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Ma J, Zhang W, Rahimialiabadi S, Ganesh NU, Sun Z, Parvez S, Peterson RT, Yeh JRJ. Instantaneous visual genotyping and facile site-specific transgenesis via CRISPR-Cas9 and phiC31 integrase. Biol Open 2024; 13:bio061666. [PMID: 39225039 PMCID: PMC11391820 DOI: 10.1242/bio.061666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Here, we introduce 'TICIT', targeted integration by CRISPR-Cas9 and integrase technologies, which utilizes the site-specific DNA recombinase - phiC31 integrase - to insert large DNA fragments into CRISPR-Cas9 target loci. This technique, which relies on first knocking in a 39-basepair phiC31 landing site via CRISPR-Cas9, enables researchers to repeatedly perform site-specific transgenesis at the exact genomic location with high precision and efficiency. We applied this approach to devise a method for the instantaneous determination of a zebrafish's genotype simply by examining its color. When a zebrafish mutant line must be propagated as heterozygotes due to homozygous lethality, employing this method allows facile identification of a population of homozygous mutant embryos even before the mutant phenotypes manifest. Thus, it should facilitate various downstream applications, such as large-scale chemical screens. We demonstrated that TICIT could also create reporter fish driven by an endogenous promoter. Further, we identified a landing site in the tyrosinase gene that could support transgene expression in a broad spectrum of tissue and cell types. In sum, TICIT enables site-specific DNA integration without requiring complex donor DNA construction. It can yield consistent transgene expression, facilitate diverse applications in zebrafish, and may be applicable to cells in culture and other model organisms.
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Affiliation(s)
- Junyan Ma
- Department of Basic Medical Science, Quanzhou Medical College, Quanzhou, Fujian 362011, China
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Weiting Zhang
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Simin Rahimialiabadi
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Nikkitha Umesh Ganesh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Zhengwang Sun
- Center for Immunology and Inflammatory Disease, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Saba Parvez
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Randall T Peterson
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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2
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. SCIENCE ADVANCES 2024; 10:eadn6603. [PMID: 38838146 PMCID: PMC11152119 DOI: 10.1126/sciadv.adn6603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Standard zebrafish transgenesis involves random transgene integration with resource-intensive screening. While phiC31 integrase-based attP/attB recombination has streamlined transgenesis in mice and Drosophila, validated attP-based landing sites for universal applications are lacking in zebrafish. Here, we developed phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET) as transgenesis approach, with two attP landing sites pIGLET14a and pIGLET24b from well-validated Tol2 transgenes. Both sites facilitate diverse transgenesis applications including reporters and Cre/loxP transgenes. The pIGLET14a and pIGLET24b landing sites consistently yield 25 to 50% germline transmission, substantially reducing the resources needed for transgenic line generation. Transgenesis into these sites enables reproducible expression patterns in F0 zebrafish embryos for enhancer discovery and testing of gene regulatory variants. Together, our new landing sites streamline targeted, reproducible zebrafish transgenesis as a robust platform for various applications while minimizing the workload for generating transgenic lines.
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Affiliation(s)
| | | | - Cassie L. Kemmler
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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3
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Eck E, Moretti B, Schlomann BH, Bragantini J, Lange M, Zhao X, VijayKumar S, Valentin G, Loureiro C, Soroldoni D, Royer LA, Oates AC, Garcia HG. Single-cell transcriptional dynamics in a living vertebrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574108. [PMID: 38260569 PMCID: PMC10802376 DOI: 10.1101/2024.01.03.574108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. We used these tools to obtain the first single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.
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Affiliation(s)
- Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, USA
| | - Bruno Moretti
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | - Brandon H. Schlomann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Merlin Lange
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | - Xiang Zhao
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Loïc A. Royer
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | - Andrew C. Oates
- Institute of Bioengineering, EPFL; Lausanne, CH
- Department of Cell and Developmental Biology, UCL; London, UK
- The Francis Crick Institute; London, UK
| | - Hernan G. Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
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4
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Mulligan TS, Mumm JS. Selective Cell Ablation Using an Improved Prodrug-Converting Nitroreductase. Methods Mol Biol 2024; 2707:223-234. [PMID: 37668916 DOI: 10.1007/978-1-0716-3401-1_15] [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
Selective cell ablation is an invaluable tool to investigate the function of cell types, the regeneration of cells, and the modeling of diseases associated with cell loss. The nitroreductase (NTR)-mediated cell ablation system is a simple method enabling the elimination of targeted cells through the expression of a nitroreductase enzyme and the application of a prodrug (such as metronidazole). The prodrug is reduced to a cytotoxic product by nitroreductase, thereby leading to DNA damage-induced cell death. In species with elevated regenerative capacity such as zebrafish, removing the prodrug allows endogenous tissue to replace the lost cells. Herein, we describe a method for the use of a markedly improved nitroreductase enzyme for spatially and temporally controlled targeted cell ablation in the zebrafish. Recently, we identified an NTR variant (NTR 2.0) that achieves effective targeted cell ablation at concentrations of metronidazole well below those causing toxic side effects. NTR 2.0 thereby enables the ablation of "resistant" cell types and novel cell ablation paradigms. These advances simplify investigations of cell function, enable interrogations of the effects of chronic inflammation on regenerative processes and facilitate modeling of degenerative diseases associated with chronic cell loss. Techniques for transgenic nitroreductase expression and prodrug application are discussed.
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Affiliation(s)
- Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
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5
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Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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6
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570868. [PMID: 38106217 PMCID: PMC10723424 DOI: 10.1101/2023.12.08.570868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Standard methods for transgenesis in zebrafish depend on random transgene integration into the genome followed by resource-intensive screening and validation. Targeted vector integration into validated genomic loci using phiC31 integrase-based attP/attB recombination has transformed mouse and Drosophila transgenesis. However, while the phiC31 system functions in zebrafish, validated loci carrying attP-based landing or safe harbor sites suitable for universal transgenesis applications in zebrafish have not been established. Here, using CRISPR-Cas9, we converted two well-validated single insertion Tol2-based zebrafish transgenes with long-standing genetic stability into two attP landing sites, called phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET). Generating fluorescent reporters, loxP-based Switch lines, CreERT2 drivers, and gene-regulatory variant reporters in the pIGLET14a and pIGLET24b landing site alleles, we document their suitability for transgenesis applications across cell types and developmental stages. For both landing sites, we routinely achieve 25-50% germline transmission of targeted transgene integrations, drastically reducing the number of required animals and necessary resources to generate individual transgenic lines. We document that phiC31 integrase-based transgenesis into pIGLET14a and pIGLET24b reproducibly results in representative reporter expression patterns in injected F0 zebrafish embryos suitable for enhancer discovery and qualitative and quantitative comparison of gene-regulatory element variants. Taken together, our new phiC31 integrase-based transgene landing sites establish reproducible, targeted zebrafish transgenesis for numerous applications while greatly reducing the workload of generating new transgenic zebrafish lines.
