101
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Genome Editing of Induced Pluripotent Stem Cells Using CRISPR/Cas9 Ribonucleoprotein Complexes to Model Genetic Ocular Diseases. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2549:321-334. [PMID: 34128206 DOI: 10.1007/7651_2021_409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Genome editing with the use of CRISPR/Cas9 ribonucleoprotein complexes of induced pluripotent stem cells can be used to model many diseases. The combination of stem cells and gene editing technologies is a valuable tool to study ocular disorders, as many have been identified to be caused by specific genetic mutations. This protocol provides experimentally derived guidelines for genome editing of human induced pluripotent stem cells (iPSCs) using CRISPR/Cas9 ribonucleoprotein complexes to generate iPSCs harboring single nucleotide variants from ocular disorders. Edited iPSC can be further differentiated into retinal cells in order to study disease mechanisms as well as screen potential therapies.
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102
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Yamada K, Maeno A, Araki S, Kikuchi M, Suzuki M, Ishizaka M, Satoh K, Akama K, Kawabe Y, Suzuki K, Kobayashi D, Hamano N, Kawamura A. An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters. Development 2021; 148:269044. [PMID: 34096572 DOI: 10.1242/dev.198325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.
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Affiliation(s)
- Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akiteru Maeno
- Plant Resource Development, Division of Genetic Resource Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Soh Araki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Morimichi Kikuchi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Masato Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Koumi Satoh
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Yuki Kawabe
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kenya Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Daiki Kobayashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nanami Hamano
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
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103
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Davis AE, Castranova D, Weinstein BM. Rapid Generation of Pigment Free, Immobile Zebrafish Embryos and Larvae in Any Genetic Background Using CRISPR-Cas9 dgRNPs. Zebrafish 2021; 18:235-242. [PMID: 34077687 DOI: 10.1089/zeb.2021.0011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The ability to carry out high-resolution, high-magnification optical imaging of living animals is one of the most attractive features of the zebrafish as a model organism. However, increasing amounts of pigmentation as development proceeds and difficulties in maintaining sustained immobilization of healthy, living animals remain challenges for live imaging. Chemical treatments can be used to suppress pigment formation and movement, but these treatments can lead to developmental defects. Genetic mutants can also be used to eliminate pigment formation and immobilize animals, but maintaining these mutants in lines carrying other combinations of transgenes and mutants is difficult and laborious. In this study, we show that CRISPR duplex guide ribonucleoproteins (dgRNPs) targeting the slc45a2 (albino) and chrna1 (nic1) genes can be used to efficiently suppress pigment formation in and immobilize F0 injected animals. CRISPR dgRNPs can be used to generate pigment-free, immobile zebrafish embryos and larvae in any transgenic and/or mutant-carrying background, greatly facilitating high-resolution imaging and analysis of the many transgenic and mutant lines available in the zebrafish.
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Affiliation(s)
- Andrew E Davis
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Daniel Castranova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
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104
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Sheets L, Holmgren M, Kindt KS. How Zebrafish Can Drive the Future of Genetic-based Hearing and Balance Research. J Assoc Res Otolaryngol 2021; 22:215-235. [PMID: 33909162 PMCID: PMC8110678 DOI: 10.1007/s10162-021-00798-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Over the last several decades, studies in humans and animal models have successfully identified numerous molecules required for hearing and balance. Many of these studies relied on unbiased forward genetic screens based on behavior or morphology to identify these molecules. Alongside forward genetic screens, reverse genetics has further driven the exploration of candidate molecules. This review provides an overview of the genetic studies that have established zebrafish as a genetic model for hearing and balance research. Further, we discuss how the unique advantages of zebrafish can be leveraged in future genetic studies. We explore strategies to design novel forward genetic screens based on morphological alterations using transgenic lines or behavioral changes following mechanical or acoustic damage. We also outline how recent advances in CRISPR-Cas9 can be applied to perform reverse genetic screens to validate large sequencing datasets. Overall, this review describes how future genetic studies in zebrafish can continue to advance our understanding of inherited and acquired hearing and balance disorders.
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Affiliation(s)
- Lavinia Sheets
- Department of Otolaryngology-Head & Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Melanie Holmgren
- Department of Otolaryngology-Head & Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie S Kindt
- Section On Sensory Cell Development and Function, National Institutes On Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA.
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105
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Lusk S, Casey MA, Kwan KM. 4-Dimensional Imaging of Zebrafish Optic Cup Morphogenesis. J Vis Exp 2021:10.3791/62155. [PMID: 34125104 PMCID: PMC8848516 DOI: 10.3791/62155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Visual system function requires the establishment of precise tissue and organ structures. In the vertebrate eye, structural defects are a common cause of visual impairment, yet mechanisms of eye morphogenesis are still poorly understood. The basic organization of the embryonic eye is conserved throughout vertebrates, thus live imaging of zebrafish embryos has become a powerful approach to directly observe eye development at real time under normal and pathological conditions. Dynamic cell processes including movements, morphologies, interactions, division, and death can be visualized in the embryo. We have developed methods for uniform labeling of subcellular structures and timelapse confocal microscopy of early eye development in zebrafish. This protocol outlines the method of generating capped mRNA for injection into the 1-cell zebrafish embryo, mounting embryos at optic vesicle stage (~12 hours post fertilization, hpf), and performing multi-dimensional timelapse imaging of optic cup morphogenesis on a laser scanning confocal microscope, such that multiple datasets are acquired sequentially in the same imaging session. Such an approach yields data that can be used for a variety of purposes, including cell tracking, volume measurements, three-dimensional (3D) rendering, and visualization. Our approaches allow us to pinpoint the cellular and molecular mechanisms driving optic cup development, in both wild type and genetic mutant conditions. These methods can be employed directly by other groups or adapted to visualize many additional aspects of zebrafish eye development.
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Affiliation(s)
- Sarah Lusk
- Department of Human Genetics, University of Utah
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106
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Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes. Proc Natl Acad Sci U S A 2021; 118:2101634118. [PMID: 34031155 DOI: 10.1073/pnas.2101634118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Determining how plasticity of developmental traits responds to environmental conditions is a challenge that must combine evolutionary sciences, ecology, and developmental biology. During metamorphosis, fish alter their morphology and color pattern according to environmental cues. We observed that juvenile clownfish (Amphiprion percula) modulate the developmental timing of their adult white bar formation during metamorphosis depending on the sea anemone species in which they are recruited. We observed an earlier formation of white bars when clownfish developed with Stichodactyla gigantea (Sg) than with Heteractis magnifica (Hm). As these bars, composed of iridophores, form during metamorphosis, we hypothesized that timing of their development may be thyroid hormone (TH) dependent. We treated clownfish larvae with TH and found that white bars developed earlier than in control fish. We further observed higher TH levels, associated with rapid white bar formation, in juveniles recruited in Sg than in Hm, explaining the faster white bar formation. Transcriptomic analysis of Sg recruits revealed higher expression of duox, a dual oxidase implicated in TH production as compared to Hm recruits. Finally, we showed that duox is an essential regulator of iridophore pattern timing in zebrafish. Taken together, our results suggest that TH controls the timing of adult color pattern formation and that shifts in duox expression and TH levels are associated with ecological differences resulting in divergent ontogenetic trajectories in color pattern development.
