1
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Xu W, Zhang S, Qin H, Yao K. From bench to bedside: cutting-edge applications of base editing and prime editing in precision medicine. J Transl Med 2024; 22:1133. [PMID: 39707395 DOI: 10.1186/s12967-024-05957-3] [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: 09/25/2024] [Accepted: 12/08/2024] [Indexed: 12/23/2024] Open
Abstract
CRISPR-based gene editing technology theoretically allows for precise manipulation of any genetic target within living cells, achieving the desired sequence modifications. This revolutionary advancement has fundamentally transformed the field of biomedicine, offering immense clinical potential for treating and correcting genetic disorders. In the treatment of most genetic diseases, precise genome editing that avoids the generation of mixed editing byproducts is considered the ideal approach. This article reviews the current progress of base editors and prime editors, elaborating on specific examples of their applications in the therapeutic field, and highlights opportunities for improvement. Furthermore, we discuss the specific performance of these technologies in terms of safety and efficacy in clinical applications, and analyze the latest advancements and potential directions that could influence the future development of genome editing technologies. Our goal is to outline the clinical relevance of this rapidly evolving scientific field and preview a roadmap for successful DNA base editing therapies for the treatment of hereditary or idiopathic diseases.
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Affiliation(s)
- Weihui Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Shiyao Zhang
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Huan Qin
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China.
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, 430065, China.
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China.
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, 430065, China.
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2
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Arantes PR, Chen X, Sinha S, Saha A, Patel AC, Sample M, Nierzwicki Ł, Lapinaite A, Palermo G. Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e. Nucleic Acids Res 2024; 52:13931-13944. [PMID: 39569582 DOI: 10.1093/nar/gkae1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 10/16/2024] [Accepted: 11/01/2024] [Indexed: 11/22/2024] Open
Abstract
CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were developed by combining CRISPR-Cas9 with a transfer RNA (tRNA) adenosine deaminase enzyme and through directed evolution, conferring the ability to deaminate DNA. However, the molecular mechanisms driving the efficient DNA deamination in the evolved ABEs remain unresolved. Here, extensive molecular simulations and biochemical experiments reveal the biophysical basis behind the astonishing base editing efficiency of ABE8e, the most efficient ABE to date. We demonstrate that the ABE8e's DNA deaminase domain, TadA8e, forms remarkably stable dimers compared to its tRNA-deaminating progenitor and that the strength of TadA dimerization is crucial for DNA deamination. The TadA8e dimer forms robust interactions involving its R98 and R129 residues, the RuvC domain of Cas9 and the DNA. These locking interactions are exclusive to ABE8e, distinguishing it from its predecessor, ABE7.10, and are indispensable to boost DNA deamination. Additionally, we identify three critical residues that drive the evolution of ABE8e toward improved base editing by balancing the enzyme's activity and stability, reinforcing the TadA8e dimer and improving the ABE8e's functionality. These insights offer new directions to engineer superior ABEs, advancing the design of safer precision genome editing tools.
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Affiliation(s)
- Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
| | - Xiaoyu Chen
- School of Molecular Sciences, Arizona State University, 551 E University Dr, Tempe, AZ 85281, USA
- Gavin Herbert Eye Institute - Centre for Translational Vision Research, University of California Irvine School of Medicine, 850 Health Sciences Rd, Irvine, CA 92617, USA
| | - Souvik Sinha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
| | - Amun C Patel
- Department of Bioengineering, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
| | - Matthew Sample
- Department of Bioengineering, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
| | - Audrone Lapinaite
- Gavin Herbert Eye Institute - Centre for Translational Vision Research, University of California Irvine School of Medicine, 850 Health Sciences Rd, Irvine, CA 92617, USA
- Department of Ophthalmology, University of California Irvine School of Medicine, 850 Health Sciences Rd, Irvine, CA 92617, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
- Department of Chemistry, University of California Riverside, 900 University Avenue, 92512 Riverside, CA, USA
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3
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Pulman J, Botto C, Malki H, Ren D, Oudin P, De Cian A, As M, Izabelle C, Saubamea B, Forster V, Fouquet S, Robert C, Portal C, El-Amraoui A, Fisson S, Concordet JP, Dalkara D. Direct delivery of Cas9 or base editor protein and guide RNA complex enables genome editing in the retina. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102349. [PMID: 39494148 PMCID: PMC11531619 DOI: 10.1016/j.omtn.2024.102349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 09/26/2024] [Indexed: 11/05/2024]
Abstract
Genome editing by CRISPR-Cas holds promise for the treatment of retinal dystrophies. For therapeutic gene editing, transient delivery of CRISPR-Cas9 is preferable to viral delivery which leads to long-term expression with potential adverse consequences. Cas9 protein and its guide RNA, delivered as ribonucleoprotein (RNP) complexes, have been successfully delivered into the retinal pigment epithelium in vivo. However, the delivery into photoreceptors, the primary focus in retinal dystrophies, has not been achieved. Here, we investigate the feasibility of direct RNP delivery into photoreceptors and retinal pigment epithelium cells. We demonstrate that Cas9 or adenine-base editors complexed with guide RNA, can enter retinal cells without the addition of any carrier compounds. Once in the retinal cells, editing rates vary based on the efficacy of the guide RNA and the specific location edited within the genes. Cas9 RNP delivery at high concentrations, however, leads to outer retinal toxicity. This underscores the importance of improving delivery efficiency for potential therapeutic applications in the future.
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Affiliation(s)
- Juliette Pulman
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Catherine Botto
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Hugo Malki
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Duohao Ren
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry-Courcouronnes, France
| | - Paul Oudin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Anne De Cian
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS 7196, Muséum National d'Histoire Naturelle, CP26 43 rue Cuvier 75231 Paris Cedex, France
| | - Marie As
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS 7196, Muséum National d'Histoire Naturelle, CP26 43 rue Cuvier 75231 Paris Cedex, France
| | | | - Bruno Saubamea
- Université Paris Cité, Inserm, CNRS, P-MIM, PICMO, 75006 Paris, France
| | - Valerie Forster
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Stéphane Fouquet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Camille Robert
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Céline Portal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Aziz El-Amraoui
- Institut Pasteur, Université Paris Cité, INSERM AO06, Institut de l’Audition, Unit Progressive Sensory Disorders, Pathophysiology and Therapy, 63 rue de Charenton 75012 Paris, France
| | - Sylvain Fisson
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
- Université Paris-Saclay, University Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry-Courcouronnes, France
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS 7196, Muséum National d'Histoire Naturelle, CP26 43 rue Cuvier 75231 Paris Cedex, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
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4
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Kong X, Li T, Yang H. AAV-mediated gene therapies by miniature gene editing tools. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2540-2553. [PMID: 39388062 DOI: 10.1007/s11427-023-2608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/29/2024] [Indexed: 10/15/2024]
Abstract
The advent of CRISPR-Cas has revolutionized precise gene editing. While pioneering CRISPR nucleases like Cas9 and Cas12 generate targeted DNA double-strand breaks (DSB) for knockout or homology-directed repair, next generation CRISPR technologies enable gene editing without DNA DSB. Base editors directly convert bases, prime editors make diverse alterations, and dead Cas-regulator fusions allow nuanced control of gene expression, avoiding potentially risks like translocations. Meanwhile, the discovery of diminutive Cas12 orthologs and Obligate Mobile Element-Guided Activity (OMEGA) nucleases has overcome cargo limitations of adeno-associated viral vectors, expanding prospects for in vivo therapeutic delivery. Here, we review the ever-evolving landscape of cutting-edge gene editing tools, focusing on miniature Cas12 orthologs and OMEGA effectors amenable to single AAV packaging. We also summarize CRISPR therapies delivered using AAV vectors, discuss challenges such as efficiency and specificity, and look to the future of this transformative field of in vivo gene editing enabled by AAV vectors delivery.
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Affiliation(s)
- Xiangfeng Kong
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Tong Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Hui Yang
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China.
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China.
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5
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Del Arco J, Acosta J, Fernández-Lucas J. Biotechnological applications of purine and pyrimidine deaminases. Biotechnol Adv 2024; 77:108473. [PMID: 39505057 DOI: 10.1016/j.biotechadv.2024.108473] [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: 05/25/2024] [Revised: 09/21/2024] [Accepted: 10/24/2024] [Indexed: 11/08/2024]
Abstract
Deaminases, ubiquitous enzymes found in all living organisms from bacteria to humans, serve diverse and crucial functions. Notably, purine and pyrimidine deaminases, while biologically essential for regulating nucleotide pools, exhibit exceptional versatility in biotechnology. This review systematically consolidates current knowledge on deaminases, showcasing their potential uses and relevance in the field of biotechnology. Thus, their transformative impact on pharmaceutical manufacturing is highlighted as catalysts for the synthesis of nucleic acid derivatives. Additionally, the role of deaminases in food bioprocessing and production is also explored, particularly in purine content reduction and caffeine production, showcasing their versatility in this field. The review also delves into most promising biomedical applications including deaminase-based GDEPT and genome and transcriptome editing by deaminase-based systems. All in all, illustrated with practical examples, we underscore the role of purine and pyrimidine deaminases in advancing sustainable and efficient biotechnological practices. Finally, the review highlights future challenges and prospects in deaminase-based biotechnological processes, encompassing both industrial and medical perspectives.
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Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Javier Acosta
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002 Barranquilla, Colombia; Department of Biochemistry and Molecular Biology, Faculty of Biology, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
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6
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Miskalis A, Shirguppe S, Winter J, Elias G, Swami D, Nambiar A, Stilger M, Woods WS, Gosstola N, Gapinske M, Zeballos A, Moore H, Maslov S, Gaj T, Perez-Pinera P. SPLICER: a highly efficient base editing toolbox that enables in vivo therapeutic exon skipping. Nat Commun 2024; 15:10354. [PMID: 39609418 PMCID: PMC11604662 DOI: 10.1038/s41467-024-54529-y] [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: 12/15/2023] [Accepted: 11/13/2024] [Indexed: 11/30/2024] Open
Abstract
Exon skipping technologies enable exclusion of targeted exons from mature mRNA transcripts, which have broad applications in medicine and biotechnology. Existing techniques including antisense oligonucleotides, targetable nucleases, and base editors, while effective for specific applications, remain hindered by transient effects, genotoxicity, and inconsistent exon skipping. To overcome these limitations, here we develop SPLICER, a toolbox of next-generation base editors containing near-PAMless Cas9 nickase variants fused to adenosine or cytosine deaminases for the simultaneous editing of splice acceptor (SA) and splice donor (SD) sequences. Synchronized SA and SD editing improves exon skipping, reduces aberrant splicing, and enables skipping of exons refractory to single splice site editing. To demonstrate the therapeutic potential of SPLICER, we target APP exon 17, which encodes amino acids that are cleaved to form Aβ plaques in Alzheimer's disease. SPLICER reduces the formation of Aβ42 peptides in vitro and enables efficient exon skipping in a mouse model of Alzheimer's disease. Overall, SPLICER is a widely applicable and efficient exon skipping toolbox.