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Affiliation(s)
- Robert L. Lalonde
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Harrison H. Wells
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Cassie L. Kemmler
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - 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
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7
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Jimenez Gonzalez A, Baranasic D, Müller F. Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis Model Mech 2023; 16:dmm050280. [PMID: 37529920 PMCID: PMC10417509 DOI: 10.1242/dmm.050280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.
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Affiliation(s)
- Ada Jimenez Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London SW7 2AZ, UK
- MRC London Institute of Medical Sciences, London W12 0NN, UK
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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8
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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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9
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Gene expression changes during the evolution of the tetrapod limb. Biol Futur 2022; 73:411-426. [PMID: 36355308 DOI: 10.1007/s42977-022-00136-1] [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: 07/10/2021] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.
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10
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Lalonde RL, Kemmler CL, Riemslagh FW, Aman AJ, Kresoja-Rakic J, Moran HR, Nieuwenhuize S, Parichy DM, Burger A, Mosimann C. Heterogeneity and genomic loci of ubiquitous transgenic Cre reporter lines in zebrafish. Dev Dyn 2022; 251:1754-1773. [PMID: 35582941 PMCID: PMC10069295 DOI: 10.1002/dvdy.499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The most-common strategy for zebrafish Cre/lox-mediated lineage labeling experiments combines ubiquitously expressed, lox-based Switch reporter transgenes with tissue-specific Cre or 4-OH-Tamoxifen-inducible CreERT2 driver lines. Although numerous Cre driver lines have been produced, only a few broadly expressed Switch reporters exist in zebrafish and their generation by random transgene integration has been challenging due to position-effect sensitivity of the lox-flanked recombination cassettes. Here, we compare commonly used Switch reporter lines for their recombination efficiency and reporter expression pattern during zebrafish development. RESULTS Using different experimental setups, we show that ubi:Switch and hsp70l:Switch outperform current generations of the two additional Switch reporters actb2:BFP-DsRed and actb2:Stop-DsRed. Our comparisons also document preferential Cre-dependent recombination of ubi:Switch and hsp70l:Switch in distinct zebrafish tissues at early developmental stages. To investigate what genomic features may influence Cre accessibility and lox recombination efficiency in highly functional Switch lines, we mapped these transgenes and charted chromatin dynamics at their integration sites. CONCLUSIONS Our data documents the heterogeneity among lox-based Switch transgenes toward informing suitable transgene selection for lineage labeling experiments. Our work further proposes that ubi:Switch and hsp70l:Switch define genomic integration sites suitable for universal transgene or switch reporter knock-in in zebrafish.
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Affiliation(s)
- Robert L Lalonde
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cassie L Kemmler
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Fréderike W Riemslagh
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Andrew J Aman
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Jelena Kresoja-Rakic
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hannah R Moran
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Susan Nieuwenhuize
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Alexa Burger
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
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11
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Basheer F, Dhar P, Samarasinghe RM. Zebrafish Models of Paediatric Brain Tumours. Int J Mol Sci 2022; 23:9920. [PMID: 36077320 PMCID: PMC9456103 DOI: 10.3390/ijms23179920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
Paediatric brain cancer is the second most common childhood cancer and is the leading cause of cancer-related deaths in children. Despite significant advancements in the treatment modalities and improvements in the 5-year survival rate, it leaves long-term therapy-associated side effects in paediatric patients. Addressing these impairments demands further understanding of the molecularity and heterogeneity of these brain tumours, which can be demonstrated using different animal models of paediatric brain cancer. Here we review the use of zebrafish as potential in vivo models for paediatric brain tumour modelling, as well as catalogue the currently available zebrafish models used to study paediatric brain cancer pathophysiology, and discuss key findings, the unique attributes that these models add, current challenges and therapeutic significance.
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Affiliation(s)
- Faiza Basheer
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Instiute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3220, Australia
| | - Poshmaal Dhar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Instiute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3220, Australia
| | - Rasika M. Samarasinghe
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Instiute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3220, Australia
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12
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Caviglia S, Unterweger IA, Gasiūnaitė A, Vanoosthuyse AE, Cutrale F, Trinh LA, Fraser SE, Neuhauss SCF, Ober EA. FRaeppli: a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish. Development 2022; 149:276363. [DOI: 10.1242/dev.199615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022]
Abstract
ABSTRACT
Visualizing cell shapes and interactions of differentiating cells is instrumental for understanding organ development and repair. Across species, strategies for stochastic multicolour labelling have greatly facilitated in vivo cell tracking and mapping neuronal connectivity. Yet integrating multi-fluorophore information into the context of developing zebrafish tissues is challenging given their cytoplasmic localization and spectral incompatibility with common fluorescent markers. Inspired by Drosophila Raeppli, we developed FRaeppli (Fish-Raeppli) by expressing bright membrane- or nuclear-targeted fluorescent proteins for efficient cell shape analysis and tracking. High spatiotemporal activation flexibility is provided by the Gal4/UAS system together with Cre/lox and/or PhiC31 integrase. The distinct spectra of the FRaeppli fluorescent proteins allow simultaneous imaging with GFP and infrared subcellular reporters or tissue landmarks. We demonstrate the suitability of FRaeppli for live imaging of complex internal organs, such as the liver, and have tailored hyperspectral protocols for time-efficient acquisition. Combining FRaeppli with polarity markers revealed previously unknown canalicular topologies between differentiating hepatocytes, reminiscent of the mammalian liver, suggesting common developmental mechanisms. The multispectral FRaeppli toolbox thus enables the comprehensive analysis of intricate cellular morphologies, topologies and lineages at single-cell resolution in zebrafish.
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Affiliation(s)
- Sara Caviglia
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Iris A. Unterweger
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Akvilė Gasiūnaitė
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Alexandre E. Vanoosthuyse
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Stephan C. F. Neuhauss
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Elke A. Ober
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
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Chowdhury K, Lin S, Lai SL. Comparative Study in Zebrafish and Medaka Unravels the Mechanisms of Tissue Regeneration. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.783818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over evolution. Organisms with variable regenerative capacity are usually distinct in phylogeny, anatomy, and physiology. This phenomenon hinders the feasibility of studying tissue regeneration by directly comparing regenerative with non-regenerative animals, such as zebrafish (Danio rerio) and mice (Mus musculus). Medaka (Oryzias latipes) is a fish model with a complete reference genome and shares a common ancestor with zebrafish approximately 110–200 million years ago (compared to 650 million years with mice). Medaka shares similar features with zebrafish, including size, diet, organ system, gross anatomy, and living environment. However, while zebrafish regenerate almost every organ upon experimental injury, medaka shows uneven regenerative capacity. Their common and distinct biological features make them a unique platform for reciprocal analyses to understand the mechanisms of tissue regeneration. Here we summarize current knowledge about tissue regeneration in these fish models in terms of injured tissues, repairing mechanisms, available materials, and established technologies. We further highlight the concept of inter-species and inter-organ comparisons, which may reveal mechanistic insights and hint at therapeutic strategies for human diseases.