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107
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Francis CR, Claflin S, Kushner EJ. Synaptotagmin-Like Protein 2a Regulates Angiogenic Lumen Formation via Weibel-Palade Body Apical Secretion of Angiopoietin-2. Arterioscler Thromb Vasc Biol 2021; 41:1972-1986. [PMID: 33853352 DOI: 10.1161/atvbaha.121.316113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
| | - Shea Claflin
- Department of Biological Sciences, University of Denver, CO
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108
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Fleming TJ, Schrankel CS, Vyas H, Rosenblatt HD, Hamdoun A. CRISPR/Cas9 mutagenesis reveals a role for ABCB1 in gut immune responses to Vibrio diazotrophicus in sea urchin larvae. J Exp Biol 2021; 224:jeb232272. [PMID: 33653719 PMCID: PMC8077557 DOI: 10.1242/jeb.232272] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 02/08/2021] [Indexed: 12/16/2022]
Abstract
The ABC transporter ABCB1 plays an important role in the disposition of xenobiotics. Embryos of most species express high levels of this transporter in early development as a protective mechanism, but its native substrates are not known. Here, we used larvae of the sea urchin Strongylocentrotus purpuratus to characterize the early life expression and role of Sp-ABCB1a, a homolog of ABCB1. The results indicate that while Sp-ABCB1a is initially expressed ubiquitously, it becomes enriched in the developing gut. Using optimized CRISPR/Cas9 gene editing methods to achieve high editing efficiency in the F0 generation, we generated ABCB1a crispant embryos with significantly reduced transporter efflux activity. When infected with the opportunistic pathogen Vibrio diazotrophicus, Sp-ABCB1a crispant larvae demonstrated significantly stronger gut inflammation, immunocyte migration and cytokine Sp-IL-17 induction, as compared with infected control larvae. The results suggest an ancestral function of ABCB1 in host-microbial interactions, with implications for the survival of invertebrate larvae in the marine microbial environment.
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Affiliation(s)
- Travis J. Fleming
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Catherine S. Schrankel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Himanshu Vyas
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Hannah D. Rosenblatt
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
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109
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Keatinge M, Tsarouchas TM, Munir T, Porter NJ, Larraz J, Gianni D, Tsai HH, Becker CG, Lyons DA, Becker T. CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury. PLoS Genet 2021; 17:e1009515. [PMID: 33914736 PMCID: PMC8084196 DOI: 10.1371/journal.pgen.1009515] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/28/2021] [Indexed: 12/30/2022] Open
Abstract
Zebrafish exhibit robust regeneration following spinal cord injury, promoted by macrophages that control post-injury inflammation. However, the mechanistic basis of how macrophages regulate regeneration is poorly understood. To address this gap in understanding, we conducted a rapid in vivo phenotypic screen for macrophage-related genes that promote regeneration after spinal injury. We used acute injection of synthetic RNA Oligo CRISPR guide RNAs (sCrRNAs) that were pre-screened for high activity in vivo. Pre-screening of over 350 sCrRNAs allowed us to rapidly identify highly active sCrRNAs (up to half, abbreviated as haCRs) and to effectively target 30 potentially macrophage-related genes. Disruption of 10 of these genes impaired axonal regeneration following spinal cord injury. We selected 5 genes for further analysis and generated stable mutants using haCRs. Four of these mutants (tgfb1a, tgfb3, tnfa, sparc) retained the acute haCR phenotype, validating the approach. Mechanistically, tgfb1a haCR-injected and stable mutant zebrafish fail to resolve post-injury inflammation, indicated by prolonged presence of neutrophils and increased levels of il1b expression. Inhibition of Il-1β rescues the impaired axon regeneration in the tgfb1a mutant. Hence, our rapid and scalable screening approach has identified functional regulators of spinal cord regeneration, but can be applied to any biological function of interest.
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Affiliation(s)
- Marcus Keatinge
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Tahimina Munir
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola J. Porter
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Juan Larraz
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Davide Gianni
- Biogen, Cambridge, Massachusetts, United States of America
| | - Hui-Hsin Tsai
- Biogen, Cambridge, Massachusetts, United States of America
| | - Catherina G. Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David A. Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
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110
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A single-cell resolution developmental atlas of hematopoietic stem and progenitor cell expansion in zebrafish. Proc Natl Acad Sci U S A 2021; 118:2015748118. [PMID: 33785593 PMCID: PMC8040670 DOI: 10.1073/pnas.2015748118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The caudal hematopoietic tissue (CHT) is characterized as a hematopoietic organ for fetal hematopoietic stem and progenitor cell (HSPC) expansion in zebrafish. In this study, we used scRNA-seq combined with functional assays to decode the developing CHT. First, we resolved fetal HSPC heterogeneity, manifested as lineage priming and metabolic gene signatures. We further analyzed the cellular interactions among nonhematopoietic niche components and HSPCs and identified an endothelial cell-specific factor, Gpr182, followed by experimental validation of its role in promoting HSPC expansion. Finally, we uncovered the conservation and divergence of developmental hematopoiesis between human fetal liver and zebrafish CHT. Our study provides a valuable resource for fetal HSPC development and clues to establish a supportive niche for HSPC expansion in vitro. During vertebrate embryogenesis, fetal hematopoietic stem and progenitor cells (HSPCs) exhibit expansion and differentiation properties in a supportive hematopoietic niche. To profile the developmental landscape of fetal HSPCs and their local niche, here, using single-cell RNA-sequencing, we deciphered a dynamic atlas covering 28,777 cells and 9 major cell types (23 clusters) of zebrafish caudal hematopoietic tissue (CHT). We characterized four heterogeneous HSPCs with distinct lineage priming and metabolic gene signatures. Furthermore, we investigated the regulatory mechanism of CHT niche components for HSPC development, with a focus on the transcription factors and ligand–receptor networks involved in HSPC expansion. Importantly, we identified an endothelial cell-specific G protein–coupled receptor 182, followed by in vivo and in vitro functional validation of its evolutionally conserved role in supporting HSPC expansion in zebrafish and mice. Finally, comparison between zebrafish CHT and human fetal liver highlighted the conservation and divergence across evolution. These findings enhance our understanding of the regulatory mechanism underlying hematopoietic niche for HSPC expansion in vivo and provide insights into improving protocols for HSPC expansion in vitro.
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111
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Abstract
The zebrafish has emerged as a valuable and important model organism for studying vascular development and vascular biology. Here, we discuss some of the approaches used to study vessels in fish, including loss-of-function tools such as morpholinos and genetic mutants, along with methods and considerations for assessing vascular phenotypes. We also provide detailed protocols for methods used for vital imaging of the zebrafish vasculature, including microangiography and long-term time-lapse imaging. The methods we describe, and the considerations we suggest using for assessing phenotypes observed using these methods, will help ensure reliable, valid conclusions when assessing vascular phenotypes following genetic or experimental manipulation of zebrafish.
