1
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Sousa AA, Hemez C, Lei L, Traore S, Kulhankova K, Newby GA, Doman JL, Oye K, Pandey S, Karp PH, McCray PB, Liu DR. Systematic optimization of prime editing for the efficient functional correction of CFTR F508del in human airway epithelial cells. Nat Biomed Eng 2024:10.1038/s41551-024-01233-3. [PMID: 38987629 DOI: 10.1038/s41551-024-01233-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Prime editing (PE) enables precise and versatile genome editing without requiring double-stranded DNA breaks. Here we describe the systematic optimization of PE systems to efficiently correct human cystic fibrosis (CF) transmembrane conductance regulator (CFTR) F508del, a three-nucleotide deletion that is the predominant cause of CF. By combining six efficiency optimizations for PE-engineered PE guide RNAs, the PEmax architecture, the transient expression of a dominant-negative mismatch repair protein, strategic silent edits, PE6 variants and proximal 'dead' single-guide RNAs-we increased correction efficiencies for CFTR F508del from less than 0.5% in HEK293T cells to 58% in immortalized bronchial epithelial cells (a 140-fold improvement) and to 25% in patient-derived airway epithelial cells. The optimizations also resulted in minimal off-target editing, in edit-to-indel ratios 3.5-fold greater than those achieved by nuclease-mediated homology-directed repair, and in the functional restoration of CFTR ion channels to over 50% of wild-type levels (similar to those achieved via combination treatment with elexacaftor, tezacaftor and ivacaftor) in primary airway cells. Our findings support the feasibility of a durable one-time treatment for CF.
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Affiliation(s)
- Alexander A Sousa
- Merkin Institute of Transformative Technologies in Healthcare, The 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
| | - Colin Hemez
- Merkin Institute of Transformative Technologies in Healthcare, The 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
| | - Lei Lei
- Stead Family Department of Pediatrics and Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Soumba Traore
- Stead Family Department of Pediatrics and Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Katarina Kulhankova
- Stead Family Department of Pediatrics and Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, The 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
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, The 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
| | - Keyede Oye
- Merkin Institute of Transformative Technologies in Healthcare, The 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
| | - Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, The 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
| | - Philip H Karp
- Department of Internal Medicine and Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, USA
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA, USA
| | - Paul B McCray
- Stead Family Department of Pediatrics and Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, The 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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2
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Liu X, Gu D, Zhang Y, Jiang Y, Xiao Z, Xu R, Qin R, Li J, Wei P. Conditional knockdown of OsMLH1 to improve plant prime editing systems without disturbing fertility in rice. Genome Biol 2024; 25:131. [PMID: 38773623 PMCID: PMC11110357 DOI: 10.1186/s13059-024-03282-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: 02/18/2024] [Accepted: 05/16/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND High-efficiency prime editing (PE) is desirable for precise genome manipulation. The activity of mammalian PE systems can be largely improved by inhibiting DNA mismatch repair by coexpressing a dominant-negative variant of MLH1. However, this strategy has not been widely used for PE optimization in plants, possibly because of its less conspicuous effects and inconsistent performance at different sites. RESULTS We show that direct RNAi knockdown of OsMLH1 in an ePE5c system increases the efficiency of our most recently updated PE tool by 1.30- to 2.11-fold in stably transformed rice cells, resulting in as many as 85.42% homozygous mutants in the T0 generation. The high specificity of ePE5c is revealed by whole-genome sequencing. To overcome the partial sterility induced by OsMLH1 knockdown of ePE5c, a conditional excision system is introduced to remove the RNAi module by Cre-mediated site-specific recombination. Using a simple approach of enriching excision events, we generate 100% RNAi module-free plants in the T0 generation. The increase in efficiency due to OsMLH1 knockdown is maintained in the excised plants, whose fertility is not impaired. CONCLUSIONS This study provides a safe and reliable plant PE optimization strategy for improving editing efficiency without disturbing plant development via transient MMR inhibition with an excisable RNAi module of MLH1.
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Affiliation(s)
- Xiaoshuang Liu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Dongfang Gu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China
| | - Yiru Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Yingli Jiang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Zhi Xiao
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Rongfang Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China
| | - Ruiying Qin
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China
| | - Juan Li
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China.
| | - Pengcheng Wei
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
- Research Centre for Biological Breeding Technology, Advance Academy, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
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3
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Bulcaen M, Kortleven P, Liu RB, Maule G, Dreano E, Kelly M, Ensinck MM, Thierie S, Smits M, Ciciani M, Hatton A, Chevalier B, Ramalho AS, Casadevall I Solvas X, Debyser Z, Vermeulen F, Gijsbers R, Sermet-Gaudelus I, Cereseto A, Carlon MS. Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. Cell Rep Med 2024; 5:101544. [PMID: 38697102 PMCID: PMC11148721 DOI: 10.1016/j.xcrm.2024.101544] [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: 07/26/2023] [Revised: 01/16/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Prime editing is a recent, CRISPR-derived genome editing technology capable of introducing precise nucleotide substitutions, insertions, and deletions. Here, we present prime editing approaches to correct L227R- and N1303K-CFTR, two mutations that cause cystic fibrosis and are not eligible for current market-approved modulator therapies. We show that, upon DNA correction of the CFTR gene, the complex glycosylation, localization, and, most importantly, function of the CFTR protein are restored in HEK293T and 16HBE cell lines. These findings were subsequently validated in patient-derived rectal organoids and human nasal epithelial cells. Through analysis of predicted and experimentally identified candidate off-target sites in primary stem cells, we confirm previous reports on the high prime editor (PE) specificity and its potential for a curative CF gene editing therapy. To facilitate future screening of genetic strategies in a translational CF model, a machine learning algorithm was developed for dynamic quantification of CFTR function in organoids (DETECTOR: "detection of targeted editing of CFTR in organoids").
