3390/cells12101363] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
This article reviews progress in the field of cardiac genome editing, in particular, its potential utility in treating cardiac arrhythmias. First, we discuss genome editing methods by which DNA can be disrupted, inserted, deleted, or corrected in cardiomyocytes. Second, we provide an overview of in vivo genome editing in preclinical models of heritable and acquired arrhythmias. Third, we discuss recent advancements in cardiac gene transfer, including delivery methods, gene expression optimization, and potential adverse effects associated with therapeutic somatic genome editing. While genome editing for cardiac arrhythmias is still in its infancy, this approach holds great promise, especially for inherited arrhythmia syndromes with a defined genetic defect.
Collapse
Affiliation(s)
- Oliver M. Moore
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin S. Ho
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Juwan S. Copeland
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vaidya Parthasarathy
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xander H. T. Wehrens
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
45
|
Khare P, Edgecomb SX, Hamadani CM, E L Tanner E, Manickam DS. Lipid nanoparticle-mediated drug delivery to the brain. Adv Drug Deliv Rev 2023; 197:114861. [PMID: 37150326 DOI: 10.1016/j.addr.2023.114861] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/12/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
Lipid nanoparticles (LNPs) have revolutionized the field of drug delivery through their applications in siRNA delivery to the liver (Onpattro) and their use in the Pfizer-BioNTech and Moderna COVID-19 mRNA vaccines. While LNPs have been extensively studied for the delivery of RNA drugs to muscle and liver targets, their potential to deliver drugs to challenging tissue targets such as the brain remains underexplored. Multiple brain disorders currently lack safe and effective therapies and therefore repurposing LNPs could potentially be a game changer for improving drug delivery to cellular targets both at and across the blood-brain barrier (BBB). In this review, we will discuss (1) the rationale and factors involved in optimizing LNPs for brain delivery, (2) ionic liquid-coated LNPs as a potential approach for increasing LNP accumulation in the brain tissue and (3) considerations, open questions and potential opportunities in the development of LNPs for delivery to the brain.
Collapse
Affiliation(s)
- Purva Khare
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA
| | - Sara X Edgecomb
- Department of Chemistry and Biochemistry, The University of Mississippi, MS
| | | | - Eden E L Tanner
- Department of Chemistry and Biochemistry, The University of Mississippi, MS.
| | - Devika S Manickam
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA.
| |
Collapse
|
46
|
Han JL, Entcheva E. Gene Modulation with CRISPR-based Tools in Human iPSC-Cardiomyocytes. Stem Cell Rev Rep 2023; 19:886-905. [PMID: 36656467 PMCID: PMC9851124 DOI: 10.1007/s12015-023-10506-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/20/2023]
Abstract
Precise control of gene expression (knock-out, knock-in, knockdown or overexpression) is at the heart of functional genomics - an approach to dissect the contribution of a gene/protein to the system's function. The development of a human in vitro system that can be patient-specific, induced pluripotent stem cells, iPSC, and the ability to obtain various cell types of interest, have empowered human disease modeling and therapeutic development. Scalable tools have been deployed for gene modulation in these cells and derivatives, including pharmacological means, DNA-based RNA interference and standard RNA interference (shRNA/siRNA). The CRISPR/Cas9 gene editing system, borrowed from bacteria and adopted for use in mammalian cells a decade ago, offers cell-specific genetic targeting and versatility. Outside genome editing, more subtle, time-resolved gene modulation is possible by using a catalytically "dead" Cas9 enzyme linked to an effector of gene transcription in combination with a guide RNA. The CRISPRi / CRISPRa (interference/activation) system evolved over the last decade as a scalable technology for performing functional genomics with libraries of gRNAs. Here, we review key developments of these approaches and their deployment in cardiovascular research. We discuss specific use with iPSC-cardiomyocytes and the challenges in further translation of these techniques.