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112
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Klatt Shaw D, Mokalled MH. Efficient CRISPR/Cas9 mutagenesis for neurobehavioral screening in adult zebrafish. G3-GENES GENOMES GENETICS 2021; 11:6179145. [PMID: 33742663 PMCID: PMC8496216 DOI: 10.1093/g3journal/jkab089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/07/2021] [Indexed: 12/22/2022]
Abstract
Adult zebrafish are widely used to interrogate mechanisms of disease development and tissue regeneration. Yet, the prospect of large-scale genetics in adult zebrafish has traditionally faced a host of biological and technical challenges, including inaccessibility of adult tissues to high-throughput phenotyping and the spatial and technical demands of adult husbandry. Here, we describe an experimental pipeline that combines high-efficiency CRISPR/Cas9 mutagenesis with functional phenotypic screening to identify genes required for spinal cord repair in adult zebrafish. Using CRISPR/Cas9 dual-guide ribonucleic proteins, we show selective and combinatorial mutagenesis of 17 genes at 28 target sites with efficiencies exceeding 85% in adult F0 “crispants”. We find that capillary electrophoresis is a reliable method to measure indel frequencies. Using a quantifiable behavioral assay, we identify seven single- or duplicate-gene crispants with reduced functional recovery after spinal cord injury. To rule out off-target effects, we generate germline mutations that recapitulate the crispant regeneration phenotypes. This study provides a platform that combines high-efficiency somatic mutagenesis with a functional phenotypic readout to perform medium- to large-scale genetic studies in adult zebrafish.
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Affiliation(s)
- Dana Klatt Shaw
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
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113
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Ghaffari K, Pierce LX, Roufaeil M, Gibson I, Tae K, Sahoo S, Cantrell JR, Andersson O, Lau J, Sakaguchi TF. NCK-associated protein 1 like (nckap1l) minor splice variant regulates intrahepatic biliary network morphogenesis. PLoS Genet 2021; 17:e1009402. [PMID: 33739979 PMCID: PMC8032155 DOI: 10.1371/journal.pgen.1009402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/08/2021] [Accepted: 02/09/2021] [Indexed: 11/18/2022] Open
Abstract
Impaired formation of the intrahepatic biliary network leads to cholestatic liver diseases, which are frequently associated with autoimmune disorders. Using a chemical mutagenesis strategy in zebrafish combined with computational network analysis, we screened for novel genes involved in intrahepatic biliary network formation. We positionally cloned a mutation in the nckap1l gene, which encodes a cytoplasmic adaptor protein for the WAVE regulatory complex. The mutation is located in the last exon after the stop codon of the primary splice isoform, only disrupting a previously unannotated minor splice isoform, which indicates that the minor splice isoform is responsible for the intrahepatic biliary network phenotype. CRISPR/Cas9-mediated nckap1l deletion, which disrupts both the primary and minor isoforms, showed the same defects. In the liver of nckap1l mutant larvae, WAVE regulatory complex component proteins are degraded specifically in biliary epithelial cells, which line the intrahepatic biliary network, thus disrupting the actin organization of these cells. We further show that nckap1l genetically interacts with the Cdk5 pathway in biliary epithelial cells. These data together indicate that although nckap1l was previously considered to be a hematopoietic cell lineage-specific protein, its minor splice isoform acts in biliary epithelial cells to regulate intrahepatic biliary network formation.
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Affiliation(s)
- Kimia Ghaffari
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Lain X. Pierce
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Maria Roufaeil
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Isabel Gibson
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Kevin Tae
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Saswat Sahoo
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
| | - James R. Cantrell
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jasmine Lau
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Takuya F. Sakaguchi
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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114
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Alhazmi N, Carroll SH, Kawasaki K, Woronowicz KC, Hallett SA, Macias Trevino C, Li EB, Baron R, Gori F, Yelick PC, Harris MP, Liao EC. Synergistic roles of Wnt modulators R-spondin2 and R-spondin3 in craniofacial morphogenesis and dental development. Sci Rep 2021; 11:5871. [PMID: 33712657 PMCID: PMC7954795 DOI: 10.1038/s41598-021-85415-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 02/26/2021] [Indexed: 12/01/2022] Open
Abstract
Wnt signaling plays a critical role in craniofacial patterning, as well as tooth and bone development. Rspo2 and Rspo3 are key regulators of Wnt signaling. However, their coordinated function and relative requirement in craniofacial development and odontogensis are poorly understood. We showed that in zebrafish rspo2 and rspo3 are both expressed in osteoprogenitors in the embryonic craniofacial skeleton. This is in contrast to mouse development, where Rspo3 is expressed in osteoprogenitors while Rspo2 expression is not observed. In zebrafish, rspo2 and rspo3 are broadly expressed in the pulp, odontoblasts and epithelial crypts. However, in the developing molars of the mouse, Rspo3 is largely expressed in the dental follicle and alveolar mesenchyme while Rspo2 expression is restricted to the tooth germ. While Rspo3 ablation in the mouse is embryonic lethal, zebrafish rspo3-/- mutants are viable with modest decrease in Meckel’s cartilage rostral length. However, compound disruption of rspo3 and rspo2 revealed synergistic roles of these genes in cartilage morphogenesis, fin development, and pharyngeal tooth development. Adult rspo3−/− zebrafish mutants exhibit a dysmorphic cranial skeleton and decreased average tooth number. This study highlights the differential functions of Rspo2 and Rspo3 in dentocranial morphogenesis in zebrafish and in mouse.
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Affiliation(s)
- Nora Alhazmi
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Shannon H Carroll
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Shriners Hospital for Children, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kenta Kawasaki
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Shriners Hospital for Children, Boston, MA, USA
| | - Katherine C Woronowicz
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Orthopedics, Boston Children's Hospital, Boston, MA, USA
| | - Shawn A Hallett
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Claudio Macias Trevino
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edward B Li
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Roland Baron
- Harvard School of Dental Medicine, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Pamela C Yelick
- Department of Orthodontics, Division of Craniofacial and Molecular Genetics, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Orthopedics, Boston Children's Hospital, Boston, MA, USA
| | - Eric C Liao
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Shriners Hospital for Children, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, MA, USA.
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115
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Teerlink CC, Jurynec MJ, Hernandez R, Stevens J, Hughes DC, Brunker CP, Rowe K, Grunwald DJ, Facelli JC, Cannon-Albright LA. A role for the MEGF6 gene in predisposition to osteoporosis. Ann Hum Genet 2021; 85:58-72. [PMID: 33026655 PMCID: PMC8274237 DOI: 10.1111/ahg.12408] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/19/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Osteoporosis is a common skeletal disorder characterized by deterioration of bone tissue. The set of genetic factors contributing to osteoporosis is not completely specified. High-risk osteoporosis pedigrees were analyzed to identify genes that may confer susceptibility to disease. Candidate predisposition variants were identified initially by whole exome sequencing of affected-relative pairs, approximately cousins, from 10 pedigrees. Variants were filtered on the basis of population frequency, concordance between pairs of cousins, affecting a gene associated with osteoporosis, and likelihood to have functionally damaging, pathogenic consequences. Subsequently, variants were tested for segregation in 68 additional relatives of the index carriers. A rare variant in MEGF6 (rs755467862) showed strong evidence of segregation with the disease phenotype. Predicted protein folding indicated the variant (Cys200Tyr) may disrupt structure of an EGF-like calcium-binding domain of MEGF6. Functional analyses demonstrated that complete loss of the paralogous genes megf6a and megf6b in zebrafish resulted in significant delay of cartilage and bone formation. Segregation analyses, in silico protein structure modeling, and functional assays support a role for MEGF6 in predisposition to osteoporosis.
