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Asadbeigi A, Bakhtiarizadeh MR, Saffari M, Modarressi MH, Sadri N, Kafi ZZ, Fazilaty H, Ghalyanchilangeroudi A, Esmaeili H. Protection of animals against devastating RNA viruses using CRISPR-Cas13s. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102235. [PMID: 39021763 PMCID: PMC11253668 DOI: 10.1016/j.omtn.2024.102235] [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: 12/14/2023] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
The intrinsic nature of CRISPR-Cas in conferring immunity to bacteria and archaea has been repurposed to combat pathogenic agents in mammalian and plant cells. In this regard, CRISPR-Cas13 systems have proved their remarkable potential for single-strand RNA viruses targeting. Here, different types of Cas13 orthologs were applied to knockdown foot-and-mouth disease virus (FMDV), a highly contagious disease of a wide variety of species with genetically diverse strains and is widely geographically distributed. Using programmable CRISPR RNAs capable of targeting conserved regions of the viral genome, all Cas13s from CRISPR system type VI (subtype A/B/D) could comprehensively target and repress different serotypes of FMDV virus. This approach has the potential to destroy all strains of a virus as targets the ultra-conserved regions of genome. We experimentally compared the silencing efficiency of CRISPR and RNAi by designing the most effective short hairpin RNAs according to our developed scoring system and observed comparable results. This study showed successful usage of various Cas13 enzymes for suppression of FMDV, which provides a flexible strategy to battle with other animal infectious RNA viruses, an underdeveloped field in the biotechnology scope.
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Affiliation(s)
- Adnan Asadbeigi
- Cancer Institute, Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran 1417613151, Iran
| | | | - Mojtaba Saffari
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran 1417613151, Iran
| | - Mohammad Hossein Modarressi
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran 1417613151, Iran
| | - Naser Sadri
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
| | - Zahra Ziafati Kafi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
| | - Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
| | - Hossein Esmaeili
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
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2
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Ortuño-Sahagún D, Riesgo-Escovar JR. Editorial: Emerging frontiers in developmental biology in Latin America. Front Neurosci 2023; 17:1129291. [PMID: 37152601 PMCID: PMC10159055 DOI: 10.3389/fnins.2023.1129291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Affiliation(s)
- Daniel Ortuño-Sahagún
- Laboratorio de Neuroinmunobiología Molecular, Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Jalisco, Mexico
- *Correspondence: Daniel Ortuño-Sahagún
| | - Juan Rafael Riesgo-Escovar
- Developmental Neurobiology and Neurophysiology, Instituto de Neurobiología, Campus UNAM Juriquilla, Universidad Nacional Autónoma de Mexico, Santiago de Querétaro, Mexico
- Juan Rafael Riesgo-Escovar
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3
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Goel K, Ploski JE. RISC-y Business: Limitations of Short Hairpin RNA-Mediated Gene Silencing in the Brain and a Discussion of CRISPR/Cas-Based Alternatives. Front Mol Neurosci 2022; 15:914430. [PMID: 35959108 PMCID: PMC9362770 DOI: 10.3389/fnmol.2022.914430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Manipulating gene expression within and outside the nervous system is useful for interrogating gene function and developing therapeutic interventions for a variety of diseases. Several approaches exist which enable gene manipulation in preclinical models, and some of these have been approved to treat human diseases. For the last couple of decades, RNA interference (RNAi) has been a leading technique to knockdown (i.e., suppress) specific RNA expression. This has been partly due to the technology's simplicity, which has promoted its adoption throughout biomedical science. However, accumulating evidence indicates that this technology can possess significant shortcomings. This review highlights the overwhelming evidence that RNAi can be prone to off-target effects and is capable of inducing cytotoxicity in some cases. With this in mind, we consider alternative CRISPR/Cas-based approaches, which may be safer and more reliable for gene knockdown. We also discuss the pros and cons of each approach.
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Affiliation(s)
- Kanishk Goel
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Jonathan E. Ploski
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, PA, United States
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4
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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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Secreted Reporter Assay Enables Quantitative and Longitudinal Monitoring of Neuronal Activity. eNeuro 2021; 8:ENEURO.0518-20.2021. [PMID: 34531280 PMCID: PMC8489021 DOI: 10.1523/eneuro.0518-20.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/23/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022] Open
Abstract
The ability to measure changes in neuronal activity in a quantifiable and precise manner is of fundamental importance to understand neuron development and function. Repeated monitoring of neuronal activity of the same population of neurons over several days is challenging and, typically, low-throughput. Here, we describe a new biochemical reporter assay that allows for repeated measurements of neuronal activity in a cell type-specific manner. We coupled activity-dependent elements from the Arc/Arg3.1 gene with a secreted reporter, Gaussia luciferase (Gluc), to quantify neuronal activity without sacrificing the neurons. The reporter predominantly senses calcium and NMDA receptor (NMDAR)-dependent activity. By repeatedly measuring the accumulation of the reporter in cell media, we can profile the developmental dynamics of neuronal activity in cultured neurons from male and female mice. The assay also allows for longitudinal analysis of pharmacological treatments, thus distinguishing acute from delayed responses. Moreover, conditional expression of the reporter allows for monitoring cell type-specific changes. This simple, quantitative, cost-effective, automatable, and cell type-specific activity reporter is a valuable tool to study the development of neuronal activity in normal and disease-model conditions, and to identify small molecules or protein factors that selectively modulate the activity of a specific population of neurons.
