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Nemudraia A, Nemudryi A, Wiedenheft B. Repair of CRISPR-guided RNA breaks enables site-specific RNA excision in human cells. Science 2024; 384:808-814. [PMID: 38662916 PMCID: PMC11175973 DOI: 10.1126/science.adk5518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 04/14/2024] [Indexed: 05/07/2024]
Abstract
Genome editing with CRISPR RNA-guided endonucleases generates DNA breaks that are resolved by cellular DNA repair machinery. However, analogous methods to manipulate RNA remain unavailable. We show that site-specific RNA breaks generated with type-III CRISPR complexes are repaired in human cells and that this repair can be used for programmable deletions in human transcripts to restore gene function. Collectively, this work establishes a technology for precise RNA manipulation with potential therapeutic applications.
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Affiliation(s)
- Anna Nemudraia
- Department of Microbiology and Cell Biology, Montana State University; Bozeman, MT, 59717, USA
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University; Bozeman, MT, 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University; Bozeman, MT, 59717, USA
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2
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Johnson GA, Gould SI, Sánchez-Rivera FJ. Deconstructing cancer with precision genome editing. Biochem Soc Trans 2024; 52:803-819. [PMID: 38629716 PMCID: PMC11088927 DOI: 10.1042/bst20230984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Recent advances in genome editing technologies are allowing investigators to engineer and study cancer-associated mutations in their endogenous genetic contexts with high precision and efficiency. Of these, base editing and prime editing are quickly becoming gold-standards in the field due to their versatility and scalability. Here, we review the merits and limitations of these precision genome editing technologies, their application to modern cancer research, and speculate how these could be integrated to address future directions in the field.
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Affiliation(s)
- Grace A. Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Samuel I. Gould
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Francisco J. Sánchez-Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
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3
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Arabpour J, Rezaei K, Khojini JY, Razi S, Hayati MJ, Gheibihayat SM. The potential role and mechanism of circRNAs in Ferroptosis: A comprehensive review. Pathol Res Pract 2024; 255:155203. [PMID: 38368664 DOI: 10.1016/j.prp.2024.155203] [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: 12/22/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Cell death encompasses various mechanisms, including necrosis and apoptosis. Ferroptosis, a unique form of regulated cell death, emerged as a non-apoptotic process reliant on iron and reactive oxygen species (ROS). Distinguishing itself from other forms of cell death, ferroptosis exhibits distinct morphological, biochemical, and genetic features. Circular RNAs (circRNAs), a novel class of RNA molecules, play crucial regulatory roles in ferroptosis-mediated pathways and cellular processes. With their circular structure and stability, circRNAs function as microRNA sponges and participate in protein regulation, offering diverse mechanisms for cellular control. Accumulating evidence indicates that circRNAs are key players in diseases associated with ferroptosis, presenting opportunities for diagnostic and therapeutic applications. This study explores the regulatory roles of circRNAs in ferroptosis and their potential in diseases such as cancer, neurological disorders, and cardiovascular diseases. By investigating the relationship between circRNAs and ferroptosis, this research provides new insights into the diagnosis, treatment, and prognosis of ferroptosis-related diseases. Furthermore, the therapeutic implications of targeting circRNAs in cancer treatment and the modulation of ferroptosis pathways demonstrate the potential of circRNAs as diagnostic markers and therapeutic targets. Overall, understanding the involvement of circRNAs in regulating ferroptosis opens up new avenues for advancements in disease management.
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Affiliation(s)
- Javad Arabpour
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kimia Rezaei
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Javad Yaghmoorian Khojini
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Shokufeh Razi
- Department of Genetics, Faculty of Basic Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Javad Hayati
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Seyed Mohammad Gheibihayat
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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4
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Liu R, Yao J, Zhou S, Yang J, Zhang Y, Yang X, Li L, Zhang Y, Zhuang Y, Yang Y, Chen X. Spatiotemporal control of RNA metabolism and CRISPR-Cas functions using engineered photoswitchable RNA-binding proteins. Nat Protoc 2024; 19:374-405. [PMID: 38036926 DOI: 10.1038/s41596-023-00920-w] [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: 12/29/2022] [Accepted: 09/19/2023] [Indexed: 12/02/2023]
Abstract
RNA molecules perform various crucial roles in diverse cellular processes, from translating genetic information to decoding the genome, regulating gene expression and catalyzing chemical reactions. RNA-binding proteins (RBPs) play an essential role in regulating the diverse behaviors and functions of RNA in live cells, but techniques for the spatiotemporal control of RBP activities and RNA functions are rarely reported yet highly desirable. We recently reported the development of LicV, a synthetic photoswitchable RBP that can bind to a specific RNA sequence in response to blue light irradiation. LicV has been used successfully for the optogenetic control of RNA localization, splicing, translation and stability, as well as for the photoswitchable regulation of transcription and genomic locus labeling. Compared to classical genetic or pharmacologic perturbations, LicV-based light-switchable effectors have the advantages of large dynamic range between dark and light conditions and submicron and millisecond spatiotemporal resolutions. In this protocol, we provide an easy, efficient and generalizable strategy for engineering photoswitchable RBPs for the spatiotemporal control of RNA metabolism. We also provide a detailed protocol for the conversion of a CRISPR-Cas system to optogenetic control. The protocols typically take 2-3 d, including transfection and results analysis. Most of this protocol is applicable to the development of novel LicV-based photoswitchable effectors for the optogenetic control of other RNA metabolisms and CRISPR-Cas functions.
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Affiliation(s)
- Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Jing Yao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Siyu Zhou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yaqiang Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaoyan Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Leshi Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yunbin Zhang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yingping Zhuang
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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5
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Jia Q, Che Q, Zhang X, Chen J, Ren C, Wu Y, Liang W, Zhang X, Li Y, Li Z, Zhang Z, Shu Q. Knockdown of Galectin-9 alleviates rheumatoid arthritis through suppressing TNF-α-induced activation of fibroblast-like synoviocytes. Biochem Pharmacol 2024; 220:115994. [PMID: 38141929 DOI: 10.1016/j.bcp.2023.115994] [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: 11/29/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
The role of Galectin-9 (Gal-9) in the pathogenesis of rheumatoid arthritis (RA) remains unclear. This study aimed to investigate the mechanism of action and therapeutic potential of Gal-9 in RA. We detected Gal-9 expression in clinical samples, explored the mechanism of function of Gal-9 by knockdown and overexpression in fibroblast-like synoviocytes (FLSs), and further verified it in collagen-induced arthritis (CIA) model. We found that the levels of Gal-9 were considerably elevated in RA synovium than in osteoarthritis (OA) patients. A substantial decrease of Gal-9 was demonstrated after tumor necrosis factor (TNF-α) inhibitor treatment in the plasma of patients with RA. Additionally, transcriptome sequencing revealed that Gal-9 was involved in the regulation of the TNF-α pathway. Gal-9 was considerably upregulated after TNF-α stimulation in FLSs, and knockdown of Gal-9 substantially inhibited TNF-α activated proliferation, migration and inflammatory response. According to cell transcriptome sequencing results, we further confirmed that Gal-9 could achieve these effects by interacting with MAFB and affecting PI3K/AKT/mTOR pathway. Finally, we knocked down Gal-9 on the CIA model and found that it could alleviate the progression of arthritis. In conclusion, our study revealed that the knockdown of Gal-9 could inhibited TNF-α induced activation in RA through MAFB, PI3K/AKT/mTOR.
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Affiliation(s)
- Qian Jia
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Rheumatology and Immunology, Linyi People's Hospital, Linyi, China; Department of Rheumatology, Linyi People's Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Linyi, China
| | - Qincheng Che
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Rheumatology, Qilu Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Jinan, China
| | - Xiaoyu Zhang
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Rheumatology, Qilu Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Jinan, China
| | - Jie Chen
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Rheumatology, Qilu Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Jinan, China
| | - Chunfeng Ren
- Department of Rheumatology and Immunology, Jining NO.1 People's Hospital, Jining, China
| | - Yunpeng Wu
- Department of Orthopedics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Weiqiang Liang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Xiaojie Zhang
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Rheumatology, Qilu Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Jinan, China
| | - Yanshan Li
- Department of Rheumatology and Immunology, Linyi People's Hospital, Linyi, China; Department of Rheumatology, Linyi People's Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Linyi, China
| | - Zunzhong Li
- Department of Rheumatology and Immunology, Linyi People's Hospital, Linyi, China; Department of Rheumatology, Linyi People's Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Linyi, China
| | - Zhenchun Zhang
- Department of Rheumatology and Immunology, Linyi People's Hospital, Linyi, China; Department of Rheumatology, Linyi People's Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Linyi, China
| | - Qiang Shu
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Rheumatology, Qilu Hospital, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Jinan, China.