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Affiliation(s)
- Angelo Miskalis
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Shraddha Shirguppe
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jackson Winter
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Gianna Elias
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Devyani Swami
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ananthan Nambiar
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Michelle Stilger
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Wendy S Woods
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Gosstola
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Michael Gapinske
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Alejandra Zeballos
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Hayden Moore
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Sergei Maslov
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Thomas Gaj
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Pablo Perez-Pinera
- The Grainger College of Engineering, Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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7
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Hołubowicz R, Du SW, Felgner J, Smidak R, Choi EH, Palczewska G, Menezes CR, Dong Z, Gao F, Medani O, Yan AL, Hołubowicz MW, Chen PZ, Bassetto M, Risaliti E, Salom D, Workman JN, Kiser PD, Foik AT, Lyon DC, Newby GA, Liu DR, Felgner PL, Palczewski K. Safer and efficient base editing and prime editing via ribonucleoproteins delivered through optimized lipid-nanoparticle formulations. Nat Biomed Eng 2024:10.1038/s41551-024-01296-2. [PMID: 39609561 DOI: 10.1038/s41551-024-01296-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 10/25/2024] [Indexed: 11/30/2024]
Abstract
Delivering ribonucleoproteins (RNPs) for in vivo genome editing is safer than using viruses encoding for Cas9 and its respective guide RNA. However, transient RNP activity does not typically lead to optimal editing outcomes. Here we show that the efficiency of delivering RNPs can be enhanced by cell-penetrating peptides (covalently fused to the protein or as excipients) and that lipid nanoparticles (LNPs) encapsulating RNPs can be optimized for enhanced RNP stability, delivery efficiency and editing potency. Specifically, after screening for suitable ionizable cationic lipids and by optimizing the concentration of the synthetic lipid DMG-PEG 2000, we show that the encapsulation, via microfluidic mixing, of adenine base editor and prime editor RNPs within LNPs using the ionizable lipid SM102 can result in in vivo editing-efficiency enhancements larger than 300-fold (with respect to the delivery of the naked RNP) without detectable off-target edits. We believe that chemically defined LNP formulations optimized for RNP-encapsulation stability and delivery efficiency will lead to safer genome editing.
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Grants
- R01EY009339, R01EY030873, P30EY034070, P30CA062203 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- T32GM008620, F30EY033642 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- P30EY034070 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- T32GM148383 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01EY032948, R21NS113264 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R00HL163805 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- UG3AI150551, U01AI142756, R35GM118062, RM1HG009490 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- 75N93022C00054 NIAID NIH HHS
- I01BX004939 U.S. Department of Veterans Affairs (Department of Veterans Affairs)
- 2022/47/B/NZ5/03023, 2020/39/D/NZ4/01881, 2019/34/E/NZ5/00434 Narodowe Centrum Nauki (National Science Centre)
- FENG.02.01-IP.05-T005/23 Fundacja na rzecz Nauki Polskiej (Foundation for Polish Science)
- N66001-21-C-4013 United States Department of Defense | Defense Threat Reduction Agency (DTRA)
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Affiliation(s)
- Rafał Hołubowicz
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Samuel W Du
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Jiin Felgner
- Adeline Yen Mah Vaccine Center, Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Roman Smidak
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Elliot H Choi
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Grazyna Palczewska
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Carolline Rodrigues Menezes
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Zhiqian Dong
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Fangyuan Gao
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Omar Medani
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Alexander L Yan
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Program in Neuroscience, Amherst College, Amherst, MA, USA
| | - Maria W Hołubowicz
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Paul Z Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marco Bassetto
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
- Research Service, Tibor Rubin VA Long Beach Medical Center, Long Beach, CA, USA
| | - Eleonora Risaliti
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - David Salom
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - J Noah Workman
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Philip D Kiser
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
- Research Service, Tibor Rubin VA Long Beach Medical Center, Long Beach, CA, USA
- Department of Clinical Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Andrzej T Foik
- International Centre for Translational Eye Research (ICTER), Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - David C Lyon
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Philip L Felgner
- Adeline Yen Mah Vaccine Center, Department of Physiology and Biophysics, University of California, Irvine, CA, USA.
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA.
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA.
- Department of Chemistry, University of California, Irvine, CA, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
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8
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Du SW, Newby GA, Salom D, Gao F, Menezes CR, Suh S, Choi EH, Chen PZ, Liu DR, Palczewski K. In vivo photoreceptor base editing ameliorates rhodopsin-E150K autosomal-recessive retinitis pigmentosa in mice. Proc Natl Acad Sci U S A 2024; 121:e2416827121. [PMID: 39556729 PMCID: PMC11621631 DOI: 10.1073/pnas.2416827121] [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: 08/22/2024] [Accepted: 09/28/2024] [Indexed: 11/20/2024] Open
Abstract
Rhodopsin, the prototypical class-A G-protein coupled receptor, is a highly sensitive receptor for light that enables phototransduction in rod photoreceptors. Rhodopsin plays not only a sensory role but also a structural role as a major component of the rod outer segment disc, comprising over 90% of the protein content of the disc membrane. Mutations in RHO which lead to structural or functional abnormalities, including the autosomal recessive E150K mutation, result in rod dysfunction and death. Therefore, correction of deleterious rhodopsin mutations could rescue inherited retinal degeneration, as demonstrated for other visual genes such as RPE65 and PDE6B. In this study, we describe a CRISPR/Cas9 adenine base editing strategy to correct the E150K mutation and demonstrate precise in vivo editing in a Rho-E150K mouse model of autosomal recessive retinitis pigmentosa (RP). Using ultraviolet-visible spectroscopy, mass spectrometry, and the G-protein activation assay, we characterized wild-type rhodopsin and rhodopsin variants containing bystander base edits. Subretinal injection of dual-adeno-associated viruses delivering our base editing strategy yielded up to 44% Rho correction in homozygous Rho-E150K mice. Injection at postnatal day 15, but not later time points, restored rhodopsin expression, partially rescued retinal function, and partially preserved retinal structure. These findings demonstrate that in vivo base editing can restore the function of mutated structural and functional proteins in animal models of disease, including rhodopsin-associated RP and suggest that the timing of gene-editing is a crucial determinant of successful treatment outcomes for degenerative genetic diseases.
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Affiliation(s)
- Samuel W. Du
- Gavin Herbert Eye Institute—Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA92617
- Department of Physiology and Biophysics, University of California, Irvine, CA92617
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- HHMI, Harvard University, Cambridge, MA02138
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD21205
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD21205
| | - David Salom
- Gavin Herbert Eye Institute—Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA92617
| | - Fangyuan Gao
- Gavin Herbert Eye Institute—Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA92617
| | - Carolline Rodrigues Menezes
- Gavin Herbert Eye Institute—Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA92617
- Department of Physiology and Biophysics, University of California, Irvine, CA92617
| | - Susie Suh
- Gavin Herbert Eye Institute—Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA92617
| | - Elliot H. Choi
- Gavin Herbert Eye Institute—Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA92617
| | - Paul Z. Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- HHMI, Harvard University, Cambridge, MA02138
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- HHMI, Harvard University, Cambridge, MA02138
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute—Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA92617
- Department of Physiology and Biophysics, University of California, Irvine, CA92617
- Department of Chemistry, University of California, Irvine, CA92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697
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9
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Chen Y, van Til NP, Bosma PJ. Gene Therapy for Inherited Liver Disease: To Add or to Edit. Int J Mol Sci 2024; 25:12514. [PMID: 39684224 DOI: 10.3390/ijms252312514] [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: 08/23/2024] [Revised: 11/06/2024] [Accepted: 11/12/2024] [Indexed: 12/18/2024] Open
Abstract
Patients suffering from an inherited severe liver disorder require lifelong treatment to prevent premature death. Until recently, the only curative treatment option was liver transplantation, which requires lifelong immune suppression. Now, liver-directed gene therapy, which is a much less invasive procedure, has become a market-approved treatment for hemophilia A and B. This may pave the way for it to become the treatment of choice for many other recessive inherited liver disorders with loss-of-function mutations. Inherited liver disease with toxic-gain-of-function or intrinsic hepatocyte damage may require alternative applications, such as integrating vectors or genome editing technologies, that can provide permanent or specific modification of the genome. We present an overview of currently available gene therapy strategies, i.e., gene supplementation, gene editing, and gene repair investigated in preclinical and clinical studies to treat inherited severe liver disorders. The advantages and limitations of these gene therapy applications are discussed in relation to the underlying disease mechanism.
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Affiliation(s)
- Yue Chen
- Amsterdam University Medical Center, Tytgat Institute for Liver and Intestinal Research, AG&M, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Niek P van Til
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Piter J Bosma
- Amsterdam University Medical Center, Tytgat Institute for Liver and Intestinal Research, AG&M, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
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10
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Raguram A, An M, Chen PZ, Liu DR. Directed evolution of engineered virus-like particles with improved production and transduction efficiencies. Nat Biotechnol 2024:10.1038/s41587-024-02467-x. [PMID: 39537813 DOI: 10.1038/s41587-024-02467-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024]
Abstract
Engineered virus-like particles (eVLPs) are promising vehicles for transient delivery of proteins and RNAs, including gene editing agents. We report a system for the laboratory evolution of eVLPs that enables the discovery of eVLP variants with improved properties. The system uses barcoded guide RNAs loaded within DNA-free eVLP-packaged cargos to uniquely label each eVLP variant in a library, enabling the identification of desired variants following selections for desired properties. We applied this system to mutate and select eVLP capsids with improved eVLP production properties or transduction efficiencies in human cells. By combining beneficial capsid mutations, we developed fifth-generation (v5) eVLPs, which exhibit a 2-4-fold increase in cultured mammalian cell delivery potency compared to previous-best v4 eVLPs. Analyses of v5 eVLPs suggest that these capsid mutations optimize packaging and delivery of desired ribonucleoprotein cargos rather than native viral genomes and substantially alter eVLP capsid structure. These findings suggest the potential of barcoded eVLP evolution to support the development of improved eVLPs.
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Affiliation(s)
- Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
| | - Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Paul Z Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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11
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Wu Y, Li X, Liu H, Yang X, Li R, Zhao H, Shang Z. Organoids in the oral and maxillofacial region: present and future. Int J Oral Sci 2024; 16:61. [PMID: 39482304 PMCID: PMC11528035 DOI: 10.1038/s41368-024-00324-w] [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: 12/19/2023] [Revised: 06/18/2024] [Accepted: 09/12/2024] [Indexed: 11/03/2024] Open
Abstract
The oral and maxillofacial region comprises a variety of organs made up of multiple soft and hard tissue, which are anatomically vulnerable to the pathogenic factors of trauma, inflammation, and cancer. The studies of this intricate entity have been long-termly challenged by a lack of versatile preclinical models. Recently, the advancements in the organoid industry have provided novel strategies to break through this dilemma. Here, we summarize the existing biological and engineering approaches that were employed to generate oral and maxillofacial organoids. Then, we detail the use of modified co-culture methods, such as cell cluster co-inoculation and air-liquid interface culture technology to reconstitute the vascular network and immune microenvironment in assembled organoids. We further retrospect the existing oral and maxillofacial assembled organoids and their potential to recapitulate the homeostasis in parental tissues such as tooth, salivary gland, and mucosa. Finally, we discuss how the next-generation organoids may benefit to regenerative and precision medicine for treatment of oral-maxillofacial illness.