Collapse
Affiliation(s)
- Julie Leann Han
- Department of Biomedical Engineering, The George Washington University, 800 22nd St NW, Suite 5000, Washington, DC, 20052, USA
| | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, 800 22nd St NW, Suite 5000, Washington, DC, 20052, USA.
| |
Collapse
|
47
|
Kyriakopoulou E, Monnikhof T, van Rooij E. Gene editing innovations and their applications in cardiomyopathy research. Dis Model Mech 2023; 16:dmm050088. [PMID: 37222281 PMCID: PMC10233723 DOI: 10.1242/dmm.050088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Cardiomyopathies are among the major triggers of heart failure, but their clinical and genetic complexity have hampered our understanding of these disorders and delayed the development of effective treatments. Alongside the recent identification of multiple cardiomyopathy-associated genetic variants, advances in genome editing are providing new opportunities for cardiac disease modeling and therapeutic intervention, both in vitro and in vivo. Two recent innovations in this field, prime and base editors, have improved editing precision and efficiency, and are opening up new possibilities for gene editing of postmitotic tissues, such as the heart. Here, we review recent advances in prime and base editors, the methods to optimize their delivery and targeting efficiency, their strengths and limitations, and the challenges that remain to be addressed to improve the application of these tools to the heart and their translation to the clinic.
Collapse
Affiliation(s)
- Eirini Kyriakopoulou
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, 3584CT Utrecht, The Netherlands
| | - Thomas Monnikhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, 3584CT Utrecht, The Netherlands
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, 3584CT Utrecht, The Netherlands
- Department of Cardiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| |
Collapse
|
48
|
Muto V, Benigni F, Magliocca V, Borghi R, Flex E, Pallottini V, Rosa A, Compagnucci C, Tartaglia M. CRISPR/Cas9 and piggyBac Transposon-Based Conversion of a Pathogenic Biallelic TBCD Variant in a Patient-Derived iPSC Line Allows Correction of PEBAT-Related Endophenotypes. Int J Mol Sci 2023; 24:ijms24097988. [PMID: 37175696 PMCID: PMC10178052 DOI: 10.3390/ijms24097988] [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: 03/07/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) have been established as a reliable in vitro disease model system and represent a particularly informative tool when animal models are not available or do not recapitulate the human pathophenotype. The recognized limit in using this technology is linked to some degree of variability in the behavior of the individual patient-derived clones. The development of CRISPR/Cas9-based gene editing solves this drawback by obtaining isogenic iPSCs in which the genetic lesion is corrected, allowing a straightforward comparison with the parental patient-derived iPSC lines. Here, we report the generation of a footprint-free isogenic cell line of patient-derived TBCD-mutated iPSCs edited using the CRISPR/Cas9 and piggyBac technologies. The corrected iPSC line had no genetic footprint after the removal of the selection cassette and maintained its "stemness". The correction of the disease-causing TBCD missense substitution restored proper protein levels of the chaperone and mitotic spindle organization, as well as reduced cellular death, which were used as read-outs of the TBCD KO-related endophenotype. The generated line represents an informative in vitro model to understand the impact of pathogenic TBCD mutations on nervous system development and physiology.
Collapse
Affiliation(s)
- Valentina Muto
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Federica Benigni
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
- Department of Science, University Roma Tre, 00146 Rome, Italy
| | - Valentina Magliocca
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Rossella Borghi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Valentina Pallottini
- Department of Science, University Roma Tre, 00146 Rome, Italy
- Neuroendocrinology Metabolism and Neuropharmacology Unit, IRCSS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Alessandro Rosa
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Claudia Compagnucci
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| |
Collapse
|
49
|
Hiramuki Y, Abe S, Uno N, Kazuki K, Takata S, Miyamoto H, Takayama H, Morimoto K, Takehara S, Osaki M, Tanihata J, Takeda S, Tomizuka K, Oshimura M, Kazuki Y. Full-length human dystrophin on human artificial chromosome compensates for mouse dystrophin deficiency in a Duchenne muscular dystrophy mouse model. Sci Rep 2023; 13:4360. [PMID: 36928364 PMCID: PMC10020543 DOI: 10.1038/s41598-023-31481-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Dystrophin maintains membrane integrity as a sarcolemmal protein. Dystrophin mutations lead to Duchenne muscular dystrophy, an X-linked recessive disorder. Since dystrophin is one of the largest genes consisting of 79 exons in the human genome, delivering a full-length dystrophin using virus vectors is challenging for gene therapy. Human artificial chromosome is a vector that can load megabase-sized genome without any interference from the host chromosome. Chimeric mice carrying a 2.4-Mb human dystrophin gene-loaded human artificial chromosome (DYS-HAC) was previously generated, and dystrophin expression from DYS-HAC was confirmed in skeletal muscles. Here we investigated whether human dystrophin expression from DYS-HAC rescues the muscle phenotypes seen in dystrophin-deficient mice. Human dystrophin was normally expressed in the sarcolemma of skeletal muscle and heart at expected molecular weights, and it ameliorated histological and functional alterations in dystrophin-deficient mice. These results indicate that the 2.4-Mb gene is enough for dystrophin to be correctly transcribed and translated, improving muscular dystrophy. Therefore, this technique using HAC gives insight into developing new treatments and novel humanized Duchenne muscular dystrophy mouse models with human dystrophin gene mutations.