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6
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Dey B, Kumar A, Patel AB. Pathomechanistic Networks of Motor System Injury in Amyotrophic Lateral Sclerosis. Curr Neuropharmacol 2024; 22:1778-1806. [PMID: 37622689 PMCID: PMC11284732 DOI: 10.2174/1570159x21666230824091601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/25/2023] [Accepted: 06/06/2023] [Indexed: 08/26/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is the most common, adult-onset, progressive motor neurodegenerative disorder that results in death within 3 years of the clinical diagnosis. Due to the clinicopathological heterogeneity, any reliable biomarkers for diagnosis or prognosis of ALS have not been identified till date. Moreover, the only three clinically approved treatments are not uniformly effective in slowing the disease progression. Over the last 15 years, there has been a rapid advancement in research on the complex pathomechanistic landscape of ALS that has opened up new avenues for successful clinical translation of targeted therapeutics. Multiple studies suggest that the age-dependent interaction of risk-associated genes with environmental factors and endogenous modifiers is critical to the multi-step process of ALS pathogenesis. In this review, we provide an updated discussion on the dysregulated cross-talk between intracellular homeostasis processes, the unique molecular networks across selectively vulnerable cell types, and the multisystemic nature of ALS pathomechanisms. Importantly, this work highlights the alteration in epigenetic and epitranscriptomic landscape due to gene-environment interactions, which have been largely overlooked in the context of ALS pathology. Finally, we suggest that precision medicine research in ALS will be largely benefitted from the stratification of patient groups based on the clinical phenotype, onset and progression, genome, exposome, and metabolic identities.
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Affiliation(s)
- Bedaballi Dey
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, Telangana, India
- AcSIR-Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
| | - Arvind Kumar
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, Telangana, India
- AcSIR-Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
| | - Anant Bahadur Patel
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, Telangana, India
- AcSIR-Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
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7
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Chen K, Wang Y. CRISPR/Cas systems for in situ imaging of intracellular nucleic acids: Concepts and applications. Biotechnol Bioeng 2023; 120:3446-3464. [PMID: 37641170 DOI: 10.1002/bit.28543] [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: 05/20/2023] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Accurate and precise localization of intracellular nucleic acids is crucial for regulating genetic information transcription and diagnosing diseases. Although intracellular nucleic acid imaging methods are available for various cell types, their widespread utilization is impeded by the intricate nature of the process and its exorbitant cost. Recently, numerous intracellular nucleic acid labeling techniques based on clustered regularly interspaced short palindromic repeats (CRISPR) have been established due to their modularity, flexibility, and specificity. In this work, we present various CRISPR methods that are currently employed for visualizing intracellular genomic sequences and RNA, based on their detection principles and application scenarios. Furthermore, we discuss the advantages and drawbacks of the existing CRISPR imaging methods, as well as future research directions. We anticipate that with continued refinement, more advanced CRISPR-based imaging techniques can be developed to better elucidate the localization and dynamics of intracellular nucleic acids, thereby providing a powerful tool for molecular biology research and clinical molecular pathology diagnosis.
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Affiliation(s)
- Kun Chen
- Department of Clinical Laboratory, Peking University Cancer Hospital & Institute, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Beijing, China
| | - Yufei Wang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, NMPA Key Laboratory for Quality Control of In Vitro Diagnostics, Beijing Engineering Research Center of Immunological Reagents Clinical Research, Beijing, China
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8
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Ikenoshita S, Matsuo K, Yabuki Y, Kawakubo K, Asamitsu S, Hori K, Usuki S, Hirose Y, Bando T, Araki K, Ueda M, Sugiyama H, Shioda N. A cyclic pyrrole-imidazole polyamide reduces pathogenic RNA in CAG/CTG triplet repeat neurological disease models. J Clin Invest 2023; 133:e164792. [PMID: 37707954 PMCID: PMC10645379 DOI: 10.1172/jci164792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Expansion of CAG and CTG (CWG) triplet repeats causes several inherited neurological diseases. The CWG repeat diseases are thought to involve complex pathogenic mechanisms through expanded CWG repeat-derived RNAs in a noncoding region and polypeptides in a coding region, respectively. However, an effective therapeutic approach has not been established for the CWG repeat diseases. Here, we show that a CWG repeat DNA-targeting compound, cyclic pyrrole-imidazole polyamide (CWG-cPIP), suppressed the pathogenesis of coding and noncoding CWG repeat diseases. CWG-cPIP bound to the hairpin form of mismatched CWG DNA, interfering with transcription elongation by RNA polymerase through a preferential activity toward repeat-expanded DNA. We found that CWG-cPIP selectively inhibited pathogenic mRNA transcripts from expanded CWG repeats, reducing CUG RNA foci and polyglutamine accumulation in cells from patients with myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Treatment with CWG-cPIP ameliorated behavioral deficits in adeno-associated virus-mediated CWG repeat-expressing mice and in a genetic mouse model of HD, without cytotoxicity or off-target effects. Together, we present a candidate compound that targets expanded CWG repeat DNA independently of its genomic location and reduces both pathogenic RNA and protein levels. CWG-cPIP may be used for the treatment of CWG repeat diseases and improvement of clinical outcomes.
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Affiliation(s)
- Susumu Ikenoshita
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Department of Neurology, Graduate School of Medical Sciences
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Kosuke Kawakubo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Karin Hori
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, Japan
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis and
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Kyoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
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9
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Wang B, Yang H. Progress of CRISPR-based programmable RNA manipulation and detection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1804. [PMID: 37282821 DOI: 10.1002/wrna.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Prokaryotic clustered regularly interspaced short palindromic repeats and CRISPR associated (CRISPR-Cas) systems provide adaptive immunity by using RNA-guided endonucleases to recognize and eliminate invading foreign nucleic acids. Type II Cas9, type V Cas12, type VI Cas13, and type III Csm/Cmr complexes have been well characterized and developed as programmable platforms for selectively targeting and manipulating RNA molecules of interest in prokaryotic and eukaryotic cells. These Cas effectors exhibit remarkable diversity of ribonucleoprotein (RNP) composition, target recognition and cleavage mechanisms, and self discrimination mechanisms, which are leveraged for various RNA targeting applications. Here, we summarize the current understanding of mechanistic and functional characteristics of these Cas effectors, give an overview on RNA detection and manipulation toolbox established so far including knockdown, editing, imaging, modification, and mapping RNA-protein interactions, and discuss the future directions for CRISPR-based RNA targeting tools. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Beibei Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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10
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Tota EM, Devaraj NK. RNA-TAG Mediated Protein-RNA Conjugation. Chembiochem 2023; 24:e202300454. [PMID: 37500587 PMCID: PMC11182364 DOI: 10.1002/cbic.202300454] [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: 06/19/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Combinations of biological macromolecules can provide researchers with precise control and unique methods for regulating, studying, and manipulating cellular processes. For instance, combining the unmatched encodability afforded by nucleic acids with the diverse functionality of proteins has transformed our approach to solving several problems in chemical biology. Despite these benefits, there remains a need for new methods to site-specifically generate conjugates between different classes of biomolecules. Here we present a fully enzymatic strategy for combining nucleic acids and proteins using SNAP-tag and RNA-TAG (transglycosylation at guanosine) technologies via a bifunctional preQ1-benzylguanine small molecule probe. We demonstrate the robust ability of this technology to assemble site-specific SNAP-tag - RNA conjugates with RNAs of varying length and use our conjugation strategy to recruit an endonuclease to an RNA of interest for targeted degradation. We foresee that combining SNAP-tag and RNA-TAG will facilitate researchers to predictably engineer novel macromolecular complexes.
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Affiliation(s)
- Ember M Tota
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, La Jolla, CA 92093, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, La Jolla, CA 92093, USA
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11
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Huang S, Dai R, Zhang Z, Zhang H, Zhang M, Li Z, Zhao K, Xiong W, Cheng S, Wang B, Wan Y. CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis. Int J Mol Sci 2023; 24:13447. [PMID: 37686249 PMCID: PMC10487896 DOI: 10.3390/ijms241713447] [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: 07/21/2023] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
CRISPR/Cas systems have found widespread applications in gene editing due to their high accuracy, high programmability, ease of use, and affordability. Benefiting from the cleavage properties (trans- or cis-) of Cas enzymes, the scope of CRISPR/Cas systems has expanded beyond gene editing and they have been utilized in various fields, particularly in live-cell imaging and bioanalysis. In this review, we summarize some fundamental working mechanisms and concepts of the CRISPR/Cas systems, describe the recent advances and design principles of CRISPR/Cas mediated techniques employed in live-cell imaging and bioanalysis, highlight the main applications in the imaging and biosensing of a wide range of molecular targets, and discuss the challenges and prospects of CRISPR/Cas systems in live-cell imaging and biosensing. By illustrating the imaging and bio-sensing processes, we hope this review will guide the best use of the CRISPR/Cas in imaging and quantifying biological and clinical elements and inspire new ideas for better tool design in live-cell imaging and bioanalysis.
