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Kamachi Y, Kawahara A. CRISPR-Cas9-Mediated Genome Modifications in Zebrafish. Methods Mol Biol 2023; 2637:313-324. [PMID: 36773157 DOI: 10.1007/978-1-0716-3016-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
CRISPR-Cas9 genome editing technology has been successfully applied to generate various genetic modifications in zebrafish. The CRISPR-Cas9 system, which originally consisted of three components, CRISPR RNA (crRNA), trans-activating crRNA (tracrRNA), and Cas9, efficiently induces DNA double-strand breaks (DSBs) at targeted genomic loci, often resulting in frameshift-mediated target gene disruption (knockout). However, it remains difficult to perform the targeted integration of exogenous DNA fragments (knock-in) with CRISPR-Cas9. DSBs can be restored through DNA repair mechanisms, such as nonhomologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and homology-directed repair (HDR). One of our two research groups established a method for the precise MMEJ-mediated targeted integrations of exogenous genes containing homologous microhomology sequences flanking a targeted genomic locus in zebrafish. The other group recently developed a method for knocking in ~200 nt sequences encoding composite tags using long single-stranded DNA (ssDNA) donors. This chapter summarizes the CRISPR-Cas9-mediated genome modification strategy in zebrafish.
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Affiliation(s)
- Yusuke Kamachi
- School of Environmental Science and Engineering, Kochi University of Technology, Tosayamada-cho, Kami, Kochi, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Graduate School of Medical Science, University of Yamanashi, Chuo, Yamanashi, Japan.
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Liang W, He J, Mao C, Yu C, Meng Q, Xue J, Wu X, Li S, Wang Y, Yi H. Gene editing monkeys: Retrospect and outlook. Front Cell Dev Biol 2022; 10:913996. [PMID: 36158194 PMCID: PMC9493099 DOI: 10.3389/fcell.2022.913996] [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: 04/06/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Animal models play a key role in life science research, especially in the study of human disease pathogenesis and drug screening. Because of the closer proximity to humans in terms of genetic evolution, physiology, immunology, biochemistry, and pathology, nonhuman primates (NHPs) have outstanding advantages in model construction for disease mechanism study and drug development. In terms of animal model construction, gene editing technology has been widely applied to this area in recent years. This review summarizes the current progress in the establishment of NHPs using gene editing technology, which mainly focuses on rhesus and cynomolgus monkeys. In addition, we discuss the limiting factors in the applications of genetically modified NHP models as well as the possible solutions and improvements. Furthermore, we highlight the prospects and challenges of the gene-edited NHP models.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
| | - Junli He
- Department of Pediatrics, Shenzhen University General Hospital, Shenzhen, China
| | - Chenyu Mao
- University of Pennsylvania, Philadelphia, PA, United States
| | - Chengwei Yu
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Qingxue Meng
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Xueliang Wu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Shanliang Li
- Department of Pharmacology, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
| | - Yukai Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- National Stem Cell Resource Center, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
| | - Hongyang Yi
- National Clinical Research Centre for Infectious Diseases, The Third People’s Hospital of Shenzhen and The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Weizheng Liang, ; Shanliang Li, ; Yukai Wang, ; Hongyang Yi,
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Ouyang S, Qin WM, Niu YJ, Ding YH, Deng Y. An EGFP Knock-in Zebrafish Experimental Model Used in Evaluation of the Amantadine Drug Safety During Early Cardiogenesis. Front Cardiovasc Med 2022; 9:839166. [PMID: 35449877 PMCID: PMC9016130 DOI: 10.3389/fcvm.2022.839166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundDrug exposure during gestation or in prematurely born children represents a significant risk to congenital heart disease (CHD). Amantadine is an antiviral agent also effective in the treatment of Parkinson’s disease. However, while its potential side effects associated with tetralogy of fallot (ToF) and birth defects were implicated, its underlying etiologic mechanisms of action remain unknown. Here, we report teratogenic effects of amantadine drug during early cardiogenesis through developing a novel zebrafish (Danio rerio) knock-in (KI) animal model and explore the underlying mechanisms.MethodsHomologous recombination (HR) pathway triggered by CRISPR/Cas9 system was utilized to generate an enhanced green fluorescent protein (EGFP) KI zebrafish animal model. Dynamic fluorescence imaging coupled with a whole-mount in-situ hybridization (WISH) assay was employed to compare the spatial and temporal expression patterns of the EGFP reporter in the KI animal model with the KI-targeted endogenous gene. Heart morphology and EGFP expression dynamics in the KI animal models were monitored to assess cardiac side effects of different doses of amantadine hydrochloride. Expression of key genes required for myocardium differentiation and left–right (LR) asymmetry was analyzed using WISH and quantitative reverse transcription-PCR (RT-PCR).ResultsA novel EGFP KI line targeted at the ventricular myosin heavy chain (vmhc) gene locus was successfully generated, in which EGFP reporter could faithfully recapitulate the endogenous expression dynamics of the ventricle chamber-specific expression of the vmhc gene. Amantadine drug treatment-induced ectopic expression of vmhc gene in the atrium and caused cardiac-looping or LR asymmetry defects to dose-dependently during early cardiogenesis, concomitant with dramatically reduced expression levels of key genes required for myocardium differentiation and LR asymmetry.ConclusionWe generated a novel zebrafish KI animal model in which EGFP reports the ventricle chamber-specific expression of vmhc gene dynamics that is useful to effectively assess drug safety on the cardiac morphology in vivo. Specifically, this study identified teratogenic effects of amantadine drug during early cardiogenesis dose dependent, which could be likely conveyed by inhibiting expression of key genes required for cardiac myocardium differentiation and LR asymmetry.
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Affiliation(s)
- Shi Ouyang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wu-Ming Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yu-Juan Niu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institute), Qingdao University, Qingdao, China
| | - Yong-He Ding
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institute), Qingdao University, Qingdao, China
- *Correspondence: Yong-He Ding,
| | - Yun Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
- Yun Deng,
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Wang J, Cao H. Zebrafish and Medaka: Important Animal Models for Human Neurodegenerative Diseases. Int J Mol Sci 2021; 22:10766. [PMID: 34639106 PMCID: PMC8509648 DOI: 10.3390/ijms221910766] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 02/06/2023] Open
Abstract
Animal models of human neurodegenerative disease have been investigated for several decades. In recent years, zebrafish (Danio rerio) and medaka (Oryzias latipes) have become popular in pathogenic and therapeutic studies about human neurodegenerative diseases due to their small size, the optical clarity of embryos, their fast development, and their suitability to large-scale therapeutic screening. Following the emergence of a new generation of molecular biological technologies such as reverse and forward genetics, morpholino, transgenesis, and gene knockout, many human neurodegenerative disease models, such as Parkinson's, Huntington's, and Alzheimer's, were constructed in zebrafish and medaka. These studies proved that zebrafish and medaka genes are functionally conserved in relation to their human homologues, so they exhibit similar neurodegenerative phenotypes to human beings. Therefore, fish are a suitable model for the investigation of pathologic mechanisms of neurodegenerative diseases and for the large-scale screening of drugs for potential therapy. In this review, we summarize the studies in modelling human neurodegenerative diseases in zebrafish and medaka in recent years.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7#, Wuhan 430072, China;
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7#, Wuhan 430072, China;
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Pensado-López A, Veiga-Rúa S, Carracedo Á, Allegue C, Sánchez L. Experimental Models to Study Autism Spectrum Disorders: hiPSCs, Rodents and Zebrafish. Genes (Basel) 2020; 11:E1376. [PMID: 33233737 PMCID: PMC7699923 DOI: 10.3390/genes11111376] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/26/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Autism Spectrum Disorders (ASD) affect around 1.5% of the global population, which manifest alterations in communication and socialization, as well as repetitive behaviors or restricted interests. ASD is a complex disorder with known environmental and genetic contributors; however, ASD etiology is far from being clear. In the past decades, many efforts have been put into developing new models to study ASD, both in vitro and in vivo. These models have a lot of potential to help to validate some of the previously associated risk factors to the development of the disorder, and to test new potential therapies that help to alleviate ASD symptoms. The present review is focused on the recent advances towards the generation of models for the study of ASD, which would be a useful tool to decipher the bases of the disorder, as well as to conduct drug screenings that hopefully lead to the identification of useful compounds to help patients deal with the symptoms of ASD.