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14
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Škorić-Milosavljević D, Tadros R, Bosada FM, Tessadori F, van Weerd JH, Woudstra OI, Tjong FV, Lahrouchi N, Bajolle F, Cordell HJ, Agopian A, Blue GM, Barge-Schaapveld DQ, Gewillig M, Preuss C, Lodder EM, Barnett P, Ilgun A, Beekman L, van Duijvenboden K, Bokenkamp R, Müller-Nurasyid M, Vliegen HW, Konings TC, van Melle JP, van Dijk AP, van Kimmenade RR, Roos-Hesselink JW, Sieswerda GT, Meijboom F, Abdul-Khaliq H, Berger F, Dittrich S, Hitz MP, Moosmann J, Riede FT, Schubert S, Galan P, Lathrop M, Munter HM, Al-Chalabi A, Shaw CE, Shaw PJ, Morrison KE, Veldink JH, van den Berg LH, Evans S, Nobrega MA, Aneas I, Radivojkov-Blagojević M, Meitinger T, Oechslin E, Mondal T, Bergin L, Smythe JF, Altamirano-Diaz L, Lougheed J, Bouma BJ, Chaix MA, Kline J, Bassett AS, Andelfinger G, van der Palen RL, Bouvagnet P, Clur SAB, Breckpot J, Kerstjens-Frederikse WS, Winlaw DS, Bauer UM, Mital S, Goldmuntz E, Keavney B, Bonnet D, Mulder BJ, Tanck MW, Bakkers J, Christoffels VM, Boogerd CJ, Postma AV, Bezzina CR. Common Genetic Variants Contribute to Risk of Transposition of the Great Arteries. Circ Res 2022; 130:166-180. [PMID: 34886679 PMCID: PMC8768504 DOI: 10.1161/circresaha.120.317107] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
Abstract
RATIONALE Dextro-transposition of the great arteries (D-TGA) is a severe congenital heart defect which affects approximately 1 in 4,000 live births. While there are several reports of D-TGA patients with rare variants in individual genes, the majority of D-TGA cases remain genetically elusive. Familial recurrence patterns and the observation that most cases with D-TGA are sporadic suggest a polygenic inheritance for the disorder, yet this remains unexplored. OBJECTIVE We sought to study the role of common single nucleotide polymorphisms (SNPs) in risk for D-TGA. METHODS AND RESULTS We conducted a genome-wide association study in an international set of 1,237 patients with D-TGA and identified a genome-wide significant susceptibility locus on chromosome 3p14.3, which was subsequently replicated in an independent case-control set (rs56219800, meta-analysis P=8.6x10-10, OR=0.69 per C allele). SNP-based heritability analysis showed that 25% of variance in susceptibility to D-TGA may be explained by common variants. A genome-wide polygenic risk score derived from the discovery set was significantly associated to D-TGA in the replication set (P=4x10-5). The genome-wide significant locus (3p14.3) co-localizes with a putative regulatory element that interacts with the promoter of WNT5A, which encodes the Wnt Family Member 5A protein known for its role in cardiac development in mice. We show that this element drives reporter gene activity in the developing heart of mice and zebrafish and is bound by the developmental transcription factor TBX20. We further demonstrate that TBX20 attenuates Wnt5a expression levels in the developing mouse heart. CONCLUSIONS This work provides support for a polygenic architecture in D-TGA and identifies a susceptibility locus on chromosome 3p14.3 near WNT5A. Genomic and functional data support a causal role of WNT5A at the locus.
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Affiliation(s)
- Doris Škorić-Milosavljević
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
| | - Rafik Tadros
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada (R.T., M.-A.C.)
| | - Fernanda M. Bosada
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
| | - Jan Hendrik van Weerd
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Odilia I. Woudstra
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Fleur V.Y. Tjong
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Fanny Bajolle
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Germany (F.B., S.S.)
| | - Heather J. Cordell
- Population Health Sciences Institute, Newcastle University, Newcastle, United Kingdom (H.J.C.)
| | - A.J. Agopian
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, TX (A.J.A.)
| | - Gillian M. Blue
- Heart Centre for Children, The Children’s Hospital at Westmead and Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Australia (G.M.B., D.S.W.)
| | | | | | - Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Québec, Canada (C.P., G.A.)
- The Jackson Laboratory, Bar Harbor, ME (C.P.)
| | - Elisabeth M. Lodder
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
| | - Phil Barnett
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Leander Beekman
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Regina Bokenkamp
- Division of Pediatric Cardiology, Department of Pediatrics (R.B., R.L.F.v.d.P.), Leiden University Medical Center, The Netherlands
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany (M.M.-N.)
- IBE, Faculty of Medicine, LMU Munich, Germany (M.M.-N.)
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany (M.M.-N.)
| | - Hubert W. Vliegen
- Department of Cardiology (H.W.V.), Leiden University Medical Center, The Netherlands
| | - Thelma C. Konings
- Department of Cardiology, Amsterdam University Medical Centers, VU Amsterdam, The Netherlands (T.C.K.)
| | - Joost P. van Melle
- Department of Cardiology, University Medical Center Groningen, University of Groningen, The Netherlands (J.P.v.M.)
| | - Arie P.J. van Dijk
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands (A.P.J.v.D., R.R.J.v.K.)
| | - Roland R.J. van Kimmenade
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands (A.P.J.v.D., R.R.J.v.K.)
- Department of Cardiology, Maastricht University Medical Center, The Netherlands (R.R.J.v.K.)
| | - Jolien W. Roos-Hesselink
- Department of Cardiology, Erasmus Medical Center, Erasmus University, Rotterdam, The Netherlands (J.W.R.-H.)
| | - Gertjan T. Sieswerda
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Folkert Meijboom
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Hashim Abdul-Khaliq
- Saarland University Medical Center, Department of Pediatric Cardiology, Homburg, Germany (H.A.-K.)
| | - Felix Berger
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de référence Malformations Cardiaques Congénitales Complexes - M3C, Hôpital Necker Enfants Malades, APHP and Université Paris Descartes, Sorbonne Paris Cité, Paris, France (F.B., D.B.)
- Charité, Universitätsmedizin Berlin, Department for Paediatric Cardiology, Germany (F.B.)
| | - Sven Dittrich
- Department of Pediatric Cardiology, Friedrich-Alexander-University of Erlangen-Nuernberg (FAU), Germany (S.D., J.M.)
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein/Campus Kiel, DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany (M.-P.H.)
- Department of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany (M.-P.H.)
| | - Julia Moosmann
- Department of Pediatric Cardiology, Friedrich-Alexander-University of Erlangen-Nuernberg (FAU), Germany (S.D., J.M.)
| | - Frank-Thomas Riede
- Leipzig Heart Center, Department of Pediatric Cardiology, University of Leipzig, Germany (F.-T.R.)
| | - Stephan Schubert
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Germany (F.B., S.S.)