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Affiliation(s)
- Shuo Huang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Rui Dai
- Institute of Oceanography, Hainan University, Haikou 570228, China;
| | - Zhiqi Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Han Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Meng Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Zhangjun Li
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Kangrui Zhao
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Wenjun Xiong
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Siyu Cheng
- College of Art and Design, Hainan University, Haikou 570228, China;
| | - Buhua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
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12
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Nikom D, Zheng S. Alternative splicing in neurodegenerative disease and the promise of RNA therapies. Nat Rev Neurosci 2023; 24:457-473. [PMID: 37336982 DOI: 10.1038/s41583-023-00717-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Alternative splicing generates a myriad of RNA products and protein isoforms of different functions from a single gene. Dysregulated alternative splicing has emerged as a new mechanism broadly implicated in the pathogenesis of neurodegenerative diseases such as Alzheimer disease, amyotrophic lateral sclerosis, frontotemporal dementia, Parkinson disease and repeat expansion diseases. Understanding the mechanisms and functional outcomes of abnormal splicing in neurological disorders is vital in developing effective therapies to treat mis-splicing pathology. In this Review, we discuss emerging research and evidence of the roles of alternative splicing defects in major neurodegenerative diseases and summarize the latest advances in RNA-based therapeutic strategies to target these disorders.
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Affiliation(s)
- David Nikom
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA
| | - Sika Zheng
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA.
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA.
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA.
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13
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Porquet F, Weidong L, Jehasse K, Gazon H, Kondili M, Blacher S, Massotte L, Di Valentin E, Furling D, Gillet NA, Klein AF, Seutin V, Willems L. Specific DMPK-promoter targeting by CRISPRi reverses myotonic dystrophy type 1-associated defects in patient muscle cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:857-871. [PMID: 37273786 PMCID: PMC10238591 DOI: 10.1016/j.omtn.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a neuromuscular disease that originates from an expansion of CTG microsatellites in the 3' untranslated region of the DMPK gene, thus leading to the expression of transcripts containing expanded CUG repeats (CUGexp). The pathophysiology is explained by a toxic RNA gain of function where CUGexp RNAs form nuclear aggregates that sequester and alter the function of MBNL splicing factors, triggering splicing misregulation linked to the DM1 symptoms. There is currently no cure for DM1, and most therapeutic strategies aim at eliminating CUGexp-DMPK transcripts. Here, we investigate a DMPK-promoter silencing strategy using CRISPR interference as a new alternative approach. Different sgRNAs targeting the DMPK promoter are evaluated in DM1 patient muscle cells. The most effective guides allowed us to reduce the level of DMPK transcripts and CUGexp-RNA aggregates up to 80%. The CUGexp-DMPK repression corrects the overall transcriptome, including spliceopathy, and reverses a physiological parameter in DM1 muscle cells. Its action is specific and restricted to the DMPK gene, as confirmed by genome-wide expression analysis. Altogether, our findings highlight DMPK-promoter silencing by CRISPRi as a promising therapeutic approach for DM1.
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Affiliation(s)
- Florent Porquet
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Lin Weidong
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Kévin Jehasse
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Hélène Gazon
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Maria Kondili
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Silvia Blacher
- Laboratory of Biology of Tumor and Development, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Laurent Massotte
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | | | - Denis Furling
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Nicolas Albert Gillet
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, 5000 Namur, Belgium
| | - Arnaud François Klein
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Vincent Seutin
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Luc Willems
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
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El Boujnouni N, van der Bent ML, Willemse M, ’t Hoen PA, Brock R, Wansink DG. Block or degrade? Balancing on- and off-target effects of antisense strategies against transcripts with expanded triplet repeats in DM1. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:622-636. [PMID: 37200862 PMCID: PMC10185704 DOI: 10.1016/j.omtn.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/13/2023] [Indexed: 05/20/2023]
Abstract
Antisense oligonucleotide (ASO) therapies for myotonic dystrophy type 1 (DM1) are based on elimination of transcripts containing an expanded repeat or inhibition of sequestration of RNA-binding proteins. This activity is achievable by both degradation of expanded transcripts and steric hindrance, although it is unknown which approach is superior. We compared blocking ASOs with RNase H-recruiting gapmers of equivalent chemistries. Two DMPK target sequences were selected: the triplet repeat and a unique sequence upstream thereof. We assessed ASO effects on transcript levels, ribonucleoprotein foci and disease-associated missplicing, and performed RNA sequencing to investigate on- and off-target effects. Both gapmers and the repeat blocker led to significant DMPK knockdown and a reduction in (CUG)exp foci. However, the repeat blocker was more effective in MBNL1 protein displacement and had superior efficiency in splicing correction at the tested dose of 100 nM. By comparison, on a transcriptome level, the blocking ASO had the fewest off-target effects. In particular, the off-target profile of the repeat gapmer asks for cautious consideration in further therapeutic development. Altogether, our study demonstrates the importance of evaluating both on-target and downstream effects of ASOs in a DM1 context, and provides guiding principles for safe and effective targeting of toxic transcripts.
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Affiliation(s)
- Najoua El Boujnouni
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - M. Leontien van der Bent
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Marieke Willemse
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Peter A.C. ’t Hoen
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Roland Brock
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 293, Bahrain
- Corresponding author Roland Brock, Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| | - Derick G. Wansink
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Corresponding author Derick G. Wansink, Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
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15
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Cuccurullo C, Striano P, Coppola A. Familial Adult Myoclonus Epilepsy: A Non-Coding Repeat Expansion Disorder of Cerebellar-Thalamic-Cortical Loop. Cells 2023; 12:1617. [PMID: 37371086 DOI: 10.3390/cells12121617] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Familial adult myoclonus Epilepsy (FAME) is a non-coding repeat expansion disorder that has been reported under different acronyms and initially linked to four main loci: FAME1 (8q23.3-q24.1), FAME 2 (2p11.1-q12.1), FAME3 (5p15.31-p15.1), and FAME4 (3q26.32-3q28). To date, it is known that the genetic mechanism underlying FAME consists of the expansion of similar non-coding pentanucleotide repeats, TTTCA and TTTTA, in different genes. FAME is characterized by cortical tremor and myoclonus usually manifesting within the second decade of life, and infrequent seizures by the third or fourth decade. Cortical tremor is the core feature of FAME and is considered part of a spectrum of cortical myoclonus. Neurophysiological investigations as jerk-locked back averaging (JLBA) and corticomuscular coherence analysis, giant somatosensory evoked potentials (SEPs), and the presence of long-latency reflex I (or C reflex) at rest support cortical tremor as the result of the sensorimotor cortex hyperexcitability. Furthermore, the application of transcranial magnetic stimulation (TMS) protocols in FAME patients has recently shown that inhibitory circuits are also altered within the primary somatosensory cortex and the concomitant involvement of subcortical networks. Moreover, neuroimaging studies and postmortem autoptic studies indicate cerebellar alterations and abnormal functional connectivity between the cerebellum and cerebrum in FAME. Accordingly, the pathophysiological mechanism underlying FAME has been hypothesized to reside in decreased sensorimotor cortical inhibition through dysfunction of the cerebellar-thalamic-cortical loop, secondary to primary cerebellar pathology. In this context, the non-coding pentameric expansions have been proposed to cause cerebellar damage through an RNA-mediated toxicity mechanism. The elucidation of the underlying pathological mechanisms of FAME paves the way to novel therapeutic possibilities, such as RNA-targeting treatments, possibly applicable to other neurodegenerative non-coding disorders.
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Affiliation(s)
- Claudia Cuccurullo
- Department of Neuroscience, Reproductive Sciences and Odontostomatology, Federico II University of Naples, 80131 Naples, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, 16126 Genova, Italy
| | - Antonietta Coppola
- Department of Neuroscience, Reproductive Sciences and Odontostomatology, Federico II University of Naples, 80131 Naples, Italy
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16
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [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: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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17
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Advancement in CRISPR/Cas9 Technology to Better Understand and Treat Neurological Disorders. Cell Mol Neurobiol 2023; 43:1019-1035. [PMID: 35751791 DOI: 10.1007/s10571-022-01242-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022]
Abstract
Neurological disorders have complicated pathophysiology that may involve several genetic mutations. Conventional treatment has limitations as they only treat apparent symptoms. Although, personalized medicine is emerging as a promising neuro-intervention, lack of precision is the major pitfall. Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system is evolving as a technological platform that may overcome the therapeutic limitations towards precision medicine. In the future, targeting genes in neurological disorders may be the mainstay of modern therapy. The present review on CRISPR/Cas9 and its application in various neurological disorders may provide a platform for its future clinical relevance towards developing precise and personalized medicine.