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Affiliation(s)
- Alba Pensado-López
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain; (A.P.-L.); (S.V.-R.)
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - Sara Veiga-Rúa
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain; (A.P.-L.); (S.V.-R.)
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - Ángel Carracedo
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIMUS, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Catarina Allegue
- Genomic Medicine Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - Laura Sánchez
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain; (A.P.-L.); (S.V.-R.)
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Fortier G, Butti Z, Patten SA. Modelling C9orf72-Related Amyotrophic Lateral Sclerosis in Zebrafish. Biomedicines 2020; 8:E440. [PMID: 33096681 PMCID: PMC7589578 DOI: 10.3390/biomedicines8100440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 12/12/2022] Open
Abstract
A hexanucleotide repeat expansion within the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and its discovery has revolutionized our understanding of this devastating disease. Model systems are a valuable tool for studying ALS pathobiology and potential therapies. The zebrafish (Danio rerio) has particularly become a useful model organism to study neurological diseases, including ALS, due to high genetic and physiological homology to mammals, and sensitivity to various genetic and pharmacological manipulations. In this review we summarize the zebrafish models that have been used to study the pathology of C9orf72-related ALS. We discuss their value in providing mechanistic insights and their potential use for drug discovery.
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Affiliation(s)
- Gabrielle Fortier
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC H7V 1B7, Canada; (G.F.); (Z.B.)
| | - Zoé Butti
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC H7V 1B7, Canada; (G.F.); (Z.B.)
| | - Shunmoogum A. Patten
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC H7V 1B7, Canada; (G.F.); (Z.B.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal (UQAM), Montréal, QC H2X 3Y7, Canada
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Sorriento D, Iaccarino G. Commentary: Studies in Zebrafish Demonstrate That CNNM2 and NT5C2 Are Most Likely the Causal Genes at the Blood Pressure-Associated Locus on Human Chromosome 10q24.32. Front Cardiovasc Med 2020; 7:582101. [PMID: 33195469 PMCID: PMC7604340 DOI: 10.3389/fcvm.2020.582101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/15/2020] [Indexed: 11/23/2022] Open
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Nguyen VT, Bian L, Tamaoki J, Otsubo S, Muratani M, Kawahara A, Kobayashi M. Generation and characterization of keap1a- and keap1b-knockout zebrafish. Redox Biol 2020; 36:101667. [PMID: 32828016 PMCID: PMC7452054 DOI: 10.1016/j.redox.2020.101667] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/07/2020] [Accepted: 07/29/2020] [Indexed: 12/30/2022] Open
Abstract
The Keap1–Nrf2 pathway is an evolutionarily conserved mechanism that protects cells from oxidative stress and electrophiles. Under homeostatic conditions, Keap1 interacts with Nrf2 and leads to its rapid proteasomal degradation, but when cells are exposed to oxidative stress/electrophiles, Keap1 senses them, resulting in an improper Keap1–Nrf2 interaction and Nrf2 stabilization. Keap1 is therefore considered both an “inhibitor” of and “stress sensor” for Nrf2 activation. Interestingly, fish and amphibians have two Keap1s (Keap1a and Keap1b), while there is only one in mammals, birds and reptiles. A phylogenetic analysis suggested that mammalian Keap1 is an ortholog of fish Keap1b, not Keap1a. In this study, we investigated the differences and similarities between Keap1a and Keap1b using zebrafish genetics. We generated zebrafish knockout lines of keap1a and keap1b. Homozygous mutants of both knockout lines were viable and fertile. In both mutant larvae, the basal expression of Nrf2 target genes and antioxidant activity were up-regulated in an Nrf2-dependent manner, suggesting that both Keap1a and Keap1b can function as Nrf2 inhibitors. We also analyzed the effects of the Nrf2 activator sulforaphane in these mutants and found that keap1a-, but not keap1b-, knockout larvae responded to sulforaphane, suggesting that the stress/chemical-sensing abilities of the two Keap1s are different. Fish and amphibians have two Keap1s: Keap1a and Keap1b. Mammalian Keap1 is an ortholog of fish Keap1b, not Keap1a. Both Keap1a and Keap1b can function as Nrf2 inhibitors. The sulforaphane-sensing abilities of Keap1a and Keap1b are different.
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Affiliation(s)
- Vu Thanh Nguyen
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan; Division of Aquaculture Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Lixuan Bian
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Junya Tamaoki
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Shiro Otsubo
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Makoto Kobayashi
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.
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Cheresiz SV, Volgin AD, Kokorina Evsyukova A, Bashirzade AAO, Demin KA, de Abreu MS, Amstislavskaya TG, Kalueff AV. Understanding neurobehavioral genetics of zebrafish. J Neurogenet 2020; 34:203-215. [PMID: 31902276 DOI: 10.1080/01677063.2019.1698565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Due to its fully sequenced genome, high genetic homology to humans, external fertilization, fast development, transparency of embryos, low cost and active reproduction, the zebrafish (Danio rerio) has become a novel promising model organism in biomedicine. Zebrafish are a useful tool in genetic and neuroscience research, including linking various genetic mutations to brain mechanisms using forward and reverse genetics. These approaches have produced novel models of rare genetic CNS disorders and common brain illnesses, such as addiction, aggression, anxiety and depression. Genetically modified zebrafish also foster neuroanatomical studies, manipulating neural circuits and linking them to different behaviors. Here, we discuss recent advances in neurogenetics of zebrafish, and evaluate their unique strengths, inherent limitations and the rapidly growing potential for elucidating the conserved roles of genes in neuropsychiatric disorders.
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Affiliation(s)
- Sergey V Cheresiz
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Andrey D Volgin
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Alexandra Kokorina Evsyukova
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Alim A O Bashirzade
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Konstantin A Demin
- Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil.,The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Tamara G Amstislavskaya
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia.,The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China.,Ural Federal University, Ekaterinburg, Russia.,Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.,Russian Scientific Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
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Pierpont ME, Brueckner M, Chung WK, Garg V, Lacro RV, McGuire AL, Mital S, Priest JR, Pu WT, Roberts A, Ware SM, Gelb BD, Russell MW. Genetic Basis for Congenital Heart Disease: Revisited: A Scientific Statement From the American Heart Association. Circulation 2019; 138:e653-e711. [PMID: 30571578 DOI: 10.1161/cir.0000000000000606] [Citation(s) in RCA: 331] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review provides an updated summary of the state of our knowledge of the genetic contributions to the pathogenesis of congenital heart disease. Since 2007, when the initial American Heart Association scientific statement on the genetic basis of congenital heart disease was published, new genomic techniques have become widely available that have dramatically changed our understanding of the causes of congenital heart disease and, clinically, have allowed more accurate definition of the pathogeneses of congenital heart disease in patients of all ages and even prenatally. Information is presented on new molecular testing techniques and their application to congenital heart disease, both isolated and associated with other congenital anomalies or syndromes. Recent advances in the understanding of copy number variants, syndromes, RASopathies, and heterotaxy/ciliopathies are provided. Insights into new research with congenital heart disease models, including genetically manipulated animals such as mice, chicks, and zebrafish, as well as human induced pluripotent stem cell-based approaches are provided to allow an understanding of how future research breakthroughs for congenital heart disease are likely to happen. It is anticipated that this review will provide a large range of health care-related personnel, including pediatric cardiologists, pediatricians, adult cardiologists, thoracic surgeons, obstetricians, geneticists, genetic counselors, and other related clinicians, timely information on the genetic aspects of congenital heart disease. The objective is to provide a comprehensive basis for interdisciplinary care for those with congenital heart disease.