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Affiliation(s)
- Craig C. Teerlink
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, 84132, USA
| | - Michael J Jurynec
- Department of Orthopaedics , University of Utah, Salt Lake City, 84108, USA
| | - Rolando Hernandez
- Department of Biomedical Informatics, University of Utah, Salt Lake City, 84108, USA
| | - Jeff Stevens
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, 84132, USA
| | - Dana C. Hughes
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, 84132, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, 84132, USA
| | - Cherie P. Brunker
- Department of Internal Medicine, University of Utah, Salt Lake City, 84132, USA
- Intermountain Healthcare, Salt Lake City, UT, 84113, USA
| | - Kerry Rowe
- Intermountain Healthcare, Salt Lake City, UT, 84113, USA
| | - David J. Grunwald
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Julio C. Facelli
- Department of Biomedical Informatics, University of Utah, Salt Lake City, 84108, USA
| | - Lisa A. Cannon-Albright
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, 84132, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, 84148, USA
- Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
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116
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de Oliveira MB, Meier K, Jung S, Bartels-Klein E, Coxam B, Geudens I, Szymborska A, Skoczylas R, Fechner I, Koltowska K, Gerhardt H. Vasohibin 1 selectively regulates secondary sprouting and lymphangiogenesis in the zebrafish trunk. Development 2021; 148:dev194993. [PMID: 33547133 PMCID: PMC7904002 DOI: 10.1242/dev.194993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/14/2021] [Indexed: 01/25/2023]
Abstract
Previous studies have shown that Vasohibin 1 (Vash1) is stimulated by VEGFs in endothelial cells and that its overexpression interferes with angiogenesis in vivo Recently, Vash1 was found to mediate tubulin detyrosination, a post-translational modification that is implicated in many cell functions, such as cell division. Here, we used the zebrafish embryo to investigate the cellular and subcellular mechanisms of Vash1 on endothelial microtubules during formation of the trunk vasculature. We show that microtubules within venous-derived secondary sprouts are strongly and selectively detyrosinated in comparison with other endothelial cells, and that this difference is lost upon vash1 knockdown. Vash1 depletion in zebrafish specifically affected secondary sprouting from the posterior cardinal vein, increasing endothelial cell divisions and cell number in the sprouts. We show that altering secondary sprout numbers and structure upon Vash1 depletion leads to defective lymphatic vessel formation and ectopic lymphatic progenitor specification in the zebrafish trunk.
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Affiliation(s)
- Marta Bastos de Oliveira
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Katja Meier
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Simone Jung
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Eireen Bartels-Klein
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Baptiste Coxam
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Ilse Geudens
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden
- Vascular Patterning Laboratory, Center for Cancer Biology, VIB, Leuven B-3000, Belgium
| | - Anna Szymborska
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Renae Skoczylas
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden
| | - Ines Fechner
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
| | - Katarzyna Koltowska
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden
| | - Holger Gerhardt
- Integrative Vascular Biology Laboratory, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Potsdamer Str. 58, 10785 Berlin, Germany
- Vascular Patterning Laboratory, Center for Cancer Biology, VIB, Leuven B-3000, Belgium
- Vascular Patterning Laboratory, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B-3000, Belgium
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straβe 2, 10178 Berlin, Germany
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117
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Klatt Shaw D, Saraswathy VM, Zhou L, McAdow AR, Burris B, Butka E, Morris SA, Dietmann S, Mokalled MH. Localized EMT reprograms glial progenitors to promote spinal cord repair. Dev Cell 2021; 56:613-626.e7. [PMID: 33609461 DOI: 10.1016/j.devcel.2021.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/17/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
Abstract
Anti-regenerative scarring obstructs spinal cord repair in mammals and presents a major hurdle for regenerative medicine. In contrast, adult zebrafish possess specialized glial cells that spontaneously repair spinal cord injuries by forming a pro-regenerative bridge across the severed tissue. To identify the mechanisms that regulate differential regenerative capacity between mammals and zebrafish, we first defined the molecular identity of zebrafish bridging glia and then performed cross-species comparisons with mammalian glia. Our transcriptomics show that pro-regenerative zebrafish glia activate an epithelial-to-mesenchymal transition (EMT) gene program and that EMT gene expression is a major factor distinguishing mammalian and zebrafish glia. Functionally, we found that localized niches of glial progenitors undergo EMT after spinal cord injury in zebrafish and, using large-scale CRISPR-Cas9 mutagenesis, we identified the gene regulatory network that activates EMT and drives functional regeneration. Thus, non-regenerative mammalian glia lack an essential EMT-driving gene regulatory network that reprograms pro-regenerative zebrafish glia after injury.
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Affiliation(s)
- Dana Klatt Shaw
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anthony R McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brooke Burris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emily Butka
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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118
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Ranawakage DC, Okada K, Sugio K, Kawaguchi Y, Kuninobu-Bonkohara Y, Takada T, Kamachi Y. Efficient CRISPR-Cas9-Mediated Knock-In of Composite Tags in Zebrafish Using Long ssDNA as a Donor. Front Cell Dev Biol 2021; 8:598634. [PMID: 33681181 PMCID: PMC7928300 DOI: 10.3389/fcell.2020.598634] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the unprecedented gene editing capability of CRISPR-Cas9-mediated targeted knock-in, the efficiency and precision of this technology still require further optimization, particularly for multicellular model organisms, such as the zebrafish (Danio rerio). Our study demonstrated that an ∼200 base-pair sequence encoding a composite tag can be efficiently "knocked-in" into the zebrafish genome using a combination of the CRISPR-Cas9 ribonucleoprotein complex and a long single-stranded DNA (lssDNA) as a donor template. Here, we targeted the sox3, sox11a, and pax6a genes to evaluate the knock-in efficiency of lssDNA donors with different structures in somatic cells of injected embryos and for their germline transmission. The structures and sequence characteristics of the lssDNA donor templates were found to be crucial to achieve a high rate of precise and heritable knock-ins. The following were our key findings: (1) lssDNA donor strand selection is important; however, strand preference and its dependency appear to vary among the target loci or their sequences. (2) The length of the 3' homology arm of the lssDNA donor affects knock-in efficiency in a site-specific manner; particularly, a shorter 50-nt arm length leads to a higher knock-in efficiency than a longer 300-nt arm for the sox3 and pax6a knock-ins. (3) Some DNA sequence characteristics of the knock-in donors and the distance between the CRISPR-Cas9 cleavage site and the tag insertion site appear to adversely affect the repair process, resulting in imprecise editing. By implementing the proposed method, we successfully obtained precisely edited sox3, sox11a, and pax6a knock-in alleles that contained a composite tag composed of FLAGx3 (or PAx3), Bio tag, and HiBiT tag (or His tag) with moderate to high germline transmission rates as high as 21%. Furthermore, the knock-in allele-specific quantitative polymerase chain reaction (qPCR) for both the 5' and 3' junctions indicated that knock-in allele frequencies were higher at the 3' side of the lssDNAs, suggesting that the lssDNA-templated knock-in was mediated by unidirectional single-strand template repair (SSTR) in zebrafish embryos.