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18
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Morelli KH, Smargon AA, Yeo GW. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders. RNA (NEW YORK, N.Y.) 2023; 29:489-497. [PMID: 36693761 PMCID: PMC10019361 DOI: 10.1261/rna.079519.122] [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] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Disruptions in RNA processing play critical roles in the pathogenesis of neurological diseases. In this Perspective, we discuss recent progress in the development of RNA-targeting therapeutic modalities. We focus on progress, limitations, and opportunities in a new generation of therapies engineered from RNA binding proteins and other endogenous RNA regulatory macromolecules to treat human neurological disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
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19
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Teng Y, Zhu M, Qiu Z. G-Quadruplexes in Repeat Expansion Disorders. Int J Mol Sci 2023; 24:ijms24032375. [PMID: 36768697 PMCID: PMC9916761 DOI: 10.3390/ijms24032375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
The repeat expansions are the main genetic cause of various neurodegeneration diseases. More than ten kinds of repeat sequences with different lengths, locations, and structures have been confirmed in the past two decades. G-rich repeat sequences, such as CGG and GGGGCC, are reported to form functional G-quadruplexes, participating in many important bioprocesses. In this review, we conducted an overview concerning the contribution of G-quadruplex in repeat expansion disorders and summarized related mechanisms in current pathological studies, including the increasing genetic instabilities in replication and transcription, the toxic RNA foci formed in neurons, and the loss/gain function of proteins and peptides. Furthermore, novel strategies targeting G-quadruplex repeats were developed based on the understanding of disease mechanism. Small molecules and proteins binding to G-quadruplex in repeat expansions were investigated to protect neurons from dysfunction and delay the progression of neurodegeneration. In addition, the effects of environment on the stability of G-quadruplex were discussed, which might be critical factors in the pathological study of repeat expansion disorders.
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20
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Huang Y, Gao BQ, Meng Q, Yang LZ, Ma XK, Wu H, Pan YH, Yang L, Li D, Chen LL. CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos. Genome Biol 2023; 24:15. [PMID: 36658633 PMCID: PMC9854193 DOI: 10.1186/s13059-023-02848-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Understanding gene transcription and mRNA-protein (mRNP) dynamics in single cells in a multicellular organism has been challenging. The catalytically dead CRISPR-Cas13 (dCas13) system has been used to visualize RNAs in live cells without genetic manipulation. We optimize this system to track developmentally expressed mRNAs in zebrafish embryos and to understand features of endogenous transcription kinetics and mRNP export. RESULTS We report that zygotic microinjection of purified CRISPR-dCas13-fluorescent proteins and modified guide RNAs allows single- and dual-color tracking of developmentally expressed mRNAs in zebrafish embryos from zygotic genome activation (ZGA) until early segmentation period without genetic manipulation. Using this approach, we uncover non-synchronized de novo transcription between inter-alleles, synchronized post-mitotic re-activation in pairs of alleles, and transcriptional memory as an extrinsic noise that potentially contributes to synchronized post-mitotic re-activation. We also reveal rapid dCas13-engaged mRNP movement in the nucleus with a corralled and diffusive motion, but a wide varying range of rate-limiting mRNP export, which can be shortened by Alyref and Nxf1 overexpression. CONCLUSIONS This optimized dCas13-based toolkit enables robust spatial-temporal tracking of endogenous mRNAs and uncovers features of transcription and mRNP motion, providing a powerful toolkit for endogenous RNA visualization in a multicellular developmental organism.
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Affiliation(s)
- Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Bao-Qing Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Quan Meng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hao Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yu-Hang Pan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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21
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RNA-targeting strategies as a platform for ocular gene therapy. Prog Retin Eye Res 2023; 92:101110. [PMID: 35840489 DOI: 10.1016/j.preteyeres.2022.101110] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023]
Abstract
Genetic medicine is offering hope as new therapies are emerging for many previously untreatable diseases. The eye is at the forefront of these advances, as exemplified by the approval of Luxturna® by the United States Food and Drug Administration (US FDA) in 2017 for the treatment of one form of Leber Congenital Amaurosis (LCA), an inherited blindness. Luxturna® was also the first in vivo human gene therapy to gain US FDA approval. Numerous gene therapy clinical trials are ongoing for other eye diseases, and novel delivery systems, discovery of new drug targets and emerging technologies are currently driving the field forward. Targeting RNA, in particular, is an attractive therapeutic strategy for genetic disease that may have safety advantages over alternative approaches by avoiding permanent changes in the genome. In this regard, antisense oligonucleotides (ASO) and RNA interference (RNAi) are the currently popular strategies for developing RNA-targeted therapeutics. Enthusiasm has been further fuelled by the emergence of clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR associated (Cas) systems that allow targeted manipulation of nucleic acids. RNA-targeting CRISPR-Cas systems now provide a novel way to develop RNA-targeted therapeutics and may provide superior efficiency and specificity to existing technologies. In addition, RNA base editing technologies using CRISPR-Cas and other modalities also enable precise alteration of single nucleotides. In this review, we showcase advances made by RNA-targeting systems for ocular disease, discuss applications of ASO and RNAi technologies, highlight emerging CRISPR-Cas systems and consider the implications of RNA-targeting therapeutics in the development of future drugs to treat eye disease.
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22
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Morelli KH, Wu Q, Gosztyla ML, Liu H, Yao M, Zhang C, Chen J, Marina RJ, Lee K, Jones KL, Huang MY, Li A, Smith-Geater C, Thompson LM, Duan W, Yeo GW. An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models. Nat Neurosci 2023; 26:27-38. [PMID: 36510111 PMCID: PMC9829537 DOI: 10.1038/s41593-022-01207-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 10/18/2022] [Indexed: 12/14/2022]
Abstract
Huntington's disease (HD) is a fatal, dominantly inherited neurodegenerative disorder caused by CAG trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Since the reduction of pathogenic mutant HTT messenger RNA is therapeutic, we developed a mutant allele-sensitive CAGEX RNA-targeting CRISPR-Cas13d system (Cas13d-CAGEX) that eliminates toxic CAGEX RNA in fibroblasts derived from patients with HD and induced pluripotent stem cell-derived neurons. We show that intrastriatal delivery of Cas13d-CAGEX via an adeno-associated viral vector selectively reduces mutant HTT mRNA and protein levels in the striatum of heterozygous zQ175 mice, a model of HD. This also led to improved motor coordination, attenuated striatal atrophy and reduction of mutant HTT protein aggregates. These phenotypic improvements lasted for at least eight months without adverse effects and with minimal off-target transcriptomic effects. Taken together, we demonstrate proof of principle of an RNA-targeting CRISPR-Cas13d system as a therapeutic approach for HD, a strategy with implications for the treatment of other dominantly inherited disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qian Wu
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hongshuai Liu
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Minmin Yao
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chuangchuang Zhang
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaxu Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ryan J Marina
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kari Lee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten L Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Megan Y Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Allison Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Charlene Smith-Geater
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - Leslie M Thompson
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Wenzhen Duan
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
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23
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Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
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Abstract
PURPOSE OF REVIEW Myotonic dystrophy type 1 (DM1) and myotonic dystrophy type 2 (DM2) are genetic disorders affecting skeletal and smooth muscle, heart, brain, eyes, and other organs. The multisystem involvement and disease variability of myotonic dystrophy have presented challenges for clinical care and research. This article focuses on the diagnosis and management of the disease. In addition, recent advances in characterizing the diverse clinical manifestations and variability of the disease are discussed. RECENT FINDINGS Studies of the multisystem involvement of myotonic dystrophy, including the most lethal cardiac and respiratory manifestations and their molecular underpinnings, expand our understanding of the myotonic dystrophy phenotype. Advances have been made in understanding the molecular mechanisms of both types of myotonic dystrophy, providing opportunities for developing targeted therapeutics, some of which have entered clinical trials in DM1. SUMMARY Continued efforts focus on advancing our molecular and clinical understanding of DM1 and DM2. Accurately measuring and monitoring the diverse and variable clinical manifestations of myotonic dystrophy in clinic and in research is important to provide adequate care, prevent complications, and find treatments that improve symptoms and life quality.
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25
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CRISPR-Based Tools for Fighting Rare Diseases. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121968. [PMID: 36556333 PMCID: PMC9787644 DOI: 10.3390/life12121968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022]
Abstract
Rare diseases affect the life of a tremendous number of people globally. The CRISPR-Cas system emerged as a powerful genome engineering tool and has facilitated the comprehension of the mechanism and development of therapies for rare diseases. This review focuses on current efforts to develop the CRISPR-based toolbox for various rare disease therapy applications and compares the pros and cons of different tools and delivery methods. We further discuss the therapeutic applications of CRISPR-based tools for fighting different rare diseases.
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26
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Nelson AL, Fontana G, Miclau E, Rongstad M, Murphy W, Huard J, Ehrhart N, Bahney C. Therapeutic approaches to activate the canonical Wnt pathway for bone regeneration. J Tissue Eng Regen Med 2022; 16:961-976. [PMID: 36112528 PMCID: PMC9826348 DOI: 10.1002/term.3349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 01/12/2023]
Abstract
Activation of the canonical Wingless-related integration site (Wnt) pathway has been shown to increase bone formation and therefore has therapeutic potential for use in orthopedic conditions. However, attempts at developing an effective strategy to achieve Wnt activation has been met with several challenges. The inherent hydrophobicity of Wnt ligands makes isolating and purifying the protein difficult. To circumvent these challenges, many have sought to target extracellular inhibitors of the Wnt pathway, such as Wnt signaling pathway inhibitors Sclerostin and Dickkopf-1, or to use small molecules, ions and proteins to increase target Wnt genes. Here, we review systemic and localized bioactive approaches to enhance bone formation or improve bone repair through antibody-based therapeutics, synthetic Wnt surrogates and scaffold doping to target canonical Wnt. We conclude with a brief review of emerging technologies, such as mRNA therapy and Clustered Regularly Interspaced Short Palindromic Repeats technology, which serve as promising approaches for future clinical translation.