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Yamashita A, Deguchi J, Honda Y, Yamada T, Miyawaki I, Nishimura Y, Tanaka T. Increased susceptibility to oxidative stress-induced toxicological evaluation by genetically modified nrf2a-deficient zebrafish. J Pharmacol Toxicol Methods 2018; 96:34-45. [PMID: 30594530 DOI: 10.1016/j.vascn.2018.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 10/10/2018] [Accepted: 12/26/2018] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Oxidative stress plays an important role in drug-induced toxicity. Oxidative stress-mediated toxicities can be detected using conventional animal models but their sensitivity is insufficient, and novel models to improve susceptibility to oxidative stress have been researched. In recent years, gene targeting methods in zebrafish have been developed, making it possible to generate homozygous null mutants. In this study, we established zebrafish deficient in the nuclear factor erythroid 2-related factor 2a (nrf2a), a key antioxidant-responsive gene, and its potential to detect oxidative stress-mediated toxicity was examined. METHODS Nrf2a-deficient zebrafish were generated using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 technique. The loss of nrf2a function was confirmed by the tolerability to hydrogen peroxide and hydrogen peroxide-induced gene expression profiles being related to antioxidant response element (ARE)-dependent signaling. Subsequently, vulnerability of nrf2a-deficient zebrafish to acetaminophen (APAP)- or doxorubicin (DOX)-induced toxicity was investigated. RESULTS Nrf2a-deficient zebrafish showed higher mortality than wild type accompanied by less induction of ARE-dependent genes with hydrogen peroxide treatment. Subsequently, this model showed increased severity and incidence of APAP-induced hepatotoxicity or DOX-induced cardiotoxicity than wild type. DISCUSSION Our results demonstrated that anti-oxidative response might not fully function in this model, and resulted in higher sensitivity to drug-induced oxidative stress. Our data support the usefulness of nrf2a-deficient model as a tool for evaluation of oxidative stress-related toxicity in drug discovery research.
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Affiliation(s)
- Akihito Yamashita
- Department of Systems Pharmacology, Mie University Graduate School of Medicine, Mie, Japan; Preclinical Research Unit, Sumitomo Dainippon Pharma Co., Ltd., Osaka, Japan.
| | - Jiro Deguchi
- Preclinical Research Unit, Sumitomo Dainippon Pharma Co., Ltd., Osaka, Japan
| | - Yayoi Honda
- Preclinical Research Unit, Sumitomo Dainippon Pharma Co., Ltd., Osaka, Japan
| | - Toru Yamada
- Preclinical Research Unit, Sumitomo Dainippon Pharma Co., Ltd., Osaka, Japan
| | - Izuru Miyawaki
- Preclinical Research Unit, Sumitomo Dainippon Pharma Co., Ltd., Osaka, Japan
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Mie, Japan
| | - Toshio Tanaka
- Department of Systems Pharmacology, Mie University Graduate School of Medicine, Mie, Japan; Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine, Mie, Japan; Mie University Medical Zebrafish Research Center, Mie, Japan; Department of Bioinformatics, Mie University Life Science Research Center, Mie, Japan; Department of Omics Medicine, Mie University Industrial Technology Innovation Institute, Mie, Japan
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12
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Zebrafish: an emerging real-time model system to study Alzheimer's disease and neurospecific drug discovery. Cell Death Discov 2018; 4:45. [PMID: 30302279 PMCID: PMC6170431 DOI: 10.1038/s41420-018-0109-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
Zebrafish (Danio rerio) is emerging as an increasingly successful model for translational research on human neurological disorders. In this review, we appraise the high degree of neurological and behavioural resemblance of zebrafish with humans. It is highly validated as a powerful vertebrate model for investigating human neurodegenerative diseases. The neuroanatomic and neurochemical pathways of zebrafish brain exhibit a profound resemblance with the human brain. Physiological, emotional and social behavioural pattern similarities between them have also been well established. Interestingly, zebrafish models have been used successfully to simulate the pathology of Alzheimer’s disease (AD) as well as Tauopathy. Their relatively simple nervous system and the optical transparency of the embryos permit real-time neurological imaging. Here, we further elaborate on the use of recent real-time imaging techniques to obtain vital insights into the neurodegeneration that occurs in AD. Zebrafish is adeptly suitable for Ca2+ imaging, which provides a better understanding of neuronal activity and axonal dystrophy in a non-invasive manner. Three-dimensional imaging in zebrafish is a rapidly evolving technique, which allows the visualisation of the whole organism for an elaborate in vivo functional and neurophysiological analysis in disease condition. Suitability to high-throughput screening and similarity with humans makes zebrafish an excellent model for screening neurospecific compounds. Thus, the zebrafish model can be pivotal in bridging the gap from the bench to the bedside. This fish is becoming an increasingly successful model to understand AD with further scope for investigation in neurodevelopment and neurodegeneration, which promises exciting research opportunities in the future.
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Luo JJ, Bian WP, Liu Y, Huang HY, Yin Q, Yang XJ, Pei DS. CRISPR/Cas9-based genome engineering of zebrafish using a seamless integration strategy. FASEB J 2018; 32:5132-5142. [PMID: 29812974 DOI: 10.1096/fj.201800077rr] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Numerous feasible methods for inserting large fragments of exogenous DNA sequences into the zebrafish genome have been developed, as has genome editing technology using programmable nucleases. However, the coding sequences of targeted endogenous genes are disrupted, and the expression patterns of inserted exogenous genes cannot completely recapitulate those of endogenous genes. Here we describe the establishment of a novel strategy for endogenous promoter-driven and microhomology-mediated end-joining-dependent integration of a donor vector using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9. We successfully integrated mCherry into the final coding sequence of targeted genes to generate seamless transgenic zebrafish lines with high efficiency. This novel seamless transgenesis technique not only maintained the integrity of the endogenous gene but also did not disrupt the function of targeted gene. Therefore, our microhomology-mediated end-joining-mediated transgenesis strategy may have broader applications in gene therapy. Moreover, this novel seamless gene-editing strategy in zebrafish provides a valuable new transgenesis technique, which was driven by endogenous promoters and in vivo animal reporter modes for translational medicine. It is expected to be a standard gene-editing technique in the field of zebrafish, leading to some important breakthroughs for studies in early embryogenesis.-Luo, J.-J., Bian, W.-P., Liu, Y., Huang, H.-Y., Yin, Q., Yang, X.-J., Pei, D.-S. CRISPR/Cas9-based genome engineering of zebrafish using a seamless integration strategy.
