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Poukalov KK, Valero MC, Muscato DR, Adams LM, Chun H, Lee YI, Andrade NS, Zeier Z, Sweeney HL, Wang ET. Myospreader improves gene editing in skeletal muscle by myonuclear propagation. Proc Natl Acad Sci U S A 2024; 121:e2321438121. [PMID: 38687782 PMCID: PMC11087771 DOI: 10.1073/pnas.2321438121] [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: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 05/02/2024] Open
Abstract
Successful CRISPR/Cas9-based gene editing in skeletal muscle is dependent on efficient propagation of Cas9 to all myonuclei in the myofiber. However, nuclear-targeted gene therapy cargos are strongly restricted to their myonuclear domain of origin. By screening nuclear localization signals and nuclear export signals, we identify "Myospreader," a combination of short peptide sequences that promotes myonuclear propagation. Appending Myospreader to Cas9 enhances protein stability and myonuclear propagation in myoblasts and myofibers. AAV-delivered Myospreader dCas9 better inhibits transcription of toxic RNA in a myotonic dystrophy mouse model. Furthermore, Myospreader Cas9 achieves higher rates of gene editing in CRISPR reporter and Duchenne muscular dystrophy mouse models. Myospreader reveals design principles relevant to all nuclear-targeted gene therapies and highlights the importance of the spatial dimension in therapeutic development.
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Affiliation(s)
- Kiril K. Poukalov
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL32610
- Center for NeuroGenetics, University of Florida, Gainesville, FL32610
- Genetics Institute, University of Florida, Gainesville, FL32610
| | - M. Carmen Valero
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL32610
- Center for NeuroGenetics, University of Florida, Gainesville, FL32610
- Genetics Institute, University of Florida, Gainesville, FL32610
| | - Derek R. Muscato
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL32610
- Center for NeuroGenetics, University of Florida, Gainesville, FL32610
- Genetics Institute, University of Florida, Gainesville, FL32610
| | - Leanne M. Adams
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL32610
- Center for NeuroGenetics, University of Florida, Gainesville, FL32610
- Genetics Institute, University of Florida, Gainesville, FL32610
| | - Heejae Chun
- Department of Pharmacology, University of Florida, Gainesville, FL32610
- Myology Institute, University of Florida, Gainesville, FL32610
| | - Young il Lee
- Department of Pharmacology, University of Florida, Gainesville, FL32610
- Myology Institute, University of Florida, Gainesville, FL32610
| | - Nadja S. Andrade
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL33136
| | - Zane Zeier
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL33136
| | - H. Lee Sweeney
- Department of Pharmacology, University of Florida, Gainesville, FL32610
- Myology Institute, University of Florida, Gainesville, FL32610
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL32610
- Center for NeuroGenetics, University of Florida, Gainesville, FL32610
- Genetics Institute, University of Florida, Gainesville, FL32610
- Myology Institute, University of Florida, Gainesville, FL32610
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Zhang W, Wang H, Luo Z, Jian Y, Gong C, Wang H, Lin X, Liu M, Wang Y, Shao H. Hitchhiking of Cas9 with nucleus-localized proteins impairs its controllability and leads to efficient genome editing of NLS-free Cas9. Mol Ther 2024; 32:920-934. [PMID: 38341611 PMCID: PMC11163216 DOI: 10.1016/j.ymthe.2024.02.008] [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: 08/17/2023] [Revised: 01/09/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
CRISPR-Cas9 is the most commonly used genome-editing tool in eukaryotic cells. To modulate Cas9 entry into the nucleus to enable control of genome editing, we constructed a light-controlled CRISPR-Cas9 system to control exposure of the Cas9 protein nuclear localization signal (NLS). Although blue-light irradiation was found to effectively control the entry of Cas9 protein into the nucleus with confocal microscopy observation, effective gene editing occurred in controls with next-generation sequencing analysis. To further clarify this phenomenon, a CRISPR-Cas9 editing system without the NLS and a CRISPR-Cas9 editing system containing a nuclear export signal were also constructed. Interestingly, both Cas9 proteins could achieve effective editing of target sites with significantly reduced off-target effects. Thus, we speculated that other factors might mediate Cas9 entry into the nucleus. However, NLS-free Cas9 was found to produce effective target gene editing even following inhibition of cell mitosis to prevent nuclear import caused by nuclear membrane disassembly. Furthermore, multiple nucleus-localized proteins were found to interact with Cas9, which could mediate the "hitchhiking" of NLS-free Cas9 into the nucleus. These findings will inform future attempts to construct controllable gene-editing systems and provide new insights into the evolution of the nucleus and compatible protein functions.