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Affiliation(s)
- Mattijs Bulcaen
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium.
| | - Phéline Kortleven
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Ronald B Liu
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; School of Engineering, University of Edinburgh, EH9 3JL Edinburgh, UK
| | - Giulia Maule
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Elise Dreano
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Mairead Kelly
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Marjolein M Ensinck
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Sam Thierie
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Maxime Smits
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Matteo Ciciani
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Aurelie Hatton
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Benoit Chevalier
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Anabela S Ramalho
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | | | - Zeger Debyser
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - François Vermeulen
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium; Department of Pediatrics, UZ Leuven, 3000 Leuven, Belgium
| | - Rik Gijsbers
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Isabelle Sermet-Gaudelus
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France; Cystic Fibrosis National Pediatric Reference Center, Pneumo-Allergologie Pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), 75015 Paris, France; European Reference Network, ERN-Lung CF, 60596 Frankfurt am Mein, Germany
| | - Anna Cereseto
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Marianne S Carlon
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium.
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4
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Dimitrievska M, Bansal D, Vitale M, Strouboulis J, Miccio A, Nicolaides KH, El Hoss S, Shangaris P, Jacków-Malinowska J. Revolutionising healing: Gene Editing's breakthrough against sickle cell disease. Blood Rev 2024; 65:101185. [PMID: 38493007 DOI: 10.1016/j.blre.2024.101185] [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: 10/25/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Recent advancements in gene editing illuminate new potential therapeutic approaches for Sickle Cell Disease (SCD), a debilitating monogenic disorder caused by a point mutation in the β-globin gene. Despite the availability of several FDA-approved medications for symptomatic relief, allogeneic hematopoietic stem cell transplantation (HSCT) remains the sole curative option, underscoring a persistent need for novel treatments. This review delves into the growing field of gene editing, particularly the extensive research focused on curing haemoglobinopathies like SCD. We examine the use of techniques such as CRISPR-Cas9 and homology-directed repair, base editing, and prime editing to either correct the pathogenic variant into a non-pathogenic or wild-type one or augment fetal haemoglobin (HbF) production. The article elucidates ways to optimize these tools for efficacious gene editing with minimal off-target effects and offers insights into their effective delivery into cells. Furthermore, we explore clinical trials involving alternative SCD treatment strategies, such as LentiGlobin therapy and autologous HSCT, distilling the current findings. This review consolidates vital information for the clinical translation of gene editing for SCD, providing strategic insights for investigators eager to further the development of gene editing for SCD.
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Affiliation(s)
- Marija Dimitrievska
- St John's Institute of Dermatology, King's College London, London SE1 9RT, UK
| | - Dravie Bansal
- St John's Institute of Dermatology, King's College London, London SE1 9RT, UK
| | - Marta Vitale
- St John's Institute of Dermatology, King's College London, London SE1 9RT, UK
| | - John Strouboulis
- Red Cell Hematology Lab, Comprehensive Cancer Center, School of Cancer & Pharmaceutical Sciences, King's College London, United Kingdom
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Kypros H Nicolaides
- Women and Children's Health, School of Life Course & Population Sciences, Kings College London, London, United Kingdom; Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, United Kingdom
| | - Sara El Hoss
- Red Cell Hematology Lab, Comprehensive Cancer Center, School of Cancer & Pharmaceutical Sciences, King's College London, United Kingdom.
| | - Panicos Shangaris
- Women and Children's Health, School of Life Course & Population Sciences, Kings College London, London, United Kingdom; Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, United Kingdom; Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
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5
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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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6
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Zeng H, Daniel TC, Lingineni A, Chee K, Talloo K, Gao X. Recent advances in prime editing technologies and their promises for therapeutic applications. Curr Opin Biotechnol 2024; 86:103071. [PMID: 38330875 PMCID: PMC10947817 DOI: 10.1016/j.copbio.2024.103071] [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: 09/15/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 02/10/2024]
Abstract
Prime editing (PE) is a groundbreaking genome editing technology offering unparalleled precision in targeted genome modifications and has great potential for therapeutic applications. This review delves into the core principles of PE and emphasizes its advancements, applications, and prospects. We begin with a brief introduction to PE principles, followed by a detailed examination of recent improvements in efficiency, precision, and the scale of feasible edits. These improvements have been made to the PE systems through guide RNA engineering, protein engineering, DNA repair pathway screening, chromosomal or epigenomic modification, and in silico design and optimization tools. Furthermore, we highlight in vivo studies showcasing the therapeutic potential of PE to model and treat genetic diseases. Moreover, we discuss PE's versatile applications in saturation genome editing and its applicability to nonhuman organisms. In conclusion, we address the challenges and opportunities linked with PE, emphasizing its profound impact on biological research and therapeutics.
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Affiliation(s)
- Hongzhi Zeng
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005, USA
| | - Tyler C Daniel
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005, USA
| | - Ananya Lingineni
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Kelly Chee
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Komal Talloo
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005, USA; Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Precision Engineering for Health, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Bonnycastle LL, Swift AJ, Mansell EC, Lee A, Winnicki E, Li ES, Robertson CC, Parsons VA, Huynh T, Krilow C, Mohlke KL, Erdos MR, Narisu N, Collins FS. Generation of Human Isogenic Induced Pluripotent Stem Cell Lines with CRISPR Prime Editing. CRISPR J 2024; 7:53-67. [PMID: 38353623 PMCID: PMC10880268 DOI: 10.1089/crispr.2023.0066] [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: 10/17/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
We developed an efficient CRISPR prime editing protocol and generated isogenic-induced pluripotent stem cell (iPSC) lines carrying heterozygous or homozygous alleles for putatively causal single nucleotide variants at six type 2 diabetes loci (ABCC8, MTNR1B, TCF7L2, HNF4A, CAMK1D, and GCK). Our two-step sequence-based approach to first identify transfected cell pools with the highest fraction of edited cells significantly reduced the downstream efforts to isolate single clones of edited cells. We found that prime editing can make targeted genetic changes in iPSC and optimization of system components and guide RNA designs that were critical to achieve acceptable efficiency. Systems utilizing PEmax, epegRNA modifications, and MLH1dn provided significant benefit, producing editing efficiencies of 36-73%. Editing success and pegRNA design optimization required for each variant differed depending on the sequence at the target site. With attention to design, prime editing is a promising approach to generate isogenic iPSC lines, enabling the study of specific genetic changes in a common genetic background.