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Affiliation(s)
- Anna Laura Nelson
- Center for Regenerative and Personalized MedicineSteadman Philippon Research Institute (SPRI)VailColoradoUSA,School of Biomedical EngineeringColorado State UniversityFort CollinsColoradoUSA
| | - GianLuca Fontana
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Elizabeth Miclau
- Center for Regenerative and Personalized MedicineSteadman Philippon Research Institute (SPRI)VailColoradoUSA
| | - Mallory Rongstad
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - William Murphy
- Department of Orthopedics and RehabilitationUniversity of Wisconsin‐MadisonMadisonWisconsinUSA,Department of Biomedical EngineeringUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Johnny Huard
- Center for Regenerative and Personalized MedicineSteadman Philippon Research Institute (SPRI)VailColoradoUSA,Department of Clinical SciencesColorado State UniversityFort CollinsColoradoUSA
| | - Nicole Ehrhart
- School of Biomedical EngineeringColorado State UniversityFort CollinsColoradoUSA,Department of Clinical SciencesColorado State UniversityFort CollinsColoradoUSA
| | - Chelsea Bahney
- Center for Regenerative and Personalized MedicineSteadman Philippon Research Institute (SPRI)VailColoradoUSA,School of Biomedical EngineeringColorado State UniversityFort CollinsColoradoUSA,Department of Clinical SciencesColorado State UniversityFort CollinsColoradoUSA,Orthopaedic Trauma InstituteUniversity of California, San Francisco (UCSF)San FranciscoCaliforniaUSA
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27
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Qin Y, Li S, Li XJ, Yang S. CRISPR-Based Genome-Editing Tools for Huntington's Disease Research and Therapy. Neurosci Bull 2022; 38:1397-1408. [PMID: 35608753 PMCID: PMC9672252 DOI: 10.1007/s12264-022-00880-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/17/2022] [Indexed: 10/18/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominantly-inherited neurodegenerative disease, which is caused by CAG trinucleotide expansion in exon 1 of the Huntingtin (HTT) gene. Although HD is a rare disease, its monogenic nature makes it an ideal model in which to understand pathogenic mechanisms and to develop therapeutic strategies for neurodegenerative diseases. Clustered regularly-interspaced short palindromic repeats (CRISPR) is the latest technology for genome editing. Being simple to use and highly efficient, CRISPR-based genome-editing tools are rapidly gaining popularity in biomedical research and opening up new avenues for disease treatment. Here, we review the development of CRISPR-based genome-editing tools and their applications in HD research to offer a translational perspective on advancing the genome-editing technology to HD treatment.
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Affiliation(s)
- Yiyang Qin
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Su Yang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
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28
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Alharbi KS, Javed Shaikh MA, Afzal O, Alfawaz Altamimi AS, Hassan almalki W, Kazmi I, Al-Abbasi FA, Alzarea SI, Babu MR, Singh SK, Chellappan DK, Dua K, Gupta G. Oligonucleotides: A novel area of interest for drug delivery in neurodegenerative diseases. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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29
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Guh CY, Shen HJ, Chen LW, Chiu PC, Liao IH, Lo CC, Chen Y, Hsieh YH, Chang TC, Yen CP, Chen YY, Chen TWW, Chen LY, Wu CS, Egly JM, Chu HPC. XPF activates break-induced telomere synthesis. Nat Commun 2022; 13:5781. [PMID: 36184605 PMCID: PMC9527253 DOI: 10.1038/s41467-022-33428-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Alternative Lengthening of Telomeres (ALT) utilizes a recombination mechanism and break-induced DNA synthesis to maintain telomere length without telomerase, but it is unclear how cells initiate ALT. TERRA, telomeric repeat-containing RNA, forms RNA:DNA hybrids (R-loops) at ALT telomeres. We show that depleting TERRA using an RNA-targeting Cas9 system reduces ALT-associated PML bodies, telomere clustering, and telomere lengthening. TERRA interactome reveals that TERRA interacts with an extensive subset of DNA repair proteins in ALT cells. One of TERRA interacting proteins, the endonuclease XPF, is highly enriched at ALT telomeres and recruited by telomeric R-loops to induce DNA damage response (DDR) independent of CSB and SLX4, and thus triggers break-induced telomere synthesis and lengthening. The attraction of BRCA1 and RAD51 at telomeres requires XPF in FANCM-deficient cells that accumulate telomeric R-loops. Our results suggest that telomeric R-loops activate DDR via XPF to promote homologous recombination and telomere replication to drive ALT.
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Affiliation(s)
- Chia-Yu Guh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Hong-Jhih Shen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Liv WeiChien Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Pei-Chen Chiu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - I-Hsin Liao
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Chen-Chia Lo
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Yunfei Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Yu-Hung Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Ting-Chia Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Chien-Ping Yen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
| | - Yi-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tom Wei-Wu Chen
- Department of Oncology, National Taiwan University Hospital and Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Liuh-Yow Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Shyi Wu
- Department of Pharmacology, National Taiwan University, Taipei, Taiwan
| | - Jean-Marc Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Strasbourg, France.,College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsueh-Ping Catherine Chu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan.
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30
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Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022; 5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [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: 05/14/2022] [Accepted: 08/17/2022] [Indexed: 01/31/2023] Open
Abstract
CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.
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Affiliation(s)
- Oana Pelea
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tudor A. Fulga
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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31
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Burris BJD, Molina Vargas AM, Park BJ, O'Connell MR. Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13. Methods 2022; 206:58-68. [PMID: 35987443 PMCID: PMC9511595 DOI: 10.1016/j.ymeth.2022.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 01/03/2023] Open
Abstract
Prokaryotic adaptive immune systems use Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR Associated (Cas) proteins to target and cleave foreign genetic elements in an RNA-guided manner [1-3]. Type VI CRISPR-Cas systems contain a single effector ribonuclease, Cas13, that binds and processes a CRISPR-RNA (crRNA; also known as a guide-RNA), forming an RNA-guided RNA-targeting effector complex [4,5]. Previous studies have shown that Cas13 can be engineered to target and modulate RNA processes in human cells, illustrating the versatility and specificity of Cas13 as an RNA knockdown (KD), splicing, editing, or imaging tool [6-8]. While Cas13 has been successfully used by several groups, our lab has observed significant variability in Cas13 KD ability depending which protocol is being followed [9-12]. To further understand this variability and generate a robust Cas13 KD protocol we thoroughly tested which Cas13 ortholog to use, the duration of KD experiments, the amount of plasmid DNA transfected, methods for analyzing KD efficiency, and report an optimized method for carrying out and analyzing Cas13 mediated RNA KD experiments. The method outlined in this paper illustrates a faster and more reliable protocol to iteratively test gRNA performance and target gene KD.
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Affiliation(s)
- Brandon Joseph Davis Burris
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Adrian Moises Molina Vargas
- Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA; Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, NY 14642, USA
| | - Brandon J Park
- Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA; Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, NY 14642, USA
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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32
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van der Bent ML, Evers MM, Vallès A. Emerging Therapies for Huntington's Disease - Focus on N-Terminal Huntingtin and Huntingtin Exon 1. Biologics 2022; 16:141-160. [PMID: 36213816 PMCID: PMC9532260 DOI: 10.2147/btt.s270657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/14/2022] [Indexed: 11/12/2022]
Abstract
Huntington's disease is a devastating heritable neurodegenerative disorder that is caused by the presence of a trinucleotide CAG repeat expansion in the Huntingtin gene, leading to a polyglutamine tract in the protein. Various mechanisms lead to the production of N-terminal Huntingtin protein fragments, which are reportedly more toxic than the full-length protein. In this review, we summarize the current knowledge on the production and toxicity of N-terminal Huntingtin protein fragments. Further, we expand on various therapeutic strategies targeting N-terminal Huntingtin on the protein, RNA and DNA level. Finally, we compare the therapeutic approaches that are clinically most advanced, including those that do not target N-terminal Huntingtin, discussing differences in mode of action and translational applicability.
