1
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Li J, Miramontes TG, Czopka T, Monk KR. Synaptic input and Ca 2+ activity in zebrafish oligodendrocyte precursor cells contribute to myelin sheath formation. Nat Neurosci 2024; 27:219-231. [PMID: 38216650 DOI: 10.1038/s41593-023-01553-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
In the nervous system, only one type of neuron-glial synapse is known to exist: that between neurons and oligodendrocyte precursor cells (OPCs), yet their composition, assembly, downstream signaling and in vivo functions remain largely unclear. Here, we address these questions using in vivo microscopy in zebrafish spinal cord and identify postsynaptic molecules PSD-95 and gephyrin in OPCs. The puncta containing these molecules in OPCs increase during early development and decrease upon OPC differentiation. These puncta are highly dynamic and frequently assemble at 'hotspots'. Gephyrin hotspots and synapse-associated Ca2+ activity in OPCs predict where a subset of myelin sheaths forms in differentiated oligodendrocytes. Further analyses reveal that spontaneous synaptic release is integral to OPC Ca2+ activity, while evoked synaptic release contributes only in early development. Finally, disruption of the synaptic genes dlg4a/dlg4b, gphnb and nlgn3b impairs OPC differentiation and myelination. Together, we propose that neuron-OPC synapses are dynamically assembled and can predetermine myelination patterns through Ca2+ signaling.
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Affiliation(s)
- Jiaxing Li
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA.
| | | | - Tim Czopka
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kelly R Monk
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA.
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2
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Shiraki T, Kawakami K. Generation of Transgenic Fish Harboring CRISPR/Cas9-Mediated Somatic Mutations Via a tRNA-Based Multiplex sgRNA Expression. Methods Mol Biol 2024; 2707:305-318. [PMID: 37668921 DOI: 10.1007/978-1-0716-3401-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The controlled expression of Cas9 and/or sgRNA in transgenic zebrafish made it possible to knock out a gene in a spatially and/or temporally controlled manner. This transgenic approach can be more useful if multiple sgRNAs are efficiently expressed since we can improve the biallelic frame-shift mutation rate and circumvent the functional redundancy of genes and genetic compensation. We developed the tRNA-based system to express multiple functional sgRNAs from a single transcript in zebrafish and found that it is applicable to the transgenic expression of multiple sgRNAs. In this chapter, we describe a procedure for the generation of plasmids containing multiple sgRNAs flanked by tRNAs and a method to induce multiple CRISPR/Cas9-mediated genome modifications in transgenic zebrafish.
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Affiliation(s)
- Tomoya Shiraki
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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3
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Hageter J, Starkey J, Horstick EJ. Thalamic regulation of a visual critical period and motor behavior. Cell Rep 2023; 42:112287. [PMID: 36952349 PMCID: PMC10514242 DOI: 10.1016/j.celrep.2023.112287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/24/2023] Open
Abstract
During the visual critical period (CP), sensory experience refines the structure and function of visual circuits. The basis of this plasticity was long thought to be limited to cortical circuits, but recently described thalamic plasticity challenges this dogma and demonstrates greater complexity underlying visual plasticity. Yet how visual experience modulates thalamic neurons or how the thalamus modulates CP timing is incompletely understood. Using a larval zebrafish, thalamus-centric ocular dominance model, we show functional changes in the thalamus and a role of inhibitory signaling to establish CP timing using a combination of functional imaging, optogenetics, and pharmacology. Hemisphere-specific changes in genetically defined thalamic neurons correlate with changes in visuomotor behavior, establishing a role of thalamic plasticity in modulating motor performance. Our work demonstrates that visual plasticity is broadly conserved and that visual experience leads to neuron-level functional changes in the thalamus that require inhibitory signaling to establish critical period timing.
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Affiliation(s)
- John Hageter
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Jacob Starkey
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Eric J Horstick
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA; Department of Neuroscience, West Virginia University, Morgantown, WV 26506, USA.
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4
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Gaillard AL, Mohamad T, Quan FB, de Cian A, Mosimann C, Tostivint H, Pézeron G. Urp1 and Urp2 act redundantly to maintain spine shape in zebrafish larvae. Dev Biol 2023; 496:36-51. [PMID: 36736605 DOI: 10.1016/j.ydbio.2023.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Urp1 and Urp2 are two neuropeptides, members of the Urotensin 2 family, that have been recently involved in the control of body axis morphogenesis in zebrafish. They are produced by a population of sensory spinal neurons, called cerebrospinal fluid contacting neurons (CSF-cNs), under the control of signals relying on the Reissner fiber, an extracellular thread bathing in the CSF. Here, we have investigated further the function of Urp1 and Urp2 (Urp1/2) in body axis formation and maintenance. We showed that urp1;urp2 double mutants develop strong body axis defects during larval growth, revealing the redundancy between the two neuropeptides. These defects were similar to those previously reported in uts2r3 mutants. We observed that this phenotype is not associated with congenital defects in vertebrae formation, but by using specific inhibitors, we found that, at least in the embryo, the action of Urp1/2 signaling depends on myosin II contraction. Finally, we provide evidence that while the Urp1/2 signaling is functioning during larval growth, it is dispensable for embryonic development. Taken together, our results show that Urp1/2 signaling is required in larvae to promote correct vertebral body axis, most likely by regulating muscle tone.
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Affiliation(s)
- Anne-Laure Gaillard
- Molecular Physiology and Adaptation (PhyMA - UMR7221), Muséum National d'Histoire naturelle, CNRS, Paris, France
| | - Teddy Mohamad
- Molecular Physiology and Adaptation (PhyMA - UMR7221), Muséum National d'Histoire naturelle, CNRS, Paris, France
| | - Feng B Quan
- Molecular Physiology and Adaptation (PhyMA - UMR7221), Muséum National d'Histoire naturelle, CNRS, Paris, France
| | - Anne de Cian
- Structure and Instability of Genomes (String - UMR 7196 - U1154), Muséum National d'Histoire naturelle, CNRS, INSERM, Paris, France
| | - Christian Mosimann
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Hervé Tostivint
- Molecular Physiology and Adaptation (PhyMA - UMR7221), Muséum National d'Histoire naturelle, CNRS, Paris, France
| | - Guillaume Pézeron
- Molecular Physiology and Adaptation (PhyMA - UMR7221), Muséum National d'Histoire naturelle, CNRS, Paris, France.
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5
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Henke K, Farmer DT, Niu X, Kraus JM, Galloway JL, Youngstrom DW. Genetically engineered zebrafish as models of skeletal development and regeneration. Bone 2023; 167:116611. [PMID: 36395960 PMCID: PMC11080330 DOI: 10.1016/j.bone.2022.116611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Zebrafish (Danio rerio) are aquatic vertebrates with significant homology to their terrestrial counterparts. While zebrafish have a centuries-long track record in developmental and regenerative biology, their utility has grown exponentially with the onset of modern genetics. This is exemplified in studies focused on skeletal development and repair. Herein, the numerous contributions of zebrafish to our understanding of the basic science of cartilage, bone, tendon/ligament, and other skeletal tissues are described, with a particular focus on applications to development and regeneration. We summarize the genetic strengths that have made the zebrafish a powerful model to understand skeletal biology. We also highlight the large body of existing tools and techniques available to understand skeletal development and repair in the zebrafish and introduce emerging methods that will aid in novel discoveries in skeletal biology. Finally, we review the unique contributions of zebrafish to our understanding of regeneration and highlight diverse routes of repair in different contexts of injury. We conclude that zebrafish will continue to fill a niche of increasing breadth and depth in the study of basic cellular mechanisms of skeletal biology.