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6
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Carpenter JC, Lignani G. Gene Editing and Modulation: the Holy Grail for the Genetic Epilepsies? Neurotherapeutics 2021; 18:1515-1523. [PMID: 34235638 PMCID: PMC8608979 DOI: 10.1007/s13311-021-01081-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2021] [Indexed: 02/04/2023] Open
Abstract
Epilepsy is a complex neurological disorder for which there are a large number of monogenic subtypes. Monogenic epilepsies are often severe and disabling, featuring drug-resistant seizures and significant developmental comorbidities. These disorders are potentially amenable to a precision medicine approach, of which genome editing using CRISPR/Cas represents the holy grail. Here we consider mutations in some of the most 'common' rare epilepsy genes and discuss the different CRISPR/Cas approaches that could be taken to cure these disorders. We consider scenarios where CRISPR-mediated gene modulation could serve as an effective therapeutic strategy and discuss whether a single gene corrective approach could hold therapeutic potential in the context of homeostatic compensation in the developing, highly dynamic brain. Despite an incomplete understanding of the mechanisms of the genetic epilepsies and current limitations of gene editing tools, CRISPR-mediated approaches have game-changing potential in the treatment of genetic epilepsy over the next decade.
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Affiliation(s)
- Jenna C Carpenter
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK
| | - Gabriele Lignani
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK.
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Eksi YE, Sanlioglu AD, Akkaya B, Ozturk BE, Sanlioglu S. Genome engineering and disease modeling via programmable nucleases for insulin gene therapy: Promises of CRISPR/Cas9 technology. World J Stem Cells 2021; 13:485-502. [PMID: 34249224 PMCID: PMC8246254 DOI: 10.4252/wjsc.v13.i6.485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/02/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Targeted genome editing is a continually evolving technology employing programmable nucleases to specifically change, insert, or remove a genomic sequence of interest. These advanced molecular tools include meganucleases, zinc finger nucleases, transcription activator-like effector nucleases and RNA-guided engineered nucleases (RGENs), which create double-strand breaks at specific target sites in the genome, and repair DNA either by homologous recombination in the presence of donor DNA or via the error-prone non-homologous end-joining mechanism. A recently discovered group of RGENs known as CRISPR/Cas9 gene-editing systems allowed precise genome manipulation revealing a causal association between disease genotype and phenotype, without the need for the reengineering of the specific enzyme when targeting different sequences. CRISPR/Cas9 has been successfully employed as an ex vivo gene-editing tool in embryonic stem cells and patient-derived stem cells to understand pancreatic beta-cell development and function. RNA-guided nucleases also open the way for the generation of novel animal models for diabetes and allow testing the efficiency of various therapeutic approaches in diabetes, as summarized and exemplified in this manuscript.
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Affiliation(s)
- Yunus E Eksi
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
| | - Ahter D Sanlioglu
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
| | - Bahar Akkaya
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
| | - Bilge Esin Ozturk
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Salih Sanlioglu
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
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8
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Perrier S, Michell-Robinson MA, Bernard G. POLR3-Related Leukodystrophy: Exploring Potential Therapeutic Approaches. Front Cell Neurosci 2021; 14:631802. [PMID: 33633543 PMCID: PMC7902007 DOI: 10.3389/fncel.2020.631802] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022] Open
Abstract
Leukodystrophies are a class of rare inherited central nervous system (CNS) disorders that affect the white matter of the brain, typically leading to progressive neurodegeneration and early death. Hypomyelinating leukodystrophies are characterized by the abnormal formation of the myelin sheath during development. POLR3-related or 4H (hypomyelination, hypodontia, and hypogonadotropic hypogonadism) leukodystrophy is one of the most common types of hypomyelinating leukodystrophy for which no curative treatment or disease-modifying therapy is available. This review aims to describe potential therapies that could be further studied for effectiveness in pre-clinical studies, for an eventual translation to the clinic to treat the neurological manifestations associated with POLR3-related leukodystrophy. Here, we discuss the therapeutic approaches that have shown promise in other leukodystrophies, as well as other genetic diseases, and consider their use in treating POLR3-related leukodystrophy. More specifically, we explore the approaches of using stem cell transplantation, gene replacement therapy, and gene editing as potential treatment options, and discuss their possible benefits and limitations as future therapeutic directions.