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Affiliation(s)
- Wenfeng Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China.
| | - Haozheng Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Zhongtao Luo
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Yingzhen Jian
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Chenyu Gong
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Hui Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Xinjian Lin
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Meilin Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Yangmin Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Hongwei Shao
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China.
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Zhao X, Deng H, Feng Y, Wang Y, Yao X, Ma Y, Zhang L, Jie J, Yang P, Yang Y. Immune-cell-mediated tissue engineering strategies for peripheral nerve injury and regeneration. J Mater Chem B 2024; 12:2217-2235. [PMID: 38345580 DOI: 10.1039/d3tb02557h] [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: 02/29/2024]
Abstract
During the process of peripheral nerve repair, there are many complex pathological and physiological changes, including multi-cellular responses and various signaling molecules, and all these events establish a dynamic microenvironment for axon repair, regeneration, and target tissue/organ reinnervation. The immune system plays an indispensable role in the process of nerve repair and function recovery. An effective immune response not only involves innate-immune and adaptive-immune cells but also consists of chemokines and cytokines released by these immune cells. The elucidation of the orchestrated interplay of immune cells with nerve regeneration and functional restoration is meaningful for the exploration of therapeutic strategies. This review mainly enumerates the general immune cell response to peripheral nerve injury and focuses on their contributions to functional recovery. The tissue engineering-mediated strategies to regulate macrophages and T cells through physical and biochemical factors combined with scaffolds are discussed. The dynamic immune responses during peripheral nerve repair and immune-cell-mediated tissue engineering methods are presented, which provide a new insight and inspiration for immunomodulatory therapies in peripheral nerve regeneration.
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Affiliation(s)
- Xueying Zhao
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Hui Deng
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Yuan Feng
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Yuehan Wang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Xiaomin Yao
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Yuyang Ma
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Luzhong Zhang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Jing Jie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nantong University, 226001, Nantong, P. R. China.
| | - Pengxiang Yang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
| | - Yumin Yang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 226001, Nantong, P. R. China.
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Wang Z, Chen X, Chen N, Yan H, Wu K, Li J, Ru Q, Deng R, Liu X, Kang R. Mechanical Factors Regulate Annulus Fibrosus (AF) Injury Repair and Remodeling: A Review. ACS Biomater Sci Eng 2024; 10:219-233. [PMID: 38149967 DOI: 10.1021/acsbiomaterials.3c01091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Low back pain is a common chronic disease that can severely affect the patient's work and daily life. The breakdown of spinal mechanical homeostasis caused by intervertebral disc (IVD) degeneration is a leading cause of low back pain. Annulus fibrosus (AF), as the outer layer structure of the IVD, is often the first affected part. AF injury caused by consistent stress overload will further accelerate IVD degeneration. Therefore, regulating AF injury repair and remodeling should be the primary goal of the IVD repair strategy. Mechanical stimulation has been shown to promote AF regeneration and repair, but most studies only focus on the effect of single stress on AF, and lack realistic models and methods that can mimic the actual mechanical environment of AF. In this article, we review the effects of different types of stress stimulation on AF injury repair and remodeling, suggest possible beneficial load combinations, and explore the underlying molecular mechanisms. It will provide the theoretical basis for designing better tissue engineering therapy using mechanical factors to regulate AF injury repair and remodeling in the future.
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Affiliation(s)
- Zihan Wang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Xin Chen
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Nan Chen
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Hongjie Yan
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Ke Wu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Jitao Li
- School of Physics and Telecommunications Engineering, Zhoukou Normal University, Zhoukou, Henan Province 466001, P.R. China
| | - Qingyuan Ru
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Rongrong Deng
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Xin Liu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
| | - Ran Kang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
- Department of Orthopedics, Nanjing Lishui Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu Province 210028, P.R. China
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Poukalov KK, Valero MC, Muscato DR, Adams LM, Chun H, Lee YI, Andrade NS, Zeier Z, Sweeney HL, Wang ET. Myospreader improves gene editing in skeletal muscle by myonuclear propagation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.06.565807. [PMID: 37986992 PMCID: PMC10659306 DOI: 10.1101/2023.11.06.565807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Successful CRISPR/Cas9-based gene editing in skeletal muscle is dependent on efficient propagation of Cas9 to all myonuclei in the myofiber. However, nuclear-targeted gene therapy cargos are strongly restricted to their myonuclear domain of origin. By screening nuclear localization signals and nuclear export signals, we identify "Myospreader", a combination of short peptide sequences that promotes myonuclear propagation. Appending Myospreader to Cas9 enhances protein stability and myonuclear propagation in myoblasts and myofibers. AAV-delivered Myospreader dCas9 better inhibits transcription of toxic RNA in a myotonic dystrophy mouse model. Furthermore, Myospreader Cas9 achieves higher rates of gene editing in CRISPR reporter and Duchenne muscular dystrophy mouse models. Myospreader reveals design principles relevant to all nuclear-targeted gene therapies and highlights the importance of the spatial dimension in therapeutic development.
