1
|
Grass T, Dokuzluoglu Z, Buchner F, Rosignol I, Thomas J, Caldarelli A, Dalinskaya A, Becker J, Rost F, Marass M, Wirth B, Beyer M, Bonaguro L, Rodriguez-Muela N. Isogenic patient-derived organoids reveal early neurodevelopmental defects in spinal muscular atrophy initiation. Cell Rep Med 2024; 5:101659. [PMID: 39067446 DOI: 10.1016/j.xcrm.2024.101659] [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: 07/25/2023] [Revised: 02/26/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Whether neurodevelopmental defects underlie postnatal neuronal death in neurodegeneration is an intriguing hypothesis only recently explored. Here, we focus on spinal muscular atrophy (SMA), a neuromuscular disorder caused by reduced survival of motor neuron (SMN) protein levels leading to spinal motor neuron (MN) loss and muscle wasting. Using the first isogenic patient-derived induced pluripotent stem cell (iPSC) model and a spinal cord organoid (SCO) system, we show that SMA SCOs exhibit abnormal morphological development, reduced expression of early neural progenitor markers, and accelerated expression of MN progenitor and MN markers. Longitudinal single-cell RNA sequencing reveals marked defects in neural stem cell specification and fewer MNs, favoring mesodermal progenitors and muscle cells, a bias also seen in early SMA mouse embryos. Surprisingly, SMN2-to-SMN1 conversion does not fully reverse these developmental abnormalities. These suggest that early neurodevelopmental defects may underlie later MN degeneration, indicating that postnatal SMN-increasing interventions might not completely amend SMA pathology in all patients.
Collapse
Affiliation(s)
- Tobias Grass
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany.
| | - Zeynep Dokuzluoglu
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany
| | - Felix Buchner
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany
| | - Ines Rosignol
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany; Technische Universität Dresden (TUD), Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Joshua Thomas
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany
| | - Antonio Caldarelli
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany
| | - Anna Dalinskaya
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany
| | - Jutta Becker
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Fabian Rost
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering, TUD, Dresden, Germany
| | - Michele Marass
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Center for Rare Diseases, University Hospital of Cologne, Cologne, Germany
| | - Marc Beyer
- Systems Medicine, DZNE, Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE & University of Bonn and West German Genome Center, Bonn, Germany; Immunogenomics & Neurodegeneration, DZNE, Bonn, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, DZNE, Bonn, Germany; Genomics & Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Natalia Rodriguez-Muela
- German Center for Neurodegenerative Diseases e.V. (DZNE), Dresden, Germany; Technische Universität Dresden (TUD), Center for Regenerative Therapies Dresden, Dresden, Germany; Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
2
|
Zhao M, Cheng X, Chen L, Zeng YH, Lin KJ, Li YL, Zheng ZH, Huang XJ, Zuo DD, Guo XX, Guo J, He D, Liu Y, Lin Y, Wang C, Lv WQ, Su HZ, Yao XP, Ye ZL, Chen XH, Lu YQ, Huang CW, Yang G, Zhang YX, Lin MT, Wang N, Xiong ZQ, Chen WJ. Antisense oligonucleotides enhance SLC20A2 expression and suppress brain calcification in a humanized mouse model. Neuron 2024:S0896-6273(24)00535-X. [PMID: 39121859 DOI: 10.1016/j.neuron.2024.07.013] [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: 07/18/2023] [Revised: 05/15/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024]
Abstract
Primary familial brain calcification (PFBC) is a genetic neurological disease, yet no effective treatment is currently available. Here, we identified five novel intronic variants in SLC20A2 gene from six PFBC families. Three of these variants increased aberrant SLC20A2 pre-mRNA splicing by altering the binding affinity of splicing machineries to newly characterized cryptic exons, ultimately causing premature termination of SLC20A2 translation. Inhibiting the cryptic-exon incorporation with splice-switching ASOs increased the expression levels of functional SLC20A2 in cells carrying SLC20A2 mutations. Moreover, by knocking in a humanized SLC20A2 intron 2 sequence carrying a PFBC-associated intronic variant, the SLC20A2-KI mice exhibited increased inorganic phosphate (Pi) levels in cerebrospinal fluid (CSF) and progressive brain calcification. Intracerebroventricular administration of ASOs to these SLC20A2-KI mice reduced CSF Pi levels and suppressed brain calcification. Together, our findings expand the genetic etiology of PFBC and demonstrate ASO-mediated splice modulation as a potential therapy for PFBC patients with SLC20A2 haploinsufficiency.
Collapse
Affiliation(s)
- Miao Zhao
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Xuewen Cheng
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Lin Gang Laboratory, Shanghai 201602, China.
| | - Lei Chen
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Heng Zeng
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Kai-Jun Lin
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Yun-Lu Li
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Ze-Hong Zheng
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xue-Jing Huang
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Dan-Dan Zuo
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xin-Xin Guo
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Jun Guo
- Department of Neurology, Tangdu Hospital, Air Force Medical University, Xi'an 710038, China
| | - Dian He
- Department of Neurology, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, China
| | - Ying Liu
- Department of Neurology, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, China
| | - Yu Lin
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Chong Wang
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Wen-Qi Lv
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Hui-Zhen Su
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Xiang-Ping Yao
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Zi-Ling Ye
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xiao-Hong Chen
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Ying-Qian Lu
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Chen-Wei Huang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yu-Xian Zhang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min-Ting Lin
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Ning Wang
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Zhi-Qi Xiong
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-inspired Technology, Shanghai 201602, China.
| | - Wan-Jin Chen
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China.
| |
Collapse
|
3
|
Masarwy R, Stotsky-Oterin L, Elisha A, Hazan-Halevy I, Peer D. Delivery of nucleic acid based genome editing platforms via lipid nanoparticles: Clinical applications. Adv Drug Deliv Rev 2024; 211:115359. [PMID: 38857763 DOI: 10.1016/j.addr.2024.115359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
CRISPR/Cas technology presents a promising approach for treating a wide range of diseases, including cancer and genetic disorders. Despite its potential, the translation of CRISPR/Cas into effective in-vivo gene therapy encounters challenges, primarily due to the need for safe and efficient delivery mechanisms. Lipid nanoparticles (LNPs), FDA-approved for RNA delivery, show potential for delivering also CRISPR/Cas, offering the capability to efficiently encapsulate large mRNA molecules with single guide RNAs. However, achieving precise targeting in-vivo remains a significant obstacle, necessitating further research into optimizing LNP formulations. Strategies to enhance specificity, such as modifying LNP structures and incorporating targeting ligands, are explored to improve organ and cell type targeting. Furthermore, the development of base and prime editing technology presents a potential breakthrough, offering precise modifications without generating double-strand breaks (DSBs). Prime editing, particularly when delivered via targeted LNPs, holds promise for treating diverse diseases safely and precisely. This review assesses both the progress made and the persistent challenges faced in using LNP-encapsulated CRISPR-based technologies for therapeutic purposes, with a particular focus on clinical translation.
Collapse
Affiliation(s)
- Razan Masarwy
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel; School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lior Stotsky-Oterin
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Aviad Elisha
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel; School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Inbal Hazan-Halevy
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
| | - Dan Peer
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
4
|
Gao J, Gunasekar S, Xia ZJ, Shalin K, Jiang C, Chen H, Lee D, Lee S, Pisal ND, Luo JN, Griciuc A, Karp JM, Tanzi R, Joshi N. Gene therapy for CNS disorders: modalities, delivery and translational challenges. Nat Rev Neurosci 2024; 25:553-572. [PMID: 38898231 DOI: 10.1038/s41583-024-00829-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Gene therapy is emerging as a powerful tool to modulate abnormal gene expression, a hallmark of most CNS disorders. The transformative potentials of recently approved gene therapies for the treatment of spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and active cerebral adrenoleukodystrophy are encouraging further development of this approach. However, most attempts to translate gene therapy to the clinic have failed to make it to market. There is an urgent need not only to tailor the genes that are targeted to the pathology of interest but to also address delivery challenges and thereby maximize the utility of genetic tools. In this Review, we provide an overview of gene therapy modalities for CNS diseases, emphasizing the interconnectedness of different delivery strategies and routes of administration. Important gaps in understanding that could accelerate the clinical translatability of CNS genetic interventions are addressed, and we present lessons learned from failed clinical trials that may guide the future development of gene therapies for the treatment and management of CNS disorders.