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Affiliation(s)
- Lori L. Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Amy J. Swift
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Erin C. Mansell
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Angela Lee
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Elizabeth Winnicki
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Elizabeth S. Li
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Catherine C. Robertson
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Victoria A. Parsons
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Trung Huynh
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Chad Krilow
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Michael R. Erdos
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Francis S. Collins
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
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8
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Davis JR, Banskota S, Levy JM, Newby GA, Wang X, Anzalone AV, Nelson AT, Chen PJ, Hennes AD, An M, Roh H, Randolph PB, Musunuru K, Liu DR. Efficient prime editing in mouse brain, liver and heart with dual AAVs. Nat Biotechnol 2024; 42:253-264. [PMID: 37142705 PMCID: PMC10869272 DOI: 10.1038/s41587-023-01758-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/22/2023] [Indexed: 05/06/2023]
Abstract
Realizing the promise of prime editing for the study and treatment of genetic disorders requires efficient methods for delivering prime editors (PEs) in vivo. Here we describe the identification of bottlenecks limiting adeno-associated virus (AAV)-mediated prime editing in vivo and the development of AAV-PE vectors with increased PE expression, prime editing guide RNA stability and modulation of DNA repair. The resulting dual-AAV systems, v1em and v3em PE-AAV, enable therapeutically relevant prime editing in mouse brain (up to 42% efficiency in cortex), liver (up to 46%) and heart (up to 11%). We apply these systems to install putative protective mutations in vivo for Alzheimer's disease in astrocytes and for coronary artery disease in hepatocytes. In vivo prime editing with v3em PE-AAV caused no detectable off-target effects or significant changes in liver enzymes or histology. Optimized PE-AAV systems support the highest unenriched levels of in vivo prime editing reported to date, facilitating the study and potential treatment of diseases with a genetic component.
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Affiliation(s)
- Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - 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
| | - Jonathan M Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - 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
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew V Anzalone
- 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
| | - Andrew T Nelson
- 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
| | - Peter J 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
| | - Andrew D Hennes
- 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
| | - 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
| | - Heejin Roh
- 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
| | - Peyton B Randolph
- 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
| | - Kiran Musunuru
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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9
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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 2024:10.1038/s41587-023-02078-y. [PMID: 38191664 PMCID: PMC11228131 DOI: 10.1038/s41587-023-02078-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [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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10
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Yu X, Huo G, Yu J, Li H, Li J. Prime editing: Its systematic optimization and current applications in disease treatment and agricultural breeding. Int J Biol Macromol 2023; 253:127025. [PMID: 37769783 DOI: 10.1016/j.ijbiomac.2023.127025] [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: 08/16/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
Abstract
CRISPR/Cas-mediated genome-editing technology has accelerated the development of the life sciences. Prime editing has raised genome editing to a new level because it allows for all 12 types of base substitutions, targeted insertions and deletions, large DNA fragment integration, and even combinations of these edits without generating DNA double-strand breaks. This versatile and game-changing technology has successfully been applied to human cells and plants, and it currently plays important roles in basic research, gene therapy, and crop breeding. Although prime editing has substantially expanded the range of possibilities for genome editing, its efficiency requires improvement. In this review, we briefly introduce prime editing and highlight recent optimizations that have improved the efficiency of prime editors. We also describe how the dual-pegRNA strategy has expanded current editing capabilities, and we summarize the potential of prime editing in treating mammalian diseases and improving crop breeding. Finally, we discuss the limitations of current prime editors and future prospects for optimizing these editors.
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Affiliation(s)
- Xiaoxiao Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Guanzhong Huo
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Jintai Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; College of Modern Science and Technology, Hebei Agricultural University, Baoding, China
| | - Huiyuan Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jun Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
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11
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Fu Y, He X, Gao XD, Li F, Ge S, Yang Z, Fan X. Prime editing: current advances and therapeutic opportunities in human diseases. Sci Bull (Beijing) 2023; 68:3278-3291. [PMID: 37973465 DOI: 10.1016/j.scib.2023.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/06/2023] [Accepted: 10/28/2023] [Indexed: 11/19/2023]
Abstract
Gene editing ushers in a new era of disease treatment since many genetic diseases are caused by base-pair mutations in genomic DNA. With the rapid development of genome editing technology, novel editing tools such as base editing and prime editing (PE) have attracted public attention, heralding a great leap forward in this field. PE, in particular, is characterized by no need for double-strand breaks (DSBs) or homology sequence templates with variable application scenarios, including point mutations as well as insertions or deletions. With higher editing efficiency and fewer byproducts than traditional editing tools, PE holds great promise as a therapeutic strategy for human diseases. Subsequently, a growing demand for the standard construction of PE system has spawned numerous easy-to-access internet resources and tools for personalized prime editing guide RNA (pegRNA) design and off-target site prediction. In this review, we mainly introduce the innovation and evolutionary strategy of PE systems and the auxiliary tools for PE design and analysis. Additionally, its application and future potential in the clinical field have been summarized and envisaged.