- Heart and Diabetes Center NRW, Center of Congenital Heart Disease, Ruhr-University of Bochum, Bad Oeynhausen, Germany (S.S.)
| | - Pilar Galan
- Sorbonne Paris Nord (Paris 13) University, Inserm U1153, Inrae U1125, Cnam, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center – University of Paris (CRESS), Bobigny, France (P.G.)
| | - Mark Lathrop
- McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Québec, Canada (M.L., H.M.M.)
| | - Hans M. Munter
- McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Québec, Canada (M.L., H.M.M.)
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King’s College London, United Kingdom (A.A.-C.)
| | - Christopher E. Shaw
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, United Kingdom (C.E.S.)
- Centre for Brain Research, University of Auckland, New Zealand (C.E.S.)
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield and NIHR Sheffield Biomedical Research Centre for Translational Neuroscience, United Kingdom (P.J.S.)
| | - Karen E. Morrison
- Faculty of Medicine Health & Life Sciences, Queens University Belfast, United Kingdom (K.E.M.)
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands (J.H.V., L.H.v.d.B.)
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands (J.H.V., L.H.v.d.B.)
| | - Sylvia Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (S.E.)
| | | | - Ivy Aneas
- Department of Human Genetics, University of Chicago, IL (M.A.N., I.A.)
| | | | - Thomas Meitinger
- Helmholtz Zentrum Munich, Institut of Human Genetics, Neuherberg, Germany (M.R.-B., T.M.)
- Division of Cardiology, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada (T.M.)
| | - Erwin Oechslin
- Peter Munk Cardiac Center, Toronto Congenital Cardiac Centre for Adults and University of Toronto, Canada (E.O.)
| | - Tapas Mondal
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Germany (T.M.)
| | - Lynn Bergin
- Division of Cardiology, Department of Medicine, London Health Sciences Centre, ON, Canada (L.B.)
| | - John F. Smythe
- Division of Cardiology, Department of Pediatrics, Kingston General Hospital, ON, Canada (J.F.S.)
| | | | - Jane Lougheed
- Division of Cardiology, Department of Pediatrics, Children’s Hospital of Eastern Ontario, Ottawa, Canada (J.L.)
| | - Berto J. Bouma
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Marie-A. Chaix
- Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada (R.T., M.-A.C.)
| | - Jennie Kline
- Department of Epidemiology, Mailman School of Public Health, Columbia University, NY (J.K.)
| | - Anne S. Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health (A.S.B.)
- Department of Psychiatry, University of Toronto, Toronto General Hospital, University Health Network, Ontario, Canada (A.S.B.)
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Québec, Canada (C.P., G.A.)
| | - Roel L.F. van der Palen
- Division of Pediatric Cardiology, Department of Pediatrics (R.B., R.L.F.v.d.P.), Leiden University Medical Center, The Netherlands
| | - Patrice Bouvagnet
- CPDPN, Hôpital MFME, CHU Martinique, Fort de France, Martinique, France (P.B.)
| | - Sally-Ann B. Clur
- Department of Pediatric Cardiology, Emma Children’s Hospital Amsterdam University Medical Centers (AMC), The Netherlands (S.-A.B.C.)
- Centre for Congenital Heart Disease Amsterdam-Leiden (CAHAL) (S.-A.B.C.)
| | - Jeroen Breckpot
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
- Center for Human Genetics University Hospitals KU Leuven, Belgium (J.B.)
| | | | - David S. Winlaw
- Heart Centre for Children, The Children’s Hospital at Westmead and Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Australia (G.M.B., D.S.W.)
| | - Ulrike M.M. Bauer
- National Register for Congenital Heart Defects, DZHK (German Centre for Cardiovascular Research), Berlin, Germany (U.M.M.B.)
| | - Seema Mital
- Hospital for Sick Children, University of Toronto, Ontario, Canada (S.M.)
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (E.G.)
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom (B.K.)
| | - Damien Bonnet
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de référence Malformations Cardiaques Congénitales Complexes - M3C, Hôpital Necker Enfants Malades, APHP and Université Paris Descartes, Sorbonne Paris Cité, Paris, France (F.B., D.B.)
| | - Barbara J. Mulder
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Michael W.T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health (APH), Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (M.W.T.T.)
| | - Jeroen Bakkers
- Division of Heart and Lungs, Department of Medical Physiology, University Medical Center Utrecht, the Netherlands (J.B.)
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Cornelis J. Boogerd
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
| | - Alex V. Postma
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Connie R. Bezzina
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
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15
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Weiss JM, Lumaquin-Yin D, Montal E, Suresh S, Leonhardt CS, White RM. Shifting the focus of zebrafish toward a model of the tumor microenvironment. eLife 2022; 11:69703. [PMID: 36538362 PMCID: PMC9767465 DOI: 10.7554/elife.69703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/21/2022] [Indexed: 12/29/2022] Open
Abstract
Cancer cells exist in a complex ecosystem with numerous other cell types in the tumor microenvironment (TME). The composition of this tumor/TME ecosystem will vary at each anatomic site and affects phenotypes such as initiation, metastasis, and drug resistance. A mechanistic understanding of the large number of cell-cell interactions between tumor and TME requires models that allow us to both characterize as well as genetically perturb this complexity. Zebrafish are a model system optimized for this problem, because of the large number of existing cell-type-specific drivers that can label nearly any cell in the TME. These include stromal cells, immune cells, and tissue resident normal cells. These cell-type-specific promoters/enhancers can be used to drive fluorophores to facilitate imaging and also CRISPR cassettes to facilitate perturbations. A major advantage of the zebrafish is the ease by which large numbers of TME cell types can be studied at once, within the same animal. While these features make the zebrafish well suited to investigate the TME, the model has important limitations, which we also discuss. In this review, we describe the existing toolset for studying the TME using zebrafish models of cancer and highlight unique biological insights that can be gained by leveraging this powerful resource.
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Affiliation(s)
- Joshua M Weiss
- Weill-Cornel Medical College, Tri-Institutional M.D./Ph.D. ProgramNew YorkUnited States
| | - Dianne Lumaquin-Yin
- Weill-Cornel Medical College, Tri-Institutional M.D./Ph.D. ProgramNew YorkUnited States
| | - Emily Montal
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Shruthy Suresh
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Carl S Leonhardt
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Richard M White
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States,Department of Medicine, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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16
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Bhatia S, Kleinjan DJ, Uttley K, Mann A, Dellepiane N, Bickmore WA. Quantitative spatial and temporal assessment of regulatory element activity in zebrafish. eLife 2021; 10:65601. [PMID: 34796872 PMCID: PMC8604437 DOI: 10.7554/elife.65601] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Mutations or genetic variation in noncoding regions of the genome harbouring cis-regulatory elements (CREs), or enhancers, have been widely implicated in human disease and disease risk. However, our ability to assay the impact of these DNA sequence changes on enhancer activity is currently very limited because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type and disease-associated mutant human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. The activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing simultaneous visualisation of where and when in development the wild-type allele is active and how this activity is altered by mutation.