Collapse
Affiliation(s)
- Jingjing Gao
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA.
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
| | - Swetharajan Gunasekar
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziting Judy Xia
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kiruba Shalin
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Christopher Jiang
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hao Chen
- Marine College, Shandong University, Weihai, China
| | - Dongtak Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sohyung Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nishkal D Pisal
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - James N Luo
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Ana Griciuc
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Jeffrey M Karp
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Rudolph Tanzi
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Nitin Joshi
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
5
|
Leandro K, Rufino-Ramos D, Breyne K, Di Ianni E, Lopes SM, Jorge Nobre R, Kleinstiver BP, Perdigão PRL, Breakefield XO, Pereira de Almeida L. Exploring the potential of cell-derived vesicles for transient delivery of gene editing payloads. Adv Drug Deliv Rev 2024; 211:115346. [PMID: 38849005 DOI: 10.1016/j.addr.2024.115346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024]
Abstract
Gene editing technologies have the potential to correct genetic disorders by modifying, inserting, or deleting specific DNA sequences or genes, paving the way for a new class of genetic therapies. While gene editing tools continue to be improved to increase their precision and efficiency, the limited efficacy of in vivo delivery remains a major hurdle for clinical use. An ideal delivery vehicle should be able to target a sufficient number of diseased cells in a transient time window to maximize on-target editing and mitigate off-target events and immunogenicity. Here, we review major advances in novel delivery platforms based on cell-derived vesicles - extracellular vesicles and virus-like particles - for transient delivery of gene editing payloads. We discuss major findings regarding packaging, in vivo biodistribution, therapeutic efficacy, and safety concerns of cell-derived vesicles delivery of gene editing cargos and their potential for clinical translation.
Collapse
Affiliation(s)
- Kevin Leandro
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal
| | - David Rufino-Ramos
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Emilio Di Ianni
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Sara M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Rui Jorge Nobre
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; ViraVector - Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra 3004-504, Portugal
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Pedro R L Perdigão
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Luís Pereira de Almeida
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; ViraVector - Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra 3004-504, Portugal.
| |
Collapse
|
6
|
Hatanaka F, Suzuki K, Shojima K, Yu J, Takahashi Y, Sakamoto A, Prieto J, Shokhirev M, Nuñez Delicado E, Rodriguez Esteban C, Izpisua Belmonte JC. Therapeutic strategy for spinal muscular atrophy by combining gene supplementation and genome editing. Nat Commun 2024; 15:6191. [PMID: 39048567 PMCID: PMC11269569 DOI: 10.1038/s41467-024-50095-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
Defect in the SMN1 gene causes spinal muscular atrophy (SMA), which shows loss of motor neurons, muscle weakness and atrophy. While current treatment strategies, including small molecules or viral vectors, have shown promise in improving motor function and survival, achieving a definitive and long-term correction of SMA's endogenous mutations and phenotypes remains highly challenging. We have previously developed a CRISPR-Cas9 based homology-independent targeted integration (HITI) strategy, enabling unidirectional DNA knock-in in both dividing and non-dividing cells in vivo. In this study, we demonstrated its utility by correcting an SMA mutation in mice. When combined with Smn1 cDNA supplementation, it exhibited long-term therapeutic benefits in SMA mice. Our observations may provide new avenues for the long-term and efficient treatment of inherited diseases.
Collapse
Affiliation(s)
- Fumiyuki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA
| | - Keiichiro Suzuki
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 560-8531, Japan
- Graduate School of Engineering Science, Osaka University, Osaka, 560-8531, Japan
- Graduate School of Frontier Bioscience, Osaka University, Osaka, 565-0871, Japan
| | - Kensaku Shojima
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of General Internal Medicine, Hyogo Medical University School of Medicine, Hyogo, 663-8131, Japan
| | - Jingting Yu
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA
| | - Akihisa Sakamoto
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Javier Prieto
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Maxim Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Estrella Nuñez Delicado
- Universidad Catolica, San Antonio de Murcia, Campus de los Jeronimos, 135, 30107, Guadalupe, Spain
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA.
| |
Collapse
|
7
|
Shirguppe S, Gapinske M, Swami D, Gosstola N, Acharya P, Miskalis A, Joulani D, Szkwarek MG, Bhattacharjee A, Elias G, Stilger M, Winter J, Woods WS, Anand D, Lim CKW, Gaj T, Perez-Pinera P. In vivo CRISPR base editing for treatment of Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602282. [PMID: 39005280 PMCID: PMC11245100 DOI: 10.1101/2024.07.05.602282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Huntington's disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons. Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies for preventing this process hold potential for treating the disorder. By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuated striatal and cortical atrophy. Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.
Collapse
|
8
|
Lian M, Chen T, Chen M, Peng X, Yang Y, Luo X, Chi Y, Wang J, Tang C, Zhou X, Zhang K, Qin C, Lai L, Zhou J, Zou Q. A modified glycosylase base editor without predictable DNA off-target effects. FEBS Lett 2024. [PMID: 38946058 DOI: 10.1002/1873-3468.14970] [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: 10/24/2023] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
Glycosylase base editor (GBE) can induce C-to-G transversion in mammalian cells, showing great promise for the treatment of human genetic disorders. However, the limited efficiency of transversion and the possibility of off-target effects caused by Cas9 restrict its potential clinical applications. In our recent study, we have successfully developed TaC9-CBE and TaC9-ABE by separating nCas9 and deaminase, which eliminates the Cas9-dependent DNA off-target effects without compromising editing efficiency. We developed a novel GBE called TaC9-GBEYE1, which utilizes the deaminase and UNG-nCas9 guided by TALE and sgRNA, respectively. TaC9-GBEYE1 showed comparable levels of on-target editing efficiency to traditional GBE at 19 target sites, without any off-target effects caused by Cas9 or TALE. The TaC9-GBEYE1 is a safe tool for gene therapy.
Collapse
Affiliation(s)
- Meng Lian
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Research Unit of Generation of Large Animal Disease Models, Guangzhou, China
| | - Tao Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaohua Peng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yang Yang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xian Luo
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yue Chi
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Jinling Wang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaoqing Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Kun Zhang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liangxue Lai
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Research Unit of Generation of Large Animal Disease Models, Guangzhou, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jizeng Zhou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| |
Collapse
|
9
|
Peng X, Chi Y, Wang J, Li S, Liu Y, Tang C, Zhou X, Lu X, Gao Y, Lai L, Chen M, Zou Q. Improvement of TaC9-ABE mediated correction of human SMN2 gene. Biotechnol Bioeng 2024. [PMID: 38923503 DOI: 10.1002/bit.28780] [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: 02/06/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
Spinal muscular atrophy (SMA) is a devastating neuromuscular disease caused by mutations in the survival motor neuron 1 (SMN1) gene. Gene editing technology repairs the conversion of the 6th base T to C in exon 7 of the paralogous SMN2 gene, compensating for the SMN protein expression and promoting the survival and function of motor neurons. However, low editing efficiency and unintended off-target effects limit the application of this technology. Here, we optimized a TaC9-adenine base editor (ABE) system by combining Cas9 nickase with the transcription activator-like effector (TALE)-adenosine deaminase fusion protein to effectively and precisely edit SMN2 without detectable Cas9 dependent off-target effects in human cell lines. We also generated human SMA-induced pluripotent stem cells (SMA-iPSCs) through the mutation of the splice acceptor or deletion of the exon 7 of SMN1. TaC9-R10 induced 45% SMN2 T6 > C conversion in the SMA-iPSCs. The SMN2 T6 > C splice-corrected SMA-iPSCs were directionally differentiated into motor neurons, exhibiting SMN protein recovery and antiapoptosis ability. Therefore, the TaC9-ABE system with dual guides from the combination of Cas9 with TALE could be a potential therapeutic strategy for SMA with high efficacy and safety.