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Affiliation(s)
- Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - D'Juan T Farmer
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA.
| | - Xubo Niu
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Jessica M Kraus
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
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6
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Plata ALD, Robles E. NMDA Receptor Antagonist MK801 Reduces Dendritic Spine Density and Stability in Zebrafish Pyramidal Neurons. Neuroscience 2022; 498:50-63. [PMID: 35718218 DOI: 10.1016/j.neuroscience.2022.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/02/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022]
Abstract
NMDA-type glutamate receptors play a critical role in activity-dependent neurite growth. We employed cell type-specific genetic labeling in zebrafish to examine the effects of NMDA receptor antagonism on the morphological development of tectal pyramidal neurons (PyrNs). Our data demonstrate that the NMDA receptor antagonist MK801 reduces PyrN spine density and stability without significantly altering dendritic growth and branching. However, the axons that synapse onto PyrN dendritic spines do exhibit reduced arbor growth and branching in response to MK801 treatment. Axons that synapse with PyrNs, but not on spines, are unaffected by MK801 treatment. These findings may reflect different roles for NMDARs during the development of spiny and aspiny dendrites.
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Affiliation(s)
- Amanda Lamarca Dela Plata
- Department of Biological Sciences and Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Estuardo Robles
- Department of Biological Sciences and Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
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7
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Kalvaitytė M, Balciunas D. Conditional mutagenesis strategies in zebrafish. Trends Genet 2022; 38:856-868. [PMID: 35662532 DOI: 10.1016/j.tig.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Abstract
Gene disruption or knockout is an essential tool for elucidating gene function. Conditional knockout methodology was developed to further advance these studies by enabling gene disruption at a predefined time and/or in discrete cells. While the conditional knockout method is widely used in the mouse, technical limitations have stifled direct adoption of this methodology in other animal models including the zebrafish. Recent advances in genome editing have enabled engineering of distinct classes of conditional mutants in zebrafish. To further accelerate the development and application of conditional mutants, we will review diverse methods of conditional knockout engineering and discuss the advantages of different conditional alleles.
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Affiliation(s)
| | - Darius Balciunas
- Life Sciences Center, Vilnius University, Vilnius, Lithuania; Department of Biology, Temple University, Philadelphia, PA, USA.
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8
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Allanki S, Strilic B, Scheinberger L, Onderwater YL, Marks A, Günther S, Preussner J, Kikhi K, Looso M, Stainier DYR, Reischauer S. Interleukin-11 signaling promotes cellular reprogramming and limits fibrotic scarring during tissue regeneration. SCIENCE ADVANCES 2021; 7:eabg6497. [PMID: 34516874 PMCID: PMC8442930 DOI: 10.1126/sciadv.abg6497] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/16/2021] [Indexed: 05/02/2023]
Abstract
Damage-induced fibrotic scarring limits tissue regeneration in mammals and is a leading cause of morbidity. In contrast, species like zebrafish can regenerate damaged tissues without excessive fibrosis. However, whether specific signaling pathways can both limit fibrosis and promote regeneration is unclear. Here, we show that interleukin-11 (Il-11)/Stat3 signaling has such a dual function. Zebrafish lacking Il-11 receptor function display severely compromised heart, fin, and scale regeneration. Deep phenotyping and transcriptional analysis of adult hearts and fins show that Il-11 signaling drives cellular reprogramming to orchestrate global and tissue-specific regenerative programs and broadly antagonizes hallmarks of adult mammalian scarring. Mechanistically, our data indicate that IL-11 signaling in endothelial cells antagonizes profibrotic transforming growth factor–β signaling and endothelial-to-mesenchymal transition, limiting scarring and promoting cardiomyocyte repopulation, after injury. Overall, our findings position damage-induced Il-11/Stat3 signaling in a key role limiting fibrosis and promoting regeneration, revealing novel targets for regenerative therapies.
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Affiliation(s)
- Srinivas Allanki
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, 60596 Frankfurt am Main, Germany
- Medical Clinic I (Cardiology/Angiology) and Campus Kerckhoff, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Boris Strilic
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Lilly Scheinberger
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Yeszamin L. Onderwater
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Alora Marks
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Stefan Günther
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Jens Preussner
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, 60596 Frankfurt am Main, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Khrievono Kikhi
- Flow Cytometry Service Group, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Mario Looso
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, 60596 Frankfurt am Main, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Sven Reischauer
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Medical Clinic I (Cardiology/Angiology) and Campus Kerckhoff, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
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9
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Zhang C, Li J, Tarique I, Zhang Y, Lu T, Wang J, Chen A, Wen F, Zhang Z, Zhang Y, Shao M. A Time-Saving Strategy to Generate Double Maternal Mutants by an Oocyte-Specific Conditional Knockout System in Zebrafish. BIOLOGY 2021; 10:biology10080777. [PMID: 34440009 PMCID: PMC8389640 DOI: 10.3390/biology10080777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 12/23/2022]
Abstract
Simple Summary Maternally supplied mRNAs and proteins, termed maternal factors, are produced by over 14,000 coding genes in zebrafish. They play exclusive roles in controlling the formation of oocytes and the development of early embryos. These maternal factors can also compensate for the loss of function of its corresponding zygotic gene products. Thus, eliminating both maternal and zygotic gene products is essential to elucidate the functions of more than half of zebrafish genes. However, it is always challenging to inactivate maternal factors, because traditional genetic methods are either technically demanding or time-consuming. Our recent work established a rapid conditional knockout method to generate maternal or maternal and zygotic mutants in one fish generation. Here, we further test the feasibility of this approach to knock out two maternal genes with functional redundancy simultaneously. As a proof of principle, we successfully generated double maternal mutant embryos for dvl2 and dvl3a genes in three months for the first time. The cell movement defects in mutant embryos obtained by this approach mimic the genuine mutant embryos generated after fifteen months of time-consuming screening following the previously reported mosaic strategy. Therefore, this method has the potential to speed up the functional study of paralogous maternal genes. Abstract Maternal products are those mRNAs and proteins deposited during oogenesis, which play critical roles in controlling oocyte formation, fertilization, and early embryonic development. However, loss-of-function studies for these maternal factors are still lacking, mainly because of the prolonged period of transgenerational screening and technical barriers that prevent the generation of maternal (M) and maternal and zygotic (MZ) mutant embryos. By the transgenic expression of multiple sgRNAs targeting a single gene of interest in the background of a transgenic line Tg(zpc:zcas9) with oocyte-specific cas9 expression, we have successfully obtained maternal or maternal–zygotic mutant for single genes in F1 embryos. In this work, we tandemly connected a maternal GFP marker and eight sgRNA expression units to target dvl2 and dvl3a simultaneously and introduced this construct to the genome of Tg(zpc:zcas9) by meganuclease I-Sce I. As expected, we confirmed the existence of Mdvl2;Mdvl3a embryos with strong defective convergence and extension movement during gastrulation among outcrossed GFP positive F1 offspring. The MZdvl2;MZdvl3a embryos were also obtained by crossing the mutant carrying mosaic F0 female with dvl2+/−;dvl3a−/− male fish. This proof-of-principle thus highlights the potential of this conditional knockout strategy to circumvent the current difficulty in the study of genes with multiple functionally redundant paralogs.
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Affiliation(s)
- Chong Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Jiaguang Li
- Taishan College, Shandong University, Qingdao 266237, China; (J.L.); (Z.Z.)
| | - Imran Tarique
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Yizhuang Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Tong Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Jiasheng Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Aijun Chen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Fenfen Wen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Zhuoyu Zhang
- Taishan College, Shandong University, Qingdao 266237, China; (J.L.); (Z.Z.)
| | - Yanjun Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
- Taishan College, Shandong University, Qingdao 266237, China; (J.L.); (Z.Z.)