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Affiliation(s)
- Yufei Wu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xiang Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hanzhe Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xiao Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Rui Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hui Zhao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
- Department of Oral and Maxillofacial-Head and Neck Oncology, School of Stomatology-Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Zhengjun Shang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
- Department of Oral and Maxillofacial-Head and Neck Oncology, School of Stomatology-Hospital of Stomatology, Wuhan University, Wuhan, China.
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12
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Liu Z, Chen S, Davis AE, Lo C, Wang Q, Li T, Ning K, Zhang Q, Zhao J, Wang S, Sun Y. Efficient Rescue of Retinal Degeneration in Pde6a Mice by Engineered Base Editing and Prime Editing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405628. [PMID: 39297417 PMCID: PMC11558111 DOI: 10.1002/advs.202405628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 09/04/2024] [Indexed: 11/14/2024]
Abstract
Retinitis pigmentosa (RP) is a complex spectrum of inherited retinal diseases marked by the gradual loss of photoreceptor cells, ultimately leading to blindness. Among these, mutations in PDE6A, responsible for encoding a cGMP-specific phosphodiesterase, stand out as pivotal in autosomal recessive RP (RP43). Unfortunately, no effective therapy currently exists for this specific form of RP. However, recent advancements in genome editing, such as base editing (BE) and prime editing (PE), offer a promising avenue for precise and efficient gene therapy. Here, it is illustrated that the engineered BE and PE systems, particularly PE, exhibit high efficiency in rescuing a target point mutation with minimal bystander effects in an RP mouse model carrying the Pde6a (c.2009A > G, p.D670G) mutation. The optimized BE and PE systems are first screened in N2a cells and subsequently assessed in electroporated mouse retinas. Notably, the optimal PE system, delivered via dual adeno-associated virus (AAV), precisely corrects the pathogenic mutation with average 9.4% efficiency, with no detectable bystander editing. This correction restores PDE6A protein expression, preserved photoreceptors, and rescued retinal function in Pde6a mice. Therefore, this study offers a proof-of-concept demonstration for the treatment of Pde6a-related retinal degeneration using BE and PE systems.
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Affiliation(s)
- Zhiquan Liu
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Siyu Chen
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Alexander E. Davis
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Chien‐Hui Lo
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Qing Wang
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Tingting Li
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
- Department of OphthalmologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Ke Ning
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Qi Zhang
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Jingyu Zhao
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Sui Wang
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
| | - Yang Sun
- Department of OphthalmologyStanford University School of MedicinePalo AltoCA94304USA
- Palo Alto Veterans AdministrationPalo AltoCA94304USA
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13
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Ramani B, Rose IVL, Teyssier N, Pan A, Danner-Bocks S, Sanghal T, Yadanar L, Tian R, Ma K, Palop JJ, Kampmann M. CRISPR screening by AAV episome-sequencing (CrAAVe-seq) is a highly scalable cell type-specific in vivo screening platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.13.544831. [PMID: 37398301 PMCID: PMC10312723 DOI: 10.1101/2023.06.13.544831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
There is a significant need for scalable CRISPR-based genetic screening methods that can be applied directly in mammalian tissues in vivo while enabling cell type-specific analysis. To address this, we developed an adeno-associated virus (AAV)-based CRISPR screening platform, CrAAVe-seq, that incorporates a Cre-sensitive sgRNA construct for pooled screening within targeted cell populations in the mouse tissues. We demonstrate the utility of this approach by screening two distinct large sgRNA libraries, together targeting over 5,000 genes, in mouse brains to create a robust profile of neuron-essential genes. We validate two genes as strongly neuron-essential in both primary mouse neurons and in vivo, confirming the predictive power of our platform. By comparing results from individual mice and across different cell populations, we highlight the reproducibility and scalability of the platform and show that it is highly sensitive even for screening smaller neuronal subpopulations. We systematically characterize the impact of sgRNA library size, mouse cohort size, the size of the targeted cell population, viral titer, and multiplicity of infection on screen performance to establish general guidelines for large-scale in vivo screens.
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Affiliation(s)
- Biswarathan Ramani
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Noam Teyssier
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew Pan
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Spencer Danner-Bocks
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Tanya Sanghal
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Lin Yadanar
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Keran Ma
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jorge J Palop
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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14
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Zhou X, Gao J, Luo L, Huang C, Wu J, Wang X. Comprehensive evaluation and prediction of editing outcomes for near-PAMless adenine and cytosine base editors. Commun Biol 2024; 7:1389. [PMID: 39455714 PMCID: PMC11511846 DOI: 10.1038/s42003-024-07078-5] [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: 04/18/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
Base editors enable the direct conversion of target bases without inducing double-strand breaks, showing great potential for disease modeling and gene therapy. Yet, their applicability has been constrained by the necessity for specific protospacer adjacent motif (PAM). We generate four versions of near-PAMless base editors and systematically evaluate their editing patterns and efficiencies using an sgRNA-target library of 45,747 sequences. Near-PAMless base editors significantly expanded the targeting scope, with both PAM and target flanking sequences as determinants for editing outcomes. We develop BEguider, a deep learning model, to accurately predict editing results for near-PAMless base editors. We also provide experimentally measured editing outcomes of 20,541 ClinVar sites, demonstrating that variants previously inaccessible by NGG PAM base editors can now be precisely generated or corrected. We make our predictive tool and data available online to facilitate development and application of near-PAMless base editors in both research and clinical settings.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Common Mechanism Research for Major Diseases; Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingjing Gao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Clinical Laboratory Medicine, Wenzhou Central Hospital, Wenzhou, China
| | - Liheng Luo
- State Key Laboratory of Common Mechanism Research for Major Diseases; Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changcai Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jiayu Wu
- State Key Laboratory of Common Mechanism Research for Major Diseases; Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyue Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases; Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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15
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Gong X, Hertle RW. Infantile Nystagmus Syndrome-Associated Inherited Retinal Diseases: Perspectives from Gene Therapy Clinical Trials. Life (Basel) 2024; 14:1356. [PMID: 39598155 PMCID: PMC11595273 DOI: 10.3390/life14111356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/27/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a clinically and genetically diverse group of progressive degenerative disorders that can result in severe visual impairment or complete blindness. Despite their predominantly monogenic inheritance patterns, the genetic complexity of over 300 identified disease-causing genes presents a significant challenge in correlating clinical phenotypes with genotypes. Achieving a molecular diagnosis is crucial for providing patients with definitive diagnostic clarity and facilitating access to emerging gene-based therapies and ongoing clinical trials. Recent advances in next-generation sequencing technologies have markedly enhanced our ability to identify genes and genetic defects leading to IRDs, thereby propelling the development of gene-based therapies. The clinical success of voretigene neparvovec (Luxturna), the first approved retinal gene therapy for RPE65-associated Leber congenital amaurosis (LCA), has spurred considerable research and development in gene-based therapies, highlighting the importance of reviewing the current status of gene therapy for IRDs, particularly those utilizing adeno-associated virus (AAV)-based therapies. As novel disease-causing mutations continue to be discovered and more targeted gene therapies are developed, integrating these treatment opportunities into the standard care for IRD patients becomes increasingly critical. This review provides an update on the diverse phenotypic-genotypic landscape of IRDs, with a specific focus on recent advances in the understanding of IRDs in children with infantile nystagmus syndrome (INS). We highlight the complexities of the genotypic-phenotypic landscape of INS-associated IRDs, including conditions such as achromatopsia, LCA, congenital stationary night blindness, and subtypes of retinitis pigmentosa. Additionally, we provide an updated overview of AAV-based gene therapies for these diseases and discuss the potential of gene-based therapies for underlying IRDs that lead to INS, offering a valuable resource for pediatric patients potentially eligible for ongoing clinical trials.
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Affiliation(s)
- Xiaoming Gong
- Department of Ophthalmology, Akron Children’s Hospital, Akron, OH 44308, USA;
- Vision Center of Excellence, Rebecca D. Considine Research Institute, Akron Children’s Hospital, Akron, OH 44308, USA
| | - Richard W. Hertle
- Department of Ophthalmology, Akron Children’s Hospital, Akron, OH 44308, USA;
- Vision Center of Excellence, Rebecca D. Considine Research Institute, Akron Children’s Hospital, Akron, OH 44308, USA
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16
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Badwal AK, Singh S. A comprehensive review on the current status of CRISPR based clinical trials for rare diseases. Int J Biol Macromol 2024; 277:134097. [PMID: 39059527 DOI: 10.1016/j.ijbiomac.2024.134097] [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: 02/11/2024] [Revised: 07/03/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024]
Abstract
A considerable fraction of population in the world suffers from rare diseases. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its related Cas proteins offer a modern form of curative gene therapy for treating the rare diseases. Hereditary transthyretin amyloidosis, hereditary angioedema, duchenne muscular dystrophy and Rett syndrome are a few examples of such rare diseases. CRISPR/Cas9, for example, has been used in the treatment of β-thalassemia and sickle cell disease (Frangoul et al., 2021; Pavani et al., 2021) [1,2]. Neurological diseases such as Huntington's have also been focused in some studies involving CRISPR/Cas (Yang et al., 2017; Yan et al., 2023) [3,4]. Delivery of these biologicals via vector and non vector mediated methods depends on the type of target cells, characteristics of expression, time duration of expression, size of foreign genetic material etc. For instance, retroviruses find their applicability in case of ex vivo delivery in somatic cells due to their ability to integrate in the host genome. These have been successfully used in gene therapy involving X-SCID patients although, incidence of inappropriate activation has been reported. On the other hand, ex vivo gene therapy for β-thalassemia involved use of BB305 lentiviral vector for high level expression of CRISPR biological in HSCs. The efficacy and safety of these biologicals will decide their future application as efficient genome editing tools as they go forward in further stages of human clinical trials. This review focuses on CRISPR/Cas based therapies which are at various stages of clinical trials for treatment of rare diseases and the constraints and ethical issues associated with them.
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Affiliation(s)
- Amneet Kaur Badwal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali 160062, Punjab, India
| | - Sushma Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali 160062, Punjab, India.