Collapse
Affiliation(s)
- Xiaohua Peng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Yue Chi
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Jinling Wang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Shuangpeng Li
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | | | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Xiaoqing Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Xuan Lu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Yue Gao
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| |
Collapse
|
10
|
Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
Collapse
Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| |
Collapse
|
11
|
Leow DMK, Ng YK, Wang LC, Koh HW, Zhao T, Khong ZJ, Tabaglio T, Narayanan G, Giadone RM, Sobota RM, Ng SY, Teo AKK, Parson SH, Rubin LL, Ong WY, Darras BT, Yeo CJ. Hepatocyte-intrinsic SMN deficiency drives metabolic dysfunction and liver steatosis in spinal muscular atrophy. J Clin Invest 2024; 134:e173702. [PMID: 38722695 PMCID: PMC11178536 DOI: 10.1172/jci173702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/25/2024] [Indexed: 06/18/2024] Open
Abstract
Spinal Muscular Atrophy (SMA) is typically characterized as a motor neuron disease, but extra-neuronal phenotypes are present in almost every organ in severely affected patients and animal models. Extra-neuronal phenotypes were previously underappreciated as patients with severe SMA phenotypes usually died in infancy; however, with current treatments for motor neurons increasing patient lifespan, impaired function of peripheral organs may develop into significant future comorbidities and lead to new treatment-modified phenotypes. Fatty liver is seen in SMA animal models , but generalizability to patients and whether this is due to hepatocyte-intrinsic Survival Motor Neuron (SMN) protein deficiency and/or subsequent to skeletal muscle denervation is unknown. If liver pathology in SMA is SMN-dependent and hepatocyte-intrinsic, this suggests SMN repleting therapies must target extra-neuronal tissues and motor neurons for optimal patient outcome. Here we showed that fatty liver is present in SMA and that SMA patient-specific iHeps were susceptible to steatosis. Using proteomics, functional studies and CRISPR/Cas9 gene editing, we confirmed that fatty liver in SMA is a primary SMN-dependent hepatocyte-intrinsic liver defect associated with mitochondrial and other hepatic metabolism implications. These pathologies require monitoring and indicate need for systematic clinical surveillance and additional and/or combinatorial therapies to ensure continued SMA patient health.
Collapse
Affiliation(s)
- Damien Meng-Kiat Leow
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yang Kai Ng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | - Loo Chien Wang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | - Hiromi W.L. Koh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | - Zi Jian Khong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | | | - Richard M. Giadone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge Massachusetts, USA
| | - Radoslaw M. Sobota
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | - Shi-Yan Ng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
- National Neuroscience Institute, Singapore, Singapore
| | - Adrian Kee Keong Teo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
| | - Simon H. Parson
- Institute of Education in Healthcare and Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland
| | - Lee L. Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge Massachusetts, USA
| | - Wei-Yi Ong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Basil T. Darras
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Crystal J.J. Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- National Neuroscience Institute, Singapore, Singapore
- Institute of Education in Healthcare and Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
12
|
Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Bhat V, Lettre G, Ascher DB, Cassa CA, Sherwood RI, Pinello L. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nat Genet 2024; 56:925-937. [PMID: 38658794 DOI: 10.1038/s41588-024-01726-6] [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: 09/07/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
CRISPR base editing screens enable analysis of disease-associated variants at scale; however, variable efficiency and precision confounds the assessment of variant-induced phenotypes. Here, we provide an integrated experimental and computational pipeline that improves estimation of variant effects in base editing screens. We use a reporter construct to measure guide RNA (gRNA) editing outcomes alongside their phenotypic consequences and introduce base editor screen analysis with activity normalization (BEAN), a Bayesian network that uses per-guide editing outcomes provided by the reporter and target site chromatin accessibility to estimate variant impacts. BEAN outperforms existing tools in variant effect quantification. We use BEAN to pinpoint common regulatory variants that alter low-density lipoprotein (LDL) uptake, implicating previously unreported genes. Additionally, through saturation base editing of LDLR, we accurately quantify missense variant pathogenicity that is consistent with measurements in UK Biobank patients and identify underlying structural mechanisms. This work provides a widely applicable approach to improve the power of base editing screens for disease-associated variant characterization.
Collapse
Affiliation(s)
- Jayoung Ryu
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sam Barkal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Jankowiak
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yunzhuo Zhou
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matthew Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Quang Vinh Phan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhijian Li
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Manuel Tognon
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Computer Science Department, University of Verona, Verona, Italy
| | - Lara Brown
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael I Love
- Department of Genetics, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineel Bhat
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Quebec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Christopher A Cassa
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Luca Pinello
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
13
|
Pozzobon M, Bean C. Mitochondria replacement from transplanted amniotic fluid stem cells: a promising therapy for non-neuronal defects in spinal muscular atrophy. Neural Regen Res 2024; 19:971-972. [PMID: 37862193 PMCID: PMC10749600 DOI: 10.4103/1673-5374.385304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 10/22/2023] Open
Affiliation(s)
- Michela Pozzobon
- Women’s and Children’s Health Department, University of Padova; Foundation Institute of Pediatric Research Città della Speranza, Padova, Italy
| | - Camilla Bean
- Women’s and Children’s Health Department, University of Padova; Foundation Institute of Pediatric Research Città della Speranza, Padova, Italy
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Chrzanowski S, Batra R. CRISPR-Based Gene Editing Techniques in Pediatric Neurological Disorders. Pediatr Neurol 2024; 153:166-174. [PMID: 38394831 DOI: 10.1016/j.pediatrneurol.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
The emergence of gene editing technologies offers a unique opportunity to develop mutation-specific treatments for pediatric neurological disorders. Gene editing systems can potentially alter disease trajectory by correcting dysfunctional mutations or therapeutically altering gene expression. Clustered regularly interspaced short palindromic repeats (CRISPR)-based approaches are attractive gene therapy platforms to personalize treatments because of their specificity, ease of design, versatility, and cost. However, many such approaches remain in the early stages of development, with ongoing efforts to optimize editing efficiency, minimize unintended off-target effects, and mitigate pathologic immune responses. Given the rapid evolution of CRISPR-based therapies, it is prudent for the clinically based child neurologist to have a conceptual understanding of what such therapies may entail, including both benefits and risks and how such therapies may be clinically applied. In this review, we describe the fundamentals of CRISPR-based therapies, discuss the opportunities and challenges that have arisen, and highlight preclinical work in several pediatric neurological diseases.
Collapse
Affiliation(s)
- Stephen Chrzanowski
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts.
| | | |
Collapse
|
16
|
Lazzarotto CR, Katta V, Li Y, Urbina E, Lee G, Tsai SQ. CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of base editor genome-wide activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.586621. [PMID: 38585919 PMCID: PMC10996588 DOI: 10.1101/2024.03.28.586621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Base editors ( BE ) enable programmable conversion of nucleotides in genomic DNA without double-stranded breaks and have substantial promise to become new transformative genome editing medicines. Sensitive and unbiased detection of base editor off-target effects is important for identifying safety risks unique to base editors and translation to human therapeutics, as well as accurate use in life sciences research. However, current methods for understanding the global activities of base editors have limitations in terms of sensitivity or bias. Here we present CHANGE-seq-BE, a novel method to directly assess the off-target profile of base editors that is simultaneously sensitive and unbiased. CHANGE-seq-BE is based on the principle of selective sequencing of adenine base editor modified genomic DNA in vitro , and provides an accessible, rapid, and comprehensive method for identifying genome-wide off-target mutations of base editors.
Collapse
|
17
|
Qi J, Yang S, Jiang Y, Cheng J, Wang S, Rao Q, Jiang X. Liquid Metal-Polymer Conductor-Based Conformal Cyborg Devices. Chem Rev 2024; 124:2081-2137. [PMID: 38393351 DOI: 10.1021/acs.chemrev.3c00317] [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: 02/25/2024]
Abstract
Gallium-based liquid metal (LM) exhibits exceptional properties such as high conductivity and biocompatibility, rendering it highly valuable for the development of conformal bioelectronics. When combined with polymers, liquid metal-polymer conductors (MPC) offer a versatile platform for fabricating conformal cyborg devices, enabling functions such as sensing, restoration, and augmentation within the human body. This review focuses on the synthesis, fabrication, and application of MPC-based cyborg devices. The synthesis of functional materials based on LM and the fabrication techniques for MPC-based devices are elucidated. The review provides a comprehensive overview of MPC-based cyborg devices, encompassing their applications in sensing diverse signals, therapeutic interventions, and augmentation. The objective of this review is to serve as a valuable resource that bridges the gap between the fabrication of MPC-based conformal devices and their potential biomedical applications.