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Affiliation(s)
| | | | | | | | | | | | - Yusuke Kamachi
- School of Environmental Science and Engineering, Kochi University of Technology, Kochi, Japan
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119
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Gasanov EV, Jędrychowska J, Pastor M, Wiweger M, Methner A, Korzh VP. An improved method for precise genome editing in zebrafish using CRISPR-Cas9 technique. Mol Biol Rep 2021; 48:1951-1957. [PMID: 33481178 PMCID: PMC7925485 DOI: 10.1007/s11033-020-06125-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/24/2020] [Indexed: 11/02/2022]
Abstract
Current methods of CRISPR-Cas9-mediated site-specific mutagenesis create deletions and small insertions at the target site which are repaired by imprecise non-homologous end-joining. Targeting of the Cas9 nuclease relies on a short guide RNA (gRNA) corresponding to the genome sequence approximately at the intended site of intervention. We here propose an improved version of CRISPR-Cas9 genome editing that relies on two complementary guide RNAs instead of one. Two guide RNAs delimit the intervention site and allow the precise deletion of several nucleotides at the target site. As proof of concept, we generated heterozygous deletion mutants of the kcng4b, gdap1, and ghitm genes in the zebrafish Danio rerio using this method. A further analysis by high-resolution DNA melting demonstrated a high efficiency and a low background of unpredicted mutations. The use of two complementary gRNAs improves CRISPR-Cas9 specificity and allows the creation of predictable and precise mutations in the genome of D. rerio.
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Affiliation(s)
- Eugene V Gasanov
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena Str. 4, 02-109, Warsaw, Poland.
| | - Justyna Jędrychowska
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena Str. 4, 02-109, Warsaw, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Zwirki i Wigury Str. 61, 02-091, Warsaw, Poland
| | - Michal Pastor
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena Str. 4, 02-109, Warsaw, Poland
- Institute of Biochemistry and Biophysics of Polish Academy of Sciences, Pawinskiego Str. 5a, 02-106, Warsaw, Poland
| | - Malgorzata Wiweger
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena Str. 4, 02-109, Warsaw, Poland
| | - Axel Methner
- Institute of Molecular Medicine, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Vladimir P Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena Str. 4, 02-109, Warsaw, Poland
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120
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Kuil LE, Chauhan RK, Cheng WW, Hofstra RMW, Alves MM. Zebrafish: A Model Organism for Studying Enteric Nervous System Development and Disease. Front Cell Dev Biol 2021; 8:629073. [PMID: 33553169 PMCID: PMC7859111 DOI: 10.3389/fcell.2020.629073] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022] Open
Abstract
The Enteric Nervous System (ENS) is a large network of enteric neurons and glia that regulates various processes in the gastrointestinal tract including motility, local blood flow, mucosal transport and secretion. The ENS is derived from stem cells coming from the neural crest that migrate into and along the primitive gut. Defects in ENS establishment cause enteric neuropathies, including Hirschsprung disease (HSCR), which is characterized by an absence of enteric neural crest cells in the distal part of the colon. In this review, we discuss the use of zebrafish as a model organism to study the development of the ENS. The accessibility of the rapidly developing gut in zebrafish embryos and larvae, enables in vivo visualization of ENS development, peristalsis and gut transit. These properties make the zebrafish a highly suitable model to bring new insights into ENS development, as well as in HSCR pathogenesis. Zebrafish have already proven fruitful in studying ENS functionality and in the validation of novel HSCR risk genes. With the rapid advancements in gene editing techniques and their unique properties, research using zebrafish as a disease model, will further increase our understanding on the genetics underlying HSCR, as well as possible treatment options for this disease.
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Affiliation(s)
- Laura E. Kuil
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Rajendra K. Chauhan
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - William W. Cheng
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
- Stem Cells and Regenerative Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Maria M. Alves
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
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121
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Parab S, Quick RE, Matsuoka RL. Endothelial cell-type-specific molecular requirements for angiogenesis drive fenestrated vessel development in the brain. eLife 2021; 10:64295. [PMID: 33459592 PMCID: PMC7840183 DOI: 10.7554/elife.64295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/17/2021] [Indexed: 02/06/2023] Open
Abstract
Vascular endothelial cells (vECs) in the brain exhibit structural and functional heterogeneity. Fenestrated, permeable brain vasculature mediates neuroendocrine function, body-fluid regulation, and neural immune responses; however, its vascular formation remains poorly understood. Here, we show that specific combinations of vascular endothelial growth factors (Vegfs) are required to selectively drive fenestrated vessel formation in the zebrafish myelencephalic choroid plexus (mCP). We found that the combined, but not individual, loss of Vegfab, Vegfc, and Vegfd causes severely impaired mCP vascularization with little effect on neighboring non-fenestrated brain vessel formation, demonstrating fenestrated-vEC-specific angiogenic requirements. This Vegfs-mediated vessel-selective patterning also involves Ccbe1. Expression analyses, cell-type-specific ablation, and paracrine activity-deficient vegfc mutant characterization suggest that vEC-autonomous Vegfc and meningeal fibroblast-derived Vegfab and Vegfd are critical for mCP vascularization. These results define molecular cues and cell types critical for directing fenestrated CP vascularization and indicate that vECs’ distinct molecular requirements for angiogenesis underlie brain vessel heterogeneity.
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Affiliation(s)
- Sweta Parab
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, United States
| | - Rachael E Quick
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, United States
| | - Ryota L Matsuoka
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, United States
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122
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Kroll F, Powell GT, Ghosh M, Gestri G, Antinucci P, Hearn TJ, Tunbak H, Lim S, Dennis HW, Fernandez JM, Whitmore D, Dreosti E, Wilson SW, Hoffman EJ, Rihel J. A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes. eLife 2021; 10:e59683. [PMID: 33416493 PMCID: PMC7793621 DOI: 10.7554/elife.59683] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
Hundreds of human genes are associated with neurological diseases, but translation into tractable biological mechanisms is lagging. Larval zebrafish are an attractive model to investigate genetic contributions to neurological diseases. However, current CRISPR-Cas9 methods are difficult to apply to large genetic screens studying behavioural phenotypes. To facilitate rapid genetic screening, we developed a simple sequencing-free tool to validate gRNAs and a highly effective CRISPR-Cas9 method capable of converting >90% of injected embryos directly into F0 biallelic knockouts. We demonstrate that F0 knockouts reliably recapitulate complex mutant phenotypes, such as altered molecular rhythms of the circadian clock, escape responses to irritants, and multi-parameter day-night locomotor behaviours. The technique is sufficiently robust to knockout multiple genes in the same animal, for example to create the transparent triple knockout crystal fish for imaging. Our F0 knockout method cuts the experimental time from gene to behavioural phenotype in zebrafish from months to one week.