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Affiliation(s)
- Juan-Juan Luo
- Center for Neuroscience, Shantou University Medical College, Shantou, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China; and
| | - Wan-Ping Bian
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China; and
| | - Yi Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China; and
- University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Yang Huang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China; and
| | - Qian Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China; and
| | - Xiao-Jun Yang
- Center for Neuroscience, Shantou University Medical College, Shantou, China
| | - De-Sheng Pei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China; and
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Sorlien EL, Witucki MA, Ogas J. Efficient Production and Identification of CRISPR/Cas9-generated Gene Knockouts in the Model System Danio rerio. J Vis Exp 2018. [PMID: 30222157 PMCID: PMC6231919 DOI: 10.3791/56969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Characterization of the clustered, regularly interspaced, short, palindromic repeat (CRISPR) system of Streptococcus pyogenes has enabled the development of a customizable platform to rapidly generate gene modifications in a wide variety of organisms, including zebrafish. CRISPR-based genome editing uses a single guide RNA (sgRNA) to target a CRISPR-associated (Cas) endonuclease to a genomic DNA (gDNA) target of interest, where the Cas endonuclease generates a double-strand break (DSB). Repair of DSBs by error-prone mechanisms lead to insertions and/or deletions (indels). This can cause frameshift mutations that often introduce a premature stop codon within the coding sequence, thus creating a protein-null allele. CRISPR-based genome engineering requires only a few molecular components and is easily introduced into zebrafish embryos by microinjection. This protocol describes the methods used to generate CRISPR reagents for zebrafish microinjection and to identify fish exhibiting germline transmission of CRISPR-modified genes. These methods include in vitro transcription of sgRNAs, microinjection of CRISPR reagents, identification of indels induced at the target site using a PCR-based method called a heteroduplex mobility assay (HMA), and characterization of the indels using both a low throughput and a powerful next-generation sequencing (NGS)-based approach that can analyze multiple PCR products collected from heterozygous fish. This protocol is streamlined to minimize both the number of fish required and the types of equipment needed to perform the analyses. Furthermore, this protocol is designed to be amenable for use by laboratory personal of all levels of experience including undergraduates, enabling this powerful tool to be economically employed by any research group interested in performing CRISPR-based genomic modification in zebrafish.
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Affiliation(s)
| | | | - Joseph Ogas
- Department of Biochemistry, Purdue University;
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15
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Shin JH, Jung S, Ramakrishna S, Kim HH, Lee J. In vivo gene correction with targeted sequence substitution through microhomology-mediated end joining. Biochem Biophys Res Commun 2018; 502:116-122. [PMID: 29787760 DOI: 10.1016/j.bbrc.2018.05.130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 11/21/2022]
Abstract
Genome editing technology using programmable nucleases has rapidly evolved in recent years. The primary mechanism to achieve precise integration of a transgene is mainly based on homology-directed repair (HDR). However, an HDR-based genome-editing approach is less efficient than non-homologous end-joining (NHEJ). Recently, a microhomology-mediated end-joining (MMEJ)-based transgene integration approach was developed, showing feasibility both in vitro and in vivo. We expanded this method to achieve targeted sequence substitution (TSS) of mutated sequences with normal sequences using double-guide RNAs (gRNAs), and a donor template flanking the microhomologies and target sequence of the gRNAs in vitro and in vivo. Our method could realize more efficient sequence substitution than the HDR-based method in vitro using a reporter cell line, and led to the survival of a hereditary tyrosinemia mouse model in vivo. The proposed MMEJ-based TSS approach could provide a novel therapeutic strategy, in addition to HDR, to achieve gene correction from a mutated sequence to a normal sequence.
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Affiliation(s)
- Jeong Hong Shin
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
| | - Soobin Jung
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea; Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, South Korea; Yonsei-IBS Institute, Yonsei University, Seoul, South Korea.
| | - Junwon Lee
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea; Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, South Korea.
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16
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Sharma N, Khurana N, Muthuraman A. Lower vertebrate and invertebrate models of Alzheimer's disease - A review. Eur J Pharmacol 2017; 815:312-323. [PMID: 28943103 DOI: 10.1016/j.ejphar.2017.09.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/20/2017] [Accepted: 09/13/2017] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease is a common neurodegenerative disorder which is characterized by the presence of beta- amyloid protein and neurofibrillary tangles (NFTs) in the brain. Till now, various higher vertebrate models have been in use to study the pathophysiology of this disease. But, these models possess some limitations like ethical restrictions, high cost, difficult maintenance of large quantity and lesser reproducibility. Besides, various lower chordate animals like Danio rerio, Drosophila melanogaster, Caenorhabditis elegans and Ciona intestinalis have been proved to be an important model for the in vivo determination of targets of drugs with least limitations. In this article, we reviewed different studies conducted on theses models for the better understanding of the pathophysiology of AD and their subsequent application as a potential tool in the preclinical evaluation of new drugs.
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Affiliation(s)
- Neha Sharma
- Department of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Navneet Khurana
- Department of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Arunachalam Muthuraman
- Department of Pharmacology, Akal College of Pharmacy and Technical Education, Mastuana Sahib, Sangrur, Punjab, India; Department of Pharmacology, JSS College of Pharmacy, Jagadguru Sri Shivarathreeshwara University, Mysuru 570015, Karnataka, India.
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17
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Abstract
In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Through a powerful combination of genetics and experimental embryology, significant inroads have been made into the regulation of embryonic axis formation, organogenesis, and the development of neural networks. Research with this model has also expanded into other areas, including the genetic regulation of aging, regeneration, and animal behavior. Zebrafish are a popular model because of the ease with which they can be maintained, their small size and low cost, the ability to obtain hundreds of embryos on a daily basis, and the accessibility, translucency, and rapidity of early developmental stages. This primer describes the swift progress of genetic approaches in zebrafish and highlights recent advances that have led to new insights into vertebrate biology.
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Novel Hypomorphic Alleles of the Mouse Tyrosinase Gene Induced by CRISPR-Cas9 Nucleases Cause Non-Albino Pigmentation Phenotypes. PLoS One 2016; 11:e0155812. [PMID: 27224051 PMCID: PMC4880214 DOI: 10.1371/journal.pone.0155812] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/04/2016] [Indexed: 11/20/2022] Open
Abstract
Tyrosinase is a key enzyme in melanin biosynthesis. Mutations in the gene encoding tyrosinase (Tyr) cause oculocutaneous albinism (OCA1) in humans. Alleles of the Tyr gene have been useful in studying pigment biology and coat color formation. Over 100 different Tyr alleles have been reported in mice, of which ≈24% are spontaneous mutations, ≈60% are radiation-induced, and the remaining alleles were obtained by chemical mutagenesis and gene targeting. Therefore, most mutations were random and could not be predicted a priori. Using the CRISPR-Cas9 system, we targeted two distinct regions of exon 1 to induce pigmentation changes and used an in vivo visual phenotype along with heteroduplex mobility assays (HMA) as readouts of CRISPR-Cas9 activity. Most of the mutant alleles result in complete loss of tyrosinase activity leading to an albino phenotype. In this study, we describe two novel in-frame deletion alleles of Tyr, dhoosara (Sanskrit for gray) and chandana (Sanskrit for sandalwood). These alleles are hypomorphic and show lighter pigmentation phenotypes of the body and eyes. This study demonstrates the utility of CRISPR-Cas9 system in generating domain-specific in-frame deletions and helps gain further insights into structure-function of Tyr gene.