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17
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An M, Raguram A, Du SW, Banskota S, Davis JR, Newby GA, Chen PZ, Palczewski K, Liu DR. Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo. Nat Biotechnol 2024; 42:1526-1537. [PMID: 38191664 PMCID: PMC11228131 DOI: 10.1038/s41587-023-02078-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Prime editing enables precise installation of genomic substitutions, insertions and deletions in living systems. Efficient in vitro and in vivo delivery of prime editing components, however, remains a challenge. Here we report prime editor engineered virus-like particles (PE-eVLPs) that deliver prime editor proteins, prime editing guide RNAs and nicking single guide RNAs as transient ribonucleoprotein complexes. We systematically engineered v3 and v3b PE-eVLPs with 65- to 170-fold higher editing efficiency in human cells compared to a PE-eVLP construct based on our previously reported base editor eVLP architecture. In two mouse models of genetic blindness, single injections of v3 PE-eVLPs resulted in therapeutically relevant levels of prime editing in the retina, protein expression restoration and partial visual function rescue. Optimized PE-eVLPs support transient in vivo delivery of prime editor ribonucleoproteins, enhancing the potential safety of prime editing by reducing off-target editing and obviating the possibility of oncogenic transgene integration.
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Affiliation(s)
- Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samuel W Du
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Paul Z Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
- Department of Chemistry, University of California, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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18
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Torella L, Santana-Gonzalez N, Zabaleta N, Gonzalez Aseguinolaza G. Gene editing in liver diseases. FEBS Lett 2024; 598:2348-2371. [PMID: 39079936 DOI: 10.1002/1873-3468.14989] [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: 04/12/2024] [Revised: 06/01/2024] [Accepted: 06/19/2024] [Indexed: 10/16/2024]
Abstract
The deliberate and precise modification of the host genome using engineered nucleases represents a groundbreaking advancement in modern medicine. Several clinical trials employing these approaches to address metabolic liver disorders have been initiated, with recent remarkable outcomes observed in patients with transthyretin amyloidosis, highlighting the potential of these therapies. Recent technological improvements, particularly CRISPR Cas9-based technology, have revolutionized gene editing, enabling in vivo modification of the cellular genome for therapeutic purposes. These modifications include gene supplementation, correction, or silencing, offering a wide range of therapeutic possibilities. Moving forward, we anticipate witnessing the unfolding therapeutic potential of these strategies in the coming years. The aim of our review is to summarize preclinical data on gene editing in animal models of inherited liver diseases and the clinical data obtained thus far, emphasizing both therapeutic efficacy and potential limitations of these medical interventions.
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Affiliation(s)
- Laura Torella
- DNA & RNA Medicine Division, Gene Therapy for Rare Diseases Department, Center for Applied Medical Research (CIMA), University of Navarra, IdisNA, Pamplona, Spain
| | - Nerea Santana-Gonzalez
- DNA & RNA Medicine Division, Gene Therapy for Rare Diseases Department, Center for Applied Medical Research (CIMA), University of Navarra, IdisNA, Pamplona, Spain
| | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA
| | - Gloria Gonzalez Aseguinolaza
- DNA & RNA Medicine Division, Gene Therapy for Rare Diseases Department, Center for Applied Medical Research (CIMA), University of Navarra, IdisNA, Pamplona, Spain
- Vivet Therapeutics, Pamplona, Spain
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19
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Truong VA, Chang YH, Dang TQ, Tu Y, Tu J, Chang CW, Chang YH, Liu GS, Hu YC. Programmable editing of primary MicroRNA switches stem cell differentiation and improves tissue regeneration. Nat Commun 2024; 15:8358. [PMID: 39333549 PMCID: PMC11436717 DOI: 10.1038/s41467-024-52707-6] [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: 09/11/2023] [Accepted: 09/19/2024] [Indexed: 09/29/2024] Open
Abstract
Programmable RNA editing is harnessed for modifying mRNA. Besides mRNA, miRNA also regulates numerous biological activities, but current RNA editors have yet to be exploited for miRNA manipulation. To engineer primary miRNA (pri-miRNA), the miRNA precursor, we present a customizable editor REPRESS (RNA Editing of Pri-miRNA for Efficient Suppression of miRNA) and characterize critical parameters. The optimized REPRESS is distinct from other mRNA editing tools in design rationale, hence enabling editing of pri-miRNAs that are not editable by other RNA editing systems. We edit various pri-miRNAs in different cells including adipose-derived stem cells (ASCs), hence attenuating mature miRNA levels without disturbing host gene expression. We further develop an improved REPRESS (iREPRESS) that enhances and prolongs pri-miR-21 editing for at least 10 days, with minimal perturbation of transcriptome and miRNAome. iREPRESS reprograms ASCs differentiation, promotes in vitro cartilage formation and augments calvarial bone regeneration in rats, thus implicating its potentials for engineering miRNA and applications such as stem cell reprogramming and tissue regeneration.
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Affiliation(s)
- Vu Anh Truong
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Han Chang
- Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Thuc Quyen Dang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi Tu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jui Tu
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Hao Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Guei-Sheung Liu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan.
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20
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Li G, Dong X, Luo J, Yuan T, Li T, Zhao G, Zhang H, Zhou J, Zeng Z, Cui S, Wang H, Wang Y, Yu Y, Yuan Y, Zuo E, Xu C, Huang J, Zhou Y. Engineering TadA ortholog-derived cytosine base editor without motif preference and adenosine activity limitation. Nat Commun 2024; 15:8090. [PMID: 39284833 PMCID: PMC11405849 DOI: 10.1038/s41467-024-52485-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024] Open
Abstract
The engineered TadA variants used in cytosine base editors (CBEs) present distinctive advantages, including a smaller size and fewer off-target effects compared to cytosine base editors that rely on natural deaminases. However, the current TadA variants demonstrate a preference for base editing in DNA with specific motif sequences and possess dual deaminase activity, acting on both cytosine and adenosine in adjacent positions, limiting their application scope. To address these issues, we employ TadA orthologs screening and multi sequence alignment (MSA)-guided protein engineering techniques to create a highly effective cytosine base editor (aTdCBE) without motif and adenosine deaminase activity limitations. Notably, the delivery of aTdCBE to a humanized mouse model of Duchenne muscular dystrophy (DMD) mice achieves robust exon 55 skipping and restoration of dystrophin expression. Our advancement in engineering TadA ortholog for cytosine editing enriches the base editing toolkits for gene-editing therapy and other potential applications.
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Affiliation(s)
- Guoling Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Xue Dong
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Jiamin Luo
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Tanglong Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tong Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Guoli Zhao
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; NHC Key Laboratory of Myopia and Related Eye Diseases; Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China
| | - Hainan Zhang
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Jingxing Zhou
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Zhenhai Zeng
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; NHC Key Laboratory of Myopia and Related Eye Diseases; Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China
| | - Shuna Cui
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Haoqiang Wang
- 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
| | - Yuan Yuan
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China
| | - Erwei Zuo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | | | - Jinhai Huang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; NHC Key Laboratory of Myopia and Related Eye Diseases; Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China.
| | - Yingsi Zhou
- HuidaGene Therapeutics Co., Ltd., Shanghai, 200131, China.
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21
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Mandalawatta HP, Rajendra K, Fairfax K, Hewitt AW. Emerging trends in virus and virus-like particle gene therapy delivery to the brain. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102280. [PMID: 39206077 PMCID: PMC11350507 DOI: 10.1016/j.omtn.2024.102280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Recent advances in gene therapy and gene-editing techniques offer the very real potential for successful treatment of neurological diseases. However, drug delivery constraints continue to impede viable therapeutic interventions targeting the brain due to its anatomical complexity and highly restrictive microvasculature that is impervious to many molecules. Realizing the therapeutic potential of gene-based therapies requires robust encapsulation and safe and efficient delivery to the target cells. Although viral vectors have been widely used for targeted delivery of gene-based therapies, drawbacks such as host genome integration, prolonged expression, undesired off-target mutations, and immunogenicity have led to the development of alternative strategies. Engineered virus-like particles (eVLPs) are an emerging, promising platform that can be engineered to achieve neurotropism through pseudotyping. This review outlines strategies to improve eVLP neurotropism for therapeutic brain delivery of gene-editing agents.
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Affiliation(s)
| | - K.C. Rajendra
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Kirsten Fairfax
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
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22
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Tarallo A, Parenti G, Brunetti-Pierri N. Precision medicine in action for Pompe disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102265. [PMID: 39100736 PMCID: PMC11296008 DOI: 10.1016/j.omtn.2024.102265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Affiliation(s)
- Antonietta Tarallo
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Giancarlo Parenti
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
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23
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Liu F, Li R, Zhu Z, Yang Y, Lu F. Current developments of gene therapy in human diseases. MedComm (Beijing) 2024; 5:e645. [PMID: 39156766 PMCID: PMC11329757 DOI: 10.1002/mco2.645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 08/20/2024] Open
Abstract
Gene therapy has witnessed substantial advancements in recent years, becoming a constructive tactic for treating various human diseases. This review presents a comprehensive overview of these developments, with a focus on their diverse applications in different disease contexts. It explores the evolution of gene delivery systems, encompassing viral (like adeno-associated virus; AAV) and nonviral approaches, and evaluates their inherent strengths and limitations. Moreover, the review delves into the progress made in targeting specific tissues and cell types, spanning the eye, liver, muscles, and central nervous system, among others, using these gene technologies. This targeted approach is crucial in addressing a broad spectrum of genetic disorders, such as inherited lysosomal storage diseases, neurodegenerative disorders, and cardiovascular diseases. Recent clinical trials and successful outcomes in gene therapy, particularly those involving AAV and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins, are highlighted, illuminating the transformative potentials of this approach in disease treatment. The review summarizes the current status of gene therapy, its prospects, and its capacity to significantly ameliorate patient outcomes and quality of life. By offering comprehensive analysis, this review provides invaluable insights for researchers, clinicians, and stakeholders, enriching the ongoing discourse on the trajectory of disease treatment.
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Affiliation(s)
- Fanfei Liu
- Department of OphthalmologyWest China HospitalChengduSichuanChina
| | - Ruiting Li
- State Key Laboratory of BiotherapyWest China HospitalChengduSichuanChina
| | - Zilin Zhu
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Yang Yang
- Department of OphthalmologyWest China HospitalChengduSichuanChina
- State Key Laboratory of BiotherapyWest China HospitalChengduSichuanChina
| | - Fang Lu
- Department of OphthalmologyWest China HospitalChengduSichuanChina
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24
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Simoni C, Barbon E, Muro AF, Cantore A. In vivo liver targeted genome editing as therapeutic approach: progresses and challenges. Front Genome Ed 2024; 6:1458037. [PMID: 39246827 PMCID: PMC11378722 DOI: 10.3389/fgeed.2024.1458037] [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: 07/01/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024] Open
Abstract
The liver is an essential organ of the body that performs several vital functions, including the metabolism of biomolecules, foreign substances, and toxins, and the production of plasma proteins, such as coagulation factors. There are hundreds of genetic disorders affecting liver functions and, for many of them, the only curative option is orthotopic liver transplantation, which nevertheless entails many risks and long-term complications. Some peculiar features of the liver, such as its large blood flow supply and the tolerogenic immune environment, make it an attractive target for in vivo gene therapy approaches. In recent years, several genome-editing tools mainly based on the clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) system have been successfully exploited in the context of liver-directed preclinical or clinical therapeutic applications. These include gene knock-out, knock-in, activation, interference, or base and prime editing approaches. Despite many achievements, important challenges still need to be addressed to broaden clinical applications, such as the optimization of the delivery methods, the improvement of the editing efficiency, and the risk of on-target or off-target unwanted effects and chromosomal rearrangements. In this review, we highlight the latest progress in the development of in vivo liver-targeted genome editing approaches for the treatment of genetic disorders. We describe the technological advancements that are currently under investigation, the challenges to overcome for clinical applicability, and the future perspectives of this technology.