Collapse
Affiliation(s)
- Yosuke Hiramuki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Satoshi Abe
- Trans Chromosomics Inc., 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Narumi Uno
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
- Laboratory of Bioengineering, Faculty of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kanako Kazuki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Shuta Takata
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Hitomaru Miyamoto
- Department of Chromosome Biomedical Engineering, Integrated Medical Sciences, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Haruka Takayama
- Trans Chromosomics Inc., 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Kayoko Morimoto
- Trans Chromosomics Inc., 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Shoko Takehara
- Trans Chromosomics Inc., 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Mitsuhiko Osaki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
- Division of Experimental Pathology, Department of Functional Morphology, Faculty of Medicine, Tottori University, Yonago, Tottori, 683‑8503, Japan
| | - Jun Tanihata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, 187-8502, Japan
- Department of Cell Physiology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, 187-8502, Japan
| | - Kazuma Tomizuka
- Laboratory of Bioengineering, Faculty of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Mitsuo Oshimura
- Trans Chromosomics Inc., 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
- Department of Chromosome Biomedical Engineering, Integrated Medical Sciences, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
- Department of Chromosome Biomedical Engineering, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Sciences, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
- Chromosome Engineering Research Group, The Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| |
Collapse
|
50
|
Müthel S, Marg A, Ignak B, Kieshauer J, Escobar H, Stadelmann C, Spuler S. Cas9-induced single cut enables highly efficient and template-free repair of a muscular dystrophy causing founder mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:494-511. [PMID: 36865086 PMCID: PMC9972404 DOI: 10.1016/j.omtn.2023.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/01/2023] [Indexed: 02/07/2023]
Abstract
With thousands of patients worldwide, CAPN3 c.550delA is the most frequent mutation causing severe, progressive, and untreatable limb girdle muscular dystrophy. We aimed to genetically correct this founder mutation in primary human muscle stem cells. We designed editing strategies providing CRISPR-Cas9 as plasmid and mRNA first in patient-derived induced pluripotent stem cells and applied this strategy then in primary human muscle stem cells from patients. Mutation-specific targeting yielded highly efficient and precise correction of CAPN3 c.550delA to wild type for both cell types. Most likely a single cut generated by SpCas9 resulted in a 5' staggered overhang of one base pair, which triggered an overhang-dependent base replication of an A:T at the mutation site. This recovered the open reading frame and the CAPN3 DNA sequence was repaired template-free to wild type, which led to CAPN3 mRNA and protein expression. Off-target analysis using amplicon sequencing of 43 in silico predicted sites demonstrates the safety of this approach. Our study extends previous usage of single cut DNA modification since our gene product has been repaired into the wild-type CAPN3 sequence with the perspective of a real cure.
Collapse
Affiliation(s)
- Stefanie Müthel
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Muscle Research Unit at the Experimental and Clinical Research Center, a Cooperation Between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) and the Charité–Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, 10117 Berlin, Germany
| | - Andreas Marg
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Muscle Research Unit at the Experimental and Clinical Research Center, a Cooperation Between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) and the Charité–Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, 10117 Berlin, Germany
| | - Busem Ignak
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Muscle Research Unit at the Experimental and Clinical Research Center, a Cooperation Between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) and the Charité–Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, 10117 Berlin, Germany
| | - Janine Kieshauer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Muscle Research Unit at the Experimental and Clinical Research Center, a Cooperation Between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) and the Charité–Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, 10117 Berlin, Germany
| | - Helena Escobar
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Muscle Research Unit at the Experimental and Clinical Research Center, a Cooperation Between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) and the Charité–Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, 10117 Berlin, Germany
| | - Christian Stadelmann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Muscle Research Unit at the Experimental and Clinical Research Center, a Cooperation Between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) and the Charité–Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, 10117 Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Simone Spuler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Muscle Research Unit at the Experimental and Clinical Research Center, a Cooperation Between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC) and the Charité–Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, 10117 Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|