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Affiliation(s)
- Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan Kleinjan
- Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kirsty Uttley
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Anita Mann
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Nefeli Dellepiane
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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17
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Matinyan N, Karkhanis MS, Gonzalez Y, Jain A, Saltzman A, Malovannaya A, Sarrion-Perdigones A, Dierick HA, Venken KJT. Multiplexed drug-based selection and counterselection genetic manipulations in Drosophila. Cell Rep 2021; 36:109700. [PMID: 34525356 PMCID: PMC8480232 DOI: 10.1016/j.celrep.2021.109700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/10/2021] [Accepted: 08/20/2021] [Indexed: 01/27/2023] Open
Abstract
The power of Drosophila melanogaster as a model system relies on tractable germline genetic manipulations. Despite Drosophila's expansive genetics toolbox, such manipulations are still accomplished one change at a time and depend predominantly on phenotypic screening. We describe a drug-based genetic platform consisting of four selection and two counterselection markers, eliminating the need to screen for modified progeny. These markers work reliably individually or in combination to produce specific genetic outcomes. We demonstrate three example applications of multiplexed drug-based genetics by generating (1) transgenic animals, expressing both components of binary overexpression systems in a single transgenesis step; (2) dual selectable and counterselectable balancer chromosomes; and (3) selectable, fluorescently tagged P[acman] bacterial artificial chromosome (BAC) strains. We perform immunoprecipitation followed by proteomic analysis on one tagged BAC line, demonstrating our platform's applicability to biological discovery. Lastly, we provide a plasmid library resource to facilitate custom transgene design and technology transfer to other model systems.
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Affiliation(s)
- Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mansi S Karkhanis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Saltzman
- Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Herman A Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX 77030, USA.
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18
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Progress in Gene-Editing Technology of Zebrafish. Biomolecules 2021; 11:biom11091300. [PMID: 34572513 PMCID: PMC8468279 DOI: 10.3390/biom11091300] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 12/26/2022] Open
Abstract
As a vertebrate model, zebrafish (Danio rerio) plays a vital role in the field of life sciences. Recently, gene-editing technology has become increasingly innovative, significantly promoting scientific research on zebrafish. However, the implementation of these methods in a reasonable and accurate manner to achieve efficient gene-editing remains challenging. In this review, we systematically summarize the development and latest progress in zebrafish gene-editing technology. Specifically, we outline trends in double-strand break-free genome modification and the prospective applications of fixed-point orientation transformation of any base at any location through a multi-method approach.
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19
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Foo YY, Motakis E, Tiang Z, Shen S, Lai JKH, Chan WX, Wiputra H, Chen N, Chen CK, Winkler C, Foo RSY, Yap CH. Effects of extended pharmacological disruption of zebrafish embryonic heart biomechanical environment on cardiac function, morphology, and gene expression. Dev Dyn 2021; 250:1759-1777. [PMID: 34056790 DOI: 10.1002/dvdy.378] [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: 01/14/2021] [Revised: 04/24/2021] [Accepted: 05/13/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Biomechanical stimuli are known to be important to cardiac development, but the mechanisms are not fully understood. Here, we pharmacologically disrupted the biomechanical environment of wild-type zebrafish embryonic hearts for an extended duration and investigated the consequent effects on cardiac function, morphological development, and gene expression. RESULTS Myocardial contractility was significantly diminished or abolished in zebrafish embryonic hearts treated for 72 hours from 2 dpf with 2,3-butanedione monoxime (BDM). Image-based flow simulations showed that flow wall shear stresses were abolished or significantly reduced with high oscillatory shear indices. At 5 dpf, after removal of BDM, treated embryonic hearts were maldeveloped, having disrupted cardiac looping, smaller ventricles, and poor cardiac function (lower ejected flow, bulboventricular regurgitation, lower contractility, and slower heart rate). RNA sequencing of cardiomyocytes of treated hearts revealed 922 significantly up-regulated genes and 1,698 significantly down-regulated genes. RNA analysis and subsequent qPCR and histology validation suggested that biomechanical disruption led to an up-regulation of inflammatory and apoptotic genes and down-regulation of ECM remodeling and ECM-receptor interaction genes. Biomechanics disruption also prevented the formation of ventricular trabeculation along with notch1 and erbb4a down-regulation. CONCLUSIONS Extended disruption of biomechanical stimuli caused maldevelopment, and potential genes responsible for this are identified.
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Affiliation(s)
- Yoke Yin Foo
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Efthymios Motakis
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zenia Tiang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Shuhao Shen
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jason Kuan Han Lai
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Wei Xuan Chan
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Hadi Wiputra
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Nanguang Chen
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Cardiology, Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Christoph Winkler
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Roger Sik Yin Foo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Choon Hwai Yap
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.,Department of Bioengineering, Imperial College London, London, UK
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20
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Cheung KY, Jesuthasan SJ, Baxendale S, van Hateren NJ, Marzo M, Hill CJ, Whitfield TT. Olfactory Rod Cells: A Rare Cell Type in the Larval Zebrafish Olfactory Epithelium With a Large Actin-Rich Apical Projection. Front Physiol 2021; 12:626080. [PMID: 33716772 PMCID: PMC7952648 DOI: 10.3389/fphys.2021.626080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
We report the presence of a rare cell type, the olfactory rod cell, in the developing zebrafish olfactory epithelium. These cells each bear a single actin-rich rod-like apical projection extending 5–10 μm from the epithelial surface. Live imaging with a ubiquitous Lifeact-RFP label indicates that the olfactory rods can oscillate. Olfactory rods arise within a few hours of the olfactory pit opening, increase in numbers and size during larval stages, and can develop in the absence of olfactory cilia. Olfactory rod cells differ in morphology from the known classes of olfactory sensory neuron, but express reporters driven by neuronal promoters. A sub-population of olfactory rod cells expresses a Lifeact-mRFPruby transgene driven by the sox10 promoter. Mosaic expression of this transgene reveals that olfactory rod cells have rounded cell bodies located apically in the olfactory epithelium and have no detectable axon. We offer speculation on the possible function of these cells in the Discussion.
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Affiliation(s)
- King Yee Cheung
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Suresh J Jesuthasan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Sarah Baxendale
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Nicholas J van Hateren
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Mar Marzo
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Christopher J Hill
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Tanya T Whitfield
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
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21
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Hans S, Zöller D, Hammer J, Stucke J, Spieß S, Kesavan G, Kroehne V, Eguiguren JS, Ezhkova D, Petzold A, Dahl A, Brand M. Cre-Controlled CRISPR mutagenesis provides fast and easy conditional gene inactivation in zebrafish. Nat Commun 2021; 12:1125. [PMID: 33602923 PMCID: PMC7893016 DOI: 10.1038/s41467-021-21427-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Conditional gene inactivation is a powerful tool to determine gene function when constitutive mutations result in detrimental effects. The most commonly used technique to achieve conditional gene inactivation employs the Cre/loxP system and its ability to delete DNA sequences flanked by two loxP sites. However, targeting a gene with two loxP sites is time and labor consuming. Here, we show Cre-Controlled CRISPR (3C) mutagenesis to circumvent these issues. 3C relies on gRNA and Cre-dependent Cas9-GFP expression from the same transgene. Exogenous or transgenic supply of Cre results in Cas9-GFP expression and subsequent mutagenesis of the gene of interest. The recombined cells become fluorescently visible enabling their isolation and subjection to various omics techniques. Hence, 3C mutagenesis provides a valuable alternative to the production of loxP-flanked alleles. It might even enable the conditional inactivation of multiple genes simultaneously and should be applicable to other model organisms amenable to single integration transgenesis.