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Site-Specific Integration of Exogenous Genes Using Genome Editing Technologies in Zebrafish. Int J Mol Sci 2016; 17:ijms17050727. [PMID: 27187373 PMCID: PMC4881549 DOI: 10.3390/ijms17050727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/26/2016] [Accepted: 05/05/2016] [Indexed: 12/12/2022] Open
Abstract
The zebrafish (Danio rerio) is an ideal vertebrate model to investigate the developmental molecular mechanism of organogenesis and regeneration. Recent innovation in genome editing technologies, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system, have allowed researchers to generate diverse genomic modifications in whole animals and in cultured cells. The CRISPR/Cas9 and TALEN techniques frequently induce DNA double-strand breaks (DSBs) at the targeted gene, resulting in frameshift-mediated gene disruption. As a useful application of genome editing technology, several groups have recently reported efficient site-specific integration of exogenous genes into targeted genomic loci. In this review, we provide an overview of TALEN- and CRISPR/Cas9-mediated site-specific integration of exogenous genes in zebrafish.
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Wen J, Sun X, Chen H, Liu H, Lai R, Li J, Wang Y, Zhang J, Sheng W. Mutation of rnf213a by TALEN causes abnormal angiogenesis and circulation defects in zebrafish. Brain Res 2016; 1644:70-8. [PMID: 27125596 DOI: 10.1016/j.brainres.2016.04.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/18/2016] [Accepted: 04/22/2016] [Indexed: 01/23/2023]
Abstract
Moyamoya disease (MMD) is characterized by a stenosis at the terminal of the internal carotid artery and an abnormal vascular network at the base of the brain. RNF213 is a susceptibility gene for MMD in East Asians. The role of RNF213 in the etiology of MMD remains unknown. Here we generated rnf213a mutant zebrafish using transcription activator-like effector nuclease (TALEN) technique and described the characteristics of a zebrafish embryonic model of MMD. rnf213a mutant zebrafish developed abnormal angiogenesis in intersegmental vessels and cranial secondary vessels. Endothelial cells exhibited the defects in morphogenesis and formation of vascular tubes despite normal cell to cell contacts under electron microscope. Circulatory disorder was induced by abnormal sprouts in the trunk and head. Reduced circulation in the abnormal vessels was revealed by microangiography. No blood flow permeated across the vessels wall despite the extremely abnormal structure. rnf213a mutant showed lower erythrocyte velocity in dorsal aorta than that in wild-type siblings. In this study, we provided a promising in vivo model for MMD, and this model would aid to understand the function of rnf213a in angiogenesis.
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Affiliation(s)
- Jun Wen
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xunsha Sun
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huimin Chen
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huijiao Liu
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Rong Lai
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiaoxing Li
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yufang Wang
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.
| | - Wenli Sheng
- Department of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department, National Key Discipline, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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21
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McCammon JM, Sive H. Challenges in understanding psychiatric disorders and developing therapeutics: a role for zebrafish. Dis Model Mech 2016; 8:647-56. [PMID: 26092527 PMCID: PMC4486859 DOI: 10.1242/dmm.019620] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The treatment of psychiatric disorders presents three major challenges to the research and clinical community: defining a genotype associated with a disorder, characterizing the molecular pathology of each disorder and developing new therapies. This Review addresses how cellular and animal systems can help to meet these challenges, with an emphasis on the role of the zebrafish. Genetic changes account for a large proportion of psychiatric disorders and, as gene variants that predispose to psychiatric disease are beginning to be identified in patients, these are tractable for study in cellular and animal systems. Defining cellular and molecular criteria associated with each disorder will help to uncover causal physiological changes in patients and will lead to more objective diagnostic criteria. These criteria should also define co-morbid pathologies within the nervous system or in other organ systems. The definition of genotypes and of any associated pathophysiology is integral to the development of new therapies. Cell culture-based approaches can address these challenges by identifying cellular pathology and by high-throughput screening of gene variants and potential therapeutics. Whole-animal systems can define the broadest function of disorder-associated gene variants and the organismal impact of candidate medications. Given its evolutionary conservation with humans and its experimental tractability, the zebrafish offers several advantages to psychiatric disorder research. These include assays ranging from molecular to behavioural, and capability for chemical screening. There is optimism that the multiple approaches discussed here will link together effectively to provide new diagnostics and treatments for psychiatric patients. Summary: In this review, we discuss strengths and limitations of prevalent laboratory models that are used for understanding psychiatric disorders and developing therapeutics, with emphasis on the zebrafish.
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Affiliation(s)
- Jasmine M McCammon
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Hazel Sive
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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22
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Zebrafish as a model for understanding enteric nervous system interactions in the developing intestinal tract. Methods Cell Biol 2016; 134:139-64. [PMID: 27312493 DOI: 10.1016/bs.mcb.2016.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The enteric nervous system (ENS) forms intimate connections with many other intestinal cell types, including immune cells and bacterial consortia resident in the intestinal lumen. In this review, we highlight contributions of the zebrafish model to understanding interactions among these cells. Zebrafish is a powerful model for forward genetic screens, several of which have uncovered genes previously unknown to be important for ENS development. More recently, zebrafish has emerged as a model for testing functions of genes identified in human patients or large-scale human susceptibility screens. In several cases, zebrafish studies have revealed mechanisms connecting intestinal symptoms with other, seemingly unrelated disease phenotypes. Importantly, chemical library screens in zebrafish have provided startling new insights into potential effects of common drugs on ENS development. A key feature of the zebrafish model is the ability to rear large numbers of animals germ free or in association with only specific bacterial species. Studies utilizing these approaches have demonstrated the importance of bacterial signals for normal intestinal development. These types of studies also show how luminal bacteria and the immune system can contribute to inflammatory processes that can feedback to influence ENS development. The excellent optical properties of zebrafish embryos and larvae, coupled with the ease of generating genetically marked cells of both the host and its resident bacteria, allow visualization of multiple intestinal cell types in living larvae and should promote a more in-depth understanding of intestinal cell interactions, especially interactions between other intestinal cell types and the ENS.
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Abstract
The recent remarkable innovation of an RNA-guided nuclease system, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system, enables us the modification of specific genomic loci in various model animals including zebrafish. With this system, multiple guide RNAs simultaneously injected with the Cas9 nuclease into zebrafish embryos cause multiple genome modifications at different genomic loci with high efficiency; therefore, a simple method to detect individual mutations at distinct loci is desired. In this chapter, we describe a procedure for inducing multiple CRISPR/Cas9-mediated genome modifications in zebrafish and a convenient method to detect CRISPR/Cas9-induced insertion and/or deletion (indel) mutations using a heteroduplex mobility assay (HMA).
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Affiliation(s)
- Satoshi Ota
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
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26
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Abstract
Using TALEN or CRISPR/Cas system to induce small indels into coding sequences has been implicated in broad applications for reverse genetic studies of many organisms including zebrafish. However, complete deletion of a large gene or noncoding gene(s) or removing a large genomic fragment spanning several genes or other chromosomal elements is preferred in various cases, as well as inducing chromosomal inversions. Here, we describe the detailed protocols for the generation of chromosomal deletion mutations mediated by Cas9 and a pair of gRNAs and the evaluation for the efficiencies in F0 founder fish and of germline transmission.
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Affiliation(s)
- An Xiao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, No 5 Yiheyuan Rd., Haidian District, Beijing, 100871, P. R. China
- Department of Internal Medicine, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, No 5 Yiheyuan Rd., Haidian District, Beijing, 100871, P. R. China.