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Affiliation(s)
- Kiril K. Poukalov
- Department of Molecular Genetics & Microbiology, University of Florida
- Center for NeuroGenetics, University of Florida
- Genetics Institute, University of Florida
| | - M. Carmen Valero
- Department of Molecular Genetics & Microbiology, University of Florida
- Center for NeuroGenetics, University of Florida
- Genetics Institute, University of Florida
| | - Derek R. Muscato
- Department of Molecular Genetics & Microbiology, University of Florida
- Center for NeuroGenetics, University of Florida
- Genetics Institute, University of Florida
| | - Leanne M. Adams
- Department of Molecular Genetics & Microbiology, University of Florida
- Center for NeuroGenetics, University of Florida
- Genetics Institute, University of Florida
| | - Heejae Chun
- Department of Pharmacology, University of Florida
- Myology Institute, University of Florida
| | - Young il Lee
- Department of Pharmacology, University of Florida
- Myology Institute, University of Florida
| | - Nadja S. Andrade
- Department of Psychiatry & Behavioral Sciences, University of Miami
| | - Zane Zeier
- Department of Psychiatry & Behavioral Sciences, University of Miami
| | - H. Lee Sweeney
- Department of Pharmacology, University of Florida
- Myology Institute, University of Florida
| | - Eric T. Wang
- Department of Molecular Genetics & Microbiology, University of Florida
- Center for NeuroGenetics, University of Florida
- Genetics Institute, University of Florida
- Myology Institute, University of Florida
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Kraus C, Sontheimer EJ. Applications of Anti-CRISPR Proteins in Genome Editing and Biotechnology. J Mol Biol 2023; 435:168120. [PMID: 37100169 DOI: 10.1016/j.jmb.2023.168120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
In the ten years since the discovery of the first anti-CRISPR (Acr) proteins, the number of validated Acrs has expanded rapidly, as has our understanding of the diverse mechanisms they employ to suppress natural CRISPR-Cas immunity. Many, though not all, function via direct, specific interaction with Cas protein effectors. The abilities of Acr proteins to modulate the activities and properties of CRISPR-Cas effectors have been exploited for an ever-increasing spectrum of biotechnological uses, most of which involve the establishment of control over genome editing systems. This control can be used to minimize off-target editing, restrict editing based on spatial, temporal, or conditional cues, limit the spread of gene drive systems, and select for genome-edited bacteriophages. Anti-CRISPRs have also been developed to overcome bacterial immunity, facilitate viral vector production, control synthetic gene circuits, and other purposes. The impressive and ever-growing diversity of Acr inhibitory mechanisms will continue to allow the tailored applications of Acrs.
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Affiliation(s)
| | - Erik J Sontheimer
- RNA Therapeutics Institute; Program in Molecular Medicine, and; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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Shin S, Jang S, Lim D. Small Molecules for Enhancing the Precision and Safety of Genome Editing. Molecules 2022; 27:6266. [PMID: 36234804 PMCID: PMC9573751 DOI: 10.3390/molecules27196266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing technologies have revolutionized biology, biotechnology, and medicine, and have spurred the development of new therapeutic modalities. However, there remain several barriers to the safe use of CRISPR technologies, such as unintended off-target DNA cleavages. Small molecules are important resources to solve these problems, given their facile delivery and fast action to enable temporal control of the CRISPR systems. Here, we provide a comprehensive overview of small molecules that can precisely modulate CRISPR-associated (Cas) nucleases and guide RNAs (gRNAs). We also discuss the small-molecule control of emerging genome editors (e.g., base editors) and anti-CRISPR proteins. These molecules could be used for the precise investigation of biological systems and the development of safer therapeutic modalities.
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Affiliation(s)
- Siyoon Shin
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Seeun Jang
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Donghyun Lim
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
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