Collapse
Affiliation(s)
- Jie Qi
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering. Southern University of Science and Technology, No. 1088, Xueyuan Rd, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 511436, P. R. China
| | - Shuaijian Yang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering. Southern University of Science and Technology, No. 1088, Xueyuan Rd, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Yizhou Jiang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering. Southern University of Science and Technology, No. 1088, Xueyuan Rd, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, P. R. China
| | - Jinhao Cheng
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering. Southern University of Science and Technology, No. 1088, Xueyuan Rd, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Saijie Wang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering. Southern University of Science and Technology, No. 1088, Xueyuan Rd, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Qingyan Rao
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering. Southern University of Science and Technology, No. 1088, Xueyuan Rd, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering. Southern University of Science and Technology, No. 1088, Xueyuan Rd, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| |
Collapse
|
18
|
Xu F, Zheng C, Xu W, Zhang S, Liu S, Chen X, Yao K. Breaking genetic shackles: The advance of base editing in genetic disorder treatment. Front Pharmacol 2024; 15:1364135. [PMID: 38510648 PMCID: PMC10953296 DOI: 10.3389/fphar.2024.1364135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The rapid evolution of gene editing technology has markedly improved the outlook for treating genetic diseases. Base editing, recognized as an exceptionally precise genetic modification tool, is emerging as a focus in the realm of genetic disease therapy. We provide a comprehensive overview of the fundamental principles and delivery methods of cytosine base editors (CBE), adenine base editors (ABE), and RNA base editors, with a particular focus on their applications and recent research advances in the treatment of genetic diseases. We have also explored the potential challenges faced by base editing technology in treatment, including aspects such as targeting specificity, safety, and efficacy, and have enumerated a series of possible solutions to propel the clinical translation of base editing technology. In conclusion, this article not only underscores the present state of base editing technology but also envisions its tremendous potential in the future, providing a novel perspective on the treatment of genetic diseases. It underscores the vast potential of base editing technology in the realm of genetic medicine, providing support for the progression of gene medicine and the development of innovative approaches to genetic disease therapy.
Collapse
Affiliation(s)
- Fang Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Caiyan Zheng
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Weihui Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shiyao Zhang
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shanshan Liu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaopeng Chen
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| |
Collapse
|
19
|
Xu R, Treeby BE, Martin E. Safety Review of Therapeutic Ultrasound for Spinal Cord Neuromodulation and Blood-Spinal Cord Barrier Opening. ULTRASOUND IN MEDICINE & BIOLOGY 2024; 50:317-331. [PMID: 38182491 DOI: 10.1016/j.ultrasmedbio.2023.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 01/07/2024]
Abstract
New focused ultrasound spinal cord applications have emerged, particularly those improving therapeutic agent delivery to the spinal cord via blood-spinal cord barrier opening and the neuromodulation of spinal cord tracts. One hurdle in the development of these applications is safety. It may be possible to use safety trends from seminal and subsequent works in focused ultrasound to guide the development of safety guidelines for spinal cord applications. We collated data from decades of pre-clinical studies and illustrate a clear relationship between damage, time-averaged spatial peak intensity and exposure duration. This relationship suggests a thermal mechanism underlies ultrasound-induced spinal cord damage. We developed minimum and mean thresholds for damage from these pre-clinical studies. When these thresholds were plotted against the parameters used in recent pre-clinical ultrasonic spinal cord neuromodulation studies, the majority of the neuromodulation studies were near or above the minimum threshold. This suggests that a thermal neuromodulatory effect may exist for ultrasonic spinal cord neuromodulation, and that the thermal dose must be carefully controlled to avoid damage to the spinal cord. By contrast, the intensity-exposure duration threshold had no predictive value when applied to blood-spinal cord barrier opening studies that employed injected contrast agents. Most blood-spinal cord barrier opening studies observed slight to severe damage, except for small animal studies that employed an active feedback control method to limit pressures based on measured bubble oscillation behavior. The development of new focused ultrasound spinal cord applications perhaps reflects the recent success in the development of focused ultrasound brain applications, and recent work has begun on the translation of these technologies from brain to spinal cord. However, a great deal of work remains to be done, particularly with respect to developing and accepting safety standards for these applications.
Collapse
Affiliation(s)
- Rui Xu
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK.
| | - Bradley E Treeby
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Eleanor Martin
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| |
Collapse
|
20
|
Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
Collapse
Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| |
Collapse
|
21
|
Sharma G, Paganin M, Lauria F, Perenthaler E, Viero G. The SMN-ribosome interplay: a new opportunity for Spinal Muscular Atrophy therapies. Biochem Soc Trans 2024; 52:465-479. [PMID: 38391004 PMCID: PMC10903476 DOI: 10.1042/bst20231116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The underlying cause of Spinal Muscular Atrophy (SMA) is in the reduction of survival motor neuron (SMN) protein levels due to mutations in the SMN1 gene. The specific effects of SMN protein loss and the resulting pathological alterations are not fully understood. Given the crucial roles of the SMN protein in snRNP biogenesis and its interactions with ribosomes and translation-related proteins and mRNAs, a decrease in SMN levels below a specific threshold in SMA is expected to affect translational control of gene expression. This review covers both direct and indirect SMN interactions across various translation-related cellular compartments and processes, spanning from ribosome biogenesis to local translation and beyond. Additionally, it aims to outline deficiencies and alterations in translation observed in SMA models and patients, while also discussing the implications of the relationship between SMN protein and the translation machinery within the context of current and future therapies.
Collapse
|
22
|
Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
Collapse
Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
23
|
Zhang E, Neugebauer ME, Krasnow NA, Liu DR. Phage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference. Nat Commun 2024; 15:1697. [PMID: 38402281 PMCID: PMC10894238 DOI: 10.1038/s41467-024-45969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 02/26/2024] Open
Abstract
TadA-derived cytosine base editors (TadCBEs) enable programmable C•G-to-T•A editing while retaining the small size, high on-target activity, and low off-target activity of TadA deaminases. Existing TadCBEs, however, exhibit residual A•T-to-G•C editing at certain positions and lower editing efficiencies at some sequence contexts and with non-SpCas9 targeting domains. To address these limitations, we use phage-assisted evolution to evolve CBE6s from a TadA-mediated dual cytosine and adenine base editor, discovering mutations at N46 and Y73 in TadA that prevent A•T-to-G•C editing and improve C•G-to-T•A editing with expanded sequence-context compatibility, respectively. In E. coli, CBE6 variants offer high C•G-to-T•A editing and no detected A•T-to-G•C editing in any sequence context. In human cells, CBE6 variants exhibit broad Cas domain compatibility and retain low off-target editing despite exceeding BE4max and previous TadCBEs in on-target editing efficiency. Finally, we show that the high selectivity of CBE6 variants is well-suited for therapeutically relevant stop codon installation without creating unwanted missense mutations from residual A•T-to-G•C editing.
Collapse
Affiliation(s)
- Emily Zhang
- 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
| | - Monica E Neugebauer
- 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
| | - Nicholas A Krasnow
- 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
| | - 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.
| |
Collapse
|
24
|
Alves CRR, Ha LL, Yaworski R, Sutton ER, Lazzarotto CR, Christie KA, Reilly A, Beauvais A, Doll RM, de la Cruz D, Maguire CA, Swoboda KJ, Tsai SQ, Kothary R, Kleinstiver BP. Optimization of base editors for the functional correction of SMN2 as a treatment for spinal muscular atrophy. Nat Biomed Eng 2024; 8:118-131. [PMID: 38057426 PMCID: PMC10922509 DOI: 10.1038/s41551-023-01132-z] [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: 01/21/2023] [Accepted: 10/12/2023] [Indexed: 12/08/2023]
Abstract
Spinal muscular atrophy (SMA) is caused by mutations in SMN1. SMN2 is a paralogous gene with a C•G-to-T•A transition in exon 7, which causes this exon to be skipped in most SMN2 transcripts, and results in low levels of the protein survival motor neuron (SMN). Here we show, in fibroblasts derived from patients with SMA and in a mouse model of SMA that, irrespective of the mutations in SMN1, adenosine base editors can be optimized to target the SMN2 exon-7 mutation or nearby regulatory elements to restore the normal expression of SMN. After optimizing and testing more than 100 guide RNAs and base editors, and leveraging Cas9 variants with high editing fidelity that are tolerant of different protospacer-adjacent motifs, we achieved the reversion of the exon-7 mutation via an A•T-to-G•C edit in up to 99% of fibroblasts, with concomitant increases in the levels of the SMN2 exon-7 transcript and of SMN. Targeting the SMN2 exon-7 mutation via base editing or other CRISPR-based methods may provide long-lasting outcomes to patients with SMA.