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Affiliation(s)
- Yidian Fu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xiaoyu He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge MA 02138, USA
| | - Fang Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
| | - Zhi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
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12
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Han W, Qiu HY, Sun S, Fu ZC, Wang GQ, Qian X, Wang L, Zhai X, Wei J, Wang Y, Guo YL, Cao GH, Ji RJ, Zhang YZ, Ma H, Wang H, Zhao M, Wu J, Bi L, Chen QB, Li Z, Yu L, Mou X, Yin H, Yang L, Chen J, Yang B, Zhang Y. Base editing of the HBG promoter induces potent fetal hemoglobin expression with no detectable off-target mutations in human HSCs. Cell Stem Cell 2023; 30:1624-1639.e8. [PMID: 37989316 DOI: 10.1016/j.stem.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/13/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Reactivating silenced γ-globin expression through the disruption of repressive regulatory domains offers a therapeutic strategy for treating β-hemoglobinopathies. Here, we used transformer base editor (tBE), a recently developed cytosine base editor with no detectable off-target mutations, to disrupt transcription-factor-binding motifs in hematopoietic stem cells. By performing functional screening of six motifs with tBE, we found that directly disrupting the BCL11A-binding motif in HBG1/2 promoters triggered the highest γ-globin expression. Via a side-by-side comparison with other clinical and preclinical strategies using Cas9 nuclease or conventional BEs (ABE8e and hA3A-BE3), we found that tBE-mediated disruption of the BCL11A-binding motif at the HBG1/2 promoters triggered the highest fetal hemoglobin in healthy and β-thalassemia patient hematopoietic stem/progenitor cells while exhibiting no detectable DNA or RNA off-target mutations. Durable therapeutic editing by tBE persisted in repopulating hematopoietic stem cells, demonstrating that tBE-mediated editing in HBG1/2 promoters is a safe and effective strategy for treating β-hemoglobinopathies.
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Affiliation(s)
- Wenyan Han
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hou-Yuan Qiu
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Shangwu Sun
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Can Fu
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Quan Wang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Xiaowen Qian
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Lijie Wang
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Xiaowen Zhai
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jia Wei
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yichuan Wang
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Yi-Lin Guo
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Hua Cao
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Rui-Jin Ji
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yi-Zhou Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Hongxia Ma
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Hongsheng Wang
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Mingli Zhao
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lili Bi
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Qiu-Bing Chen
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Zifeng Li
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Ling Yu
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaodun Mou
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Hao Yin
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Department of Pathology and Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; TaiKang Centre for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China; State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Shanghai 200031, China.
| | - Bei Yang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Shanghai 200031, China.
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan University, Wuhan, China.
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13
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Han W, Gao BQ, Zhu J, He Z, Li J, Yang L, Chen J. Design and application of the transformer base editor in mammalian cells and mice. Nat Protoc 2023; 18:3194-3228. [PMID: 37794072 DOI: 10.1038/s41596-023-00877-w] [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: 12/17/2022] [Accepted: 06/21/2023] [Indexed: 10/06/2023]
Abstract
Fusing apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like cytidine deaminase with catalytically impaired Cas proteins (e.g., nCas9 or dCas9) provides a novel gene-editing technology, base editing, that grants targeted base substitutions with high efficiency. However, genome-wide and transcriptome-wide off-target mutations are observed in base editing, which raises safety concerns regarding therapeutic applications. Previously, we developed a new base editing system, the transformer base editor (tBE), to induce efficient editing with no observable genome-wide or transcriptome-wide off-target mutations both in mammalian cells and in mice. Here we describe a detailed protocol for the design and application of the tBE. Steps for designing single-guide RNA (sgRNA) and helper sgRNA pairs, making constructs, determining the genome-wide and transcriptome-wide off-target mutations, producing the tBE-containing adeno-associated viruses, delivering adeno-associated viruses into mice and examining the in vivo editing effects are included in this protocol. High-precision base editing by the tBE can be completed within 2-3 weeks (in mammalian cells) or within 6-8 weeks (in mice), with sgRNA-helper sgRNA pairs. The whole process can be collaboratively accomplished by researchers using standard techniques from molecular biology, bioinformatics and mouse husbandry.
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Affiliation(s)
- Wenyan Han
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Bao-Qing Gao
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Junjie Zhu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zongxing He
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jianfeng Li
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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14
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Xia K, Wang F, Tan Z, Zhang S, Lai X, Ou W, Yang C, Chen H, Peng H, Luo P, Hu A, Tu X, Wang T, Ke Q, Deng C, Xiang AP. Precise Correction of Lhcgr Mutation in Stem Leydig Cells by Prime Editing Rescues Hereditary Primary Hypogonadism in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300993. [PMID: 37697644 PMCID: PMC10582410 DOI: 10.1002/advs.202300993] [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: 02/13/2023] [Revised: 07/20/2023] [Indexed: 09/13/2023]
Abstract
Hereditary primary hypogonadism (HPH), caused by gene mutation related to testosterone synthesis in Leydig cells, usually impairs male sexual development and spermatogenesis. Genetically corrected stem Leydig cells (SLCs) transplantation may provide a new approach for treating HPH. Here, a novel nonsense-point-mutation mouse model (LhcgrW495X ) is first generated based on a gene mutation relative to HPH patients. To verify the efficacy and feasibility of SLCs transplantation in treating HPH, wild-type SLCs are transplanted into LhcgrW495X mice, in which SLCs obviously rescue HPH phenotypes. Through comparing several editing strategies, optimized PE2 protein (PEmax) system is identified as an efficient and precise approach to correct the pathogenic point mutation in Lhcgr. Furthermore, delivering intein-split PEmax system via lentivirus successfully corrects the mutation in SLCs from LhcgrW495X mice ex vivo. Gene-corrected SLCs from LhcgrW495X mice exert ability to differentiate into functional Leydig cells in vitro. Notably, the transplantation of gene-corrected SLCs effectively regenerates Leydig cells, recovers testosterone production, restarts sexual development, rescues spermatogenesis, and produces fertile offspring in LhcgrW495X mice. Altogether, these results suggest that PE-based gene editing in SLCs ex vivo is a promising strategy for HPH therapy and is potentially leveraged to address more hereditary diseases in reproductive system.