- Correspondence:
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10
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Zhang C, Lu T, Zhang Y, Li J, Tarique I, Wen F, Chen A, Wang J, Zhang Z, Zhang Y, Shi DL, Shao M. Rapid generation of maternal mutants via oocyte transgenic expression of CRISPR-Cas9 and sgRNAs in zebrafish. SCIENCE ADVANCES 2021; 7:eabg4243. [PMID: 34362733 PMCID: PMC8346210 DOI: 10.1126/sciadv.abg4243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/21/2021] [Indexed: 05/08/2023]
Abstract
Maternal products are exclusive factors to drive oogenesis and early embryonic development. As disrupting maternal gene functions is either time-consuming or technically challenging, early developmental programs regulated by maternal factors remain mostly elusive. We provide a transgenic approach to inactivate maternal genes in zebrafish primary oocytes. By introducing three tandem single guide RNA (sgRNA) expression cassettes and a green fluorescent protein (GFP) reporter into Tg(zpc:zcas9) embryos, we efficiently obtained maternal nanog and ctnnb2 mutants among GFP-positive F1 offspring. Notably, most of these maternal mutants displayed either sgRNA site-spanning genomic deletions or unintended large deletions extending distantly from the sgRNA targets, suggesting a prominent deletion-prone tendency of genome editing in the oocyte. Thus, our method allows maternal gene knockout in the absence of viable and fertile homozygous mutant adults. This approach is particularly time-saving and can be applied for functional screening of maternal factors and generating genomic deletions in zebrafish.
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Affiliation(s)
- Chong Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Tong Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yizhuang Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaguang Li
- Shandong University Taishan College, Qingdao 266237, China
| | - Imran Tarique
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Fenfen Wen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Aijun Chen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiasheng Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Zhuoyu Zhang
- Shandong University Taishan College, Qingdao 266237, China
| | - Yanjun Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - De-Li Shi
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
- Developmental Biology Laboratory, CNRS-UMR7622, Institut de Biologie Paris-Seine, Sorbonne University, Paris 75005, France
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
- Shandong University Taishan College, Qingdao 266237, China
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11
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Isiaku AI, Zhang Z, Pazhakh V, Manley HR, Thompson ER, Fox LC, Yerneni S, Blombery P, Lieschke GJ. Transient, flexible gene editing in zebrafish neutrophils and macrophages for determination of cell-autonomous functions. Dis Model Mech 2021; 14:271018. [PMID: 34296745 PMCID: PMC8319549 DOI: 10.1242/dmm.047431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/04/2021] [Indexed: 11/28/2022] Open
Abstract
Zebrafish are an important model for studying phagocyte function, but rigorous experimental systems to distinguish whether phagocyte-dependent effects are neutrophil or macrophage specific have been lacking. We have developed and validated transgenic lines that enable superior demonstration of cell-autonomous neutrophil and macrophage genetic requirements. We coupled well-characterized neutrophil- and macrophage-specific Gal4 driver lines with UAS:Cas9 transgenes for selective expression of Cas9 in either neutrophils or macrophages. Efficient gene editing, confirmed by both Sanger and next-generation sequencing, occurred in both lineages following microinjection of efficacious synthetic guide RNAs into zebrafish embryos. In proof-of-principle experiments, we demonstrated molecular and/or functional evidence of on-target gene editing for several genes (mCherry, lamin B receptor, trim33) in either neutrophils or macrophages as intended. These new UAS:Cas9 tools provide an improved resource for assessing individual contributions of neutrophil- and macrophage-expressed genes to the many physiological processes and diseases modelled in zebrafish. Furthermore, this gene-editing functionality can be exploited in any cell lineage for which a lineage-specific Gal4 driver is available. This article has an associated First Person interview with the first author of the paper. Summary: We developed new tools for lineage-specific gene editing in neutrophils or macrophages based on leukocyte-specific Cas9 expression, that can be used with injected synthetic gRNAs.
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Affiliation(s)
- Abdulsalam I Isiaku
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Zuobing Zhang
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia.,Department of Biological Sciences, School of Life Science, Shanxi University, Taiyuan, Shanxi Province 030006, China
| | - Vahid Pazhakh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Harriet R Manley
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ella R Thompson
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Lucy C Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Satwica Yerneni
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia.,Department of Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Parkville, VIC 3050, Australia
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12
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Wang Y, Hsu AY, Walton EM, Park SJ, Syahirah R, Wang T, Zhou W, Ding C, Lemke AP, Zhang G, Tobin DM, Deng Q. A robust and flexible CRISPR/Cas9-based system for neutrophil-specific gene inactivation in zebrafish. J Cell Sci 2021; 134:237799. [PMID: 33722979 DOI: 10.1242/jcs.258574] [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: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
CRISPR/Cas9-based tissue-specific knockout techniques are essential for probing the functions of genes in embryonic development and disease using zebrafish. However, the lack of capacity to perform gene-specific rescue or live imaging in the tissue-specific knockout background has limited the utility of this approach. Here, we report a robust and flexible gateway system for tissue-specific gene inactivation in neutrophils. Using a transgenic fish line with neutrophil-restricted expression of Cas9 and ubiquitous expression of single guide (sg)RNAs targeting rac2, specific disruption of the rac2 gene in neutrophils is achieved. Transient expression of sgRNAs targeting rac2 or cdk2 in the neutrophil-restricted Cas9 line also results in significantly decreased cell motility. Re-expressing sgRNA-resistant rac2 or cdk2 genes restores neutrophil motility in the corresponding knockout background. Moreover, active Rac and force-bearing F-actins localize to both the cell front and the contracting tail during neutrophil interstitial migration in an oscillating fashion that is disrupted when rac2 is knocked out. Together, our work provides a potent tool that can be used to advance the utility of zebrafish in identifying and characterizing gene functions in a tissue-specific manner.
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Affiliation(s)
- Yueyang Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Alan Y Hsu
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Eric M Walton
- Department of Molecular Genetics and Microbiology, and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sung Jun Park
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Ramizah Syahirah
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Tianqi Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Wenqing Zhou
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Chang Ding
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Abby Pei Lemke
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA.,Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qing Deng
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.,Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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13
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Sharma P, Sharma BS, Verma RJ. CRISPR-based genome editing of zebrafish. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:69-84. [PMID: 33934838 DOI: 10.1016/bs.pmbts.2021.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9, once discovered as an adaptive immune system in bacteria, has emerged as a disruptive technology in the field of genetic engineering. Technological advancements in the recent past has enhanced the applicability of CRISPR/Cas9 tool for gene editing, gene therapies, developmental studies and mutational analysis in various model organisms. Zebrafish, one of the excellent animal models, is preferred for conducting CRISPR/Cas9 studies to assess the functional implication of specific genes of interest. CRISPR/Cas9 mediated gene editing techniques, such as, knock-out and knock-in approaches, provide evidences to identify the role of different genes through loss-of-function studies. Also, CRISPR/Cas9 has been proved to be an efficient tool for designing disease models for gene expression studies based on phenotypic screening. The present chapter provides an overview of CRISPR/Cas9 mechanism, different strategies for DNA modifications and gene function analysis, highlighting the translational applications for future prospects, such as screening of drug toxicity and efficacy.
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Affiliation(s)
- Preeti Sharma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India; PanGenomics International Pvt Ltd, Sterling Accuris Diagnostics, Ellis Bridge, Ahmedabad, Gujarat, India.
| | - B Sharan Sharma
- Rivaara Labs Pvt Ltd, KD Hospital, Vaishnodevi Circle, Ahmedabad, Gujarat, India
| | - Ramtej J Verma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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14
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Potekhina ES, Bass DY, Kelmanson IV, Fetisova ES, Ivanenko AV, Belousov VV, Bilan DS. Drug Screening with Genetically Encoded Fluorescent Sensors: Today and Tomorrow. Int J Mol Sci 2020; 22:E148. [PMID: 33375682 PMCID: PMC7794770 DOI: 10.3390/ijms22010148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Genetically-encoded fluorescent sensors have been actively developed over the last few decades and used in live imaging and drug screening. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the obvious benefits of using genetically-encoded fluorescent sensors in drug screening. In combination with high-throughput screening (HTS), some genetically-encoded fluorescent sensors may provide high reproducibility and robustness to assays. We provide a brief overview of successful, perspective, and hopeful attempts at using genetically encoded fluorescent sensors in HTS of modulators of ion channels, Ca2+ homeostasis, GPCR activity, and for screening cytotoxic, anticancer, and anti-parasitic compounds. We discuss the advantages of sensors in whole organism drug screening models and the perspectives of the combination of human disease modeling by CRISPR techniques with genetically encoded fluorescent sensors for drug screening.