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Affiliation(s)
- Stefan Hans
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.
| | - Daniela Zöller
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Juliane Hammer
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Johanna Stucke
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Sandra Spieß
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Gokul Kesavan
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Volker Kroehne
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Juan Sebastian Eguiguren
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Diana Ezhkova
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Andreas Petzold
- Center for Molecular and Cellular Bioengineering (CMCB), DRESDEN-Concept Genome Center, Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- Center for Molecular and Cellular Bioengineering (CMCB), DRESDEN-Concept Genome Center, Technische Universität Dresden, Dresden, Germany
| | - Michael Brand
- Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.
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22
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Isaacman-Beck J, Paik KC, Wienecke CFR, Yang HH, Fisher YE, Wang IE, Ishida IG, Maimon G, Wilson RI, Clandinin TR. SPARC enables genetic manipulation of precise proportions of cells. Nat Neurosci 2020; 23:1168-1175. [PMID: 32690967 PMCID: PMC7939234 DOI: 10.1038/s41593-020-0668-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/12/2020] [Indexed: 11/17/2022]
Abstract
Many experimental approaches rely on controlling gene expression in select subsets of cells within an individual animal. However, reproducibly targeting transgene expression to specific fractions of a genetically defined cell type is challenging. We developed Sparse Predictive Activity through Recombinase Competition (SPARC), a generalizable toolkit that can express any effector in precise proportions of post-mitotic cells in Drosophila. Using this approach, we demonstrate targeted expression of many effectors in several cell types and apply these tools to calcium imaging of individual neurons and optogenetic manipulation of sparse cell populations in vivo.
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Affiliation(s)
| | - Kristine C Paik
- Department of Neurobiology, Stanford University, Stanford, CA, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Helen H Yang
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Yvette E Fisher
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Irving E Wang
- Department of Neurobiology, Stanford University, Stanford, CA, USA.,Freenome, South San Francisco, CA, USA
| | - Itzel G Ishida
- Laboratory of Integrative Brain Function and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Gaby Maimon
- Laboratory of Integrative Brain Function and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Rachel I Wilson
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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23
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Liu Y, Huang H, Wang H, Zhang Y. A novel approach for T7 bacteriophage genome integration of exogenous DNA. J Biol Eng 2020; 14:2. [PMID: 31988659 PMCID: PMC6966851 DOI: 10.1186/s13036-019-0224-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/18/2019] [Indexed: 01/16/2023] Open
Abstract
Background The comparatively small genome, well elucidated functional genomics and rapid life cycle confer T7 bacteriophage with great advantages for bio-application. Genetic manipulation of T7 genome plays a key role in T7 related applications. As one of the important aspects in T7 phage genetic modification, gene knock-in refers to two main approaches including direct genetic manipulation in vitro and recombineering. Neither of these available methods are efficient enough to support the development of innovative applications capitalizing on T7 bio-system and thus there is room for novel strategies that address this issue. Integration mediated by the ΦC31 integrase is one of the most robust site-specific recombination systems. ΦC31 integrases with enhanced activity and specificity have been developed such that it is ideal to effectuate exogenous DNA knock-in of T7 phage with advanced ΦC31 integrase. Methods Plasmid construction was conducted by routine molecular cloning technology. The engineered T7 bacteriophages were constructed through homologous recombination with corresponding plasmids and the functional T7 phage was designated as T7∆G10G11-attB. In the integration reaction, hosts with both executive plasmids (pEXM4) and donor plasmids (pMCBK) were lysed by T7∆G10G11-attB. Progenies of T7 phages that integrated with pMCBK were isolated in restrict hosts and validated by sequencing. T7∆G10G11-attB capacity limit was explored by another integration reactions with donor plasmids that contain exogenous DNA of various lengths. Results T7∆G10G11-attB exhibits abortive growth in restrictive hosts, and a bacterial attachment site recognized by ΦC31 integrase (attB) was confirmed to be present in the T7∆G10G11-attB genome via sequencing. The integration reaction demonstrated that plasmids containing the corresponding phage attachment site (attP) could be integrated into the T7∆G10G11-attB genome. The candidate recombinant phage was isolated and validated to have integrated exogenous DNA. The maximum capacity of T7∆G10G11-attB was explored, and it’s found that insertion of exogenous DNA sequences longer than 2 kbp long can be accommodated stably. Conclusion We advanced and established a novel approach for gene knock-in into the T7 genome using ΦC31 integrase.
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Affiliation(s)
- Ying Liu
- 1State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong People's Republic of China
| | - Hongxing Huang
- 1State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong People's Republic of China
| | - Hua Wang
- 2Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology and Guangdong, Provincial Key Laboratory of Stomatology, SunYat-sen University, Guangzhou, 510055 People's Republic of China
| | - Yan Zhang
- 1State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong People's Republic of China
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24
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Marques IJ, Lupi E, Mercader N. Model systems for regeneration: zebrafish. Development 2019; 146:146/18/dev167692. [DOI: 10.1242/dev.167692] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Tissue damage can resolve completely through healing and regeneration, or can produce permanent scarring and loss of function. The response to tissue damage varies across tissues and between species. Determining the natural mechanisms behind regeneration in model organisms that regenerate well can help us develop strategies for tissue recovery in species with poor regenerative capacity (such as humans). The zebrafish (Danio rerio) is one of the most accessible vertebrate models to study regeneration. In this Primer, we highlight the tools available to study regeneration in the zebrafish, provide an overview of the mechanisms underlying regeneration in this system and discuss future perspectives for the field.
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Affiliation(s)
- Ines J. Marques
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
| | - Eleonora Lupi
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Acquifer, Ditabis, Digital Biomedical Imaging Systems, Pforzheim, Germany
| | - Nadia Mercader
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Centro Nacional de Investigaciones Cardiovasculares CNIC, Madrid 2029, Spain
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25
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Collery RF, Link BA. Precise Short Sequence Insertion in Zebrafish Using a CRISPR/Cas9 Approach to Generate a Constitutively Soluble Lrp2 Protein. Front Cell Dev Biol 2019; 7:167. [PMID: 31457013 PMCID: PMC6700241 DOI: 10.3389/fcell.2019.00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/31/2019] [Indexed: 11/13/2022] Open
Abstract
LRP2 is a large transmembrane receptor expressed on absorptive epithelia where it binds many extracellular ligands to control several signaling pathways. Mutations in LRP2 are associated with buphthalmic eye enlargement, myopia and other non-ocular symptoms. Though studies have clearly shown that absence of LRP2 causes these phenotypes, and that overexpression of individual LRP2 domains can exacerbate eye enlargement caused by the absence of Lrp2, the relationship between soluble LRP2 fragments and full-length membrane-bound LRP2 is not completely understood. Here we use a CRISPR/Cas9 approach to insert a stop codon cassette into zebrafish lrp2 to prematurely truncate the protein before its transmembrane domain while leaving the entire extracellular domain intact. The resulting mutant line will be a useful tool for examining Lrp2 function in the eye, and testing hypotheses regarding its extracellular processing.