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Affiliation(s)
- Chiara Simoni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Barbon
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrés F Muro
- International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alessio Cantore
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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25
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Masarwy R, Stotsky-Oterin L, Elisha A, Hazan-Halevy I, Peer D. Delivery of nucleic acid based genome editing platforms via lipid nanoparticles: Clinical applications. Adv Drug Deliv Rev 2024; 211:115359. [PMID: 38857763 DOI: 10.1016/j.addr.2024.115359] [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: 03/30/2024] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
CRISPR/Cas technology presents a promising approach for treating a wide range of diseases, including cancer and genetic disorders. Despite its potential, the translation of CRISPR/Cas into effective in-vivo gene therapy encounters challenges, primarily due to the need for safe and efficient delivery mechanisms. Lipid nanoparticles (LNPs), FDA-approved for RNA delivery, show potential for delivering also CRISPR/Cas, offering the capability to efficiently encapsulate large mRNA molecules with single guide RNAs. However, achieving precise targeting in-vivo remains a significant obstacle, necessitating further research into optimizing LNP formulations. Strategies to enhance specificity, such as modifying LNP structures and incorporating targeting ligands, are explored to improve organ and cell type targeting. Furthermore, the development of base and prime editing technology presents a potential breakthrough, offering precise modifications without generating double-strand breaks (DSBs). Prime editing, particularly when delivered via targeted LNPs, holds promise for treating diverse diseases safely and precisely. This review assesses both the progress made and the persistent challenges faced in using LNP-encapsulated CRISPR-based technologies for therapeutic purposes, with a particular focus on clinical translation.
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Affiliation(s)
- Razan Masarwy
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel; School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lior Stotsky-Oterin
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Aviad Elisha
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel; School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Inbal Hazan-Halevy
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
| | - Dan Peer
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
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26
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Zhang G, Song Z, Huang S, Wang Y, Sun J, Qiao L, Li G, Feng Y, Han W, Tang J, Chen Y, Huang X, Liu F, Wang X, Liu J. nCas9 Engineering for Improved Target Interaction Presents an Effective Strategy to Enhance Base Editing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405426. [PMID: 38881503 PMCID: PMC11336945 DOI: 10.1002/advs.202405426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Base editors (BEs) are a recent generation of genome editing tools that couple a cytidine or adenosine deaminase activity to a catalytically impaired Cas9 moiety (nCas9) to enable specific base conversions at the targeted genomic loci. Given their strong application potential, BEs are under active developments toward greater levels of efficiency and safety. Here, a previously overlooked nCas9-centric strategy is explored for enhancement of BE. Based on a cytosine BE (CBE), 20 point mutations associated with nCas9-target interaction are tested. Subsequently, from the initial positive X-to-arginine hits, combinatorial modifications are applied to establish further enhanced CBE variants (1.1-1.3). Parallel nCas9 modifications in other versions of CBEs including A3A-Y130F-BE4max, YEE-BE4max, CGBE, and split-AncBE4max, as well as in the context of two adenine BEs (ABE), likewise enhance their respective activities. The same strategy also substantially improves the efficiencies of high-fidelity nCas9/BEs. Further evidence confirms that the stabilization of nCas9-substrate interactions underlies the enhanced BE activities. In support of their translational potential, the engineered CBE and ABE variants respectively enable 82% and 25% higher rates of editing than the controls in primary human T-cells. This study thus demonstrates a highly adaptable strategy for enhancing BE, and for optimizing other forms of Cas9-derived tools.
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Affiliation(s)
| | - Ziguo Song
- International Joint Agriculture Research Center for Animal Bio‐BreedingMinistry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | | | - Yafeng Wang
- Department of Rheumatology and ImmunologyNanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjing210008China
| | - Jiayuan Sun
- International Joint Agriculture Research Center for Animal Bio‐BreedingMinistry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Lu Qiao
- Zhejiang LabHangzhouZhejiang311121China
| | - Guanglei Li
- Gene Editing CenterSchool of Life Science and TechnologyShanghaiTech University100 Haike Rd., Pudong New AreaShanghai201210China
| | | | - Wei Han
- Zhejiang LabHangzhouZhejiang311121China
| | - Jin Tang
- Zhejiang LabHangzhouZhejiang311121China
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio‐BreedingMinistry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | | | - Furui Liu
- Zhejiang LabHangzhouZhejiang311121China
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio‐BreedingMinistry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi712100China
| | - Jianghuai Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease StudyModel Animal Research Center at Medical School of Nanjing UniversityNanjing210061China
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27
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Maurya R, Vikal A, Narang RK, Patel P, Kurmi BD. Recent advancements and applications of ophthalmic gene therapy strategies: A breakthrough in ocular therapeutics. Exp Eye Res 2024; 245:109983. [PMID: 38942133 DOI: 10.1016/j.exer.2024.109983] [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: 02/15/2024] [Revised: 06/03/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Over the past twenty years, ocular gene therapy has primarily focused on addressing diseases linked to various genetic factors. The eye is an ideal candidate for gene therapy due to its unique characteristics, such as easy accessibility and the ability to target both corneal and retinal conditions, including retinitis pigmentosa (RP), Leber congenital amaurosis (LCA), age-related macular degeneration (AMD), and Stargardt disease. Currently, literature documents 33 clinical trials in this field, with the most promising results emerging from trials focused on LCA. These successes have catalyzed further research into other ocular conditions such as glaucoma, AMD, RP, and choroideremia. The effectiveness of gene therapy relies on the efficient delivery of genetic material to specific cells, ensuring sustained and optimal gene expression over time. Viral vectors have been widely used for this purpose, although concerns about potential risks such as immune reactions and genetic mutations have led to the development of non-viral vector systems. Preliminary laboratory research and clinical investigations have shown a connection between vector dosage and the intensity of immune response and inflammation in the eye. The method of administration significantly influences these reactions, with subretinal delivery resulting in a milder humoral response compared to the intravitreal route. This review discusses various ophthalmic diseases, including both corneal and retinal conditions, and their underlying mechanisms, highlighting recent advances and applications in ocular gene therapies.
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Affiliation(s)
- Rashmi Maurya
- Department of Pharmaceutics, ISF College of Pharmacy, GT Road, Moga, 142001, Punjab, India
| | - Akash Vikal
- Department of Pharmaceutics, ISF College of Pharmacy, GT Road, Moga, 142001, Punjab, India
| | - Raj Kumar Narang
- Department of Pharmaceutics, ISF College of Pharmacy, GT Road, Moga, 142001, Punjab, India; ISF College of Pharmacy & Research, Rattian Road, Moga, 142048, Punjab, India
| | - Preeti Patel
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Moga, 142001, Punjab, India
| | - Balak Das Kurmi
- Department of Pharmaceutics, ISF College of Pharmacy, GT Road, Moga, 142001, Punjab, India.
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28
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Tonetto E, Cucci A, Follenzi A, Bernardi F, Pinotti M, Balestra D. DNA base editing corrects common hemophilia A mutations and restores factor VIII expression in in vitro and ex vivo models. J Thromb Haemost 2024; 22:2171-2183. [PMID: 38718928 DOI: 10.1016/j.jtha.2024.04.020] [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: 01/22/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Replacement and nonreplacement therapies effectively control bleeding in hemophilia A (HA) but imply lifelong interventions. Authorized gene addition therapy could provide a cure but still poses questions on durability. FVIIIgene correction would definitively restore factor (F)VIII production, as shown in animal models through nuclease-mediated homologous recombination (HR). However, low efficiency and potential off-target double-strand break still limit HR translatability. OBJECTIVES To correct common model single point mutations leading to severe HA through the recently developed double-strand break/HR-independent base editing (BE) and prime editing (PE) approaches. METHODS Screening for efficacy of BE/PE systems in HEK293T cells transiently expressing FVIII variants and validation at DNA (sequencing) and protein (enzyme-linked immunosorbent assay; activated partial thromboplastin time) level in stable clones. Evaluation of rescue in engineered blood outgrowth endothelial cells by lentiviral-mediated delivery of BE. RESULTS Transient assays identified the best-performing BE/PE systems for each variant, with the highest rescue of FVIII expression (up to 25% of wild-type recombinant FVIII) for the p.R2166∗ and p.R2228Q mutations. In stable clones, we demonstrated that the mutation reversion on DNA (∼24%) was consistent with the rescue of FVIII secretion and activity of 20% to 30%. The lentiviral-mediated delivery of the selected BE systems was attempted in engineered blood outgrowth endothelial cells harboring the p.R2166∗ and p.R2228Q variants, which led to an appreciable and dose-dependent rescue of secreted functional FVIII. CONCLUSION Overall data provide the first proof-of-concept for effective BE/PE-mediated correction of HA-causing mutations, which encourage studies in mouse models to develop a personalized cure for large cohorts of patients through a single intervention.
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Affiliation(s)
- Elena Tonetto
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Alessia Cucci
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Antonia Follenzi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy.
| | - Dario Balestra
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
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Zhou Y, Zhang C, Xiao W, Herzog RW, Han R. Systemic delivery of full-length dystrophin in Duchenne muscular dystrophy mice. Nat Commun 2024; 15:6141. [PMID: 39034316 PMCID: PMC11271493 DOI: 10.1038/s41467-024-50569-6] [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: 01/22/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
Current gene therapy for Duchenne muscular dystrophy (DMD) utilizes adeno-associated virus (AAV) to deliver micro-dystrophin (µDys), which does not provide full protection for striated muscles as it lacks many important functional domains of full-length (FL) dystrophin. Here we develop a triple vector system to deliver FL-dystrophin into skeletal and cardiac muscles. We split FL-dystrophin into three fragments linked to two orthogonal pairs of split intein, allowing efficient assembly of FL-dystrophin. The three fragments packaged in myotropic AAV (MyoAAV4A) restore FL-dystrophin expression in both skeletal and cardiac muscles in male mdx4cv mice. Dystrophin-glycoprotein complex components are also restored at the sarcolemma of dystrophic muscles. MyoAAV4A-delivered FL-dystrophin significantly improves muscle histopathology, contractility, and overall strength comparable to µDys, but unlike µDys, it also restores defective cavin 4 localization and associated signaling in mdx4cv heart. Therefore, our data support the feasibility of a mutation-independent FL-dystrophin gene therapy for DMD, warranting further clinical development.