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Affiliation(s)
- Kai Xia
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Fulin Wang
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Zhipeng Tan
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Suyuan Zhang
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Xingqiang Lai
- Cardiovascular DepartmentThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdong518033China
| | - Wangsheng Ou
- State Key Laboratory of Ophthalmology Zhong Shan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouGuangdong510000China
| | - Cuifeng Yang
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Hong Chen
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Hao Peng
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Peng Luo
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Anqi Hu
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Xiang'an Tu
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Tao Wang
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Qiong Ke
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Chunhua Deng
- Department of Urology and AndrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education National‐Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510080China
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15
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Zhao W, Li J, Wang X, Xu W, Gao B, Xiang J, Hou Y, Liu W, Wu J, Qi Q, Wei J, Yang X, Lu L, Yang L, Chen J, Yang B. Prime editor-mediated functional reshaping of ACE2 prevents the entry of multiple human coronaviruses, including SARS-CoV-2 variants. MedComm (Beijing) 2023; 4:e356. [PMID: 37701533 PMCID: PMC10492923 DOI: 10.1002/mco2.356] [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: 03/14/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 09/14/2023] Open
Abstract
The spike protein of SARS-CoV-2 hijacks the host angiotensin converting enzyme 2 (ACE2) to meditate its entry and is the primary target for vaccine development. Nevertheless, SARS-CoV-2 keeps evolving and the latest Omicron subvariants BQ.1 and XBB have gained exceptional immune evasion potential through mutations in their spike proteins, leading to sharply reduced efficacy of current spike-focused vaccines and therapeutics. Compared with the fast-evolving spike protein, targeting host ACE2 offers an alternative antiviral strategy that is more resistant to viral evolution and can even provide broad prevention against SARS-CoV and HCoV-NL63. Here, we use prime editor (PE) to precisely edit ACE2 at structurally selected sites. We demonstrated that residue changes at Q24/D30/K31 and/or K353 of ACE2 could completely ablate the binding of tested viruses while maintaining its physiological role in host angiotensin II conversion. PE-mediated ACE2 editing at these sites suppressed the entry of pseudotyped SARS-CoV-2 major variants of concern and even SARS-CoV or HCoV-NL63. Moreover, it significantly inhibited the replication of the Delta variant live virus. Our work investigated the unexplored application potential of prime editing in high-risk infectious disease control and demonstrated that such gene editing-based host factor reshaping strategy can provide broad-spectrum antiviral activity and a high barrier to viral escape or resistance.
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Affiliation(s)
- Wenwen Zhao
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Gene Editing CenterSchool of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Clinical Research and Trial CenterShanghaiChina
| | - Jifang Li
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Gene Editing CenterSchool of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Clinical Research and Trial CenterShanghaiChina
| | - Xiao Wang
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Gene Editing CenterSchool of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghaiChina
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)School of Basic Medical SciencesFudan UniversityShanghaiChina
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan UniversityShanghaiChina
- Biosafety Level 3 LaboratoryShanghai Medical CollegeShanghai Frontiers Science Center of Pathogenic Microbes and InfectionFudan UniversityShanghaiChina
| | - Bao‐Qing Gao
- Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina
| | - Jiangchao Xiang
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Gene Editing CenterSchool of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Clinical Research and Trial CenterShanghaiChina
| | - Yaofeng Hou
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Clinical Research and Trial CenterShanghaiChina
| | - Wei Liu
- School of Physical Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Jing Wu
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Gene Editing CenterSchool of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Qilian Qi
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Jia Wei
- Center for Molecular MedicineChildren's HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Medical EpigeneticsInternational Laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyInstitutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Xiaoyu Yang
- School of Physical Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Li Yang
- Center for Molecular MedicineChildren's HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Medical EpigeneticsInternational Laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyInstitutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Jia Chen
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Gene Editing CenterSchool of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Clinical Research and Trial CenterShanghaiChina
- Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghaiChina
| | - Bei Yang
- Shanghai Frontiers Science Center for Biomacromolecules and Precision MedicineShanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Clinical Research and Trial CenterShanghaiChina
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16
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Choi EH, Suh S, Sears AE, Hołubowicz R, Kedhar SR, Browne AW, Palczewski K. Genome editing in the treatment of ocular diseases. Exp Mol Med 2023; 55:1678-1690. [PMID: 37524870 PMCID: PMC10474087 DOI: 10.1038/s12276-023-01057-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/14/2023] [Indexed: 08/02/2023] Open
Abstract
Genome-editing technologies have ushered in a new era in gene therapy, providing novel therapeutic strategies for a wide range of diseases, including both genetic and nongenetic ocular diseases. These technologies offer new hope for patients suffering from previously untreatable conditions. The unique anatomical and physiological features of the eye, including its immune-privileged status, size, and compartmentalized structure, provide an optimal environment for the application of these cutting-edge technologies. Moreover, the development of various delivery methods has facilitated the efficient and targeted administration of genome engineering tools designed to correct specific ocular tissues. Additionally, advancements in noninvasive ocular imaging techniques and electroretinography have enabled real-time monitoring of therapeutic efficacy and safety. Herein, we discuss the discovery and development of genome-editing technologies, their application to ocular diseases from the anterior segment to the posterior segment, current limitations encountered in translating these technologies into clinical practice, and ongoing research endeavors aimed at overcoming these challenges.
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Affiliation(s)
- Elliot H Choi
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Susie Suh
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Avery E Sears
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Rafał Hołubowicz
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Sanjay R Kedhar
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Andrew W Browne
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, 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.