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Saralahti A, Rämet M. Zebrafish and Streptococcal Infections. Scand J Immunol 2015; 82:174-83. [PMID: 26095827 DOI: 10.1111/sji.12320] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/28/2015] [Indexed: 12/11/2022]
Abstract
Streptococcal bacteria are a versatile group of gram-positive bacteria capable of infecting several host organisms, including humans and fish. Streptococcal species are common colonizers of the human respiratory and gastrointestinal tract, but they also cause some of the most common life-threatening, invasive infections in humans and aquaculture. With its unique characteristics and efficient tools for genetic and imaging applications, the zebrafish (Danio rerio) has emerged as a powerful vertebrate model for infectious diseases. Several zebrafish models introduced so far have shown that zebrafish are suitable models for both zoonotic and human-specific infections. Recently, several zebrafish models mimicking human streptococcal infections have also been developed. These models show great potential in providing novel information about the pathogenic mechanisms and host responses associated with human streptococcal infections. Here, we review the zebrafish infection models for the most relevant streptococcal species: the human-specific Streptococcus pneumoniae and Streptococcus pyogenes, and the zoonotic Streptococcus iniae and Streptococcus agalactiae. The recent success and the future potential of these models for the study of host-pathogen interactions in streptococcal infections are also discussed.
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Affiliation(s)
- A Saralahti
- BioMediTech, University of Tampere, Tampere, Finland
| | - M Rämet
- BioMediTech, University of Tampere, Tampere, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland.,PEDEGO Research Center, Medical Research Center Oulu, University of Oulu, Oulu, Finland
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28
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Venken KJT, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:233-67. [PMID: 26447401 DOI: 10.1002/wdev.214] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 08/03/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
A central challenge in investigating biological phenomena is the development of techniques to modify genomic DNA with nucleotide precision that can be transmitted through the germ line. Recent years have brought a boon in these technologies, now collectively known as genome engineering. Defined genomic manipulations at the nucleotide level enable a variety of reverse engineering paradigms, providing new opportunities to interrogate diverse biological functions. These genetic modifications include controlled removal, insertion, and substitution of genetic fragments, both small and large. Small fragments up to a few kilobases (e.g., single nucleotide mutations, small deletions, or gene tagging at single or multiple gene loci) to large fragments up to megabase resolution can be manipulated at single loci to create deletions, duplications, inversions, or translocations of substantial sections of whole chromosome arms. A specialized substitution of chromosomal portions that presumably are functionally orthologous between different organisms through syntenic replacement, can provide proof of evolutionary conservation between regulatory sequences. Large transgenes containing endogenous or synthetic DNA can be integrated at defined genomic locations, permitting an alternative proof of evolutionary conservation, and sophisticated transgenes can be used to interrogate biological phenomena. Precision engineering can additionally be used to manipulate the genomes of organelles (e.g., mitochondria). Novel genome engineering paradigms are often accelerated in existing, easily genetically tractable model organisms, primarily because these paradigms can be integrated in a rigorous, existing technology foundation. The Drosophila melanogaster fly model is ideal for these types of studies. Due to its small genome size, having just four chromosomes, the vast amount of cutting-edge genetic technologies, and its short life-cycle and inexpensive maintenance requirements, the fly is exceptionally amenable to complex genetic analysis using advanced genome engineering. Thus, highly sophisticated methods developed in the fly model can be used in nearly any sequenced organism. Here, we summarize different ways to perform precise inheritable genome engineering using integrases, recombinases, and DNA nucleases in the D. melanogaster. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Koen J T Venken
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Paul J Vandeventer
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Audrey E Christiansen
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Kristi L Hoffman
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
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Martin PS, Kloesel B, Norris RA, Lindsay M, Milan D, Body SC. Embryonic Development of the Bicuspid Aortic Valve. J Cardiovasc Dev Dis 2015; 2:248-272. [PMID: 28529942 PMCID: PMC5438177 DOI: 10.3390/jcdd2040248] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital valvular heart defect with an overall frequency of 0.5%–1.2%. BAVs result from abnormal aortic cusp formation during valvulogenesis, whereby adjacent cusps fuse into a single large cusp resulting in two, instead of the normal three, aortic cusps. Individuals with BAV are at increased risk for ascending aortic disease, aortic stenosis and coarctation of the aorta. The frequent occurrence of BAV and its anatomically discrete but frequent co-existing diseases leads us to suspect a common cellular origin. Although autosomal-dominant transmission of BAV has been observed in a few pedigrees, notably involving the gene NOTCH1, no single-gene model clearly explains BAV inheritance, implying a complex genetic model involving interacting genes. Several sequencing studies in patients with BAV have identified rare and uncommon mutations in genes of cardiac embryogenesis. But the extensive cell-cell signaling and multiple cellular origins involved in cardiac embryogenesis preclude simplistic explanations of this disease. In this review, we examine the series of events from cellular and transcriptional embryogenesis of the heart, to development of the aortic valve.
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Affiliation(s)
- Peter S. Martin
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis St., Th724, Boston, MA 02115, USA; E-Mails: (P.S.M.); (B.K.)
| | - Benjamin Kloesel
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis St., Th724, Boston, MA 02115, USA; E-Mails: (P.S.M.); (B.K.)
| | - Russell A. Norris
- Department of Regenerative Medicine and Cell Biology, Children’s Research Institute, Medical University of South Carolina, 173 Ashley St, Charleston, SC 29403, USA; E-Mail:
| | - Mark Lindsay
- Cardiovascular Research Center, Richard B. Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; E-Mails: (M.L.); (D.M.)
| | - David Milan
- Cardiovascular Research Center, Richard B. Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; E-Mails: (M.L.); (D.M.)
| | - Simon C. Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis St., Th724, Boston, MA 02115, USA; E-Mails: (P.S.M.); (B.K.)
- Author to whom correspondence should be addressed: E-Mail: ; Tel.: +1-617-732-7330; Fax: +1-617-730-2813
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30
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McCammon JM, Sive H. Addressing the Genetics of Human Mental Health Disorders in Model Organisms. Annu Rev Genomics Hum Genet 2015; 16:173-97. [DOI: 10.1146/annurev-genom-090314-050048] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jasmine M. McCammon
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142;
| | - Hazel Sive
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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31
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Hisano Y, Inoue A, Taimatsu K, Ota S, Ohga R, Kotani H, Muraki M, Aoki J, Kawahara A. Comprehensive analysis of sphingosine-1-phosphate receptor mutants during zebrafish embryogenesis. Genes Cells 2015; 20:647-58. [PMID: 26094551 DOI: 10.1111/gtc.12259] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022]
Abstract
The lipid mediator sphingosine-1-phosphate (S1P) regulates various physiological and pathological phenomena such as angiogenesis and oncogenesis. Secreted S1P associates with the G-protein-coupled S1P receptors (S1PRs), leading to the activation of downstream signaling molecules. In mammals, five S1prs have been identified and the genetic disruption of a single S1pr1 gene causes vascular defects. In zebrafish, seven s1prs have been isolated. We found that individual s1prs showed unique expression patterns with some overlapping expression domains during early embryogenesis. We generated all s1pr single-mutant zebrafish by introducing premature stop codons in their coding regions using transcription activator-like effector nucleases and analyzed their phenotypes during early embryogenesis. Zygotic s1pr1, s1pr3a, s1pr3b, s1pr4, s1pr5a and s1pr5b mutants showed no developmental defects and grew into adults, whereas zygotic s1pr2 mutant showed embryonic lethality with a cardiac defect, showing quite distinct embryonic phenotypes for individual S1pr mutants between zebrafish and mouse. We further generated maternal-zygotic s1pr1, s1pr3a, s1pr3b, s1pr4, s1pr5a and s1pr5b mutants and found that these maternal-zygotic mutants also showed no obvious developmental defects, presumably suggesting the redundant functions of the S1P receptor-mediated signaling in zebrafish.