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Affiliation(s)
- Yuan Zhou
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Chen Zhang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Weidong Xiao
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Roland W Herzog
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Renzhi Han
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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30
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Zhu W, Du W, Rameshbabu AP, Armstrong AM, Silver S, Kim Y, Wei W, Shu Y, Liu X, Lewis MA, Steel KP, Chen ZY. Targeted genome editing restores auditory function in adult mice with progressive hearing loss caused by a human microRNA mutation. Sci Transl Med 2024; 16:eadn0689. [PMID: 38985856 PMCID: PMC7616320 DOI: 10.1126/scitranslmed.adn0689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
Mutations in microRNA-96 (MIR96) cause autosomal dominant deafness-50 (DFNA50), a form of delayed-onset hearing loss. Genome editing has shown efficacy in hearing recovery through intervention in neonatal mice, yet editing in the adult inner ear is necessary for clinical applications, which has not been done. Here, we developed a genome editing therapy for the MIR96 mutation 14C>A by screening different CRISPR systems and optimizing Cas9 expression and the sgRNA scaffold for efficient and specific mutation editing. AAV delivery of the KKH variant of Staphylococcus aureus Cas9 (SaCas9-KKH) and sgRNA to the cochleae of presymptomatic (3-week-old) and symptomatic (6-week-old) adult Mir9614C>A/+ mutant mice improved hearing long term, with efficacy increased by injection at a younger age. Adult inner ear delivery resulted in transient Cas9 expression without evidence of AAV genomic integration, indicating the good safety profile of our in vivo genome editing strategy. We developed a dual-AAV system, including an AAV-sgmiR96-master carrying sgRNAs against all known human MIR96 mutations. Because mouse and human MIR96 sequences share 100% homology, our approach and sgRNA selection for efficient and specific hair cell editing for long-term hearing recovery lay the foundation for the development of treatment for patients with DFNA50 caused by MIR96 mutations.
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Affiliation(s)
- Wenliang Zhu
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
| | - Wan Du
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
| | - Arun Prabhu Rameshbabu
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
| | - Ariel Miura Armstrong
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
| | - Stewart Silver
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
| | - Yehree Kim
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
| | - Wei Wei
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
| | - Yilai Shu
- ENT Institute and Otorhinolaryngology Department of Eye & ENT hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai200031, China
- Institutes of Biomedical Science, Fudan University, Shanghai200032, China
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai200031, China
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami School of Medicine, Miami, FL 33136, USA
| | - Morag A. Lewis
- Wolfson Sensory, Pain and Regeneration Centre, King’s College London, LondonWC2R 2LS, UK
| | - Karen P. Steel
- Wolfson Sensory, Pain and Regeneration Centre, King’s College London, LondonWC2R 2LS, UK
| | - Zheng-Yi Chen
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- Eaton-Peabody laboratory, Massachusetts Eye and Ear, Boston, MA02114, USA
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Shirguppe S, Gapinske M, Swami D, Gosstola N, Acharya P, Miskalis A, Joulani D, Szkwarek MG, Bhattacharjee A, Elias G, Stilger M, Winter J, Woods WS, Anand D, Lim CKW, Gaj T, Perez-Pinera P. In vivo CRISPR base editing for treatment of Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602282. [PMID: 39005280 PMCID: PMC11245100 DOI: 10.1101/2024.07.05.602282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Huntington's disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons. Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies for preventing this process hold potential for treating the disorder. By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuated striatal and cortical atrophy. Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.
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Sun Y, Wang L. Development of Anti-HIV Therapeutics: From Conventional Drug Discovery to Cutting-Edge Technology. Pharmaceuticals (Basel) 2024; 17:887. [PMID: 39065738 PMCID: PMC11280173 DOI: 10.3390/ph17070887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
The efforts to discover HIV therapeutics have continued since the first human immunodeficiency virus (HIV) infected patient was confirmed in the 1980s. Ten years later, the first HIV drug, zidovudine (AZT), targeting HIV reverse transcriptase, was developed. Meanwhile, scientists were enlightened to discover new drugs that target different HIV genes, like integrase, protease, and host receptors. Combination antiretroviral therapy (cART) is the most feasible medical intervention to suppress the virus in people with HIV (PWH) and control the epidemic. ART treatment has made HIV a chronic infection rather than a fatal disease, but ART does not eliminate latent reservoirs of HIV-1 from the host cells; strict and life-long adherence to ART is required for the therapy to be effective in patients. In this review, we first discussed the scientific history of conventional HIV drug discovery since scientists need to develop more and more drugs to solve drug-resistant issues and release the side effects. Then, we summarized the novel research technologies, like gene editing, applied to HIV treatment and their contributions to eliminating HIV as a complementary therapy.
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Affiliation(s)
| | - Lingyun Wang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA;
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Gopalappa R, Lee M, Kim G, Jung ES, Lee H, Hwang HY, Lee JG, Kim SJ, Yoo HJ, Sung YH, Kim D, Baek IJ, Kim HH. In vivo adenine base editing rescues adrenoleukodystrophy in a humanized mouse model. Mol Ther 2024; 32:2190-2206. [PMID: 38796705 PMCID: PMC11286820 DOI: 10.1016/j.ymthe.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024] Open
Abstract
X-linked adrenoleukodystrophy (ALD), an inherited neurometabolic disorder caused by mutations in ABCD1, which encodes the peroxisomal ABC transporter, mainly affects the brain, spinal cord, adrenal glands, and testes. In ALD patients, very-long-chain fatty acids (VLCFAs) fail to enter the peroxisome and undergo subsequent β-oxidation, resulting in their accumulation in the body. It has not been tested whether in vivo base editing or prime editing can be harnessed to ameliorate ALD. We developed a humanized mouse model of ALD by inserting a human cDNA containing the pathogenic variant into the mouse Abcd1 locus. The humanized ALD model showed increased levels of VLCFAs. To correct the mutation, we tested both base editing and prime editing and found that base editing using ABE8e(V106W) could correct the mutation in patient-derived fibroblasts at an efficiency of 7.4%. Adeno-associated virus (AAV)-mediated systemic delivery of NG-ABE8e(V106W) enabled robust correction of the pathogenic variant in the mouse brain (correction efficiency: ∼5.5%), spinal cord (∼5.1%), and adrenal gland (∼2%), leading to a significant reduction in the plasma levels of C26:0/C22:0. This established humanized mouse model and the successful correction of the pathogenic variant using a base editor serve as a significant step toward treating human ALD disease.
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Affiliation(s)
- Ramu Gopalappa
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - MinYoung Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Globinna Kim
- ConveRgence mEDIcine research cenTer (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Republic of Korea; Department of Cell and Genetic Engineering, ASAN Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Eul Sik Jung
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; JES Clinic, Incheon 21550, Republic of Korea
| | - Hanahrae Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hye-Yeon Hwang
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jong Geol Lee
- ConveRgence mEDIcine research cenTer (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Republic of Korea
| | - Su Jung Kim
- ConveRgence mEDIcine research cenTer (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Republic of Korea
| | - Hyun Ju Yoo
- ConveRgence mEDIcine research cenTer (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Republic of Korea
| | - Young Hoon Sung
- ConveRgence mEDIcine research cenTer (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Republic of Korea; Department of Cell and Genetic Engineering, ASAN Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Daesik Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - In-Jeoung Baek
- ConveRgence mEDIcine research cenTer (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Republic of Korea; Department of Cell and Genetic Engineering, ASAN Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Center for Nanomedicine, Institute for Basic Science, Seoul 03722, Republic of Korea; Graduate Program of Nano Biomedical Engineering, Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Woo Choo Lee Institute for Precision Drug Development, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
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Baek S, Jang J, Jung HJ, Lee H, Choe Y. Advanced Immunolabeling Method for Optical Volumetric Imaging Reveals Dystrophic Neurites of Dopaminergic Neurons in Alzheimer's Disease Mouse Brain. Mol Neurobiol 2024; 61:3976-3999. [PMID: 38049707 PMCID: PMC11236860 DOI: 10.1007/s12035-023-03823-9] [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: 05/25/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023]
Abstract
Optical brain clearing combined with immunolabeling is valuable for analyzing molecular tissue structures, including complex synaptic connectivity. However, the presence of aberrant lipid deposition due to aging and brain disorders poses a challenge for achieving antibody penetration throughout the entire brain volume. Herein, we present an efficient brain-wide immunolabeling method, the immuno-active clearing technique (iACT). The treatment of brain tissues with a zwitterionic detergent, specifically SB3-12, significantly enhanced tissue permeability by effectively mitigating lipid barriers. Notably, Quadrol treatment further refines the methodology by effectively eliminating residual detergents from cleared brain tissues, subsequently amplifying volumetric fluorescence signals. Employing iACT, we uncover disrupted axonal projections within the mesolimbic dopaminergic (DA) circuits in 5xFAD mice. Subsequent characterization of DA neural circuits in 5xFAD mice revealed proximal axonal swelling and misrouting of distal axonal compartments in proximity to amyloid-beta plaques. Importantly, these structural anomalies in DA axons correlate with a marked reduction in DA release within the nucleus accumbens. Collectively, our findings highlight the efficacy of optical volumetric imaging with iACT in resolving intricate structural alterations in deep brain neural circuits. Furthermore, we unveil the compromised integrity of DA pathways, contributing to the underlying neuropathology of Alzheimer's disease. The iACT technique thus holds significant promise as a valuable asset for advancing our understanding of complex neurodegenerative disorders and may pave the way for targeted therapeutic interventions.
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Affiliation(s)
- Soonbong Baek
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Jaemyung Jang
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Hyun Jin Jung
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Hyeyoung Lee
- Division of Applied Bioengineering, Dong-eui University, Busanjin-gu, Busan, 47340, Republic of Korea
| | - Youngshik Choe
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea.
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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401797. [PMID: 38728624 PMCID: PMC11267366 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Mudi Meng Honors CollegeChina Pharmaceutical UniversityNanjing210009China
| | - Jianping Kong
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Gongyu Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Zhaoxing Li
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| | - Yibei Xiao
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
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Neumann EN, Bertozzi TM, Wu E, Serack F, Harvey JW, Brauer PP, Pirtle CP, Coffey A, Howard M, Kamath N, Lenz K, Guzman K, Raymond MH, Khalil AS, Deverman BE, Minikel EV, Vallabh SM, Weissman JS. Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor. Science 2024; 384:ado7082. [PMID: 38935715 DOI: 10.1126/science.ado7082] [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: 02/18/2024] [Accepted: 05/02/2024] [Indexed: 06/29/2024]
Abstract
Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid-onset dementia and death. However, elimination of endogenous PrP halts prion disease progression. In this study, we describe Coupled Histone tail for Autoinhibition Release of Methyltransferase (CHARM), a compact, enzyme-free epigenetic editor capable of silencing transcription through programmable DNA methylation. Using a histone H3 tail-Dnmt3l fusion, CHARM recruits and activates endogenous DNA methyltransferases, thereby reducing transgene size and cytotoxicity. When delivered to the mouse brain by systemic injection of adeno-associated virus (AAV), Prnp-targeted CHARM ablates PrP expression across the brain. Furthermore, we have temporally limited editor expression by implementing a kinetically tuned self-silencing approach. CHARM potentially represents a broadly applicable strategy to suppress pathogenic proteins, including those implicated in other neurodegenerative diseases.