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17
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Liang SQ, Liu P, Ponnienselvan K, Suresh S, Chen Z, Kramme C, Chatterjee P, Zhu LJ, Sontheimer EJ, Xue W, Wolfe SA. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat Methods 2023; 20:898-907. [PMID: 37156841 DOI: 10.1038/s41592-023-01859-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/17/2023] [Indexed: 05/10/2023]
Abstract
Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-cognate sequences. Here we describe a genome-wide approach for the identification of potential prime editor off-target sites, which we call PE-tag. This method relies on the attachment or insertion of an amplification tag at sites of prime editor activity to allow their identification. PE-tag enables genome-wide profiling of off-target sites in vitro using extracted genomic DNA, in mammalian cell lines and in the adult mouse liver. PE-tag components can be delivered in a variety of formats for off-target site detection. Our studies are consistent with the high specificity previously described for prime editor systems, but we find that off-target editing rates are influenced by prime editing guide RNA design. PE-tag represents an accessible, rapid and sensitive approach for the genome-wide identification of prime editor activity and the evaluation of prime editor safety.
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Affiliation(s)
- Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Karthikeyan Ponnienselvan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sneha Suresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Pranam Chatterjee
- Wyss Institute, Harvard Medical School, Boston, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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18
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Everette KA, Newby GA, Levine RM, Mayberry K, Jang Y, Mayuranathan T, Nimmagadda N, Dempsey E, Li Y, Bhoopalan SV, Liu X, Davis JR, Nelson AT, Chen PJ, Sousa AA, Cheng Y, Tisdale JF, Weiss MJ, Yen JS, Liu DR. Ex vivo prime editing of patient haematopoietic stem cells rescues sickle-cell disease phenotypes after engraftment in mice. Nat Biomed Eng 2023; 7:616-628. [PMID: 37069266 PMCID: PMC10195679 DOI: 10.1038/s41551-023-01026-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/22/2023] [Indexed: 04/19/2023]
Abstract
Sickle-cell disease (SCD) is caused by an A·T-to-T·A transversion mutation in the β-globin gene (HBB). Here we show that prime editing can correct the SCD allele (HBBS) to wild type (HBBA) at frequencies of 15%-41% in haematopoietic stem and progenitor cells (HSPCs) from patients with SCD. Seventeen weeks after transplantation into immunodeficient mice, prime-edited SCD HSPCs maintained HBBA levels and displayed engraftment frequencies, haematopoietic differentiation and lineage maturation similar to those of unedited HSPCs from healthy donors. An average of 42% of human erythroblasts and reticulocytes isolated 17 weeks after transplantation of prime-edited HSPCs from four SCD patient donors expressed HBBA, exceeding the levels predicted for therapeutic benefit. HSPC-derived erythrocytes carried less sickle haemoglobin, contained HBBA-derived adult haemoglobin at 28%-43% of normal levels and resisted hypoxia-induced sickling. Minimal off-target editing was detected at over 100 sites nominated experimentally via unbiased genome-wide analysis. Our findings support the feasibility of a one-time prime editing SCD treatment that corrects HBBS to HBBA, does not require any viral or non-viral DNA template and minimizes undesired consequences of DNA double-strand breaks.
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Affiliation(s)
- Kelcee A Everette
- 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
| | - 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
| | - Rachel M Levine
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kalin Mayberry
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yoonjeong Jang
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Nikitha Nimmagadda
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Erin Dempsey
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Xiong Liu
- Molecular and Clinical Hematology Branch, National Heart, Lung, and Blood Institute/National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessie R Davis
- 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
| | - Andrew T Nelson
- 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
| | - Peter J 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
| | - Alexander A Sousa
- 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
| | - Yong Cheng
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - John F Tisdale
- Molecular and Clinical Hematology Branch, National Heart, Lung, and Blood Institute/National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathan S Yen
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, 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.
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19
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Arif T, Farooq A, Ahmad FJ, Akhtar M, Choudhery MS. Prime editing: A potential treatment option for β-thalassemia. Cell Biol Int 2023; 47:699-713. [PMID: 36480796 DOI: 10.1002/cbin.11972] [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: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022]
Abstract
The potential to therapeutically alter the genome is one of the remarkable scientific developments in recent years. Genome editing technologies have provided an opportunity to precisely alter genomic sequence(s) in eukaryotic cells as a treatment option for various genetic disorders. These technologies allow the correction of harmful mutations in patients by precise nucleotide editing. Genome editing technologies such as CRISPR (clustered regularly interspaced short palindromic repeat) and base editors have greatly contributed to the practical applications of gene editing. However, these technologies have certain limitations, including imperfect editing, undesirable mutations, off-target effects, and lack of potential to simultaneously edit multiple loci. Recently, prime editing (PE) has emerged as a new gene editing technology with the potential to overcome the above-mentioned limitations. Interestingly, PE not only has higher specificity but also does not require double-strand breaks. In addition, a minimum possibility of potential off-target mutant sites makes PE a preferred choice for therapeutic gene editing. Furthermore, PE has the potential to introduce insertion and deletions of all 12 single-base mutations at target sequences. Considering its potential, PE has been applied as a treatment option for genetic diseases including hemoglobinopathies. β-Thalassemia, for example, one of the most significant blood disorders characterized by reduced levels of functional hemoglobin, could potentially be treated using PE. Therapeutic reactivation of the γ-globin gene in adult β-thalassemia patients through PE technology is considered a promising therapeutic strategy. The current review aims to briefly discuss the genome editing strategies and potential applications of PE for the treatment of β-thalassemia. In addition, the review will also focus on challenges associated with the use of PE.