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Affiliation(s)
- François Kroll
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Gareth T Powell
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Marcus Ghosh
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Gaia Gestri
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Paride Antinucci
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Timothy J Hearn
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Hande Tunbak
- Wolfson Institute for Biomedical Research, University College LondonLondonUnited Kingdom
| | - Sumi Lim
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Harvey W Dennis
- School of Biological Sciences, Faculty of Science, University of BristolBristolUnited Kingdom
| | | | - David Whitmore
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
- Department of Molecular and Cell Biology, James Cook UniversityTownsvilleAustralia
| | - Elena Dreosti
- Wolfson Institute for Biomedical Research, University College LondonLondonUnited Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Ellen J Hoffman
- Child Study Center, Yale School of MedicineNew HavenUnited States
- Department of Neuroscience, Yale School of MedicineNew HavenUnited States
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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123
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Zhao D, Jones JL, Gasperini RJ, Charlesworth JC, Liu GS, Burdon KP. Rapid and efficient cataract gene evaluation in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes. Methods 2021; 194:37-47. [PMID: 33418061 DOI: 10.1016/j.ymeth.2020.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 02/08/2023] Open
Abstract
Cataract is the leading cause of blindness worldwide. Congenital or paediatric cataract can result in permanent visual impairment or blindness even with best attempts at treatment. A significant proportion of paediatric cataract has a genetic cause. Therefore, identifying the genes that lead to cataract formation is essential for understanding the pathological process of inherited paediatric cataract as well as to the development of new therapies. Despite clear progress in genomics technologies, verification of the biological effects of newly identified candidate genes and variants is still challenging. Here, we provide a step-by-step pipeline to evaluate cataract candidate genes in F0 zebrafish using CRISPR-Cas9 ribonucleoprotein complexes (RNP). Detailed descriptions of CRISPR-Cas9 RNP design and formulation, microinjection, optimization of CRISPR-Cas9 RNP reagent dose and delivery route, editing efficacy analysis as well as cataract formation evaluation are included. Following this protocol, any cataract candidates can be readily and efficiently evaluated within 2 weeks using basic laboratory supplies.
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Affiliation(s)
- Duran Zhao
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Johanna L Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Jac C Charlesworth
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia; Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia.
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124
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Sieliwonczyk E, Matchkov VV, Vandendriessche B, Alaerts M, Bakkers J, Loeys B, Schepers D. Inherited Ventricular Arrhythmia in Zebrafish: Genetic Models and Phenotyping Tools. Rev Physiol Biochem Pharmacol 2021; 184:33-68. [PMID: 34533615 DOI: 10.1007/112_2021_65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In the last years, the field of inheritable ventricular arrhythmia disease modelling has changed significantly with a push towards the use of novel cellular cardiomyocyte based models. However, there is a growing need for new in vivo models to study the disease pathology at the tissue and organ level. Zebrafish provide an excellent opportunity for in vivo modelling of inheritable ventricular arrhythmia syndromes due to the remarkable similarity between their cardiac electrophysiology and that of humans. Additionally, many state-of-the-art methods in gene editing and electrophysiological phenotyping are available for zebrafish research. In this review, we give a comprehensive overview of the published zebrafish genetic models for primary electrical disorders and arrhythmogenic cardiomyopathy. We summarise and discuss the strengths and weaknesses of the different technical approaches for the generation of genetically modified zebrafish disease models, as well as the electrophysiological approaches in zebrafish phenotyping. By providing this detailed overview, we aim to draw attention to the potential of the zebrafish model for studying arrhythmia syndromes at the organ level and as a platform for personalised medicine and drug testing.
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Affiliation(s)
- Ewa Sieliwonczyk
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
| | - Vladimir V Matchkov
- Department of Biomedicine, Pulmonary and Cardiovascular Pharmacology, Aarhus University, Aarhus, Denmark
| | - Bert Vandendriessche
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Maaike Alaerts
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Jeroen Bakkers
- Hubrecht Institute for Developmental and Stem Cell Biology, Utrecht, The Netherlands
| | - Bart Loeys
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dorien Schepers
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Laboratory for Molecular, Cellular and Network Excitability, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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125
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England SJ, Cerda GA, Kowalchuk A, Sorice T, Grieb G, Lewis KE. Hmx3a Has Essential Functions in Zebrafish Spinal Cord, Ear and Lateral Line Development. Genetics 2020; 216:1153-1185. [PMID: 33077489 PMCID: PMC7768253 DOI: 10.1534/genetics.120.303748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/14/2020] [Indexed: 11/30/2022] Open
Abstract
Transcription factors that contain a homeodomain DNA-binding domain have crucial functions in most aspects of cellular function and embryonic development in both animals and plants. Hmx proteins are a subfamily of NK homeodomain-containing proteins that have fundamental roles in development of sensory structures such as the eye and the ear. However, Hmx functions in spinal cord development have not been analyzed. Here, we show that zebrafish (Danio rerio) hmx2 and hmx3a are coexpressed in spinal dI2 and V1 interneurons, whereas hmx3b, hmx1, and hmx4 are not expressed in spinal cord. Using mutational analyses, we demonstrate that, in addition to its previously reported role in ear development, hmx3a is required for correct specification of a subset of spinal interneuron neurotransmitter phenotypes, as well as correct lateral line progression and survival to adulthood. Surprisingly, despite similar expression patterns of hmx2 and hmx3a during embryonic development, zebrafish hmx2 mutants are viable and have no obviously abnormal phenotypes in sensory structures or neurons that require hmx3a In addition, embryos homozygous for deletions of both hmx2 and hmx3a have identical phenotypes to severe hmx3a single mutants. However, mutating hmx2 in hypomorphic hmx3a mutants that usually develop normally, results in abnormal ear and lateral line phenotypes. This suggests that while hmx2 cannot compensate for loss of hmx3a, it does function in these developmental processes, although to a much lesser extent than hmx3a More surprisingly, our mutational analyses suggest that Hmx3a may not require its homeodomain DNA-binding domain for its roles in viability or embryonic development.
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Affiliation(s)
| | - Gustavo A Cerda
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3DY, UK
| | | | - Taylor Sorice
- Department of Biology, Syracuse University, New York 13244
| | - Ginny Grieb
- Department of Biology, Syracuse University, New York 13244
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126
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Piedade WP, Titialii-Torres K, Morris AC, Famulski JK. Proteasome-Mediated Regulation of Cdhr1a by Siah1 Modulates Photoreceptor Development and Survival in Zebrafish. Front Cell Dev Biol 2020; 8:594290. [PMID: 33330480 PMCID: PMC7719784 DOI: 10.3389/fcell.2020.594290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023] Open
Abstract
Congenital retinal dystrophies are a major cause of unpreventable and incurable blindness worldwide. Mutations in CDHR1, a retina specific cadherin, are associated with cone-rod dystrophy. The ubiquitin proteasome system (UPS) is responsible for mediating orderly and precise targeting of protein degradation to maintain biological homeostasis and coordinate proper development, including retinal development. Recently, our lab uncovered that the seven in absentia (Siah) family of E3 ubiquitin ligases play a role in optic fissure fusion and identified Cdhr1a as a potential target of Siah. Using two-color whole mount in situ hybridization and immunohistochemistry, we detected siah1 and cdhr1a co-expression as well as protein localization in the retinal outer nuclear layer (ONL), and more precisely in the connecting cilium of rods and cones between 3-5 days post fertilization (dpf). We confirmed that Siah1 targets Cdhr1a for proteasomal degradation by co-transfection and co-immunoprecipitation in cell culture. To analyze the functional importance of this interaction, we created two transgenic zebrafish lines that express siah1 or an inactive siah1 (siah1ΔRING) under the control of the heat shock promoter to modulate Siah activity during photoreceptor development. Overexpression of siah1, but not siah1ΔRING, resulted in a decrease in the number of rods and cones at 72 h post fertilization (hpf). The number of retinal ganglion cells, amacrine and bipolar cells was not affected by Siah1 overexpression, and there was no significant reduction of proliferating cells in the Siah1 overexpressing retina. We did, however, detect increased cell death, confirmed by an increase in the number of TUNEL + cells in the ONL, which was proteasome-dependent, as proteasome inhibition rescued the cell death phenotype. Furthermore, reduction in rods and cones resulting from increased Siah1 expression was rescued by injection of cdhr1a mRNA, and to an even greater extent by injection of a Siah1-insensitive cdhr1a variant mRNA. Lastly, CRISPR induced loss of Cdhr1a function phenocopied Siah1 overexpression resulting in a significant reduction of rods and cones. Taken together, our work provides the first evidence that Cdhr1a plays a role during early photoreceptor development and that Cdhr1a is regulated by Siah1 via the UPS.