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Affiliation(s)
- Edwin N Neumann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tessa M Bertozzi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Elaine Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fiona Serack
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John W Harvey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pamela P Brauer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine P Pirtle
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alissa Coffey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Howard
- Comparative Medicine, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nikita Kamath
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kenney Lenz
- Comparative Medicine, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kenia Guzman
- Comparative Medicine, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael H Raymond
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Benjamin E Deverman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric Vallabh Minikel
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sonia M Vallabh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Choi DE, Shin JW, Zeng S, Hong EP, Jang JH, Loupe JM, Wheeler VC, Stutzman HE, Kleinstiver B, Lee JM. Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease. eLife 2024; 12:RP89782. [PMID: 38869243 PMCID: PMC11175616 DOI: 10.7554/elife.89782] [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] [Indexed: 06/14/2024] Open
Abstract
An expanded CAG repeat in the huntingtin gene (HTT) causes Huntington's disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and guide RNAs (gRNAs) efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without altering HTT mRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased in the liver by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion strategies in HD and potentially other repeat expansion disorders.
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Affiliation(s)
- Doo Eun Choi
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jun Wan Shin
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Sophia Zeng
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Eun Pyo Hong
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jae-Hyun Jang
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jacob M Loupe
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Hannah E Stutzman
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
| | - Ben Kleinstiver
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
| | - Jong-Min Lee
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
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38
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Christensen CL, Kan SH, Andrade-Heckman P, Rha AK, Harb JF, Wang RY. Base editing rescues acid α-glucosidase function in infantile-onset Pompe disease patient-derived cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102220. [PMID: 38948331 PMCID: PMC11214518 DOI: 10.1016/j.omtn.2024.102220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/16/2024] [Indexed: 07/02/2024]
Abstract
Infantile-onset Pompe disease (IOPD) results from pathogenic variants in the GAA gene, which encodes acid α-glucosidase. The correction of pathogenic variants through genome editing may be a valuable one-time therapy for PD and improve upon the current standard of care. We performed adenine base editing in human dermal fibroblasts harboring three transition nonsense variants, c.2227C>T (p.Q743∗; IOPD-1), c.2560C>T (p.R854∗; IOPD-2), and c.2608C>T (p.R870∗; IOPD-3). Up to 96% adenine deamination of target variants was observed, with minimal editing across >50 off-target sites. Post-base editing, expressed GAA protein was up to 0.66-fold normal (unaffected fibroblasts), an improvement over affected fibroblasts wherein GAA was undetectable. GAA enzyme activity was between 81.91 ± 13.51 and 129.98 ± 9.33 units/mg protein at 28 days post-transfection, which falls within the normal range (50-200 units/mg protein). LAMP2 protein was significantly decreased in the most robustly edited cell line, IOPD-3, indicating reduced lysosomal burden. Taken together, the findings reported herein demonstrate that base editing results in efficacious adenine deamination, restoration of GAA expression and activity, and reduction in lysosomal burden in the most robustly edited cells. Future work will assess base editing outcomes and the impact on Pompe pathology in two mouse models, Gaa c.2227C>T and Gaa c.2560C>T.
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Affiliation(s)
| | - Shih-Hsin Kan
- CHOC Children’s Research Institute, Orange, CA 92868, USA
| | | | | | - Jerry F. Harb
- CHOC Children’s Research Institute, Orange, CA 92868, USA
| | - Raymond Y. Wang
- Division of Metabolic Disorders, CHOC Children’s Specialists, Orange, CA 92868, USA
- Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, CA 92697, USA
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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: 0] [Impact Index Per Article: 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.
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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
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Hosseini K, Fallahi J, Razban V, Sirat RZ, Varasteh M, Tarhriz V. Overview of clinical, molecular, and therapeutic features of Niemann-Pick disease (types A, B, and C): Focus on therapeutic approaches. Cell Biochem Funct 2024; 42:e4028. [PMID: 38715125 DOI: 10.1002/cbf.4028] [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: 01/20/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 06/30/2024]
Abstract
Niemann-Pick disease (NPD) is another type of metabolic disorder that is classified as lysosomal storage diseases (LSDs). The main cause of the disease is mutation in the SMPD1 (type A and B) or NPC1 or NPC2 (type C) genes, which lead to the accumulation of lipid substrates in the lysosomes of the liver, brain, spleen, lung, and bone marrow cells. This is followed by multiple cell damage, dysfunction of lysosomes, and finally dysfunction of body organs. So far, about 346, 575, and 30 mutations have been reported in SMPD1, NPC1, and NPC2 genes, respectively. Depending on the type of mutation and the clinical symptoms of the disease, the treatment will be different. The general aim of the current study is to review the clinical and molecular characteristics of patients with NPD and study various treatment methods for this disease with a focus on gene therapy approaches.
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Affiliation(s)
- Kamran Hosseini
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Vahid Razban
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | | | - Vahideh Tarhriz
- Cardiovascular Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
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41
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Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
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42
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Chen Q, Wang X, Zhang Y, Tian M, Duan J, Zhang Y, Yin H. Minimizing the ratio of ionizable lipid in lipid nanoparticles for in vivo base editing. Natl Sci Rev 2024; 11:nwae135. [PMID: 38770531 PMCID: PMC11104531 DOI: 10.1093/nsr/nwae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/22/2024] [Accepted: 04/02/2024] [Indexed: 05/22/2024] Open
Abstract
Lipid nanoparticles (LNPs) have gained clinical approval as carriers for both siRNA and mRNA. Among the crucial components of LNPs, ionizable lipids play a pivotal role in determining the efficiency of RNA delivery. In this study, we synthesized a series of ionizable lipids, denoted as HTO, with a higher count of hydroxyl groups compared to SM-102. Remarkably, LNPs based on HTO12 lipid demonstrated comparable mRNA delivery efficiency and biosafety to those based on SM-102. However, the former reduced the ratio of ionizable lipid/total lipids to mRNA in LNPs by 2.5 times compared to SM-102. The HTO12 LNP efficiently encapsulated adenine base editor mRNA and sgRNA targeting Pcsk9, leading to substantial gene editing within the liver of mice and effective reduction of the target protein. Our study underscores that ionizable lipids with multiple hydroxyl groups may facilitate an improved lipid-to-mRNA ratio to minimize the dosage of ionizable lipids for in vivo delivery.
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Affiliation(s)
- Qiubing Chen
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Xuebin Wang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Yizhou Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Ming Tian
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Junyi Duan
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Ying Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Hao Yin
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
- RNA Institute, Wuhan University, Wuhan 430071, China
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43
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Plug BC, Revers IM, Breur M, González GM, Timmerman JA, Meijns NRC, Hamberg D, Wagendorp J, Nutma E, Wolf NI, Luchicchi A, Mansvelder HD, van Til NP, van der Knaap MS, Bugiani M. Human post-mortem organotypic brain slice cultures: a tool to study pathomechanisms and test therapies. Acta Neuropathol Commun 2024; 12:83. [PMID: 38822428 PMCID: PMC11140981 DOI: 10.1186/s40478-024-01784-1] [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: 02/13/2024] [Accepted: 04/16/2024] [Indexed: 06/03/2024] Open
Abstract
Human brain experimental models recapitulating age- and disease-related characteristics are lacking. There is urgent need for human-specific tools that model the complex molecular and cellular interplay between different cell types to assess underlying disease mechanisms and test therapies. Here we present an adapted ex vivo organotypic slice culture method using human post-mortem brain tissue cultured at an air-liquid interface to also study brain white matter. We assessed whether these human post-mortem brain slices recapitulate the in vivo neuropathology and if they are suitable for pathophysiological, experimental and pre-clinical treatment development purposes, specifically regarding leukodystrophies. Human post-mortem brain tissue and cerebrospinal fluid were obtained from control, psychiatric and leukodystrophy donors. Slices were cultured up to six weeks, in culture medium with or without human cerebrospinal fluid. Human post-mortem organotypic brain slice cultures remained viable for at least six weeks ex vivo and maintained tissue structure and diversity of (neural) cell types. Supplementation with cerebrospinal fluid could improve slice recovery. Patient-derived organotypic slice cultures recapitulated and maintained known in vivo neuropathology. The cultures also showed physiologic multicellular responses to lysolecithin-induced demyelination ex vivo, indicating their suitability to study intrinsic repair mechanisms upon injury. The slice cultures were applicable for various experimental studies, as multi-electrode neuronal recordings. Finally, the cultures showed successful cell-type dependent transduction with gene therapy vectors. These human post-mortem organotypic brain slice cultures represent an adapted ex vivo model suitable for multifaceted studies of brain disease mechanisms, boosting translation from human ex vivo to in vivo. This model also allows for assessing potential treatment options, including gene therapy applications. Human post-mortem brain slice cultures are thus a valuable tool in preclinical research to study the pathomechanisms of a wide variety of brain diseases in living human tissue.
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Affiliation(s)
- Bonnie C Plug
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
| | - Ilma M Revers
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
| | - Marjolein Breur
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
| | - Gema Muñoz González
- Department of Anatomy and Neurosciences, MS Center Amsterdam, Amsterdam University Medical Centre, VU University, Amsterdam Neuroscience, De Boelelaan 1108, Amsterdam, 1081 HZ, The Netherlands
| | - Jaap A Timmerman
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam Neuroscience, De Boelelaan 1085, Amsterdam, 1081 HV, The Netherlands
| | - Niels R C Meijns
- Department of Anatomy and Neurosciences, MS Center Amsterdam, Amsterdam University Medical Centre, VU University, Amsterdam Neuroscience, De Boelelaan 1108, Amsterdam, 1081 HZ, The Netherlands
| | - Daniek Hamberg
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
| | - Jikke Wagendorp
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
| | - Erik Nutma
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
| | - Nicole I Wolf
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
| | - Antonio Luchicchi
- Department of Anatomy and Neurosciences, MS Center Amsterdam, Amsterdam University Medical Centre, VU University, Amsterdam Neuroscience, De Boelelaan 1108, Amsterdam, 1081 HZ, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam Neuroscience, De Boelelaan 1085, Amsterdam, 1081 HV, The Netherlands
| | - Niek P van Til
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam Neuroscience, De Boelelaan 1085, Amsterdam, 1081 HV, The Netherlands
| | - Marjo S van der Knaap
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam Neuroscience, De Boelelaan 1085, Amsterdam, 1081 HV, The Netherlands
| | - Marianna Bugiani
- Department of Paediatrics and Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands.