Collapse
Affiliation(s)
- Christiano R R Alves
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Neurology, Harvard Medical School, Boston, MA, USA.
| | - Leillani L Ha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca Yaworski
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Emma R Sutton
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathleen A Christie
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Aoife Reilly
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Ariane Beauvais
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
| | - Roman M Doll
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Biosciences/Cancer Biology Program, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Demitri de la Cruz
- Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Casey A Maguire
- Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Kathryn J Swoboda
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rashmi Kothary
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario, Canada
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
25
|
Zhang Y, Wu ZY. Gene therapy for monogenic disorders: challenges, strategies, and perspectives. J Genet Genomics 2024; 51:133-143. [PMID: 37586590 DOI: 10.1016/j.jgg.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
Monogenic disorders refer to a group of human diseases caused by mutations in single genes. While disease-modifying therapies have offered some relief from symptoms and delayed progression for some monogenic diseases, most of these diseases still lack effective treatments. In recent decades, gene therapy has emerged as a promising therapeutic strategy for genetic disorders. Researchers have developed various gene manipulation tools and gene delivery systems to treat monogenic diseases. Despite this progress, concerns about inefficient delivery, persistent expression, immunogenicity, toxicity, capacity limitation, genomic integration, and limited tissue specificity still need to be addressed. This review gives an overview of commonly used gene therapy and delivery tools, along with the challenges they face and potential strategies to counter them.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Key Laboratory of Medical Neurobiology of Zhejiang Province, Hangzhou, Zhejiang 310009, China
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Key Laboratory of Medical Neurobiology of Zhejiang Province, Hangzhou, Zhejiang 310009, China.
| |
Collapse
|
26
|
Portell A, Mali P. Mutation corrections in spinal muscular atrophy. Nat Biomed Eng 2024; 8:111-113. [PMID: 38129656 DOI: 10.1038/s41551-023-01166-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Andrew Portell
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
27
|
Leclerc D, Siroky MD, Miller SM. Next-generation biological vector platforms for in vivo delivery of genome editing agents. Curr Opin Biotechnol 2024; 85:103040. [PMID: 38103518 DOI: 10.1016/j.copbio.2023.103040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023]
Abstract
CRISPR-based genome editing holds promise for addressing genetic disease, infectious disease, and cancer and has rapidly advanced from primary research to clinical trials in recent years. However, the lack of safe and potent in vivo delivery methods for CRISPR components has limited most ongoing clinical trials to ex vivo gene therapy. Effective CRISPR in vivo genome editing necessitates an effective vehicle ensuring target cell transduction while minimizing off-target effects, toxicity, and immune reactions. In this review, we examine promising biological-derived platforms to deliver DNA editing agents in vivo and the engineering thereof, encompassing potent viral-based vehicles, flexible protein nanocages, and mammalian-derived particles.
Collapse
Affiliation(s)
- Delphine Leclerc
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael D Siroky
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shannon M Miller
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
28
|
Zhang H, Kelly K, Lee J, Echeverria D, Cooper D, Panwala R, Amrani N, Chen Z, Gaston N, Wagh A, Newby G, Xie J, Liu DR, Gao G, Wolfe S, Khvorova A, Watts J, Sontheimer E. Self-delivering, chemically modified CRISPR RNAs for AAV co-delivery and genome editing in vivo. Nucleic Acids Res 2024; 52:977-997. [PMID: 38033325 PMCID: PMC10810193 DOI: 10.1093/nar/gkad1125] [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: 03/09/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a 'protecting oligo'), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.
Collapse
Affiliation(s)
- Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rebecca Panwala
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Atish Wagh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Scot A Wolfe
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| |
Collapse
|
29
|
郑 婷, 朱 倍, 王 智, 李 青. [Gene therapy strategies and prospects for neurofibromatosis type 1]. ZHONGGUO XIU FU CHONG JIAN WAI KE ZA ZHI = ZHONGGUO XIUFU CHONGJIAN WAIKE ZAZHI = CHINESE JOURNAL OF REPARATIVE AND RECONSTRUCTIVE SURGERY 2024; 38:1-8. [PMID: 38225833 PMCID: PMC10796236 DOI: 10.7507/1002-1892.202309071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 01/17/2024]
Abstract
Objective To summarize the gene therapy strategies for neurofibromatosis type 1 (NF1) and related research progress. Methods The recent literature on gene therapy for NF1 at home and abroad was reviewed. The structure and function of the NF1 gene and its mutations were analyzed, and the current status as well as future prospects of the transgenic therapy and gene editing strategies were summarized. Results NF1 is an autosomal dominantly inherited tumor predisposition syndrome caused by mutations in the NF1 tumor suppressor gene, which impair the function of the neurofibromin and lead to the disease. It has complex clinical manifestations and is not yet curable. Gene therapy strategies for NF1 are still in the research and development stage. Existing studies on the transgenic therapy for NF1 have mainly focused on the construction and expression of the GTPase-activating protein-related domain in cells that lack of functional neurofibromin, confirming the feasibility of the transgenic therapy for NF1. Future research may focus on split adeno-associated virus (AAV) gene delivery, oversized AAV gene delivery, and the development of new vectors for targeted delivery of full-length NF1 cDNA. In addition, the gene editing tools of the new generation have great potential to treat monogenic genetic diseases such as NF1, but need to be further validated in terms of efficiency and safety. Conclusion Gene therapy, including both the transgenic therapy and gene editing, is expected to become an important new therapeutic approach for NF1 patients.
Collapse
Affiliation(s)
- 婷婷 郑
- 上海交通大学医学院附属第九人民医院整复外科(上海 200011)Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
- 上海交通大学医学院附属第九人民医院Ⅰ型神经纤维瘤病诊疗中心(上海 200011)Neurofibromatosis Type 1 Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
| | - 倍瑶 朱
- 上海交通大学医学院附属第九人民医院整复外科(上海 200011)Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
- 上海交通大学医学院附属第九人民医院Ⅰ型神经纤维瘤病诊疗中心(上海 200011)Neurofibromatosis Type 1 Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
| | - 智超 王
- 上海交通大学医学院附属第九人民医院整复外科(上海 200011)Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
- 上海交通大学医学院附属第九人民医院Ⅰ型神经纤维瘤病诊疗中心(上海 200011)Neurofibromatosis Type 1 Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
| | - 青峰 李
- 上海交通大学医学院附属第九人民医院整复外科(上海 200011)Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
- 上海交通大学医学院附属第九人民医院Ⅰ型神经纤维瘤病诊疗中心(上海 200011)Neurofibromatosis Type 1 Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
| |
Collapse
|
30
|
Imiołek M, Fekete S, Kizekai L, Addepalli B, Lauber M. Fast and efficient size exclusion chromatography of adeno associated viral vectors with 2.5 micrometer particle low adsorption columns. J Chromatogr A 2024; 1714:464587. [PMID: 38150795 DOI: 10.1016/j.chroma.2023.464587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
More and more transformative gene therapies (GTx) are reaching commercialization stage and many of them use Adeno Associated Viruses (AAVs) as their vector. Being larger than therapeutic antibodies, their size variant analysis poses an analytical challenge that must be addressed to speed up the development processes. Size exclusion chromatography (SEC) can provide critical information on the quality and purity of the product, but its full potential is not yet utilized by currently applied columns that are (i) packed with relatively large particles, (ii) prepared exclusively in large formats and (iii) built using metal hardware that is prone to secondary interactions. In this paper, we investigate the use of state-of-the-art sub-3 µm particles to address existing limitations. A prototype 2.5 µm column was found to deliver superior kinetic efficiency, significant reduction in run times and increased resolution of separations. No evidence for shear or sample sieving effects were found during comparisons with conventional 5 µm columns. Moreover, use of low adsorption hardware enabled the application of a wide range of mobile phase conditions and a chance to apply a more robust platform method for several AAV serotypes. The resulting method was tested for its reproducibility as well as utility for critical quality attribute assays, including multiangle light scattering based (MALS) measurements of size and molar mass. Thus, a new tool for higher resolution, higher throughput size variant analysis of AAVs has been described.