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Affiliation(s)
| | | | | | - Jakub K. Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
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127
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128
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Theis JL, Vogler G, Missinato MA, Li X, Nielsen T, Zeng XXI, Martinez-Fernandez A, Walls SM, Kervadec A, Kezos JN, Birker K, Evans JM, O'Byrne MM, Fogarty ZC, Terzic A, Grossfeld P, Ocorr K, Nelson TJ, Olson TM, Colas AR, Bodmer R. Patient-specific genomics and cross-species functional analysis implicate LRP2 in hypoplastic left heart syndrome. eLife 2020; 9:e59554. [PMID: 33006316 PMCID: PMC7581429 DOI: 10.7554/elife.59554] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Congenital heart diseases (CHDs), including hypoplastic left heart syndrome (HLHS), are genetically complex and poorly understood. Here, a multidisciplinary platform was established to functionally evaluate novel CHD gene candidates, based on whole-genome and iPSC RNA sequencing of a HLHS family-trio. Filtering for rare variants and altered expression in proband iPSCs prioritized 10 candidates. siRNA/RNAi-mediated knockdown in healthy human iPSC-derived cardiomyocytes (hiPSC-CM) and in developing Drosophila and zebrafish hearts revealed that LDL receptor-related protein LRP2 is required for cardiomyocyte proliferation and differentiation. Consistent with hypoplastic heart defects, compared to patents the proband's iPSC-CMs exhibited reduced proliferation. Interestingly, rare, predicted-damaging LRP2 variants were enriched in a HLHS cohort; however, understanding their contribution to HLHS requires further investigation. Collectively, we have established a multi-species high-throughput platform to rapidly evaluate candidate genes and their interactions during heart development, which are crucial first steps toward deciphering oligogenic underpinnings of CHDs, including hypoplastic left hearts.
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Affiliation(s)
- Jeanne L Theis
- Cardiovascular Genetics Research LaboratoryRochesterUnited States
| | - Georg Vogler
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Maria A Missinato
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Xing Li
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Tanja Nielsen
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
- Doctoral Degrees and Habilitations, Department of Biology, Chemistry, and Pharmacy, Freie Universität BerlinBerlinGermany
| | - Xin-Xin I Zeng
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | | | - Stanley M Walls
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Anaïs Kervadec
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - James N Kezos
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Katja Birker
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Megan M O'Byrne
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Zachary C Fogarty
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - André Terzic
- Department of Cardiovascular Medicine, Mayo ClinicRochesterUnited States
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Center for Regenerative Medicine, Mayo ClinicRochesterUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Paul Grossfeld
- University of California San Diego, Rady’s HospitalSan DiegoUnited States
- Division of General Internal Medicine, Mayo ClinicRochesterUnited States
| | - Karen Ocorr
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Timothy J Nelson
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Center for Regenerative Medicine, Mayo ClinicRochesterUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Timothy M Olson
- Department of Cardiovascular Medicine, Mayo ClinicRochesterUnited States
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Alexandre R Colas
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Rolf Bodmer
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
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129
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Naert T, Tulkens D, Edwards NA, Carron M, Shaidani NI, Wlizla M, Boel A, Demuynck S, Horb ME, Coucke P, Willaert A, Zorn AM, Vleminckx K. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos. Sci Rep 2020; 10:14662. [PMID: 32887910 PMCID: PMC7473854 DOI: 10.1038/s41598-020-71412-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 genome editing has revolutionized functional genomics in vertebrates. However, CRISPR/Cas9 edited F0 animals too often demonstrate variable phenotypic penetrance due to the mosaic nature of editing outcomes after double strand break (DSB) repair. Even with high efficiency levels of genome editing, phenotypes may be obscured by proportional presence of in-frame mutations that still produce functional protein. Recently, studies in cell culture systems have shown that the nature of CRISPR/Cas9-mediated mutations can be dependent on local sequence context and can be predicted by computational methods. Here, we demonstrate that similar approaches can be used to forecast CRISPR/Cas9 gene editing outcomes in Xenopus tropicalis, Xenopus laevis, and zebrafish. We show that a publicly available neural network previously trained in mouse embryonic stem cell cultures (InDelphi-mESC) is able to accurately predict CRISPR/Cas9 gene editing outcomes in early vertebrate embryos. Our observations can have direct implications for experiment design, allowing the selection of guide RNAs with predicted repair outcome signatures enriched towards frameshift mutations, allowing maximization of CRISPR/Cas9 phenotype penetrance in the F0 generation.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Dieter Tulkens
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Nicole A Edwards
- Division of Developmental Biology, Perinatal Institute, and Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital, Cincinnati, USA
| | - Marjolein Carron
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nikko-Ideen Shaidani
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Marcin Wlizla
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Annekatrien Boel
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Suzan Demuynck
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Paul Coucke
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Andy Willaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Aaron M Zorn
- Division of Developmental Biology, Perinatal Institute, and Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital, Cincinnati, USA
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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130
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Gerlai R. Evolutionary conservation, translational relevance and cognitive function: The future of zebrafish in behavioral neuroscience. Neurosci Biobehav Rev 2020; 116:426-435. [DOI: 10.1016/j.neubiorev.2020.07.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023]
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131
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Weaver ML, Piedade WP, Meshram NN, Famulski JK. Hyaloid vasculature and mmp2 activity play a role during optic fissure fusion in zebrafish. Sci Rep 2020; 10:10136. [PMID: 32576859 PMCID: PMC7311462 DOI: 10.1038/s41598-020-66451-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/18/2020] [Indexed: 02/03/2023] Open
Abstract
Vertebrate retinal development requires timely and precise fusion of the optic fissure (OF). Failure of this event leads to congenital vision impairment in the form of coloboma. Recent studies have suggested hyaloid vasculature to be involved in OF fusion. In order to examine this link, we analyzed OF fusion and hyaloid vasculogenesis in the zebrafish pax2a noi mutant line. We first determined that pax2a-/- embryos fail to accumulate F-actin in the OF prior to basement membrane (BM) degradation. Furthermore, using 3D and live imaging we observed reduced OF hyaloid vascularization in pax2a-/- embryos. When examining the connection between pax2a loss of function and hyaloid vasculature, we observed significant reduction of talin1 expression, a regulator of hyaloid vasculature. In addition, cranial VEGF expression was found to be reduced in pax2a-/- embryos. Pharmacological inhibition of VEGF signaling phenocopied the pax2a-/- vasculature, F-actin and BM degradation phenotypes. Lastly, we determined that OF associated hyaloid vasculature is a source of mmp2, mmp14a and mmp14b expression and showed that mmp2 is functionally necessary for degradation of OF BM. Taken together we propose a pax2a driven mechanism that ensures proper and timely hyaloid vasculature invasion of the OF in order to facilitate availability of the BM remodeler mmp2.