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Affiliation(s)
- Ross F Collery
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin Eye Institute, Milwaukee, WI, United States
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
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26
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Foo YY, Pant S, Tay HS, Imangali N, Chen N, Winkler C, Yap CH. 4D modelling of fluid mechanics in the zebrafish embryonic heart. Biomech Model Mechanobiol 2019; 19:221-232. [PMID: 31446522 DOI: 10.1007/s10237-019-01205-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 07/20/2019] [Indexed: 11/30/2022]
Abstract
Abnormal blood flow mechanics can result in pathological heart malformation, underlining the importance of understanding embryonic cardiac fluid mechanics. In the current study, we performed image-based computational fluid dynamics simulation of the zebrafish embryonic heart ventricles and characterized flow mechanics, organ dynamics, and energy dynamics in detail. 4D scans of 5 days post-fertilization embryonic hearts with GFP-labelled myocardium were acquired using line-scan focal modulation microscopy. This revealed that the zebrafish hearts exhibited a wave-like contractile/relaxation motion from the inlet to the outlet during both systole and diastole, which we showed to be an energy efficient configuration. No impedance pumping effects of pressure and velocity waves were observed. Due to its tube-like configuration, inflow velocities were higher near the inlet and smaller at the outlet and vice versa for outflow velocities. This resulted in an interesting spatial wall shear stress (WSS) pattern where WSS waveforms near the inlet and those near the outlet were out of phase. There was large spatial variability in WSS magnitudes. Peak WSS was in the range of 47.5-130 dyne/cm2 at the inflow and outflow tracts, but were much smaller, in the range of 4-11 dyne/cm2, in the mid-ventricular segment. Due to very low Reynolds number and the highly viscous environment, intraventricular pressure gradients were high, suggesting substantial energy losses of flow through the heart.
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Affiliation(s)
- Yoke Yin Foo
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Shilpa Pant
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Huiping Shermaine Tay
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Nurgul Imangali
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Nanguang Chen
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Christoph Winkler
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Choon Hwai Yap
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.
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27
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Wang X, Deng Z, Liu T. Marker‐Free System Using Ribosomal Promoters Enhanced Xylose/Glucose Isomerase Production inStreptomyces rubiginosus. Biotechnol J 2019; 14:e1900114. [DOI: 10.1002/biot.201900114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/05/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Microbial Metabolism, School of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghai 200030 P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghai 200030 P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan 430075 P. R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan 430075 P. R. China
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28
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Haussmann IU, Ustaoglu P, Brauer U, Hemani Y, Dix TC, Soller M. Plasmid-based gap-repair recombineered transgenes reveal a central role for introns in mutually exclusive alternative splicing in Down Syndrome Cell Adhesion Molecule exon 4. Nucleic Acids Res 2019; 47:1389-1403. [PMID: 30541104 PMCID: PMC6379703 DOI: 10.1093/nar/gky1254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/22/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing is a key feature of human genes, yet studying its regulation is often complicated by large introns. The Down Syndrome Cell Adhesion Molecule (Dscam) gene from Drosophila is one of the most complex genes generating vast molecular diversity by mutually exclusive alternative splicing. To resolve how alternative splicing in Dscam is regulated, we first developed plasmid-based UAS reporter genes for the Dscam variable exon 4 cluster and show that its alternative splicing is recapitulated by GAL4-mediated expression in neurons. We then developed gap-repair recombineering to very efficiently manipulate these large reporter plasmids in Escherichia coli using restriction enzymes or sgRNA/Cas9 DNA scission to capitalize on the many benefits of plasmids in phiC31 integrase-mediated transgenesis. Using these novel tools, we show that inclusion of Dscam exon 4 variables differs little in development and individual flies, and is robustly determined by sequences harbored in variable exons. We further show that introns drive selection of both proximal and distal variable exons. Since exon 4 cluster introns lack conserved sequences that could mediate robust long-range base-pairing to bring exons into proximity for splicing, our data argue for a central role of introns in mutually exclusive alternative splicing of Dscam exon 4 cluster.
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Affiliation(s)
- Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,School of Life Science, CSELS, Coventry University, Coventry CV1 5FB, UK
| | - Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ulrike Brauer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yash Hemani
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Thomas C Dix
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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29
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Cantu Gutierrez A, Cantu Gutierrez M, Rhyner AM, Ruiz OE, Eisenhoffer GT, Wythe JD. FishNET: An automated relational database for zebrafish colony management. PLoS Biol 2019; 17:e3000343. [PMID: 31220074 PMCID: PMC6605666 DOI: 10.1371/journal.pbio.3000343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 07/02/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022] Open
Abstract
The zebrafish Danio rerio is a powerful model system to study the genetics of development and disease. However, maintenance of zebrafish husbandry records is both time intensive and laborious, and a standardized way to manage and track the large amount of unique lines in a given laboratory or centralized facility has not been embraced by the field. Here, we present FishNET, an intuitive, open-source, relational database for managing data and information related to zebrafish husbandry and maintenance. By creating a "virtual facility," FishNET enables users to remotely inspect the rooms, racks, tanks, and lines within a given facility. Importantly, FishNET scales from one laboratory to an entire facility with several laboratories to multiple facilities, generating a cohesive laboratory and community-based platform. Automated data entry eliminates confusion regarding line nomenclature and streamlines maintenance of individual lines, while flexible query forms allow researchers to retrieve database records based on user-defined criteria. FishNET also links associated embryonic and adult biological samples with data, such as genotyping results or confocal images, to enable robust and efficient colony management and storage of laboratory information. A shared calendar function with email notifications and automated reminders for line turnover, automated tank counts, and census reports promote communication with both end users and administrators. The expected benefits of FishNET are improved vivaria efficiency, increased quality control for experimental numbers, and flexible data reporting and retrieval. FishNET's easy, intuitive record management and open-source, end-user-modifiable architecture provides an efficient solution to real-time zebrafish colony management for users throughout a facility and institution and, in some cases, across entire research hubs.