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Affiliation(s)
| | - Melvin M Evers
- uniQure biopharma B.V., Department of Research and Development, Amsterdam, the Netherlands
| | - Astrid Vallès
- uniQure biopharma B.V., Department of Research and Development, Amsterdam, the Netherlands
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33
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Chhabra R, Muthusamy V, Baveja A, Katral A, Mehta B, Zunjare RU, Hossain F. Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds. PLoS One 2022; 17:e0274732. [PMID: 36136965 PMCID: PMC9498942 DOI: 10.1371/journal.pone.0274732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/03/2022] [Indexed: 11/24/2022] Open
Abstract
Sweet corn has become a popular food worldwide. It possesses six-times more sugar than field corn due to the presence of recessive shrunken2 (sh2) gene. Despite availability of diverse sweet corn germplasm, comprehensive characterization of sh2 has not been undertaken so far. Here, entire Sh2 gene (7320 bp) among five field corn-(Sh2Sh2) and six sweet corn-(sh2sh2) inbreds was sequenced. A total of 686 SNPs and 372 InDels were identified, of which three SNPs differentiated the wild-(Sh2) and mutant-(sh2) allele. Ten InDel markers were developed to assess sh2 gene-based diversity among 23 sweet corn and 25 field corn lines. Twenty-five alleles and 47 haplotypes of sh2 were identified among 48 inbreds. Among markers, MGU-InDel-2, MGU-InDel-3, MGU-InDel-5 and MGU-InDel-8 had PIC>0.5. Major allele frequency varied from 0.458–0.958. The gene sequence of these maize inbreds was compared with 25 orthologues of monocots. Sh2 gene possessed 15–18 exons with 6-225bp among maize, while it was 6–21 exons with 30-441bp among orthologues. While intron length across maize genotypes varied between 67-2069bp, the same among orthologues was 57–2713 bp. Sh2-encoded AGPase domain was more conserved than NTP transferase domain. Nucleotide and protein sequences of sh2 in maize and orthologues revealed that rice orthologue was closer to maize than other monocots. The study also provided details of motifs and domains present in sh2 gene, physicochemical properties and secondary structure of SH2 protein in maize inbreds and orthologues. This study reports detailed characterization and diversity analysis in sh2 gene of maize and related orthologues in various monocots.
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Affiliation(s)
- Rashmi Chhabra
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Aanchal Baveja
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Brijesh Mehta
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, India
- * E-mail:
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Rhine K, Al-Azzam N, Yu T, Yeo GW. Aging RNA granule dynamics in neurodegeneration. Front Mol Biosci 2022; 9:991641. [PMID: 36188213 PMCID: PMC9523239 DOI: 10.3389/fmolb.2022.991641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/22/2022] [Indexed: 12/30/2022] Open
Abstract
Disordered RNA-binding proteins and repetitive RNA sequences are the main genetic causes of several neurodegenerative diseases, including amyotrophic lateral sclerosis and Huntington's disease. Importantly, these components also seed the formation of cytoplasmic liquid-like granules, like stress granules and P bodies. Emerging evidence demonstrates that healthy granules formed via liquid-liquid phase separation can mature into solid- or gel-like inclusions that persist within the cell. These solidified inclusions are a precursor to the aggregates identified in patients, demonstrating that dysregulation of RNA granule biology is an important component of neurodegeneration. Here, we review recent literature highlighting how RNA molecules seed proteinaceous granules, the mechanisms of healthy turnover of RNA granules in cells, which biophysical properties underly a transition to solid- or gel-like material states, and why persistent granules disrupt the cellular homeostasis of neurons. We also identify various methods that will illuminate the contributions of disordered proteins and RNAs to neurodegeneration in ongoing research efforts.
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Affiliation(s)
- Kevin Rhine
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
| | - Norah Al-Azzam
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
| | - Tao Yu
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- Stem Cell Program, University of California, San Diego, San Diego, CA, United States
- Institute for Genomic Medicine, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
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35
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Kurosaki T, Ashizawa T. The genetic and molecular features of the intronic pentanucleotide repeat expansion in spinocerebellar ataxia type 10. Front Genet 2022; 13:936869. [PMID: 36199580 PMCID: PMC9528567 DOI: 10.3389/fgene.2022.936869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is characterized by progressive cerebellar neurodegeneration and, in many patients, epilepsy. This disease mainly occurs in individuals with Indigenous American or East Asian ancestry, with strong evidence supporting a founder effect. The mutation causing SCA10 is a large expansion in an ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene. The ATTCT repeat is highly unstable, expanding to 280–4,500 repeats in affected patients compared with the 9–32 repeats in normal individuals, one of the largest repeat expansions causing neurological disorders identified to date. However, the underlying molecular basis of how this huge repeat expansion evolves and contributes to the SCA10 phenotype remains largely unknown. Recent progress in next-generation DNA sequencing technologies has established that the SCA10 repeat sequence has a highly heterogeneous structure. Here we summarize what is known about the structure and origin of SCA10 repeats, discuss the potential contribution of variant repeats to the SCA10 disease phenotype, and explore how this information can be exploited for therapeutic benefit.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
- Center for RNA Biology, University of Rochester, Rochester, NY, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
| | - Tetsuo Ashizawa
- Stanley H. Appel Department of Neurology, Houston Methodist Research Institute and Weil Cornell Medical College at Houston Methodist Houston, TX, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
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36
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Han RC, MacLaren RE. RNA gene editing in the eye and beyond: The neglected tool of the gene editing armatorium? INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 372:175-205. [PMID: 36064264 DOI: 10.1016/bs.ircmb.2022.04.009] [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] [Indexed: 11/22/2022]
Abstract
RNA editing allows correction of pathological point mutations without permanently altering genomic DNA. Theoretically targetable to any RNA type and site, its flexibility and reversibility makes it a potentially powerful gene editing tool. RNA editing offers a host of potential advantages in specific niches when compared to currently available alternative gene manipulation techniques. Unlike DNA editors, which are currently too large to be delivered in vivo using a viral vector, smaller RNA editors fit easily within the capabilities of an adeno-associated virus (AAV). Unlike gene augmentation, which is limited by gene size and viral packaging constraints, RNA editing may correct transcripts too long to fit within a viral vector. In this article we examine the development of RNA editing and discuss potential applications and pitfalls. We argue that, although in its infancy, an RNA editing approach can offer unique advantages for selected retinal diseases.
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Affiliation(s)
- Ruofan Connie Han
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom.
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; Oxford Eye Hospital, John Radcliffe, Oxford, United Kingdom
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37
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Yang LZ, Gao BQ, Huang Y, Wang Y, Yang L, Chen LL. Multi-color RNA imaging with CRISPR-Cas13b systems in living cells. CELL INSIGHT 2022; 1:100044. [PMID: 37192858 PMCID: PMC10120316 DOI: 10.1016/j.cellin.2022.100044] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 05/18/2023]
Abstract
Visualizing RNA dynamics is important for understanding RNA function. Catalytically dead (d) CRISPR-Cas13 systems have been established to image and track RNAs in living cells, but efficient dCas13 for RNA imaging is still limited. Here, we analyzed metagenomic and bacterial genomic databases to comprehensively screen Cas13 homologies for their RNA labeling capabilities in living mammalian cells. Among eight previously unreported dCas13 proteins that can be used for RNA labeling, dHgm4Cas13b and dMisCas13b displayed comparable, if not higher, efficiencies to the best-known ones when targeting endogenous MUC4 and NEAT1_2 by single guide (g) RNAs. Further examination of the labeling robustness of different dCas13 systems using the GCN4 repeats revealed that a minimum of 12 GCN4 repeats was required for dHgm4Cas13b and dMisCas13b imaging at the single RNA molecule level, while >24 GCN4 repeats were required for reported dLwaCas13a, dRfxCas13d and dPguCas13b. Importantly, by silencing pre-crRNA processing activity of dMisCas13b (ddMisCas13b) and further incorporating RNA aptamers including PP7, MS2, Pepper or BoxB to individual gRNAs, a CRISPRpalette system was developed to successfully achieve multi-color RNA visualization in living cells.
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Affiliation(s)
- Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bao-Qing Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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38
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Detection of repeat expansions in large next generation DNA and RNA sequencing data without alignment. Sci Rep 2022; 12:13124. [PMID: 35907931 PMCID: PMC9338934 DOI: 10.1038/s41598-022-17267-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Bioinformatic methods for detecting short tandem repeat expansions in short-read sequencing have identified new repeat expansions in humans, but require alignment information to identify repetitive motif enrichment at genomic locations. We present superSTR, an ultrafast method that does not require alignment. superSTR is used to process whole-genome and whole-exome sequencing data, and perform the first STR analysis of the UK Biobank, efficiently screening and identifying known and potential disease-associated STRs in the exomes of 49,953 biobank participants. We demonstrate the first bioinformatic screening of RNA sequencing data to detect repeat expansions in humans and mouse models of ataxia and dystrophy.