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Affiliation(s)
- Stefanie Perrier
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Mackenzie A. Michell-Robinson
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, Montréal Children’s Hospital and McGill University Health Centre, Montréal, QC, Canada
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9
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Duarte F, Déglon N. Genome Editing for CNS Disorders. Front Neurosci 2020; 14:579062. [PMID: 33192264 PMCID: PMC7642486 DOI: 10.3389/fnins.2020.579062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Central nervous system (CNS) disorders have a social and economic burden on modern societies, and the development of effective therapies is urgently required. Gene editing may prevent or cure a disease by inducing genetic changes at endogenous loci. Genome editing includes not only the insertion, deletion or replacement of nucleotides, but also the modulation of gene expression and epigenetic editing. Emerging technologies based on ZFs, TALEs, and CRISPR/Cas systems have extended the boundaries of genome manipulation and promoted genome editing approaches to the level of promising strategies for counteracting genetic diseases. The parallel development of efficient delivery systems has also increased our access to the CNS. In this review, we describe the various tools available for genome editing and summarize in vivo preclinical studies of CNS genome editing, whilst considering current limitations and alternative approaches to overcome some bottlenecks.
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Affiliation(s)
- Fábio Duarte
- Laboratory of Neurotherapies and NeuroModulation, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland.,Laboratory of Neurotherapies and NeuroModulation, Neuroscience Research Center, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Nicole Déglon
- Laboratory of Neurotherapies and NeuroModulation, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland.,Laboratory of Neurotherapies and NeuroModulation, Neuroscience Research Center, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
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10
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Arzate-Mejía RG, Lottenbach Z, Schindler V, Jawaid A, Mansuy IM. Long-Term Impact of Social Isolation and Molecular Underpinnings. Front Genet 2020; 11:589621. [PMID: 33193727 PMCID: PMC7649797 DOI: 10.3389/fgene.2020.589621] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
Prolonged periods of social isolation can have detrimental effects on the physiology and behavior of exposed individuals in humans and animal models. This involves complex molecular mechanisms across tissues in the body which remain partly identified. This review discusses the biology of social isolation and describes the acute and lasting effects of prolonged periods of social isolation with a focus on the molecular events leading to behavioral alterations. We highlight the role of epigenetic mechanisms and non-coding RNA in the control of gene expression as a response to social isolation, and the consequences for behavior. Considering the use of strict quarantine during epidemics, like currently with COVID-19, we provide a cautionary tale on the indiscriminate implementation of such form of social isolation and its potential damaging and lasting effects in mental health.
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Affiliation(s)
- Rodrigo G Arzate-Mejía
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | | | | | - Ali Jawaid
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
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11
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Bohnsack JP, Pandey SC. Histone modifications, DNA methylation, and the epigenetic code of alcohol use disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:1-62. [PMID: 33461661 DOI: 10.1016/bs.irn.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alcohol use disorder (AUD) is a leading cause of morbidity and mortality. Despite AUD's substantial contributions to lost economic productivity and quality of life, there are only a limited number of approved drugs for treatment of AUD in the United States. This chapter will update progress made on the epigenetic basis of AUD, with particular focus on histone post-translational modifications and DNA methylation and how these two epigenetic mechanisms interact to contribute to neuroadaptive processes leading to initiation, maintenance and progression of AUD pathophysiology. We will also evaluate epigenetic therapeutic strategies that have arisen from preclinical models of AUD and epigenetic biomarkers that have been discovered in human populations with AUD.
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Affiliation(s)
- John Peyton Bohnsack
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States; Jesse Brown VA Medical Center, Chicago, IL, United States; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States.
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12
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Taxier LR, Gross KS, Frick KM. Oestradiol as a neuromodulator of learning and memory. Nat Rev Neurosci 2020; 21:535-550. [PMID: 32879508 PMCID: PMC8302223 DOI: 10.1038/s41583-020-0362-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2020] [Indexed: 12/24/2022]
Abstract
Although hormones such as glucocorticoids have been broadly accepted in recent decades as general neuromodulators of memory processes, sex steroid hormones such as the potent oestrogen 17β-oestradiol have been less well recognized by the scientific community in this capacity. The predominance of females in studies of oestradiol and memory and the general (but erroneous) perception that oestrogens are 'female' hormones have probably prevented oestradiol from being more widely considered as a key memory modulator in both sexes. Indeed, although considerable evidence supports a crucial role for oestradiol in regulating learning and memory in females, a growing body of literature indicates a similar role in males. This Review discusses the mechanisms of oestradiol signalling and provides an overview of the effects of oestradiol on spatial, object recognition, social and fear memories. Although the primary focus is on data collected in females, effects of oestradiol on memory in males will be discussed, as will sex differences in the molecular mechanisms that regulate oestrogenic modulation of memory, which may have important implications for the development of future cognitive therapeutics.
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Affiliation(s)
- Lisa R Taxier
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kellie S Gross
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Karyn M Frick
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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