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Affiliation(s)
- Ekaterina S. Potekhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dina Y. Bass
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ilya V. Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Elena S. Fetisova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
| | - Alexander V. Ivanenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, 117997 Moscow, Russia
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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15
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Buglak DB, Kushner EJ, Marvin AP, Davis KL, Bautch VL. Excess centrosomes disrupt vascular lumenization and endothelial cell adherens junctions. Angiogenesis 2020; 23:567-575. [PMID: 32699963 PMCID: PMC7524686 DOI: 10.1007/s10456-020-09737-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/08/2020] [Indexed: 12/12/2022]
Abstract
Proper blood vessel formation requires coordinated changes in endothelial cell polarity and rearrangement of cell-cell junctions to form a functional lumen. One important regulator of cell polarity is the centrosome, which acts as a microtubule organizing center. Excess centrosomes perturb aspects of endothelial cell polarity linked to migration, but whether centrosome number influences apical-basal polarity and cell-cell junctions is unknown. Here, we show that excess centrosomes alter the apical-basal polarity of endothelial cells in angiogenic sprouts and disrupt endothelial cell-cell adherens junctions. Endothelial cells with excess centrosomes had narrower lumens in a 3D sprouting angiogenesis model, and zebrafish intersegmental vessels had reduced perfusion following centrosome overduplication. These results indicate that endothelial cell centrosome number regulates proper lumenization downstream of effects on apical-basal polarity and cell-cell junctions. Endothelial cells with excess centrosomes are prevalent in tumor vessels, suggesting how centrosomes may contribute to tumor vessel dysfunction.
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Affiliation(s)
- Danielle B Buglak
- Curriculum in Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Erich J Kushner
- Department of Biology, The University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC, 27599, USA
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Allison P Marvin
- Department of Biology, The University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC, 27599, USA
| | - Katy L Davis
- Department of Biology, The University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC, 27599, USA
| | - Victoria L Bautch
- Curriculum in Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biology, The University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC, 27599, USA.
- McAllister Heart Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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16
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Burgess J, Burrows JT, Sadhak R, Chiang S, Weiss A, D'Amata C, Molinaro AM, Zhu S, Long M, Hu C, Krause HM, Pearson BJ. An optimized QF-binary expression system for use in zebrafish. Dev Biol 2020; 465:144-156. [PMID: 32697972 DOI: 10.1016/j.ydbio.2020.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/05/2020] [Accepted: 07/09/2020] [Indexed: 11/15/2022]
Abstract
The zebrafish model organism has been of exceptional utility for the study of vertebrate development and disease through the application of tissue-specific labelling and overexpression of genes carrying patient-derived mutations. However, there remains a need for a binary expression system that is both non-toxic and not silenced over animal generations by DNA methylation. The Q binary expression system derived from the fungus Neurospora crassa is ideal, because the consensus binding site for the QF transcription factor lacks CpG dinucleotides, precluding silencing by CpG-meditated methylation. To optimize this system for zebrafish, we systematically tested several variants of the QF transcription factor: QF full length; QF2, which lacks the middle domain; QF2w, which is an attenuated version of QF2; and chimeric QFGal4. We found that full length QF and QF2 were strongly toxic to zebrafish embryos, QF2w was mildly toxic, and QFGal4 was well tolerated, when injected as RNA or expressed ubiquitously from stable transgenes. In addition, QFGal4 robustly activated a Tg(QUAS:GFPNLS) reporter transgene. To increase the utility of this system, we also modified the QF effector sequence termed QUAS, which consists of five copies of the QF binding site. Specifically, we decreased both the CpG dinucleotide content, as well as the repetitiveness of QUAS, to reduce the risk of transgene silencing via CpG methylation. Moreover, these modifications to QUAS removed leaky QF-independent neural expression that we detected in the original QUAS sequence. To demonstrate the utility of our QF optimizations, we show how the Q-system can be used for lineage tracing using a Cre-dependent Tg(ubi:QFGal4-switch) transgene. We also demonstrate that QFGal4 can be used in transient injections to tag and label endogenous genes by knocking in QFGal4 into sox2 and ubiquitin C genes.
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Affiliation(s)
- Jason Burgess
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G 0A4, Canada
| | - Jeffrey T Burrows
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G 0A4, Canada
| | - Roshan Sadhak
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sharon Chiang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alex Weiss
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G 0A4, Canada
| | - Cassandra D'Amata
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G 0A4, Canada
| | - Alyssa M Molinaro
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shujun Zhu
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G 0A4, Canada
| | - Michael Long
- The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Chun Hu
- The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Henry M Krause
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Bret J Pearson
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada.
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17
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Wang G, Muhl L, Padberg Y, Dupont L, Peterson-Maduro J, Stehling M, le Noble F, Colige A, Betsholtz C, Schulte-Merker S, van Impel A. Specific fibroblast subpopulations and neuronal structures provide local sources of Vegfc-processing components during zebrafish lymphangiogenesis. Nat Commun 2020; 11:2724. [PMID: 32483144 PMCID: PMC7264274 DOI: 10.1038/s41467-020-16552-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/07/2020] [Indexed: 12/17/2022] Open
Abstract
Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space, and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss-of-function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that this locally restricted Vegfc maturation is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single-cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis.
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Affiliation(s)
- Guangxia Wang
- Institute for Cardiovascular Organogenesis and Regeneration, WWU Münster, Münster, Germany.,Faculty of Medicine, WWU Münster, Münster, Germany.,Cells-in-Motion Cluster of Excellence, WWU Münster, Münster, Germany
| | - Lars Muhl
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Yvonne Padberg
- Institute for Cardiovascular Organogenesis and Regeneration, WWU Münster, Münster, Germany.,Faculty of Medicine, WWU Münster, Münster, Germany.,Cells-in-Motion Cluster of Excellence, WWU Münster, Münster, Germany
| | - Laura Dupont
- Laboratory of Connective Tissue Biology, GIGA, University of Liège, Liege, Belgium
| | | | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ferdinand le Noble
- Department of Cell and Developmental Biology, Zoological Institute and Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Experimental Cardiology, University of Heidelberg, Heidelberg, Germany.,DZHK (German Center for Cardiovascular Research) partner site, Heidelberg/Mannheim, Germany
| | - Alain Colige
- Laboratory of Connective Tissue Biology, GIGA, University of Liège, Liege, Belgium
| | - Christer Betsholtz
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden.,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, WWU Münster, Münster, Germany. .,Faculty of Medicine, WWU Münster, Münster, Germany. .,Cells-in-Motion Cluster of Excellence, WWU Münster, Münster, Germany.
| | - Andreas van Impel
- Institute for Cardiovascular Organogenesis and Regeneration, WWU Münster, Münster, Germany. .,Faculty of Medicine, WWU Münster, Münster, Germany. .,Cells-in-Motion Cluster of Excellence, WWU Münster, Münster, Germany.
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18
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Rubbini D, Cornet C, Terriente J, Di Donato V. CRISPR Meets Zebrafish: Accelerating the Discovery of New Therapeutic Targets. SLAS DISCOVERY 2020; 25:552-567. [PMID: 32462967 DOI: 10.1177/2472555220926920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bringing a new drug to the market costs an average of US$2.6 billion and takes more than 10 years from discovery to regulatory approval. Despite the need to reduce cost and time to increase productivity, pharma companies tend to crowd their efforts in the same indications and drug targets. This results in the commercialization of drugs that share the same mechanism of action (MoA) and, in many cases, equivalent efficacies among them-an outcome that helps neither patients nor the balance sheet of the companies trying to bring therapeutics to the same patient population. Indeed, the discovery of new therapeutic targets, based on a deeper understanding of the disease biology, would likely provide more innovative MoAs and potentially greater drug efficacies. It would also bring better chances for identifying appropriate treatments according to the patient's genetic stratification. Nowadays, we count with an enormous amount of unprocessed information on potential disease targets that could be extracted from omics data obtained from patient samples. In addition, hundreds of pharmacological and genetic screenings have been performed to identify innovative drug targets. Traditionally, rodents have been the animal models of choice to perform functional genomic studies. The high experimental cost, combined with the low throughput provided by those models, however, is a bottleneck for discovering and validating novel genetic disease associations. To overcome these limitations, we propose that zebrafish, in conjunction with the use of CRISPR/Cas9 genome-editing tools, could streamline functional genomic processes to bring biologically relevant knowledge on innovative disease targets in a shorter time frame.