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Wilson KM, Katona E, Glaria I, Carcolé M, Swift IJ, Sogorb-Esteve A, Heller C, Bouzigues A, Heslegrave AJ, Keshavan A, Knowles K, Patil S, Mohapatra S, Liu Y, Goyal J, Sanchez-Valle R, Laforce RJ, Synofzik M, Rowe JB, Finger E, Vandenberghe R, Butler CR, Gerhard A, Van Swieten JC, Seelaar H, Borroni B, Galimberti D, de Mendonça A, Masellis M, Tartaglia MC, Otto M, Graff C, Ducharme S, Schott JM, Malaspina A, Zetterberg H, Boyanapalli R, Rohrer JD, Isaacs AM. Development of a sensitive trial-ready poly(GP) CSF biomarker assay for C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis. J Neurol Neurosurg Psychiatry 2022; 93:761-771. [PMID: 35379698 PMCID: PMC9279742 DOI: 10.1136/jnnp-2021-328710] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 01/15/2023]
Abstract
OBJECTIVE A GGGGCC repeat expansion in the C9orf72 gene is the most common cause of genetic frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). As potential therapies targeting the repeat expansion are now entering clinical trials, sensitive biomarker assays of target engagement are urgently required. Our objective was to develop such an assay. METHODS We used the single molecule array (Simoa) platform to develop an immunoassay for measuring poly(GP) dipeptide repeat proteins (DPRs) generated by the C9orf72 repeat expansion in cerebrospinal fluid (CSF) of people with C9orf72-associated FTD/ALS. RESULTS AND CONCLUSIONS We show the assay to be highly sensitive and robust, passing extensive qualification criteria including low intraplate and interplate variability, a high precision and accuracy in measuring both calibrators and samples, dilutional parallelism, tolerance to sample and standard freeze-thaw and no haemoglobin interference. We used this assay to measure poly(GP) in CSF samples collected through the Genetic FTD Initiative (N=40 C9orf72 and 15 controls). We found it had 100% specificity and 100% sensitivity and a large window for detecting target engagement, as the C9orf72 CSF sample with the lowest poly(GP) signal had eightfold higher signal than controls and on average values from C9orf72 samples were 38-fold higher than controls, which all fell below the lower limit of quantification of the assay. These data indicate that a Simoa-based poly(GP) DPR assay is suitable for use in clinical trials to determine target engagement of therapeutics aimed at reducing C9orf72 repeat-containing transcripts.
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Affiliation(s)
- Katherine M Wilson
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Eszter Katona
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Idoia Glaria
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mireia Carcolé
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Imogen J Swift
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Aitana Sogorb-Esteve
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Carolin Heller
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Arabella Bouzigues
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Amanda J Heslegrave
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
| | - Ashvini Keshavan
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Kathryn Knowles
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | | | - Yuanjing Liu
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | - Jaya Goyal
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | - Raquel Sanchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic, Institut d'Investigacións Biomèdiques August Pi I Sunyer, University of Barcelona, Barcelona, Spain
| | - Robert Jr Laforce
- Clinique Interdisciplinaire de Mémoire, Département des Sciences Neurologiques, CHU de Québec, and Faculté de Médecine, Université Laval, Quebec City, Quebec, Canada
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- Center for Neurodegenerative Diseases, (DZNE), Tübingen, Germany
| | - James B Rowe
- Department of Clinical Neurosciences and Cambridge University Hospitals NHS Trust and Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Elizabeth Finger
- Department of Clinical Neurological Sciences, University of Western Ontario, University of Western Ontario, London, Ontario, Canada
| | - Rik Vandenberghe
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Neurology Service, University Hospitals, Leuven, Belgium
| | - Christopher R Butler
- Nuffield Department of Clinical Neurosciences, Medical Sciences Division, University of Oxford, Oxford, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Alexander Gerhard
- Division of Neuroscience and Experimental Psychology, Wolfson Molecular Imaging Centre, The University of Manchester, Manchester, UK
- Departments of Geriatric Medicine and Nuclear Medicine, University of Duisburg- Essen, University of Duisburg- Essen, Essen, Germany
| | | | - Harro Seelaar
- Department of Neurology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Barbara Borroni
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Daniela Galimberti
- Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Centro Dino Ferrari, University of Milan, Milan, Italy
| | | | - Mario Masellis
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - M Carmela Tartaglia
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, Ontario, Canada
- Canadian Sports Concussion Project, Toronto, Ontario, Canada
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Caroline Graff
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Bioclinicum, Karolinska Institutet, Solna, Sweden
- Unit for Hereditary Dementias, Theme Aging, Karolinska University Hospital, Solna, Sweden
| | - Simon Ducharme
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Jonathan M Schott
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Andrea Malaspina
- Barts and The London School of Medicine and Dentistry Blizard Institute, London, UK
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Henrik Zetterberg
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | | | - Jonathan D Rohrer
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Adrian M Isaacs
- UK Dementia Research Institute at UCL, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
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40
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Gene Therapy in Amyotrophic Lateral Sclerosis. Cells 2022; 11:cells11132066. [PMID: 35805149 PMCID: PMC9265980 DOI: 10.3390/cells11132066] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/30/2022] Open
Abstract
Since the discovery of Cu/Zn superoxide dismutase (SOD1) gene mutation, in 1993, as the first genetic abnormality in amyotrophic lateral sclerosis (ALS), over 50 genes have been identified as either cause or modifier in ALS and ALS/frontotemporal dementia (FTD) spectrum disease. Mutations in C9orf72, SOD1, TAR DNA binding protein 43 (TARDBP), and fused in sarcoma (FUS) genes are the four most common ones. During the last three decades, tremendous effort has been made worldwide to reveal biological pathways underlying the pathogenesis of these gene mutations in ALS/FTD. Accordingly, targeting etiologic genes (i.e., gene therapies) to suppress their toxic effects have been investigated widely. It includes four major strategies: (i) removal or inhibition of abnormal transcribed RNA using microRNA or antisense oligonucleotides (ASOs), (ii) degradation of abnormal mRNA using RNA interference (RNAi), (iii) decrease or inhibition of mutant proteins (e.g., using antibodies against misfolded proteins), and (iv) DNA genome editing with methods such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas). The promising results of these studies have led to the application of some of these strategies into ALS clinical trials, especially for C9orf72 and SOD1. In this paper, we will overview advances in gene therapy in ALS/FTD, focusing on C9orf72, SOD1, TARDBP, and FUS genes.
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41
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Mechanistic and Therapeutic Insights into Ataxic Disorders with Pentanucleotide Expansions. Cells 2022; 11:cells11091567. [PMID: 35563872 PMCID: PMC9099484 DOI: 10.3390/cells11091567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Pentanucleotide expansion diseases constitute a special class of neurodegeneration. The repeat expansions occur in non-coding regions, have likely arisen from Alu elements, and often result in autosomal dominant or recessive phenotypes with underlying cerebellar neuropathology. When transcribed (potentially bidirectionally), the expanded RNA forms complex secondary and tertiary structures that can give rise to RNA-mediated toxicity, including protein sequestration, pentapeptide synthesis, and mRNA dysregulation. Since several of these diseases have recently been discovered, our understanding of their pathological mechanisms is limited, and their therapeutic interventions underexplored. This review aims to highlight new in vitro and in vivo insights into these incurable diseases.
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42
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Molecular Therapies for Myotonic Dystrophy Type 1: From Small Drugs to Gene Editing. Int J Mol Sci 2022; 23:ijms23094622. [PMID: 35563013 PMCID: PMC9101876 DOI: 10.3390/ijms23094622] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy affecting many different body tissues, predominantly skeletal and cardiac muscles and the central nervous system. The expansion of CTG repeats in the DM1 protein-kinase (DMPK) gene is the genetic cause of the disease. The pathogenetic mechanisms are mainly mediated by the production of a toxic expanded CUG transcript from the DMPK gene. With the availability of new knowledge, disease models, and technical tools, much progress has been made in the discovery of altered pathways and in the potential of therapeutic intervention, making the path to the clinic a closer reality. In this review, we describe and discuss the molecular therapeutic strategies for DM1, which are designed to directly target the CTG genomic tract, the expanded CUG transcript or downstream signaling molecules.
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43
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Piao X, Meng D, Zhang X, Song Q, Lv H, Jia Y. Dual-gRNA approach with limited off-target effect corrects C9ORF72 repeat expansion in vivo. Sci Rep 2022; 12:5672. [PMID: 35383205 PMCID: PMC8983752 DOI: 10.1038/s41598-022-07746-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
C9ORF72 GGGGCC repeat expansion is the most common genetic cause for amyotrophic lateral sclerosis and frontotemporal dementia, which generates abnormal DNA and RNA structures and produces toxic proteins. Recently, efficacy of CRISPR/Cas9-mediated editing has been proven in treatment of disease. However, DNA low complexity surrounding C9ORF72 expansion increases the off-target risks. Here we provide a dual-gRNA design outside of the low complexity region which enables us to remove the repeat DNA in a 'cutting-deletion-fusion' manner with a high fusion efficiency (50%). Our dual-gRNA design limits off-target effect and does not significantly affect C9ORF72 expression. In neurons carrying patient C9ORF72 expansion, our approach removes the repeat DNA and corrects the RNA foci in vitro and in vivo. Therefore, we conclude that our proof-of-concept design correct C9ORF72 repeat expansion, which may have potential therapeutic value for the patients.
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Affiliation(s)
- Xuejiao Piao
- School of Medicine, Medical Science Building, Room D204, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Beijing, China
- IDG/McGovern Institute for Brain Research at Tsinghua, Beijing, China
| | - Dawei Meng
- School of Medicine, Medical Science Building, Room D204, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Beijing, China
- IDG/McGovern Institute for Brain Research at Tsinghua, Beijing, China
| | - Xue Zhang
- School of Medicine, Medical Science Building, Room D204, Tsinghua University, Beijing, 100084, China
- Peking-Tsinghua Joint Center for Life Sciences, Beijing, China
- IDG/McGovern Institute for Brain Research at Tsinghua, Beijing, China
| | - Qiang Song
- School of Medicine, Medical Science Building, Room D204, Tsinghua University, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua, Beijing, China
| | - Hailong Lv
- School of Medicine, Medical Science Building, Room D204, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Beijing, China
- IDG/McGovern Institute for Brain Research at Tsinghua, Beijing, China
| | - Yichang Jia
- School of Medicine, Medical Science Building, Room D204, Tsinghua University, Beijing, 100084, China.