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1100 DD, Amsterdam, The Netherlands.
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centre, Meibergdreef 9, Amsterdam, 1100 DD, The Netherlands.
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Sevim-Wunderlich S, Dang T, Rossius J, Schnütgen F, Kühn R. A Mouse Model of X-Linked Chronic Granulomatous Disease for the Development of CRISPR/Cas9 Gene Therapy. Genes (Basel) 2024; 15:706. [PMID: 38927642 PMCID: PMC11203339 DOI: 10.3390/genes15060706] [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: 05/07/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Chronic granulomatous disease (CGD) is an inherited immunodeficiency disease mainly caused by mutations in the X-linked CYBB gene that abrogate reactive oxygen species (ROS) production in phagocytes and microbial defense. Gene repair using the CRISPR/Cas9 system in hematopoietic stem and progenitor cells (HSPCs) is a promising technology for therapy for CGD. To support the establishment of efficient and safe gene therapies for CGD, we generated a mouse model harboring a patient-derived mutation in the CYBB gene. Our CybbC517del mouse line shows the hallmarks of CGD and provides a source for Cybb-deficient HSPCs that can be used to evaluate gene-therapy approaches in vitro and in vivo. In a setup using Cas9 RNPs and an AAV repair vector in HSPCs, we show that the mutation can be repaired in 19% of treated cells and that treatment restores ROS production by macrophages. In conclusion, our CybbC517del mouse line provides a new platform for refining and evaluating novel gene therapies and studying X-CGD pathophysiology.
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Affiliation(s)
- Seren Sevim-Wunderlich
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
| | - Tu Dang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
| | - Jana Rossius
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
| | - Frank Schnütgen
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany;
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Frankfurt Cancer Institute, Goethe-University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (S.S.-W.); (T.D.); (J.R.)
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45
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Walsh ZH, Shah P, Kothapalli N, Shah SB, Nikolenyi G, Brodtman DZ, Leuzzi G, Rogava M, Mu M, Ho P, Abuzaid S, Vasan N, AlQuraishi M, Milner JD, Ciccia A, Melms JC, Izar B. Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens. Nat Biotechnol 2024:10.1038/s41587-024-02235-x. [PMID: 38783148 DOI: 10.1038/s41587-024-02235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Single-nucleotide variants (SNVs) in key T cell genes can drive clinical pathologies and could be repurposed to improve cellular cancer immunotherapies. Here, we perform massively parallel base-editing screens to generate thousands of variants at gene loci annotated with known or potential clinical relevance. We discover a broad landscape of putative gain-of-function (GOF) and loss-of-function (LOF) mutations, including in PIK3CD and the gene encoding its regulatory subunit, PIK3R1, LCK, SOS1, AKT1 and RHOA. Base editing of PIK3CD and PIK3R1 variants in T cells with an engineered T cell receptor specific to a melanoma epitope or in different generations of CD19 chimeric antigen receptor (CAR) T cells demonstrates that discovered GOF variants, but not LOF or silent mutation controls, enhanced signaling, cytokine production and lysis of cognate melanoma and leukemia cell models, respectively. Additionally, we show that generations of CD19 CAR T cells engineered with PIK3CD GOF mutations demonstrate enhanced antigen-specific signaling, cytokine production and leukemia cell killing, including when benchmarked against other recent strategies.
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Affiliation(s)
- Zachary H Walsh
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Parin Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Neeharika Kothapalli
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shivem B Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gergo Nikolenyi
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - D Zack Brodtman
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Meri Rogava
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael Mu
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia Ho
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Sinan Abuzaid
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Mohammed AlQuraishi
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua D Milner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alberto Ciccia
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Johannes C Melms
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Benjamin Izar
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA.
- Columbia Center for Translational Immunology, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
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46
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Han R, Zhou Y, Zhang C, Xiao W, Herzog R. Systemic Delivery of Full-Length Dystrophin in DMD Mice. RESEARCH SQUARE 2024:rs.3.rs-3867299. [PMID: 38746161 PMCID: PMC11092816 DOI: 10.21203/rs.3.rs-3867299/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Current gene therapy for Duchenne muscular dystrophy (DMD) utilizes adeno-associated virus (AAV) to deliver miniaturized dystrophin (micro-dystrophin or µDys), which does not provide full protection for striated muscles as it lacks many important functional domains within full-length (FL) dystrophin. Here we develop a triple vector system to deliver FL-dystrophin into skeletal and cardiac muscles. We rationally split FL-dystrophin into three fragments (N, M, and C) linked to two orthogonal pairs of split intein, allowing efficient, unidirectional assembly of FL-dystrophin. The three fragments packaged in myotropic AAV (MyoAAV4A) restore FL-dystrophin expression in both skeletal and cardiac muscles in male mdx 4cv mice. Dystrophin-glycoprotein complex components are also restored in the sarcolemma of dystrophic muscles. MyoAAV4A-delivered FL-dystrophin significantly improves muscle histopathology, contractility, and overall strength comparable to µDys, but unlike µDys, it also restores defective ERK signaling in heart. The FL-dystrophin gene therapy therefore promises to offer superior protection for DMD.
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47
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Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
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Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
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48
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Xin Y, Feng H, He C, Lu H, Zuo E, Yan N. Development of a universal antibiotic resistance screening system for efficient enrichment of C-to-G and A-to-G base editing. Int J Biol Macromol 2024; 268:131785. [PMID: 38679258 DOI: 10.1016/j.ijbiomac.2024.131785] [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: 02/01/2024] [Revised: 03/31/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024]
Abstract
To expand the scope of genomic editing, a C-to-G transversion-based editor called CGBE has been developed for precise single-nucleotide genomic editing. However, limited editing efficiency and product purity have hindered the development and application of CGBE. In this study, we introduced the Puromycin-Resistance Screening System, referred to as CGBE/ABE-PRSS, to select genetically modified cells via the CGBE or ABE editors. The CGBE/ABE-PRSS system significantly improves the enrichment efficiency of CGBE- or ABE-modified cells, showing enhancements of up to 59.6 % compared with the controls. Our findings indicate that the CGBE/ABE-PRSS, when driven by the CMV promoter, results in a higher enrichment of edited cells compared to the CAG and EF1α promoters. Furthermore, we demonstrate that this system is compatible with different versions of both CGBE and ABE, enabling various cell species and simultaneous multiplexed genome editing without any detectable random off-targets. In conclusion, our developed CGBE/ABE-PRSS system facilitates the selection of edited cells and holds promise in both basic engineering and gene therapy applications.
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Affiliation(s)
- Ying Xin
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hu Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chenfei He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongjiang Lu
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Erwei Zuo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Nana Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China..
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49
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Böck D, Revers IM, Bomhof ASJ, Hillen AEJ, Boeijink C, Kissling L, Egli S, Moreno-Mateos MA, van der Knaap MS, van Til NP, Schwank G. In vivo base editing of a pathogenic Eif2b5 variant improves vanishing white matter phenotypes in mice. Mol Ther 2024; 32:1328-1343. [PMID: 38454603 PMCID: PMC11081866 DOI: 10.1016/j.ymthe.2024.03.009] [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: 10/17/2023] [Revised: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
Vanishing white matter (VWM) is a fatal leukodystrophy caused by recessive mutations in subunits of the eukaryotic translation initiation factor 2B. Currently, there are no effective therapies for VWM. Here, we assessed the potential of adenine base editing to correct human pathogenic VWM variants in mouse models. Using adeno-associated viral vectors, we delivered intein-split adenine base editors into the cerebral ventricles of newborn VWM mice, resulting in 45.9% ± 5.9% correction of the Eif2b5R191H variant in the cortex. Treatment slightly increased mature astrocyte populations and partially recovered the integrated stress response (ISR) in female VWM animals. This led to notable improvements in bodyweight and grip strength in females; however, locomotor disabilities were not rescued. Further molecular analyses suggest that more precise editing (i.e., lower rates of bystander editing) as well as more efficient delivery of the base editors to deep brain regions and oligodendrocytes would have been required for a broader phenotypic rescue. Our study emphasizes the potential, but also identifies limitations, of current in vivo base-editing approaches for the treatment of VWM or other leukodystrophies.
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Affiliation(s)
- Desirée Böck
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Ilma M Revers
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, 1105AZ Amsterdam, the Netherlands
| | - Anastasia S J Bomhof
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, 1105AZ Amsterdam, the Netherlands
| | - Anne E J Hillen
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, 1105AZ Amsterdam, the Netherlands
| | - Claire Boeijink
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, 1105AZ Amsterdam, the Netherlands
| | - Lucas Kissling
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Sabina Egli
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Miguel A Moreno-Mateos
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, 41013 Seville, Spain; Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, 41013 Seville, Spain
| | - Marjo S van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, 1105AZ Amsterdam, the Netherlands; Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081HV Amsterdam, the Netherlands
| | - Niek P van Til
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, 1105AZ Amsterdam, the Netherlands; Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081HV Amsterdam, the Netherlands.
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland.
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50
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Deneault E. Recent Therapeutic Gene Editing Applications to Genetic Disorders. Curr Issues Mol Biol 2024; 46:4147-4185. [PMID: 38785523 PMCID: PMC11119904 DOI: 10.3390/cimb46050255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Recent years have witnessed unprecedented progress in therapeutic gene editing, revolutionizing the approach to treating genetic disorders. In this comprehensive review, we discuss the progression of milestones leading to the emergence of the clustered regularly interspaced short palindromic repeats (CRISPR)-based technology as a powerful tool for precise and targeted modifications of the human genome. CRISPR-Cas9 nuclease, base editing, and prime editing have taken center stage, demonstrating remarkable precision and efficacy in targeted ex vivo and in vivo genomic modifications. Enhanced delivery systems, including viral vectors and nanoparticles, have further improved the efficiency and safety of therapeutic gene editing, advancing their clinical translatability. The exploration of CRISPR-Cas systems beyond the commonly used Cas9, such as the development of Cas12 and Cas13 variants, has expanded the repertoire of gene editing tools, enabling more intricate modifications and therapeutic interventions. Outstandingly, prime editing represents a significant leap forward, given its unparalleled versatility and minimization of off-target effects. These innovations have paved the way for therapeutic gene editing in a multitude of previously incurable genetic disorders, ranging from monogenic diseases to complex polygenic conditions. This review highlights the latest innovative studies in the field, emphasizing breakthrough technologies in preclinical and clinical trials, and their applications in the realm of precision medicine. However, challenges such as off-target effects and ethical considerations remain, necessitating continued research to refine safety profiles and ethical frameworks.
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Affiliation(s)
- Eric Deneault
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
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