Collapse
Affiliation(s)
- Mateusz Imiołek
- Waters Corporation, 1 Rue Michel Servet, Geneva 1211, Switzerland.
| | - Szabolcs Fekete
- Waters Corporation, 1 Rue Michel Servet, Geneva 1211, Switzerland
| | - Lavelay Kizekai
- Waters Corporation, 34 Maple Street, Milford MA 01757, United States of America
| | | | - Matthew Lauber
- Waters Corporation, 34 Maple Street, Milford MA 01757, United States of America
| |
Collapse
|
31
|
Gao S, Guan H, Bloomer H, Wich D, Song D, Khirallah J, Ye Z, Zhao Y, Chen M, Xu C, Liu L, Xu Q. Harnessing non-Watson-Crick's base pairing to enhance CRISPR effectors cleavage activities and enable gene editing in mammalian cells. Proc Natl Acad Sci U S A 2024; 121:e2308415120. [PMID: 38150477 PMCID: PMC10786293 DOI: 10.1073/pnas.2308415120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/21/2023] [Indexed: 12/29/2023] Open
Abstract
Genomic DNA of the cyanophage S-2L virus is composed of 2-aminoadenine (Z), thymine (T), guanine (G), and cytosine (C), forming the genetic alphabet ZTGC, which violates Watson-Crick base pairing rules. The Z-base has an extra amino group on the two position that allows the formation of a third hydrogen bond with thymine in DNA strands. Here, we explored and expanded applications of this non-Watson-Crick base pairing in protein expression and gene editing. Both ZTGC-DNA (Z-DNA) and ZUGC-RNA (Z-RNA) produced in vitro show detectable compatibility and can be decoded in mammalian cells, including Homo sapiens cells. Z-crRNA can guide CRISPR-effectors SpCas9 and LbCas12a to cleave specific DNA through non-Watson-Crick base pairing and boost cleavage activities compared to A-crRNA. Z-crRNA can also allow for efficient gene and base editing in human cells. Together, our results help pave the way for potential strategies for optimizing DNA or RNA payloads for gene editing therapeutics and give insights to understanding the natural Z-DNA genome.
Collapse
Affiliation(s)
- Shuliang Gao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Huiwen Guan
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Hanan Bloomer
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Douglas Wich
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Donghui Song
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Jennifer Khirallah
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Yu Zhao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Mengting Chen
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Chutian Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Lihan Liu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| |
Collapse
|
32
|
Xiao YL, Wu Y, Tang W. An adenine base editor variant expands context compatibility. Nat Biotechnol 2024:10.1038/s41587-023-01994-3. [PMID: 38168987 DOI: 10.1038/s41587-023-01994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 09/15/2023] [Indexed: 01/05/2024]
Abstract
Adenine base editors (ABEs) are precise gene-editing agents that convert A:T pairs into G:C through a deoxyinosine intermediate. Existing ABEs function most effectively when the target A is in a TA context. Here we evolve the Escherichia coli transfer RNA-specific adenosine deaminase (TadA) to generate TadA8r, which extends potent deoxyadenosine deamination to RA (R = A or G) and is faster in processing GA than TadA8.20 and TadA8e, the two most active TadA variants reported so far. ABE8r, comprising TadA8r and a Streptococcus pyogenes Cas9 nickase, expands the editing window at the protospacer adjacent motif-distal end and outperforms ABE7.10, ABE8.20 and ABE8e in correcting disease-associated G:C-to-A:T transitions in the human genome, with a controlled off-target profile. We show ABE8r-mediated editing of clinically relevant sites that are poorly accessed by existing editors, including sites in PCSK9, whose disruption reduces low-density lipoprotein cholesterol, and ABCA4-p.Gly1961Glu, the most frequent mutation in Stargardt disease.
Collapse
Affiliation(s)
- Yu-Lan Xiao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Yuan Wu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Weixin Tang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
33
|
Li WK, Zhang SQ, Peng WL, Shi YH, Yuan B, Yuan YT, Xue ZY, Wang JC, Han WJ, Chen ZF, Shan SF, Xue BQ, Chen JL, Zhang C, Zhu SJ, Tai YL, Cheng TL, Qiu ZL. Whole-brain in vivo base editing reverses behavioral changes in Mef2c-mutant mice. Nat Neurosci 2024; 27:116-128. [PMID: 38012399 DOI: 10.1038/s41593-023-01499-x] [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: 10/23/2022] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
Whole-brain genome editing to correct single-base mutations and reduce or reverse behavioral changes in animal models of autism spectrum disorder (ASD) has not yet been achieved. We developed an apolipoprotein B messenger RNA-editing enzyme, catalytic polypeptide-embedded cytosine base editor (AeCBE) system for converting C·G to T·A base pairs. We demonstrate its effectiveness by targeting AeCBE to an ASD-associated mutation of the MEF2C gene (c.104T>C, p.L35P) in vivo in mice. We first constructed Mef2cL35P heterozygous mice. Male heterozygous mice exhibited hyperactivity, repetitive behavior and social abnormalities. We then programmed AeCBE to edit the mutated C·G base pairs of Mef2c in the mouse brain through the intravenous injection of blood-brain barrier-crossing adeno-associated virus. This treatment successfully restored Mef2c protein levels in several brain regions and reversed the behavioral abnormalities in Mef2c-mutant mice. Our work presents an in vivo base-editing paradigm that could potentially correct single-base genetic mutations in the brain.
Collapse
Affiliation(s)
- Wei-Ke Li
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shu-Qian Zhang
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Wan-Ling Peng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Han Shi
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bo Yuan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Ting Yuan
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen-Yu Xue
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin-Cheng Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Wen-Jian Han
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Fang Chen
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Shi-Fang Shan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bi-Qing Xue
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jin-Long Chen
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Cheng Zhang
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shu-Jia Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Lin Tai
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tian-Lin Cheng
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
| | - Zi-Long Qiu
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Clinical Neuroscience Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| |
Collapse
|
34
|
Park CS, Habib O, Lee Y, Hur JK. Applications of CRISPR technologies to the development of gene and cell therapy. BMB Rep 2024; 57:2-11. [PMID: 38178651 PMCID: PMC10828430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
Advancements in gene and cell therapy have resulted in novel therapeutics for diseases previously considered incurable or challenging to treat. Among the various contributing technologies, genome editing stands out as one of the most crucial for the progress in gene and cell therapy. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the subsequent evolution of genetic engineering technology have markedly expanded the field of target-specific gene editing. Originally studied in the immune systems of bacteria and archaea, the CRISPR system has demonstrated wide applicability to effective genome editing of various biological systems including human cells. The development of CRISPR-based base editing has enabled directional cytosine-tothymine and adenine-to-guanine substitutions of select DNA bases at the target locus. Subsequent advances in prime editing further elevated the flexibility of the edit multiple consecutive bases to desired sequences. The recent CRISPR technologies also have been actively utilized for the development of in vivo and ex vivo gene and cell therapies. We anticipate that the medical applications of CRISPR will rapidly progress to provide unprecedented possibilities to develop novel therapeutics towards various diseases. [BMB Reports 2024; 57(1): 2-11].
Collapse
Affiliation(s)
- Chul-Sung Park
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
| | - Omer Habib
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Younsu Lee
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Junho K. Hur
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
- Department of Genetics, College of Medicine, Hanyang University, Seoul 04763, Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea
| |
Collapse
|
35
|
Wouters F, Bogie J, Wullaert A, van der Hilst J. Recent Insights in Pyrin Inflammasome Activation: Identifying Potential Novel Therapeutic Approaches in Pyrin-Associated Autoinflammatory Syndromes. J Clin Immunol 2023; 44:8. [PMID: 38129719 DOI: 10.1007/s10875-023-01621-5] [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: 08/28/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Pyrin is a cytosolic protein encoded by the MEFV gene, predominantly expressed in innate immune cells. Upon activation, it forms an inflammasome, a multimolecular complex that enables the activation and secretion of IL-1β and IL-18. In addition, the Pyrin inflammasome activates Gasdermin D leading to pyroptosis, a highly pro-inflammatory cell death. Four autoinflammatory syndromes are associated with Pyrin inflammasome dysregulation: familial Mediterranean fever, hyper IgD syndrome/mevalonate kinase deficiency, pyrin-associated autoinflammation with neutrophilic dermatosis, and pyogenic arthritis, pyoderma gangrenosum, and acne syndrome. In this review, we discuss recent advances in understanding the molecular mechanisms regulating the two-step model of Pyrin inflammasome activation. Based on these insights, we discuss current pharmacological options and identify a series of existing molecules with therapeutic potential for the treatment of pyrin-associated autoinflammatory syndromes.