- Peking-Tsinghua Joint Center for Life Sciences, Beijing, China.
- IDG/McGovern Institute for Brain Research at Tsinghua, Beijing, China.
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Cardinali B, Provenzano C, Izzo M, Voellenkle C, Battistini J, Strimpakos G, Golini E, Mandillo S, Scavizzi F, Raspa M, Perfetti A, Baci D, Lazarevic D, Garcia-Manteiga JM, Gourdon G, Martelli F, Falcone G. Time-controlled and muscle-specific CRISPR/Cas9-mediated deletion of CTG-repeat expansion in the DMPK gene. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:184-199. [PMID: 34976437 PMCID: PMC8693309 DOI: 10.1016/j.omtn.2021.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-mediated therapeutic gene editing is a promising technology for durable treatment of incurable monogenic diseases such as myotonic dystrophies. Gene-editing approaches have been recently applied to in vitro and in vivo models of myotonic dystrophy type 1 (DM1) to delete the pathogenic CTG-repeat expansion located in the 3′ untranslated region of the DMPK gene. In DM1-patient-derived cells removal of the expanded repeats induced beneficial effects on major hallmarks of the disease with reduction in DMPK transcript-containing ribonuclear foci and reversal of aberrant splicing patterns. Here, we set out to excise the triplet expansion in a time-restricted and cell-specific fashion to minimize the potential occurrence of unintended events in off-target genomic loci and select for the target cell type. To this aim, we employed either a ubiquitous promoter-driven or a muscle-specific promoter-driven Cas9 nuclease and tetracycline repressor-based guide RNAs. A dual-vector approach was used to deliver the CRISPR/Cas9 components into DM1 patient-derived cells and in skeletal muscle of a DM1 mouse model. In this way, we obtained efficient and inducible gene editing both in proliferating cells and differentiated post-mitotic myocytes in vitro as well as in skeletal muscle tissue in vivo.
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Affiliation(s)
- Beatrice Cardinali
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Claudia Provenzano
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Mariapaola Izzo
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Jonathan Battistini
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Georgios Strimpakos
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Elisabetta Golini
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Ferdinando Scavizzi
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Marcello Raspa
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Alessandra Perfetti
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Denisa Baci
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | | | - Geneviève Gourdon
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Germana Falcone
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
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45
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Liu X, Wang Y, Effah CY, Wu L, Yu F, Wei J, Mao G, Xiong Y, He L. Endocytosis and intracellular RNAs imaging of nanomaterials-based fluorescence probes. Talanta 2022; 243:123377. [DOI: 10.1016/j.talanta.2022.123377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/12/2022]
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46
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Soltanzadeh P. Myotonic Dystrophies: A Genetic Overview. Genes (Basel) 2022; 13:367. [PMID: 35205411 PMCID: PMC8872148 DOI: 10.3390/genes13020367] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 02/01/2023] Open
Abstract
Myotonic dystrophies (DM) are the most common muscular dystrophies in adults, which can affect other non-skeletal muscle organs such as the heart, brain and gastrointestinal system. There are two genetically distinct types of myotonic dystrophy: myotonic dystrophy type 1 (DM1) and myotonic dystrophy type 2 (DM2), both dominantly inherited with significant overlap in clinical manifestations. DM1 results from CTG repeat expansions in the 3'-untranslated region (3'UTR) of the DMPK (dystrophia myotonica protein kinase) gene on chromosome 19, while DM2 is caused by CCTG repeat expansions in intron 1 of the CNBP (cellular nucleic acid-binding protein) gene on chromosome 3. Recent advances in genetics and molecular biology, especially in the field of RNA biology, have allowed better understanding of the potential pathomechanisms involved in DM. In this review article, core clinical features and genetics of DM are presented followed by a discussion on the current postulated pathomechanisms and therapeutic approaches used in DM, including the ones currently in human clinical trial phase.
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Affiliation(s)
- Payam Soltanzadeh
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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47
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Arandel L, Matloka M, Klein AF, Rau F, Sureau A, Ney M, Cordier A, Kondili M, Polay-Espinoza M, Naouar N, Ferry A, Lemaitre M, Begard S, Colin M, Lamarre C, Tran H, Buée L, Marie J, Sergeant N, Furling D. Reversal of RNA toxicity in myotonic dystrophy via a decoy RNA-binding protein with high affinity for expanded CUG repeats. Nat Biomed Eng 2022; 6:207-220. [PMID: 35145256 DOI: 10.1038/s41551-021-00838-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/07/2021] [Indexed: 12/19/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an RNA-dominant disease whose pathogenesis stems from the functional loss of muscleblind-like RNA-binding proteins (RBPs), which causes the formation of alternative-splicing defects. The loss of functional muscleblind-like protein 1 (MBNL1) results from its nuclear sequestration by mutant transcripts containing pathogenic expanded CUG repeats (CUGexp). Here we show that an RBP engineered to act as a decoy for CUGexp reverses the toxicity of the mutant transcripts. In vitro, the binding of the RBP decoy to CUGexp in immortalized muscle cells derived from a patient with DM1 released sequestered endogenous MBNL1 from nuclear RNA foci, restored MBNL1 activity, and corrected the transcriptomic signature of DM1. In mice with DM1, the local or systemic delivery of the RBP decoy via an adeno-associated virus into the animals' skeletal muscle led to the long-lasting correction of the splicing defects and to ameliorated disease pathology. Our findings support the development of decoy RBPs with high binding affinities for expanded RNA repeats as a therapeutic strategy for myotonic dystrophies.
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Affiliation(s)
- Ludovic Arandel
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Magdalena Matloka
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Arnaud F Klein
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Frédérique Rau
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Alain Sureau
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Michel Ney
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Aurélien Cordier
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Maria Kondili
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Micaela Polay-Espinoza
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Naira Naouar
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Arnaud Ferry
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Mégane Lemaitre
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France.,Sorbonne Université, Inserm, Phénotypage du petit animal, Paris, France
| | - Séverine Begard
- Université de Lille, Inserm, CHU Lille, Lille Neuroscience and Cognition, Lille, France
| | - Morvane Colin
- Université de Lille, Inserm, CHU Lille, Lille Neuroscience and Cognition, Lille, France
| | - Chloé Lamarre
- Université de Lille, Inserm, CHU Lille, Lille Neuroscience and Cognition, Lille, France
| | - Hélène Tran
- Université de Lille, Inserm, CHU Lille, Lille Neuroscience and Cognition, Lille, France
| | - Luc Buée
- Université de Lille, Inserm, CHU Lille, Lille Neuroscience and Cognition, Lille, France
| | - Joëlle Marie
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Nicolas Sergeant
- Université de Lille, Inserm, CHU Lille, Lille Neuroscience and Cognition, Lille, France.
| | - Denis Furling
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France.
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48
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Díaz-Galicia E, Grünberg R, Arold ST. How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application. BIOSENSORS 2022; 12:53. [PMID: 35200314 PMCID: PMC8869480 DOI: 10.3390/bios12020053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems have a great and still largely untapped potential for in vitro applications, in particular, for RNA biosensing. However, there is currently no systematic guide on selecting the most appropriate RNA-targeting CRISPR-Cas system for a given application among thousands of potential candidates. We provide an overview of the currently described Cas effector systems and review existing Cas-based RNA detection methods. We then propose a set of systematic selection criteria for selecting CRISPR-Cas candidates for new applications. Using this approach, we identify four candidates for in vitro RNA.
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Affiliation(s)
- Escarlet Díaz-Galicia
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Raik Grünberg
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, F-34090 Montpellier, France
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49
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Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
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Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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50
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Emerging strategies for the genetic dissection of gene functions, cell types, and neural circuits in the mammalian brain. Mol Psychiatry 2022; 27:422-435. [PMID: 34561609 DOI: 10.1038/s41380-021-01292-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
The mammalian brain is composed of a large number of highly diverse cell types with different molecular, anatomical, and functional features. Distinct cellular identities are generated during development under the regulation of intricate genetic programs and manifested through unique combinations of gene expression. Recent advancements in our understanding of the molecular and cellular mechanisms underlying the assembly, function, and pathology of the brain circuitry depend on the invention and application of genetic strategies that engage intrinsic gene regulatory mechanisms. Here we review the strategies for gene regulation on DNA, RNA, and protein levels and their applications in cell type targeting and neural circuit dissection. We highlight newly emerged strategies and emphasize the importance of combinatorial approaches. We also discuss the potential caveats and pitfalls in current methods and suggest future prospects to improve their comprehensiveness and versatility.
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