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Affiliation(s)
- Davide Rubbini
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Carles Cornet
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Javier Terriente
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Vincenzo Di Donato
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
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19
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Espino-Saldaña AE, Rodríguez-Ortiz R, Pereida-Jaramillo E, Martínez-Torres A. Modeling Neuronal Diseases in Zebrafish in the Era of CRISPR. Curr Neuropharmacol 2020; 18:136-152. [PMID: 31573887 PMCID: PMC7324878 DOI: 10.2174/1570159x17666191001145550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/04/2019] [Accepted: 09/29/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Danio rerio is a powerful experimental model for studies in genetics and development. Recently, CRISPR technology has been applied in this species to mimic various human diseases, including those affecting the nervous system. Zebrafish offer multiple experimental advantages: external embryogenesis, rapid development, transparent embryos, short life cycle, and basic neurobiological processes shared with humans. This animal model, together with the CRISPR system, emerging imaging technologies, and novel behavioral approaches, lay the basis for a prominent future in neuropathology and will undoubtedly accelerate our understanding of brain function and its disorders. OBJECTIVE Gather relevant findings from studies that have used CRISPR technologies in zebrafish to explore basic neuronal function and model human diseases. METHODS We systematically reviewed the most recent literature about CRISPR technology applications for understanding brain function and neurological disorders in D. rerio. We highlighted the key role of CRISPR in driving forward our understanding of particular topics in neuroscience. RESULTS We show specific advances in neurobiology when the CRISPR system has been applied in zebrafish and describe how CRISPR is accelerating our understanding of brain organization. CONCLUSION Today, CRISPR is the preferred method to modify genomes of practically any living organism. Despite the rapid development of CRISPR technologies to generate disease models in zebrafish, more efforts are needed to efficiently combine different disciplines to find the etiology and treatments for many brain diseases.
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Affiliation(s)
- Angeles Edith Espino-Saldaña
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Campus UNAM Juriquilla, Querétaro, Qro CP76230, México
- Universidad Autónoma de Querétaro, Facultad de Ciencias Naturales, Av. de las Ciencias S/N, Querétaro, Mexico
| | - Roberto Rodríguez-Ortiz
- CONACYT - Instituto de Neurobiología, Universidad Nacional Autónoma de México. Querétaro, Qro., México
| | - Elizabeth Pereida-Jaramillo
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Campus UNAM Juriquilla, Querétaro, Qro CP76230, México
| | - Ataúlfo Martínez-Torres
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Campus UNAM Juriquilla, Querétaro, Qro CP76230, México
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20
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Failed Progenitor Specification Underlies the Cardiopharyngeal Phenotypes in a Zebrafish Model of 22q11.2 Deletion Syndrome. Cell Rep 2019; 24:1342-1354.e5. [PMID: 30067987 PMCID: PMC6261257 DOI: 10.1016/j.celrep.2018.06.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 05/08/2018] [Accepted: 06/28/2018] [Indexed: 12/13/2022] Open
Abstract
Microdeletions involving TBX1 result in variable congenital malformations known collectively as 22q11.2 deletion syndrome (22q11.2DS). Tbx1-deficient mice and zebrafish recapitulate several disease phenotypes, including pharyngeal arch artery (PAA), head muscle (HM), and cardiac outflow tract (OFT) deficiencies. In zebrafish, these structures arise from nkx2.5+ progenitors in pharyngeal arches 2-6. Because pharyngeal arch morphogenesis is compromised in Tbx1-deficient animals, the malformations were considered secondary. Here, we report that the PAA, HM, and OFT phenotypes in tbx1 mutant zebrafish are primary and arise prior to pharyngeal arch morphogenesis from failed specification of the nkx2.5+ pharyngeal lineage. Through in situ analysis and lineage tracing, we reveal that nkx2.5 and tbx1 are co-expressed in this progenitor population. Furthermore, we present evidence suggesting that gdf3-ALK4 signaling is a downstream mediator of nkx2.5+ pharyngeal lineage specification. Collectively, these studies support a cellular mechanism potentially underlying the cardiovascular and craniofacial defects observed in the 22q11.2DS population.
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21
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Bensimon-Brito A, Ramkumar S, Boezio GLM, Guenther S, Kuenne C, Helker CSM, Sánchez-Iranzo H, Iloska D, Piesker J, Pullamsetti S, Mercader N, Beis D, Stainier DYR. TGF-β Signaling Promotes Tissue Formation during Cardiac Valve Regeneration in Adult Zebrafish. Dev Cell 2019; 52:9-20.e7. [PMID: 31786069 DOI: 10.1016/j.devcel.2019.10.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/17/2019] [Accepted: 10/28/2019] [Indexed: 12/14/2022]
Abstract
Cardiac valve disease can lead to severe cardiac dysfunction and is thus a frequent cause of morbidity and mortality. Its main treatment is valve replacement, which is currently greatly limited by the poor recellularization and tissue formation potential of the implanted valves. As we still lack suitable animal models to identify modulators of these processes, here we used adult zebrafish and found that, upon valve decellularization, they initiate a rapid regenerative program that leads to the formation of new functional valves. After injury, endothelial and kidney marrow-derived cells undergo cell cycle re-entry and differentiate into new extracellular matrix-secreting valve cells. The TGF-β signaling pathway promotes the regenerative process by enhancing progenitor cell proliferation as well as valve cell differentiation. These findings reveal a key role for TGF-β signaling in cardiac valve regeneration and establish the zebrafish as a model to identify and test factors promoting cardiac valve recellularization and growth.
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Affiliation(s)
- Anabela Bensimon-Brito
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany.
| | - Srinath Ramkumar
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Giulia L M Boezio
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Stefan Guenther
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Carsten Kuenne
- Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Christian S M Helker
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Héctor Sánchez-Iranzo
- Cell Biology and Biophysics Research Unit, EMBL Heidelberg, Heidelberg 69117, Germany
| | - Dijana Iloska
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Janett Piesker
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Soni Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Nadia Mercader
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland; Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid 28049, Spain
| | - Dimitris Beis
- Developmental Biology, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany.
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22
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DeMarco E, Xu N, Baier H, Robles E. Neuron types in the zebrafish optic tectum labeled by an id2b transgene. J Comp Neurol 2019; 528:1173-1188. [PMID: 31725916 DOI: 10.1002/cne.24815] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 01/30/2023]
Abstract
The larval zebrafish optic tectum has emerged as a prominent model for understanding how neural circuits control visually guided behaviors. Further advances in this area will require tools to monitor and manipulate tectal neurons with cell type specificity. Here, we characterize the morphology and neurotransmitter phenotype of tectal neurons labeled by an id2b:gal4 transgene. Whole-brain imaging of stable transgenic id2b:gal4 larvae revealed labeling in a subset of neurons in optic tectum, cerebellum, and hindbrain. Genetic mosaic labeling of single neurons within the id2b:gal4 expression pattern enabled us to characterize three tectal neuron types with distinct morphologies and connectivities. The first is a neuron type previously identified in the optic tectum of other teleost fish: the tectal pyramidal neuron (PyrN). PyrNs are local interneurons that form two stratified dendritic arbors and one stratified axonal arbor in the tectal neuropil. The second tectal neuron type labeled by the id2b:gal4 transgene is a projection neuron that forms a stratified dendritic arbor in the tectal neuropil and an axon that exits tectum to form a topographic projection to torus longitudinalis (TL). A third neuron type labeled is a projection neuron with a nonstratified dendritic arbor and a descending axonal projection to tegmentum. These findings establish the id2b:gal4 transgenic as a useful tool for future studies aimed at elucidating the functional role of tectum, TL, and tegmentum in visually guided behaviors.