Collapse
Affiliation(s)
- Flore Wouters
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590, Diepenbeek, Belgium.
| | - Jeroen Bogie
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590, Diepenbeek, Belgium
- University MS Center Hasselt, 3900, Pelt, Belgium
| | - Andy Wullaert
- Department of Internal Medicine and Paediatrics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Inflammation Research VIB, 9052, Ghent, Belgium
- Laboratory of Protein Science, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jeroen van der Hilst
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, 3590, Diepenbeek, Belgium.
- Department of Infectious Diseases and Immune Pathology, Jessa General Hospital and Limburg Clinical Research Center, Hasselt, Belgium.
| |
Collapse
|
36
|
Woodruff R, Parekh F, Lamb K, Mekkaoui L, Allen C, Smetanova K, Huang J, Williams A, Toledo GS, Lilova K, Roddie C, Sillibourne J, Pule M. Large-scale manufacturing of base-edited chimeric antigen receptor T cells. Mol Ther Methods Clin Dev 2023; 31:101123. [PMID: 37886606 PMCID: PMC10597784 DOI: 10.1016/j.omtm.2023.101123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
Base editing is a revolutionary gene-editing technique enabling the introduction of point mutations into the genome without generating detrimental DNA double-stranded breaks. Base-editing enzymes are commonly delivered in the form of modified linear messenger RNA (mRNA) that is costly to produce. Here, we address this problem by developing a simple protocol for manufacturing base-edited cells using circular RNA (circRNA), which is less expensive to synthesize. Compared with linear mRNA, higher editing efficiencies were achieved with circRNA, enabling an 8-fold reduction in the amount of RNA required. We used this protocol to manufacture a clinical dose (1 × 108 cells) of base-edited chimeric antigen receptor (CAR) T cells lacking expression of the inhibitory receptor, PD-1. Editing efficiencies of up to 86% were obtained using 0.25 μg circRNA/1 × 106 cells. Increased editing efficiencies with circRNA were attributed to more efficient translation. These results suggest that circRNA, which is less expensive to produce than linear mRNA, is a viable option for reducing the cost of manufacturing base-edited cells at scale.
Collapse
Affiliation(s)
- Rosie Woodruff
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Farhaan Parekh
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Katarina Lamb
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Leila Mekkaoui
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Christopher Allen
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | | | - Jasmine Huang
- Imperial College London, South Kensington Campus, SW7 2AZ London, UK
| | - Alex Williams
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | | | - Koki Lilova
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Claire Roddie
- Deparment of Haematology, Cancer Institute, 72 Huntley Street, WC1E 6BT London, UK
| | - James Sillibourne
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Martin Pule
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
- Deparment of Haematology, Cancer Institute, 72 Huntley Street, WC1E 6BT London, UK
| |
Collapse
|
37
|
Michailidou F. Engineering of Therapeutic and Detoxifying Enzymes. Angew Chem Int Ed Engl 2023; 62:e202308814. [PMID: 37433049 DOI: 10.1002/anie.202308814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/13/2023]
Abstract
Therapeutic enzymes present excellent opportunities for the treatment of human disease, modulation of metabolic pathways and system detoxification. However, current use of enzyme therapy in the clinic is limited as naturally occurring enzymes are seldom optimal for such applications and require substantial improvement by protein engineering. Engineering strategies such as design and directed evolution that have been successfully implemented for industrial biocatalysis can significantly advance the field of therapeutic enzymes, leading to biocatalysts with new-to-nature therapeutic activities, high selectivity, and suitability for medical applications. This minireview highlights case studies of how state-of-the-art and emerging methods in protein engineering are explored for the generation of therapeutic enzymes and discusses gaps and future opportunities in the field of enzyme therapy.
Collapse
Affiliation(s)
- Freideriki Michailidou
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| |
Collapse
|
38
|
Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
Collapse
Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
| | | | | |
Collapse
|
39
|
Sparmann A, Vogel J. RNA-based medicine: from molecular mechanisms to therapy. EMBO J 2023; 42:e114760. [PMID: 37728251 PMCID: PMC10620767 DOI: 10.15252/embj.2023114760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
RNA-based therapeutics have the potential to revolutionize the treatment and prevention of human diseases. While early research faced setbacks, it established the basis for breakthroughs in RNA-based drug design that culminated in the extraordinarily fast development of mRNA vaccines to combat the COVID-19 pandemic. We have now reached a pivotal moment where RNA medicines are poised to make a broad impact in the clinic. In this review, we present an overview of different RNA-based strategies to generate novel therapeutics, including antisense and RNAi-based mechanisms, mRNA-based approaches, and CRISPR-Cas-mediated genome editing. Using three rare genetic diseases as examples, we highlight the opportunities, but also the challenges to wide-ranging applications of this class of drugs.
Collapse
Affiliation(s)
- Anke Sparmann
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
| | - Jörg Vogel
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
- Institute of Molecular Infection Biology (IMIB)University of WürzburgWürzburgGermany
| |
Collapse
|
40
|
Bhatia P, Sterneckert J. Base editing: a promising tool to rescue spinal muscular atrophy. Signal Transduct Target Ther 2023; 8:362. [PMID: 37743375 PMCID: PMC10518301 DOI: 10.1038/s41392-023-01583-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/10/2023] [Accepted: 07/30/2023] [Indexed: 09/26/2023] Open
Affiliation(s)
- Priyanka Bhatia
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany.
- Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, Germany.
| |
Collapse
|
41
|
Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Lettre G, Ascher DB, Cassa CA, Sherwood RI, Pinello L. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.08.23295253. [PMID: 37732177 PMCID: PMC10508837 DOI: 10.1101/2023.09.08.23295253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
CRISPR base editing screens are powerful tools for studying disease-associated variants at scale. However, the efficiency and precision of base editing perturbations vary, confounding the assessment of variant-induced phenotypic effects. Here, we provide an integrated pipeline that improves the estimation of variant impact in base editing screens. We perform high-throughput ABE8e-SpRY base editing screens with an integrated reporter construct to measure the editing efficiency and outcomes of each gRNA alongside their phenotypic consequences. We introduce BEAN, a Bayesian network that accounts for per-guide editing outcomes and target site chromatin accessibility to estimate variant impacts. We show this pipeline attains superior performance compared to existing tools in variant classification and effect size quantification. We use BEAN to pinpoint common variants that alter LDL uptake, implicating novel genes. Additionally, through saturation base editing of LDLR, we enable accurate quantitative prediction of the effects of missense variants on LDL-C levels, which aligns with measurements in UK Biobank individuals, and identify structural mechanisms underlying variant pathogenicity. This work provides a widely applicable approach to improve the power of base editor screens for disease-associated variant characterization.