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Affiliation(s)
- Taqdees Arif
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
| | - Aroosa Farooq
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
| | - Fridoon Jawad Ahmad
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
| | - Muhammad Akhtar
- School of Biological Sciences, University of Punjab Lahore, Lahore, Punjab, Pakistan
| | - Mahmood S Choudhery
- Department of Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Punjab, Pakistan
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20
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Jin S, Lin Q, Gao Q, Gao C. Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs). Nat Protoc 2023; 18:831-853. [PMID: 36434096 DOI: 10.1038/s41596-022-00773-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
Prime editors (PEs), which can install desired base edits without donor DNA or double-strand breaks, have been used in plants and can, in principle, accelerate crop improvement and breeding. However, their editing efficiency in plants is generally low. Optimizing the prime editing guide RNA (pegRNA) by designing the sequence on the basis of melting temperature, using dual-pegRNAs and engineering PEs have all been shown to enhance PE efficiency. In addition, an automated pegRNA design platform, PlantPegDesigner, has been developed on the basis of rice prime editing experimental data. In this protocol, we present detailed protocols for designing and optimizing pegRNAs using PlantPegDesigner, constructing engineered plant PE vectors with enhanced editing efficiency for prime editing, evaluating prime editing efficiencies using a reporter system and comparing the effectiveness and byproducts of PEs by deep amplicon sequencing. Using this protocol, researchers can construct optimized pegRNAs for prime editing in 4-7 d and obtain prime-edited rice or wheat plants within 3 months.
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Affiliation(s)
- Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- Qi Biodesign, Life Science Park, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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21
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Chen PJ, Liu DR. Prime editing for precise and highly versatile genome manipulation. Nat Rev Genet 2023; 24:161-177. [PMID: 36344749 PMCID: PMC10989687 DOI: 10.1038/s41576-022-00541-1] [Citation(s) in RCA: 131] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2022] [Indexed: 11/09/2022]
Abstract
Programmable gene-editing tools have transformed the life sciences and have shown potential for the treatment of genetic disease. Among the CRISPR-Cas technologies that can currently make targeted DNA changes in mammalian cells, prime editors offer an unusual combination of versatility, specificity and precision. Prime editors do not require double-strand DNA breaks and can make virtually any substitution, small insertion and small deletion within the DNA of living cells. Prime editing minimally requires a programmable nickase fused to a polymerase enzyme, and an extended guide RNA that both specifies the target site and templates the desired genome edit. In this Review, we summarize prime editing strategies to generate programmed genomic changes, highlight their limitations and recent developments that circumvent some of these bottlenecks, and discuss applications and future directions.
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Affiliation(s)
- Peter J 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 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.
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22
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Lei Z, Meng H, Zhuang Y, Zhu Q, Yi C. Chemical and Biological Approaches to Interrogate off-Target Effects of Genome Editing Tools. ACS Chem Biol 2023; 18:205-217. [PMID: 36731114 DOI: 10.1021/acschembio.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Various genome editing tools have been developed for programmable genome manipulation at specified genomic loci. However, it is crucial to comprehensively interrogate the off-target effect induced by these genome editing tools, especially when apply them onto the therapeutic applications. Here, we outlined the off-target effect that has been observed for various genome editing tools. We also reviewed detection methods to determine or evaluate the off-target editing, and we have discussed their advantages and limitations. Additionally, we have summarized current RNA editing tools for RNA therapy and medicine that may serve as alternative approaches for genome editing tools in both research and clinical applications.
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Affiliation(s)
- Zhixin Lei
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
| | - Yuan Zhuang
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing100871, China
| | - Qingguo Zhu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Chengqi Yi
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China.,Peking University Genome Editing Research Center, Peking University, Beijing100871, China
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23
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Brooks IR, Sheriff A, Moran D, Wang J, Jacków J. Challenges of Gene Editing Therapies for Genodermatoses. Int J Mol Sci 2023; 24:2298. [PMID: 36768619 PMCID: PMC9916788 DOI: 10.3390/ijms24032298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Genodermatoses encompass a wide range of inherited skin diseases, many of which are monogenic. Genodermatoses range in severity and result in early-onset cancers or life-threatening damage to the skin, and there are few curative options. As such, there is a clinical need for single-intervention treatments with curative potential. Here, we discuss the nascent field of gene editing for the treatment of genodermatoses, exploring CRISPR-Cas9 and homology-directed repair, base editing, and prime editing tools for correcting pathogenic mutations. We specifically focus on the optimisation of editing efficiency, the minimisation off-targets edits, and the tools for delivery for potential future therapies. Honing each of these factors is essential for translating gene editing therapies into the clinical setting. Therefore, the aim of this review article is to raise important considerations for investigators aiming to develop gene editing approaches for genodermatoses.
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Affiliation(s)
| | | | | | | | - Joanna Jacków
- St John’s Institute of Dermatology, King’s College London, London SE1 9RT, UK
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24
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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25
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Buffa V, Alvarez Vargas JR, Galy A, Spinozzi S, Rocca CJ. Hematopoietic stem and progenitors cells gene editing: Beyond blood disorders. Front Genome Ed 2023; 4:997142. [PMID: 36698790 PMCID: PMC9868335 DOI: 10.3389/fgeed.2022.997142] [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: 07/18/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
Lessons learned from decades-long practice in the transplantation of hematopoietic stem and progenitor cells (HSPCs) to treat severe inherited disorders or cancer, have set the stage for the current ex vivo gene therapies using autologous gene-modified hematopoietic stem and progenitor cells that have treated so far, hundreds of patients with monogenic disorders. With increased knowledge of hematopoietic stem and progenitor cell biology, improved modalities for patient conditioning and with the emergence of new gene editing technologies, a new era of hematopoietic stem and progenitor cell-based gene therapies is poised to emerge. Gene editing has the potential to restore physiological expression of a mutated gene, or to insert a functional gene in a precise locus with reduced off-target activity and toxicity. Advances in patient conditioning has reduced treatment toxicities and may improve the engraftment of gene-modified cells and specific progeny. Thanks to these improvements, new potential treatments of various blood- or immune disorders as well as other inherited diseases will continue to emerge. In the present review, the most recent advances in hematopoietic stem and progenitor cell gene editing will be reported, with a focus on how this approach could be a promising solution to treat non-blood-related inherited disorders and the mechanisms behind the therapeutic actions discussed.