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Affiliation(s)
- Elisabeth DeMarco
- Department of Biological Sciences and Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana
| | - Nina Xu
- Department of Biological Sciences and Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana
| | - Herwig Baier
- Max Planck Institute for Neurobiology, Martinsried, Germany
| | - Estuardo Robles
- Department of Biological Sciences and Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana
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23
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Redox Signaling via Lipid Peroxidation Regulates Retinal Progenitor Cell Differentiation. Dev Cell 2019; 50:73-89.e6. [DOI: 10.1016/j.devcel.2019.05.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 02/07/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022]
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24
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Genetic and epigenetic control of retinal development in zebrafish. Curr Opin Neurobiol 2019; 59:120-127. [PMID: 31255843 DOI: 10.1016/j.conb.2019.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/23/2019] [Accepted: 05/28/2019] [Indexed: 12/24/2022]
Abstract
The vertebrate retina is a complex structure composed of seven cell types (six neuron and one glia), and all of which originate from a seemingly homogeneous population of proliferative multipotent retinal progenitor cells (RPCs) that exit the cell cycle and differentiate in a spatio-temporally regulated and stereotyped fashion. This neurogenesis process requires intricate genetic regulation involving a combination of cell intrinsic transcription factors and extrinsic signaling molecules, and many critical factors have been identified that influence the timing and composition of the developing retina. Adding complexity to the process, over the past decade, a variety of epigenetic regulatory mechanisms have been shown to influence neurogenesis, and these include changes in histone modifications and the chromatin landscape and changes in DNA methylation and hydroxymethylation patterns. This review summarizes recent findings in the genetic and epigenetic regulation of retinal development, with an emphasis on the zebrafish model system, and it outlines future areas of investigation that will continue to push the field forward into the epigenomics era.
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25
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Bercier V, Rosello M, Del Bene F, Revenu C. Zebrafish as a Model for the Study of Live in vivo Processive Transport in Neurons. Front Cell Dev Biol 2019; 7:17. [PMID: 30838208 PMCID: PMC6389722 DOI: 10.3389/fcell.2019.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
Motor proteins are responsible for transport of vesicles and organelles within the cell cytoplasm. They interact with the actin cytoskeleton and with microtubules to ensure communication and supply throughout the cell. Much work has been done in vitro and in silico to unravel the key players, including the dynein motor complex, the kinesin and myosin superfamilies, and their interacting regulatory complexes, but there is a clear need for in vivo data as recent evidence suggests previous models might not recapitulate physiological conditions. The zebrafish embryo provides an excellent system to study these processes in intact animals due to the ease of genetic manipulation and the optical transparency allowing live imaging. We present here the advantages of the zebrafish embryo as a system to study live in vivo processive transport in neurons and provide technical recommendations for successful analysis.
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Affiliation(s)
- Valérie Bercier
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France.,Laboratory of Neurobiology, Center for Brain and Disease Research, Research Group Experimental Neurology, Department of Neurosciences, VIB-KU Leuven, Leuven, Belgium
| | - Marion Rosello
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Céline Revenu
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
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26
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Cayuela ML, Claes KBM, Ferreira MG, Henriques CM, van Eeden F, Varga M, Vierstraete J, Mione MC. The Zebrafish as an Emerging Model to Study DNA Damage in Aging, Cancer and Other Diseases. Front Cell Dev Biol 2019; 6:178. [PMID: 30687705 PMCID: PMC6335974 DOI: 10.3389/fcell.2018.00178] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/22/2018] [Indexed: 12/17/2022] Open
Abstract
Cancer is a disease of the elderly, and old age is its largest risk factor. With age, DNA damage accumulates continuously, increasing the chance of malignant transformation. The zebrafish has emerged as an important vertebrate model to study these processes. Key mechanisms such as DNA damage responses and cellular senescence can be studied in zebrafish throughout its life course. In addition, the zebrafish is becoming an important resource to study telomere biology in aging, regeneration and cancer. Here we review some of the tools and resources that zebrafish researchers have developed and discuss their potential use in the study of DNA damage, cancer and aging related diseases.
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Affiliation(s)
- Maria Luisa Cayuela
- Telomerase, Cancer and Aging Group, Surgery Unit, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Murcia, Spain
| | | | | | - Catarina Martins Henriques
- Department of Oncology and Metabolism, Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | | | - Máté Varga
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
- MTA-SE Lendület Nephrogenetic Laboratory, Budapest, Hungary
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27
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Xu M, Wang J, Guo X, Li T, Kuang X, Wu QF. Illumination of neural development by in vivo clonal analysis. CELL REGENERATION (LONDON, ENGLAND) 2018; 7:33-39. [PMID: 30671228 PMCID: PMC6326247 DOI: 10.1016/j.cr.2018.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/22/2018] [Accepted: 09/18/2018] [Indexed: 01/22/2023]
Abstract
Single embryonic and adult neural stem cells (NSCs) are characterized by their self-renewal and differentiation potential. Lineage tracing via clonal analysis allows for specific labeling of a single NSC and tracking of its progeny throughout development. Over the past five decades, a plethora of clonal analysis methods have been developed in tandem with integration of chemical, genetic, imaging and sequencing techniques. Applications of these approaches have gained diverse insights into the heterogeneous behavior of NSCs, lineage relationships between cells, molecular regulation of fate specification and ontogeny of complex neural tissues. In this review, we summarize the history and methods of clonal analysis as well as highlight key findings revealed by single-cell lineage tracking of stem cells in developing and adult brains across different animal models.
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Affiliation(s)
- Mingrui Xu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jingjing Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xize Guo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tingting Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Kuang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing-Feng Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Beijing 100101, China
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28
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Schulze L, Henninger J, Kadobianskyi M, Chaigne T, Faustino AI, Hakiy N, Albadri S, Schuelke M, Maler L, Del Bene F, Judkewitz B. Transparent Danionella translucida as a genetically tractable vertebrate brain model. Nat Methods 2018; 15:977-983. [PMID: 30323353 DOI: 10.1038/s41592-018-0144-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/17/2018] [Indexed: 11/09/2022]
Abstract
Understanding how distributed neuronal circuits integrate sensory information and generate behavior is a central goal of neuroscience. However, it has been difficult to study neuronal networks at single-cell resolution across the entire adult brain in vertebrates because of their size and opacity. We address this challenge here by introducing the fish Danionella translucida to neuroscience as a potential model organism. This teleost remains small and transparent even in adulthood, when neural circuits and behavior have matured. Despite having the smallest known adult vertebrate brain, D. translucida displays a rich set of complex behaviors, including courtship, shoaling, schooling, and acoustic communication. In order to carry out optical measurements and perturbations of neural activity with genetically encoded tools, we established CRISPR-Cas9 genome editing and Tol2 transgenesis techniques. These features make D. translucida a promising model organism for the study of adult vertebrate brain function at single-cell resolution.
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Affiliation(s)
- Lisanne Schulze
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jörg Henninger
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mykola Kadobianskyi
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas Chaigne
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ana Isabel Faustino
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nahid Hakiy
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Shahad Albadri
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, SU Sorbonne University, Paris, France
| | - Markus Schuelke
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Leonard Maler
- Brain and Mind Research Institute, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, SU Sorbonne University, Paris, France
| | - Benjamin Judkewitz
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Humboldt University, Berlin, Germany.