Collapse
Affiliation(s)
- Jayoung Ryu
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sam Barkal
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Yunzhuo Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matthew Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Quang Vinh Phan
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhijian Li
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Manuel Tognon
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Computer Science Department, University of Verona, Verona, Italy
| | - Lara Brown
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael I. Love
- Department of Genetics, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
42
|
Frost I, Mendoza AM, Chiou TT, Kim P, Aizenberg J, Kohn DB, De Oliveira SN, Weiss PS, Jonas SJ. Fluorinated Silane-Modified Filtroporation Devices Enable Gene Knockout in Human Hematopoietic Stem and Progenitor Cells. ACS APPLIED MATERIALS & INTERFACES 2023; 15:41299-41309. [PMID: 37616579 PMCID: PMC10485797 DOI: 10.1021/acsami.3c07045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Intracellular delivery technologies that are cost-effective, non-cytotoxic, efficient, and cargo-agnostic are needed to enable the manufacturing of cell-based therapies as well as gene manipulation for research applications. Current technologies capable of delivering large cargoes, such as plasmids and CRISPR-Cas9 ribonucleoproteins (RNPs), are plagued with high costs and/or cytotoxicity and often require substantial specialized equipment and reagents, which may not be available in resource-limited settings. Here, we report an intracellular delivery technology that can be assembled from materials available in most research laboratories, thus democratizing access to intracellular delivery for researchers and clinicians in low-resource areas of the world. These filtroporation devices permeabilize cells by pulling them through the pores of a cell culture insert by the application of vacuum available in biosafety cabinets. In a format that costs less than $10 in materials per experiment, we demonstrate the delivery of fluorescently labeled dextran, expression plasmids, and RNPs for gene knockout to Jurkat cells and human CD34+ hematopoietic stem and progenitor cell populations with delivery efficiencies of up to 40% for RNP knockout and viabilities of >80%. We show that functionalizing the surfaces of the filters with fluorinated silane moieties further enhances the delivery efficiency. These devices are capable of processing 500,000 to 4 million cells per experiment, and when combined with a 3D-printed vacuum application chamber, this throughput can be straightforwardly increased 6-12-fold in parallel experiments.
Collapse
Affiliation(s)
- Isaura
M. Frost
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
- UCLA
Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Alexandra M. Mendoza
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Tzu-Ting Chiou
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Philseok Kim
- John A. Paulson
School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Joanna Aizenberg
- John A. Paulson
School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Donald B. Kohn
- Department
of Molecular and Medical Pharmacology, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Satiro N. De Oliveira
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S. Weiss
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Steven J. Jonas
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Children’s
Discovery and Innovation Institute, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| |
Collapse
|
43
|
Signoria I, van der Pol WL, Groen EJN. Innovating spinal muscular atrophy models in the therapeutic era. Dis Model Mech 2023; 16:dmm050352. [PMID: 37787662 PMCID: PMC10565113 DOI: 10.1242/dmm.050352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a severe, monogenetic, neuromuscular disease. A thorough understanding of its genetic cause and the availability of robust models has led to the development and approval of three gene-targeting therapies. This is a unique and exciting development for the field of neuromuscular diseases, many of which remain untreatable. The development of therapies for SMA not only opens the door to future therapeutic possibilities for other genetic neuromuscular diseases, but also informs us about the limitations of such treatments. For example, treatment response varies widely and, for many patients, significant disability remains. Currently available SMA models best recapitulate the severe types of SMA, and these models are genetically and phenotypically more homogeneous than patients. Furthermore, treating patients is leading to a shift in phenotypes with increased variability in SMA clinical presentation. Therefore, there is a need to generate model systems that better reflect these developments. Here, we will first discuss current animal models of SMA and their limitations. Next, we will discuss the characteristics required to future-proof models to assist the field in the development of additional, novel therapies for SMA.
Collapse
Affiliation(s)
- Ilaria Signoria
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - W. Ludo van der Pol
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ewout J. N. Groen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| |
Collapse
|
44
|
Stampone E, Bencivenga D, Capellupo MC, Roberti D, Tartaglione I, Perrotta S, Della Ragione F, Borriello A. Genome editing and cancer therapy: handling the hypoxia-responsive pathway as a promising strategy. Cell Mol Life Sci 2023; 80:220. [PMID: 37477829 PMCID: PMC10361942 DOI: 10.1007/s00018-023-04852-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023]
Abstract
The precise characterization of oxygen-sensing pathways and the identification of pO2-regulated gene expression are both issues of critical importance. The O2-sensing system plays crucial roles in almost all the pivotal human processes, including the stem cell specification, the growth and development of tissues (such as embryogenesis), the modulation of intermediate metabolism (including the shift of the glucose metabolism from oxidative to anaerobic ATP production and vice versa), and the control of blood pressure. The solid cancer microenvironment is characterized by low oxygen levels and by the consequent activation of the hypoxia response that, in turn, allows a complex adaptive response characterized mainly by neoangiogenesis and metabolic reprogramming. Recently, incredible advances in molecular genetic methodologies allowed the genome editing with high efficiency and, above all, the precise identification of target cells/tissues. These new possibilities and the knowledge of the mechanisms of adaptation to hypoxia suggest the effective development of new therapeutic approaches based on the manipulation, targeting, and exploitation of the oxygen-sensor system molecular mechanisms.
Collapse
Affiliation(s)
- Emanuela Stampone
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Debora Bencivenga
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Maria Chiara Capellupo
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Domenico Roberti
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Immacolata Tartaglione
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Silverio Perrotta
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Fulvio Della Ragione
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy.
| | - Adriana Borriello
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy.
| |
Collapse
|
45
|
Lakhina Y, Boulis NM, Donsante A. Current and emerging targeted therapies for spinal muscular atrophy. Expert Rev Neurother 2023; 23:1189-1199. [PMID: 37843301 DOI: 10.1080/14737175.2023.2268276] [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: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION Spinal muscular atrophy (SMA) is a progressive neurodegenerative disorder caused by insufficiency or total absence of the survival motor neuron protein due to a mutation in the SMN1 gene. The copy number of its paralog, SMN2, influences disease onset and phenotype severity. Current therapeutic approaches include viral and non-viral modalities affecting gene expression. Regulatory-approved drugs Spinraza (Nusinersen), Zolgensma (Onasemnogene abeparvovec), and Evrysdi (Risdiplam) are still being investigated during clinical trials and show benefits in the long-term for symptomatic and pre-symptomatic patients. However, some ongoing interventions require repeated drug administration. AREAS COVERED In this review, the authors describe the existing therapy based on point of application, focusing on recent clinical trials of antisense oligonucleotides, viral gene therapy, and splice modulators and thepotential routes for correcting the mutation to provide therapeutic levels of SMN protein. EXPERT OPINION In the opinion of the authors, multiple treatment options for patients with SMA shifted the treatment paradigm from palliative supportive care to improvedmotor function, increased survival, and greater quality of life for such patients. They further believe that the future in SMA treatment development lies incombining existing treatment options, targeting aspects of the disease refractory to these treatments, and using gene editing technologies.
Collapse
Affiliation(s)
- Yuliya Lakhina
- Department of Neurosurgery, Emory University, Atlanta, USA
| | | | | |
Collapse
|
46
|
Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [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: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
Collapse
Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
| |
Collapse
|
47
|
Liang Y, Chen F, Wang K, Lai L. Base editors: development and applications in biomedicine. Front Med 2023; 17:359-387. [PMID: 37434066 DOI: 10.1007/s11684-023-1013-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/19/2023] [Indexed: 07/13/2023]
Abstract
Base editor (BE) is a gene-editing tool developed by combining the CRISPR/Cas system with an individual deaminase, enabling precise single-base substitution in DNA or RNA without generating a DNA double-strand break (DSB) or requiring donor DNA templates in living cells. Base editors offer more precise and secure genome-editing effects than other conventional artificial nuclease systems, such as CRISPR/Cas9, as the DSB induced by Cas9 will cause severe damage to the genome. Thus, base editors have important applications in the field of biomedicine, including gene function investigation, directed protein evolution, genetic lineage tracing, disease modeling, and gene therapy. Since the development of the two main base editors, cytosine base editors (CBEs) and adenine base editors (ABEs), scientists have developed more than 100 optimized base editors with improved editing efficiency, precision, specificity, targeting scope, and capacity to be delivered in vivo, greatly enhancing their application potential in biomedicine. Here, we review the recent development of base editors, summarize their applications in the biomedical field, and discuss future perspectives and challenges for therapeutic applications.
Collapse
Affiliation(s)
- Yanhui Liang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
| |
Collapse
|
48
|
Qin H, Xu W, Yao K. CRISPR-based genome editing in disease treatment. Trends Mol Med 2023:S1471-4914(23)00093-X. [PMID: 37263857 DOI: 10.1016/j.molmed.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Affiliation(s)
- Huan Qin
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
| | - Weihui Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China.
| |
Collapse
|
49
|
Villanueva MT. Base editing treats SMA in mice. Nat Rev Drug Discov 2023; 22:353. [PMID: 37024675 DOI: 10.1038/d41573-023-00057-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
50
|
High-precision genomic tool tackles deadly mutation. Nature 2023; 616:222. [PMID: 37012473 DOI: 10.1038/d41586-023-00906-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|