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Affiliation(s)
- Yu Hisano
- Laboratory for Developmental Gene Regulation, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-8613, Japan
| | - Kiyohito Taimatsu
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Satoshi Ota
- Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan.,Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Rie Ohga
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Hirohito Kotani
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Michiko Muraki
- Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, 332-8613, Japan
| | - Atsuo Kawahara
- Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan.,Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
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Kotani H, Taimatsu K, Ohga R, Ota S, Kawahara A. Efficient Multiple Genome Modifications Induced by the crRNAs, tracrRNA and Cas9 Protein Complex in Zebrafish. PLoS One 2015; 10:e0128319. [PMID: 26010089 PMCID: PMC4444095 DOI: 10.1371/journal.pone.0128319] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/26/2015] [Indexed: 12/22/2022] Open
Abstract
The type II clustered regularly interspaced short palindromic repeats (CRISPR) associated with Cas9 endonuclease (CRISPR/Cas9) has become a powerful genetic tool for understanding the function of a gene of interest. In zebrafish, the injection of Cas9 mRNA and guide-RNA (gRNA), which are prepared using an in vitro transcription system, efficiently induce DNA double-strand breaks (DSBs) at the targeted genomic locus. Because gRNA was originally constructed by fusing two short RNAs CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA), we examined the effect of synthetic crRNAs and tracrRNA with Cas9 mRNA or Cas9 protein on the genome editing activity. We previously reported that the disruption of tyrosinase (tyr) by tyr-gRNA/Cas9 mRNA causes a retinal pigment defect, whereas the disruption of spns2 by spns2-gRNA1/Cas9 mRNA leads to a cardiac progenitor migration defect in zebrafish. Here, we found that the injection of spns2-crRNA1, tyr-crRNA and tracrRNA with Cas9 mRNA or Cas9 protein simultaneously caused a migration defect in cardiac progenitors and a pigment defect in retinal epithelial cells. A time course analysis demonstrated that the injection of crRNAs and tracrRNA with Cas9 protein rapidly induced genome modifications compared with the injection of crRNAs and tracrRNA with Cas9 mRNA. We further show that the crRNA-tracrRNA-Cas9 protein complex is functional for the visualization of endogenous gene expression; therefore, this is a very powerful, ready-to-use system in zebrafish.
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Affiliation(s)
- Hirohito Kotani
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Kiyohito Taimatsu
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Rie Ohga
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Satoshi Ota
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
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Hisano Y, Inoue A, Okudaira M, Taimatsu K, Matsumoto H, Kotani H, Ohga R, Aoki J, Kawahara A. Maternal and Zygotic Sphingosine Kinase 2 Are Indispensable for Cardiac Development in Zebrafish. J Biol Chem 2015; 290:14841-51. [PMID: 25907554 DOI: 10.1074/jbc.m114.634717] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 01/14/2023] Open
Abstract
Sphingosine 1-phosphate (S1P) is synthesized from sphingosine by sphingosine kinases (SPHK1 and SPHK2) in invertebrates and vertebrates, whereas specific receptors for S1P (S1PRs) selectively appear in vertebrates, suggesting that S1P acquires novel functions in vertebrates. Because the developmental functions of SPHK1 and SPHK2 remain obscure in vertebrates, we generated sphk1 or sphk2 gene-disrupted zebrafish by introducing premature stop codons in their coding regions using transcription activator-like effector nucleases. Both zygotic sphk1 and sphk2 zebrafish mutants exhibited no obvious developmental defects and grew to adults. The maternal-zygotic sphk2 mutant (MZsphk2), but not the maternal-zygotic sphk1 mutant and maternal sphk2 mutant, had a defect in the cardiac progenitor migration and a concomitant decrease in S1P level, leading to a two-heart phenotype (cardia bifida). Cardia bifida in MZsphk2, which was rescued by injecting sphk2 mRNA, was a phenotype identical to that of zygotic mutants of the S1P transporter spns2 and S1P receptor s1pr2, indicating that the Sphk2-Spns2-S1pr2 axis regulates the cardiac progenitor migration in zebrafish. The contribution of maternally supplied lipid mediators during vertebrate organogenesis presents as a requirement for maternal-zygotic Sphk2.
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Affiliation(s)
- Yu Hisano
- From the Laboratory for Developmental Gene Regulation, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198,
| | - Asuka Inoue
- the Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, PRESTO and
| | - Michiyo Okudaira
- the Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578
| | - Kiyohito Taimatsu
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Hirotaka Matsumoto
- the Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578
| | - Hirohito Kotani
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Rie Ohga
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Junken Aoki
- the Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, CREST, Japan Science and Technology Agency and
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
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Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish. Sci Rep 2015; 5:8841. [PMID: 25740433 PMCID: PMC4350073 DOI: 10.1038/srep08841] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/05/2015] [Indexed: 12/23/2022] Open
Abstract
The CRISPR/Cas9 system provides a powerful tool for genome editing in various model organisms, including zebrafish. The establishment of targeted gene-disrupted zebrafish (knockouts) is readily achieved by CRISPR/Cas9-mediated genome modification. Recently, exogenous DNA integration into the zebrafish genome via homology-independent DNA repair was reported, but this integration contained various mutations at the junctions of genomic and integrated DNA. Thus, precise genome modification into targeted genomic loci remains to be achieved. Here, we describe efficient, precise CRISPR/Cas9-mediated integration using a donor vector harbouring short homologous sequences (10-40 bp) flanking the genomic target locus. We succeeded in integrating with high efficiency an exogenous mCherry or eGFP gene into targeted genes (tyrosinase and krtt1c19e) in frame. We found the precise in-frame integration of exogenous DNA without backbone vector sequences when Cas9 cleavage sites were introduced at both sides of the left homology arm, the eGFP sequence and the right homology arm. Furthermore, we confirmed that this precise genome modification was heritable. This simple method enables precise targeted gene knock-in in zebrafish.
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35
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Sasaki H, Yoshida K, Hozumi A, Sasakura Y. CRISPR/Cas9-mediated gene knockout in the ascidian Ciona intestinalis. Dev Growth Differ 2014; 56:499-510. [PMID: 25212715 PMCID: PMC4231237 DOI: 10.1111/dgd.12149] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/18/2014] [Accepted: 06/22/2014] [Indexed: 01/25/2023]
Abstract
Knockout of genes with CRISPR/Cas9 is a newly emerged approach to investigate functions of genes in various organisms. We demonstrate that CRISPR/Cas9 can mutate endogenous genes of the ascidian Ciona intestinalis, a splendid model for elucidating molecular mechanisms for constructing the chordate body plan. Short guide RNA (sgRNA) and Cas9 mRNA, when they are expressed in Ciona embryos by means of microinjection or electroporation of their expression vectors, introduced mutations in the target genes. The specificity of target choice by sgRNA is relatively high compared to the reports from some other organisms, and a single nucleotide mutation at the sgRNA dramatically reduced mutation efficiency at the on-target site. CRISPR/Cas9-mediated mutagenesis will be a powerful method to study gene functions in Ciona along with another genome editing approach using TALE nucleases.
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Affiliation(s)
- Haruka Sasaki
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
| | - Keita Yoshida
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
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36
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Horii T, Hatada I. Genome engineering using the CRISPR/Cas system. World J Med Genet 2014; 4:69-76. [DOI: 10.5496/wjmg.v4.i3.69] [Citation(s) in RCA: 7] [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: 12/28/2013] [Revised: 03/12/2014] [Accepted: 05/19/2014] [Indexed: 02/06/2023] Open
Abstract
Recently, an epoch-making genome engineering technology using clustered regularly at interspaced short palindromic repeats (CRISPR) and CRISPR associated (Cas) nucleases, was developed. Previous technologies for genome manipulation require the time-consuming design and construction of genome-engineered nucleases for each target and have, therefore, not been widely used in mouse research where standard techniques based on homologous recombination are commonly used. The CRISPR/Cas system only requires the design of sequences complementary to a target locus, making this technology fast and straightforward. In addition, CRISPR/Cas can be used to generate mice carrying mutations in multiple genes in a single step, an achievement not possible using other methods. Here, we review the uses of this technology in genetic analysis and manipulation, including achievements made possible to date and the prospects for future therapeutic applications.