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29
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A tRNA-based multiplex sgRNA expression system in zebrafish and its application to generation of transgenic albino fish. Sci Rep 2018; 8:13366. [PMID: 30190522 PMCID: PMC6127137 DOI: 10.1038/s41598-018-31476-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/20/2018] [Indexed: 01/20/2023] Open
Abstract
The CRISPR/Cas9 system can be introduced into zebrafish as transgenes. Namely, expression of single-guide RNA (sgRNA) and controlled expression of Cas9 in transgenic zebrafish enables the study of gene functions in specific cell types. This transgenic CRISPR/Cas9 approach would be more useful if multiple sgRNAs could be expressed simultaneously since we could knock-out a gene more efficiently or disrupt multiple genes simultaneously. Here we describe a novel system to express multiple sgRNAs efficiently in zebrafish, that relies on the endogenous tRNA processing machinery. We cloned nine endogenous zebrafish tRNA genes, fused them to sgRNAs, and demonstrated that an active sgRNA can be produced from a precursor transcript containing either of these tRNAs. To show a proof of principle, we constructed transgenic fish expressing Cas9 under the control of the ubiquitin promoter and a single transcript containing three distinct sgRNAs, that targeted the slc45a2 (albino) gene, fused to tRNAs under the control of the U6 promoter. We found that the Tg(ubb:SpCas9,u6c:3xslc45a2-sgRNA) harbored mutations in all of the target sites in the albino gene and showed nearly complete albino phenotypes, which were amenable to imaging experiments. Thus, the tRNA-based multiplex sgRNA expression system should facilitate gene knock-out studies in transgenic zebrafish.
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30
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Zheng SS, Han RY, Xiang L, Zhuang YY, Jin ZB. Versatile Genome Engineering Techniques Advance Human Ocular Disease Researches in Zebrafish. Front Cell Dev Biol 2018; 6:75. [PMID: 30050903 PMCID: PMC6052052 DOI: 10.3389/fcell.2018.00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Over recent decades, zebrafish has been established as a sophisticated vertebrate model for studying human ocular diseases due to its high fecundity, short generation time and genetic tractability. With the invention of morpholino (MO) technology, it became possible to study the genetic basis and relevant genes of ocular diseases in vivo. Many genes have been shown to be related to ocular diseases. However, the issue of specificity is the major concern in defining gene functions with MO technology. The emergence of the first- and second-generation genetic modification tools zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs), respectively, eliminated the potential phenotypic risk induced by MOs. Nevertheless, the efficiency of these nucleases remained relatively low until the third technique, the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, was discovered. This review highlights the application of multiple genome engineering techniques, especially the CRISPR/Cas9 system, in the study of human ocular diseases in zebrafish.
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Affiliation(s)
- Si-Si Zheng
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ru-Yi Han
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Lue Xiang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - You-Yuan Zhuang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
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31
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Cornet C, Di Donato V, Terriente J. Combining Zebrafish and CRISPR/Cas9: Toward a More Efficient Drug Discovery Pipeline. Front Pharmacol 2018; 9:703. [PMID: 30018554 PMCID: PMC6037853 DOI: 10.3389/fphar.2018.00703] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/11/2018] [Indexed: 12/13/2022] Open
Abstract
The use of zebrafish larvae in basic and applied research has grown exponentially during the last 20 years. The reasons for this success lay in its specific experimental advantages: on the one hand, the small size, the large number of progeny and the fast life cycle greatly facilitate large-scale approaches while maintaining 3Rs amenability; on the other hand, high genetic and physiological homology with humans and ease of genetic manipulation make zebrafish larvae a highly robust model for understanding human disease. Together, these advantages allow using zebrafish larvae for performing high-throughput research, both in terms of chemical and genetic phenotypic screenings. Therefore, the zebrafish larva as an animal model is placed between more reductionist in vitro high-throughput screenings and informative but low-throughput preclinical assays using mammals. However, despite its biological advantages and growing translational validation, zebrafish remains scarcely used in current drug discovery pipelines. In a context in which the pharmaceutical industry is facing a productivity crisis in bringing new drugs to the market, the combined advantages of zebrafish and the CRISPR/Cas9 system, the most powerful technology for genomic editing to date, has the potential to become a valuable tool for streamlining the generation of models mimicking human disease, the validation of novel drug targets and the discovery of new therapeutics. This review will focus on the most recent advances on CRISPR/Cas9 implementation in zebrafish and all their potential uses in biomedical research and drug discovery.
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Affiliation(s)
- Carles Cornet
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), Barcelona, Spain
| | - Vincenzo Di Donato
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), Barcelona, Spain
| | - Javier Terriente
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), Barcelona, Spain
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32
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Zebrafish Models of Rare Hereditary Pediatric Diseases. Diseases 2018; 6:diseases6020043. [PMID: 29789451 PMCID: PMC6023479 DOI: 10.3390/diseases6020043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 12/12/2022] Open
Abstract
Recent advances in sequencing technologies have made it significantly easier to find the genetic roots of rare hereditary pediatric diseases. These novel methods are not panaceas, however, and they often give ambiguous results, highlighting multiple possible causative mutations in affected patients. Furthermore, even when the mapping results are unambiguous, the affected gene might be of unknown function. In these cases, understanding how a particular genotype can result in a phenotype also needs carefully designed experimental work. Model organism genetics can offer a straightforward experimental setup for hypothesis testing. Containing orthologs for over 80% of the genes involved in human diseases, zebrafish (Danio rerio) has emerged as one of the top disease models over the past decade. A plethora of genetic tools makes it easy to create mutations in almost any gene of the zebrafish genome and these mutant strains can be used in high-throughput preclinical screens for active molecules. As this small vertebrate species offers several other advantages as well, its popularity in biomedical research is bound to increase, with “aquarium to bedside” drug development pipelines taking a more prevalent role in the near future.
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33
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Di Donato V, De Santis F, Albadri S, Auer TO, Duroure K, Charpentier M, Concordet JP, Gebhardt C, Del Bene F. An Attractive Reelin Gradient Establishes Synaptic Lamination in the Vertebrate Visual System. Neuron 2018; 97:1049-1062.e6. [PMID: 29429939 DOI: 10.1016/j.neuron.2018.01.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 11/11/2017] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
Abstract
A conserved organizational and functional principle of neural networks is the segregation of axon-dendritic synaptic connections into laminae. Here we report that targeting of synaptic laminae by retinal ganglion cell (RGC) arbors in the vertebrate visual system is regulated by a signaling system relying on target-derived Reelin and VLDLR/Dab1a on the projecting neurons. Furthermore, we find that Reelin is distributed as a gradient on the target tissue and stabilized by heparan sulfate proteoglycans (HSPGs) in the extracellular matrix (ECM). Through genetic manipulations, we show that this Reelin gradient is important for laminar targeting and that it is attractive for RGC axons. Finally, we suggest a comprehensive model of synaptic lamina formation in which attractive Reelin counter-balances repulsive Slit1, thereby guiding RGC axons toward single synaptic laminae. We establish a mechanism that may represent a general principle for neural network assembly in vertebrate species and across different brain areas.
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Affiliation(s)
- Vincenzo Di Donato
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, UPMC Paris-Sorbonne, Paris 75005, France
| | - Flavia De Santis
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, UPMC Paris-Sorbonne, Paris 75005, France
| | - Shahad Albadri
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, UPMC Paris-Sorbonne, Paris 75005, France
| | - Thomas Oliver Auer
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, UPMC Paris-Sorbonne, Paris 75005, France
| | - Karine Duroure
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, UPMC Paris-Sorbonne, Paris 75005, France
| | - Marine Charpentier
- Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Paris 75231, France
| | - Jean-Paul Concordet
- Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Paris 75231, France
| | - Christoph Gebhardt
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, UPMC Paris-Sorbonne, Paris 75005, France.
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, UPMC Paris-Sorbonne, Paris 75005, France.
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34
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Carney TJ, Mosimann C. Switch and Trace: Recombinase Genetics in Zebrafish. Trends Genet 2018; 34:362-378. [PMID: 29429760 DOI: 10.1016/j.tig.2018.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/04/2018] [Accepted: 01/08/2018] [Indexed: 01/04/2023]
Abstract
Transgenic approaches are instrumental for labeling and manipulating cells and cellular machineries in vivo. Transgenes have traditionally been static entities that remained unaltered following genome integration, limiting their versatility. The development of DNA recombinase-based methods to modify, excise, or rearrange transgene cassettes has introduced versatile control of transgene activity and function. In particular, recombinase-controlled transgenes enable regulation of exogenous gene expression, conditional mutagenesis, and genetic lineage tracing. In zebrafish, transgenesis-based recombinase genetics using Cre/lox, Flp/FRT, and ΦC31 are increasingly applied to study development and homeostasis, and to generate disease models. Intersected with the versatile imaging capacity of the zebrafish model and recent breakthroughs in genome editing, we review and discuss past, current, and potential future approaches and resources for recombinase-based techniques in zebrafish.