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Affiliation(s)
- Megan L Weaver
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Warlen P Piedade
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | - Jakub K Famulski
- Department of Biology, University of Kentucky, Lexington, KY, USA.
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132
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Xu B, Tang X, Jin M, Zhang H, Du L, Yu S, He J. Unifying developmental programs for embryonic and postembryonic neurogenesis in the zebrafish retina. Development 2020; 147:dev.185660. [PMID: 32467236 DOI: 10.1242/dev.185660] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 05/13/2020] [Indexed: 01/14/2023]
Abstract
The zebrafish retina grows for a lifetime. Whether embryonic and postembryonic retinogenesis conform to the same developmental program is an outstanding question that remains under debate. Using single-cell RNA sequencing of ∼20,000 cells of the developing zebrafish retina at four different stages, we identified seven distinct developmental states. Each state explicitly expresses a gene set. Disruption of individual state-specific marker genes results in various defects ranging from small eyes to the loss of distinct retinal cell types. Using a similar approach, we further characterized the developmental states of postembryonic retinal stem cells (RSCs) and their progeny in the ciliary marginal zone. Expression pattern analysis of state-specific marker genes showed that the developmental states of postembryonic RSCs largely recapitulated those of their embryonic counterparts, except for some differences in rod photoreceptor genesis. Thus, our findings reveal the unifying developmental program used by the embryonic and postembryonic retinogenesis in zebrafish.
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Affiliation(s)
- Baijie Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Xia Tang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China .,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Mengmeng Jin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Hui Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Lei Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Shuguang Yu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Jie He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China .,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
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133
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Li J, Ge W. Zebrafish as a model for studying ovarian development: Recent advances from targeted gene knockout studies. Mol Cell Endocrinol 2020; 507:110778. [PMID: 32142861 DOI: 10.1016/j.mce.2020.110778] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022]
Abstract
Ovarian development is a complex process controlled by precise coordination of multiple factors. The targeted gene knockout technique is a powerful tool to study the functions of these factors. The successful application of this technique in mice in the past three decades has significantly enhanced our understanding on the molecular mechanism of ovarian development. Recently, with the advent of genome editing techniques, targeted gene knockout research can be carried out in many species. Zebrafish has emerged as an excellent model system to study the control of ovarian development. Dozens of genes related to ovarian development have been knocked out in zebrafish in recent years. Much new information and perspectives on the molecular mechanism of ovarian development have been obtained from these mutant zebrafish. Some findings have challenged conventional views. Several genes have been identified for the first time in vertebrates to control ovarian development. Focusing on ovarian development, the purpose of this review is to briefly summarize recent findings using these gene knockout zebrafish models, and compare these findings with mammalian models. These established mutants and rapid development of gene knockout techniques have prompted zebrafish as an ideal animal model for studying ovarian development.
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Affiliation(s)
- Jianzhen Li
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China, 730070.
| | - Wei Ge
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau, China.
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134
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135
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Kim BH, Zhang G. Generating Stable Knockout Zebrafish Lines by Deleting Large Chromosomal Fragments Using Multiple gRNAs. G3 (BETHESDA, MD.) 2020; 10:1029-1037. [PMID: 31915253 PMCID: PMC7056962 DOI: 10.1534/g3.119.401035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/06/2020] [Indexed: 12/28/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas9 (CRISPR associated protein 9) system has been successfully adopted as a versatile genetic tool for functional manipulations, due to its convenience and effectiveness. Genetics lesions induced by single guide RNA (gRNA) are usually small indel (insertion-deletion) DNA mutations. The impact of this type of CRISPR-induced DNA mutation on the coded mRNA transcription processing and protein translation can be complex. Unexpected or unknown transcripts, generated through alternative splicing, may impede the generation of successful loss-of-function mutants. To create null or null-like loss-of-function mutant zebrafish, we employed simultaneous multiple gRNA injection into single-cell stage embryos. We demonstrated that DNA composed of multiple exons, up to 78kb in length, can be deleted in the smarca2 gene locus. Additionally, two different genes (rnf185 and rnf215) were successfully mutated in F1 fish with multiple exon deletions using this multiplex gRNA injection strategy. We expect this approach will be useful for knock-out studies in zebrafish and other vertebrate organisms, especially when the phenotype of a single gRNA-induced mutant is not clear.
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Affiliation(s)
| | - GuangJun Zhang
- Department of Comparative Pathobiology,
- Purdue University Center for Cancer Research
- Purdue Institute for Inflammation, Immunology and Infectious Diseases (PI4D), and
- Purdue Institute for Integrative Neuroscience; Purdue University, West Lafayette, Indiana 47907
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136
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Bryan CD, Casey MA, Pfeiffer RL, Jones BW, Kwan KM. Optic cup morphogenesis requires neural crest-mediated basement membrane assembly. Development 2020; 147:dev181420. [PMID: 31988185 PMCID: PMC7044464 DOI: 10.1242/dev.181420] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
Organogenesis requires precise interactions between a developing tissue and its environment. In vertebrates, the developing eye is surrounded by a complex extracellular matrix as well as multiple mesenchymal cell populations. Disruptions to either the matrix or periocular mesenchyme can cause defects in early eye development, yet in many cases the underlying mechanism is unknown. Here, using multidimensional imaging and computational analyses in zebrafish, we establish that cell movements in the developing optic cup require neural crest. Ultrastructural analysis reveals that basement membrane formation around the developing eye is also dependent on neural crest, but only specifically around the retinal pigment epithelium. Neural crest cells produce the extracellular matrix protein nidogen: impairing nidogen function disrupts eye development, and, strikingly, expression of nidogen in the absence of neural crest partially restores optic cup morphogenesis. These results demonstrate that eye formation is regulated in part by extrinsic control of extracellular matrix assembly.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Chase D Bryan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Macaulie A Casey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Rebecca L Pfeiffer
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Bryan W Jones
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Kristen M Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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137
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Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Over the past decade, advancements in high-throughput sequencing have greatly enhanced our knowledge of the mutational signatures responsible for hereditary hearing loss. In its present state, the field has a largely uncensored view of protein coding changes in a growing number of genes that have been associated with hereditary hearing loss, and many more that have been proposed as candidate genes. Sequencing data can now be generated using methods that have become widespread and affordable. The greatest hurdles facing the field concern functional validation of uncharacterized genes and rapid application to human diseases, including hearing and balance disorders. To date, over 30 hearing-related disease models exist in zebrafish. New genome editing technologies, including CRISPR/Cas9 will accelerate the functional validation of hearing loss genes and variants in zebrafish. Here, we discuss current progress in the field and recent advances in genome editing approaches.
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