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Affiliation(s)
- Valentina Buffa
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - José Roberto Alvarez Vargas
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Anne Galy
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Simone Spinozzi
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Céline J. Rocca
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France,*Correspondence: Céline J. Rocca,
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26
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Wang D, Fan X, Li M, Liu T, Lu P, Wang G, Li Y, Han J, Zhao J. Prime Editing in Mammals: The Next Generation of Precision Genome Editing. CRISPR J 2022; 5:746-768. [PMID: 36512351 DOI: 10.1089/crispr.2022.0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The recently established prime editor (PE) system is regarded as next-generation gene-editing technology. This methodology can install any base-to-base change as well as insertions and deletions without the requirement for double-stranded break formation or donor DNA templates; thus, it offers more targeting flexibility and greater editing precision than conventional CRISPR-Cas systems or base editors. In this study, we introduce the basic principles of PE and then review its most recent progress in terms of editing versatility, specificity, and efficiency in mammals. Next, we summarize key considerations regarding the selection of PE variants, prime editing guide RNA (pegRNA) design rules, and the efficiency and accuracy evaluation of PE. Finally, we highlight and discuss how PE can assist in a wide range of biological studies and how it can be applied to make precise genomic corrections in animal models, which paves the way for curing human diseases.
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Affiliation(s)
- Dawei Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiude Fan
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Mengzhu Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tianbo Liu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Peng Lu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Guangxin Wang
- Shandong Innovation Center of Intelligent Diagnosis, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yuan Li
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JunMing Han
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JiaJun Zhao
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
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Qiu HY, Ji RJ, Zhang Y. Current advances of CRISPR-Cas technology in cell therapy. CELL INSIGHT 2022; 1:100067. [PMID: 37193354 PMCID: PMC10120314 DOI: 10.1016/j.cellin.2022.100067] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 05/18/2023]
Abstract
CRISPR-Cas is a versatile genome editing technology that has been broadly applied in both basic research and translation medicine. Ever since its discovery, the bacterial derived endonucleases have been engineered to a collection of robust genome-editing tools for introducing frameshift mutations or base conversions at site-specific loci. Since the initiation of first-in-human trial in 2016, CRISPR-Cas has been tested in 57 cell therapy trials, 38 of which focusing on engineered CAR-T cells and TCR-T cells for cancer malignancies, 15 trials of engineered hematopoietic stem cells treating hemoglobinopathies, leukemia and AIDS, and 4 trials of engineered iPSCs for diabetes and cancer. Here, we aim to review the recent breakthroughs of CRISPR technology and highlight their applications in cell therapy.
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Affiliation(s)
- Hou-Yuan Qiu
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Rui-Jin Ji
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
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28
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CRISPR-Based Tools for Fighting Rare Diseases. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121968. [PMID: 36556333 PMCID: PMC9787644 DOI: 10.3390/life12121968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022]
Abstract
Rare diseases affect the life of a tremendous number of people globally. The CRISPR-Cas system emerged as a powerful genome engineering tool and has facilitated the comprehension of the mechanism and development of therapies for rare diseases. This review focuses on current efforts to develop the CRISPR-based toolbox for various rare disease therapy applications and compares the pros and cons of different tools and delivery methods. We further discuss the therapeutic applications of CRISPR-based tools for fighting different rare diseases.
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29
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Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat Commun 2022; 13:1669. [PMID: 35351879 PMCID: PMC8964725 DOI: 10.1038/s41467-022-29339-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractPrime editor (PE), which is developed by combining Cas9 nickase and an engineered reverse transcriptase, can mediate all twelve types of base substitutions and small insertions or deletions in living cells but its efficiency remains low. Here, we develop spegRNA by introducing same-sense mutations at proper positions in the reverse-transcription template of pegRNA to increase PE’s base-editing efficiency up-to 4,976-fold (on-average 353-fold). We also develop apegRNA by altering the pegRNA secondary structure to increase PE’s indel-editing efficiency up-to 10.6-fold (on-average 2.77-fold). The spegRNA and apegRNA can be combined to further enhance editing efficiency. When spegRNA and apegRNA are used in PE3 and PE5 systems, the efficiencies of sPE3, aPE3, sPE5 and aPE5 systems are all enhanced significantly. The strategies developed in this study realize highly efficient prime editing at certain previously uneditable sites.
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30
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Wang J, He Z, Wang G, Zhang R, Duan J, Gao P, Lei X, Qiu H, Zhang C, Zhang Y, Yin H. Efficient targeted insertion of large DNA fragments without DNA donors. Nat Methods 2022; 19:331-340. [PMID: 35228726 DOI: 10.1038/s41592-022-01399-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023]
Abstract
Targeted insertion of large DNA fragments holds great potential for treating genetic diseases. Prime editors can effectively insert short fragments (~44 bp) but not large ones. Here we developed GRAND editing to precisely insert large DNA fragments without DNA donors. In contrast to prime editors, which require reverse transcription templates hybridizing with the target sequence, GRAND editing employs a pair of prime editing guide RNAs, with reverse transcription templates nonhomologous to the target site but complementary to each other. This strategy exhibited an efficiency of up to 63.0% of a 150-bp insertion with minor by-products and 28.4% of a 250-bp insertion. It allowed insertions up to ~1 kb, although the efficiency remains low for fragments larger than 400 bp. We confirmed efficient insertion in multiple genomic loci of several cell lines and non-dividing cells, which expands the scope of genome editing to enable donor-free insertion of large DNA sequences.
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Affiliation(s)
- Jinlin Wang
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhou He
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guoquan Wang
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ruiwen Zhang
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Junyi Duan
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Pan Gao
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinlin Lei
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Houyuan Qiu
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Rheumatology and Immunology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chuanping Zhang
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Rheumatology and Immunology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ying Zhang
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Rheumatology and Immunology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Hao Yin
- Department of Urology, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University School of Pharmaceutical Sciences, Wuhan, China.
- RNA Institute, Wuhan University, Wuhan, China.
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.
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