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Affiliation(s)
- Tom J Carney
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore.
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
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Sánchez-Iranzo H, Galardi-Castilla M, Minguillón C, Sanz-Morejón A, González-Rosa JM, Felker A, Ernst A, Guzmán-Martínez G, Mosimann C, Mercader N. Tbx5a lineage tracing shows cardiomyocyte plasticity during zebrafish heart regeneration. Nat Commun 2018; 9:428. [PMID: 29382818 PMCID: PMC5789846 DOI: 10.1038/s41467-017-02650-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/15/2017] [Indexed: 12/30/2022] Open
Abstract
During development, mesodermal progenitors from the first heart field (FHF) form a primitive cardiac tube, to which progenitors from the second heart field (SHF) are added. The contribution of FHF and SHF progenitors to the adult zebrafish heart has not been studied to date. Here we find, using genetic tbx5a lineage tracing tools, that the ventricular myocardium in the adult zebrafish is mainly derived from tbx5a+ cells, with a small contribution from tbx5a- SHF progenitors. Notably, ablation of ventricular tbx5a+-derived cardiomyocytes in the embryo is compensated by expansion of SHF-derived cells. In the adult, tbx5a expression is restricted to the trabeculae and excluded from the outer cortical layer. tbx5a-lineage tracing revealed that trabecular cardiomyocytes can switch their fate and differentiate into cortical myocardium during adult heart regeneration. We conclude that a high degree of cardiomyocyte cell fate plasticity contributes to efficient regeneration.
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Affiliation(s)
- Héctor Sánchez-Iranzo
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - María Galardi-Castilla
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Carolina Minguillón
- CSIC-Institut de Biologia Molecular de Barcelona Parc Científic de Barcelona C/ Baldiri i Reixac, 10 08028, Barcelona, Spain
- Barcelonabeta Brain Research Center, Pasqual Maragall Foundation, 08005, Barcelona, Spain
| | - Andrés Sanz-Morejón
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Institute of Anatomy, University of Bern, 3000, Bern 9, Switzerland
| | - Juan Manuel González-Rosa
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Anastasia Felker
- Institute of Molecular Life Sciences, University of Zürich, 8057, Zürich, Switzerland
| | - Alexander Ernst
- Institute of Anatomy, University of Bern, 3000, Bern 9, Switzerland
| | | | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, 8057, Zürich, Switzerland
| | - Nadia Mercader
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
- Institute of Anatomy, University of Bern, 3000, Bern 9, Switzerland.
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Campbell LJ, Hyde DR. Opportunities for CRISPR/Cas9 Gene Editing in Retinal Regeneration Research. Front Cell Dev Biol 2017; 5:99. [PMID: 29218308 PMCID: PMC5703712 DOI: 10.3389/fcell.2017.00099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/06/2017] [Indexed: 01/22/2023] Open
Abstract
While retinal degeneration and disease results in permanent damage and vision loss in humans, the severely damaged zebrafish retina has a high capacity to regenerate lost neurons and restore visual behaviors. Advancements in understanding the molecular and cellular basis of this regeneration response give hope that strategies and therapeutics may be developed to restore sight to blind and visually-impaired individuals. Our current understanding has been facilitated by the amenability of zebrafish to molecular tools, imaging techniques, and forward and reverse genetic approaches. Accordingly, the zebrafish research community has developed a diverse array of research tools for use in developing and adult animals, including toolkits for facilitating the generation of transgenic animals, systems for inducible, cell-specific transgene expression, and the creation of knockout alleles for nearly every protein coding gene. As CRISPR/Cas9 genome editing has begun to revolutionize molecular biology research, the zebrafish community has responded in stride by developing CRISPR/Cas9 techniques for the zebrafish as well as incorporating CRISPR/Cas9 into available toolsets. The application of CRISPR/Cas9 to retinal regeneration research will undoubtedly bring us closer to understanding the mechanisms underlying retinal repair and vision restoration in the zebrafish, as well as developing therapeutic approaches that will restore vision to blind and visually-impaired individuals. This review focuses on how CRISPR/Cas9 has been integrated into zebrafish research toolsets and how this new tool will revolutionize the field of retinal regeneration research.
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Affiliation(s)
- Leah J Campbell
- Department of Biological Sciences, Center for Zebrafish Research and Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, United States
| | - David R Hyde
- Department of Biological Sciences, Center for Zebrafish Research and Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, United States
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Liu Y, Ma S, Chang J, Zhang T, Wang X, Shi R, Zhang J, Lu W, Liu Y, Xia Q. Tissue-specific genome editing of laminA/C in the posterior silk glands of Bombyx mori. J Genet Genomics 2017; 44:451-459. [DOI: 10.1016/j.jgg.2017.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
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Albadri S, Del Bene F, Revenu C. Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish. Methods 2017; 121-122:77-85. [PMID: 28300641 DOI: 10.1016/j.ymeth.2017.03.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/13/2017] [Accepted: 03/03/2017] [Indexed: 12/19/2022] Open
Abstract
With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc. but also ways to circumvent encountered issues with HDR insertions by the development of non-homologous dependent strategies. While imprecise, these homology-independent mechanisms based on non-homologous-end-joining (NHEJ) repair have been employed in zebrafish to generate reporter lines or to accurately edit an open reading frame by the use of intron-targeting modifications. Therefore, with higher efficiency and insertion rate, NHEJ-based knock-in seems to be a promising approach to target endogenous loci and to circumvent the limitations of HDR whenever it is possible and appropriate. In this perspective, we propose new strategies to generate cDNA edited or tagged insertions, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish.
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Affiliation(s)
- Shahad Albadri
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France.
| | - Céline Revenu
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
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CRISPR/Cas9-Mediated Knockin and Knockout in Zebrafish. RESEARCH AND PERSPECTIVES IN NEUROSCIENCES 2017. [DOI: 10.1007/978-3-319-60192-2_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Fodor E, Sigmond T, Ari E, Lengyel K, Takács-Vellai K, Varga M, Vellai T. Methods to Study Autophagy in Zebrafish. Methods Enzymol 2017; 588:467-496. [DOI: 10.1016/bs.mie.2016.10.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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41
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Diving into marine genomics with CRISPR/Cas9 systems. Mar Genomics 2016; 30:55-65. [DOI: 10.1016/j.margen.2016.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 12/12/2022]
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42
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Lee RTH, Ng ASM, Ingham PW. Ribozyme Mediated gRNA Generation for In Vitro and In Vivo CRISPR/Cas9 Mutagenesis. PLoS One 2016; 11:e0166020. [PMID: 27832146 PMCID: PMC5104441 DOI: 10.1371/journal.pone.0166020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/21/2016] [Indexed: 12/27/2022] Open
Abstract
CRISPR/Cas9 is now regularly used for targeted mutagenesis in a wide variety of systems. Here we report the use of ribozymes for the generation of gRNAs both in vitro and in zebrafish embryos. We show that incorporation of ribozymes increases the types of promoters and number of target sites available for mutagenesis without compromising mutagenesis efficiency. We have tested this by comparing the efficiency of mutagenesis of gRNA constructs with and without ribozymes and also generated a transgenic zebrafish expressing gRNA using a heat shock promoter (RNA polymerase II-dependent promoter) that was able to induce mutagenesis of its target. Our method provides a streamlined approach to test gRNA efficiency as well as increasing the versatility of conditional gene knock out in zebrafish.
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Affiliation(s)
- Raymond Teck Ho Lee
- Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell biology, Agency of Science, Technology and Research (A-STAR), Singapore
| | - Ashley Shu Mei Ng
- Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell biology, Agency of Science, Technology and Research (A-STAR), Singapore
| | - Philip W. Ingham
- Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell biology, Agency of Science, Technology and Research (A-STAR), Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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