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Newman M, Ebrahimie E, Lardelli M. Using the zebrafish model for Alzheimer's disease research. Front Genet 2014; 5:189. [PMID: 25071820 PMCID: PMC4075077 DOI: 10.3389/fgene.2014.00189] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/06/2014] [Indexed: 12/19/2022] Open
Abstract
Rodent models have been extensively used to investigate the cause and mechanisms behind Alzheimer’s disease. Despite many years of intensive research using these models we still lack a detailed understanding of the molecular events that lead to neurodegeneration. Although zebrafish lack the complexity of advanced cognitive behaviors evident in rodent models they have proven to be a very informative model for the study of human diseases. In this review we give an overview of how the zebrafish has been used to study Alzheimer’s disease. Zebrafish possess genes orthologous to those mutated in familial Alzheimer’s disease and research using zebrafish has revealed unique characteristics of these genes that have been difficult to observe in rodent models. The zebrafish is becoming an increasingly popular model for the investigation of Alzheimer’s disease and will complement studies using other models to help complete our understanding of this disease.
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Affiliation(s)
- Morgan Newman
- School of Molecular and Biomedical Science, University of Adelaide SA, Australia
| | - Esmaeil Ebrahimie
- School of Molecular and Biomedical Science, University of Adelaide SA, Australia
| | - Michael Lardelli
- School of Molecular and Biomedical Science, University of Adelaide SA, Australia
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Xie S, Shen B, Zhang C, Huang X, Zhang Y. sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS One 2014; 9:e100448. [PMID: 24956386 PMCID: PMC4067335 DOI: 10.1371/journal.pone.0100448] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 05/23/2014] [Indexed: 12/26/2022] Open
Abstract
Although the CRISPR/Cas9/sgRNA system efficiently cleaves intracellular DNA at desired target sites, major concerns remain on potential "off-target" cleavage that may occur throughout the whole genome. In order to improve CRISPR-Cas9 specificity for targeted genome editing and transcriptional control, we describe a bioinformatics tool "sgRNAcas9", which is a software package developed for fast design of CRISPR sgRNA with minimized off-target effects. This package consists of programs to perform a search for CRISPR target sites (protospacers) with user-defined parameters, predict genome-wide Cas9 potential off-target cleavage sites (POT), classify the POT into three categories, batch-design oligonucleotides for constructing 20-nt (nucleotides) or truncated sgRNA expression vectors, extract desired length nucleotide sequences flanking the on- or off-target cleavage sites for designing PCR primer pairs to validate the mutations by T7E1 cleavage assay. Importantly, by identifying potential off-target sites in silico, the sgRNAcas9 allows the selection of more specific target sites and aids the identification of bona fide off-target sites, significantly facilitating the design of sgRNA for genome editing applications. sgRNAcas9 software package is publicly available at BiooTools website (www.biootools.com) under the terms of the GNU General Public License.
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Affiliation(s)
- Shengsong Xie
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bin Shen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Chaobao Zhang
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xingxu Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
| | - Yonglian Zhang
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institute of Planned Parenthood Research, Shanghai, China
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Ota S, Hisano Y, Ikawa Y, Kawahara A. Multiple genome modifications by the CRISPR/Cas9 system in zebrafish. Genes Cells 2014; 19:555-64. [PMID: 24848337 DOI: 10.1111/gtc.12154] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/26/2014] [Indexed: 01/01/2023]
Abstract
The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system, which is an adaptive immune system of bacteria, has become a powerful tool for genome editing in various model organisms. Here, we demonstrate multiple genome modifications mediated by CRISPR/Cas9 in zebrafish (Danio rerio). Multiple genes including golden/gol and tyrosinase/tyr, which are involved in pigment formation, and s1pr2 and spns2, which are involved in cardiac development, were disrupted with insertion and/or deletion (indel) mutations introduced by the co-injection of multiple guide RNAs (gRNAs) and the nuclease Cas9 mRNA. We simultaneously observed two distinct phenotypes, such as, the two hearts phenotype and the hypopigmentation of skin melanophores and the retinal pigment epithelium, in the injected F0 embryos. Additionally, we detected the targeted deletion and inversion genes as a 7.1-kb fragment between the two distinct spns2 targeted sites together with indel mutations. Conversely, chromosomal translocations among five target loci were not detected. Therefore, we confirmed that the CRISPR/Cas9-induced indel mutations and a locus-specific deletion were heritable in F1 embryos. To screen founders, we improved heteroduplex mobility assay (HMA) for simultaneously detecting indel mutations in different target loci. The results suggest that the multi-locus HMA is a powerful tool for identification of multiple genome modifications mediated by the CRISPR/Cas9 system.
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Affiliation(s)
- Satoshi Ota
- Laboratory for Cardiovascular Molecular Dynamics, RIKEN Quantitative Biology Center (QBiC), Furuedai 6-2-3, Suita, Osaka, 565-0874, Japan; Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimogatou 1110, Chuo, Yamanashi, 409-3898, Japan
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Archambeault DR, Matzuk MM. Disrupting the male germ line to find infertility and contraception targets. ANNALES D'ENDOCRINOLOGIE 2014; 75:101-8. [PMID: 24793995 DOI: 10.1016/j.ando.2014.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genetically-manipulated mouse models have become indispensible for broadening our understanding of genes and pathways related to male germ cell development. Until suitable in vitro systems for studying spermatogenesis are perfected, in vivo models will remain the gold standard for inquiry into testicular function. Here, we discuss exciting advances that are allowing researchers faster, easier, and more customizable access to their mouse models of interest. Specifically, the trans-NIH Knockout Mouse Project (KOMP) is working to generate knockout mouse models of every gene in the mouse genome. The related Knockout Mouse Phenotyping Program (KOMP2) is performing systematic phenotypic analysis of this genome-wide collection of knockout mice, including fertility screening. Together, these programs will not only uncover new genes involved in male germ cell development but also provide the research community with the mouse models necessary for further investigations. In addition to KOMP/KOMP2, another promising development in the field of mouse models is the advent of CRISPR (clustered regularly interspaced short palindromic repeat)-Cas technology. Utilizing 20 nucleotide guide sequences, CRISPR/Cas has the potential to introduce sequence-specific insertions, deletions, and point mutations to produce null, conditional, activated, or reporter-tagged alleles. CRISPR/Cas can also successfully target multiple genes in a single experimental step, forgoing the multiple generations of breeding traditionally required to produce mouse models with deletions, insertions, or mutations in multiple genes. In addition, CRISPR/Cas can be used to create mouse models carrying variants identical to those identified in infertile human patients, providing the opportunity to explore the effects of such mutations in an in vivo system. Both the KOMP/KOMP2 projects and the CRISPR/Cas system provide powerful, accessible genetic approaches to the study of male germ cell development in the mouse. A more complete understanding of male germ cell biology is critical for the identification of novel targets for potential non-hormonal contraceptive intervention.
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Affiliation(s)
- Denise R Archambeault
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Martin M Matzuk
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA; Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA; Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA.
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