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Affiliation(s)
- Abiud Cantu Gutierrez
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Manuel Cantu Gutierrez
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alexander M. Rhyner
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Oscar E. Ruiz
- Department of Genetics, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - George T. Eisenhoffer
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Genetics, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Joshua D. Wythe
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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30
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Mishra S, Joshi S, Ward JE, Buys EP, Mishra D, Mishra D, Morgado I, Fisch S, Lavatelli F, Merlini G, Dorbala S, MacRae CA, Liao R. Zebrafish model of amyloid light chain cardiotoxicity: regeneration versus degeneration. Am J Physiol Heart Circ Physiol 2019; 316:H1158-H1166. [PMID: 30875258 PMCID: PMC6580397 DOI: 10.1152/ajpheart.00788.2018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/27/2019] [Accepted: 03/02/2019] [Indexed: 12/27/2022]
Abstract
Cardiac dysfunction is the most frequent cause of morbidity and mortality in amyloid light chain (AL) amyloidosis caused by a clonal immunoglobulin light chain (LC). Previously published transgenic animal models of AL amyloidosis have not recapitulated the key phenotype of cardiac dysfunction seen in AL amyloidosis, which has limited our understanding of the disease mechanisms in vivo, as well as the development of targeted AL therapeutics. We have developed a transgenic zebrafish model in which a λ LC derived from a patient with AL amyloidosis is conditionally expressed in the liver under the control of the Gal4 upstream activation sequence enhancer system. Circulating LC levels of 125 µg/ml in these transgenic zebrafish are comparable to median pathological serum LC levels. Functional analysis links abnormal contractile function with evidence of cellular and molecular proteotoxicity in the heart, including increased cell death and autophagy. However, despite pathological and functional phenotypes analogous to human AL, the lifespan of the transgenic fish is comparable to control fish without the expressed AL-LC transgene. Nuclear labeling experiments suggest increased cardiac proliferation in the transgenic fish, which can be counteracted by treatment with a small molecule proliferation inhibitor leading to increased zebrafish mortality because of cardiac apoptosis and functional deterioration. This transgenic zebrafish model provides a platform to study underlying AL disease mechanisms in vivo further. NEW & NOTEWORTHY Heart failure is a major cause of mortality in amyloid light (AL) amyloidosis, yet it has been difficult to model in animals. We report the generation of a transgenic zebrafish model for AL amyloidosis with pathological concentration of circulating human light chain protein that results in cardiac dysfunction. The light chain toxicity triggers regeneration in the zebrafish heart resulting in functional compensation early in life, but with age develops into cardiac dysfunction.
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Affiliation(s)
- Shikha Mishra
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Shaurya Joshi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Jennifer E Ward
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Eva P Buys
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Deepak Mishra
- Department of Biological Engineering, Massachusetts Institute of Technology , Boston, Massachusetts
| | - Deepa Mishra
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Isabel Morgado
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Sudeshna Fisch
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Francesca Lavatelli
- Amyloidosis Research and Treatment Center, Fondazione Istituto Di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia , Pavia , Italy
| | - Giampaolo Merlini
- Amyloidosis Research and Treatment Center, Fondazione Istituto Di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia , Pavia , Italy
| | - Sharmila Dorbala
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Calum A MacRae
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
| | - Ronglih Liao
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
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31
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Letrado P, de Miguel I, Lamberto I, Díez-Martínez R, Oyarzabal J. Zebrafish: Speeding Up the Cancer Drug Discovery Process. Cancer Res 2018; 78:6048-6058. [PMID: 30327381 DOI: 10.1158/0008-5472.can-18-1029] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/29/2018] [Accepted: 08/23/2018] [Indexed: 11/16/2022]
Abstract
Zebrafish (Danio rerio) is an ideal in vivo model to study a wide variety of human cancer types. In this review, we provide a comprehensive overview of zebrafish in the cancer drug discovery process, from (i) approaches to induce malignant tumors, (ii) techniques to monitor cancer progression, and (iii) strategies for compound administration to (iv) a compilation of the 355 existing case studies showing the impact of zebrafish models on cancer drug discovery, which cover a broad scope of scenarios. Finally, based on the current state-of-the-art analysis, this review presents some highlights about future directions using zebrafish in cancer drug discovery and the potential of this model as a prognostic tool in prospective clinical studies. Cancer Res; 78(21); 6048-58. ©2018 AACR.
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Affiliation(s)
- Patricia Letrado
- Ikan Biotech SL, The Zebrafish Lab Department, Centro Europeo de Empresas e Innovación de Navarra (CEIN), Noain, Spain.,Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Irene de Miguel
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Iranzu Lamberto
- Ikan Biotech SL, The Zebrafish Lab Department, Centro Europeo de Empresas e Innovación de Navarra (CEIN), Noain, Spain
| | - Roberto Díez-Martínez
- Ikan Biotech SL, The Zebrafish Lab Department, Centro Europeo de Empresas e Innovación de Navarra (CEIN), Noain, Spain.
| | - Julen Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
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32
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de Pater E, Trompouki E. Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis. Front Cell Dev Biol 2018; 6:124. [PMID: 30374440 PMCID: PMC6196227 DOI: 10.3389/fcell.2018.00124] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is an optimal system for studying stem cell maintenance and lineage differentiation under physiological and pathological conditions. In vertebrate organisms, billions of differentiated hematopoietic cells need to be continuously produced to replenish the blood cell pool. Disruptions in this process have immediate consequences for oxygen transport, responses against pathogens, maintenance of hemostasis and vascular integrity. Zebrafish is a widely used and well-established model for studying the hematopoietic system. Several new hematopoietic regulators were identified in genetic and chemical screens using the zebrafish model. Moreover, zebrafish enables in vivo imaging of hematopoietic stem cell generation and differentiation during embryogenesis, and adulthood. Finally, zebrafish has been used to model hematopoietic diseases. Recent technological advances in single-cell transcriptome analysis, epigenetic regulation, proteomics, metabolomics, and processing of large data sets promise to transform the current understanding of normal, abnormal, and malignant hematopoiesis. In this perspective, we discuss how the zebrafish model has proven beneficial for studying physiological and pathological hematopoiesis and how these novel technologies are transforming the field.
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Affiliation(s)
- Emma de Pater
- Department of Hematology, Erasmus MC, Rotterdam, Netherlands
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
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33
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A Collection of Transgenic Medaka Strains for Efficient Site-Directed Transgenesis Mediated by phiC31 Integrase. G3-GENES GENOMES GENETICS 2018; 8:2585-2593. [PMID: 29848622 PMCID: PMC6071608 DOI: 10.1534/g3.118.200130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genetic analysis is facilitated by the efficient production of transgenic strains expressing a DNA of interest as a single copy at a designated chromosomal location. However, technical progress toward this goal in medaka fish (Oryzias latipes), a vertebrate model organism, has been slow. It is well known that phiC31 integrase enables efficient site-directed transgenesis by catalyzing the recombination of an attP DNA motif in a host genome with an attB motif in a targeting vector. This system was pioneered in medaka using the Sleeping Beauty transposon system, and the attP site was established at three chromosomal locations. However, this number appeared insufficient with regard to genetic linkage between the attP-landing site and a genetically modified locus of interest. Here, to establish a collection of transgenic strains of medaka, we introduced an attP motif into the medaka genome using the Ac/Ds maize transposon system and established 12 independent transgenic strains harboring a single copy of the attP motif in at least 11 of the 24 medaka chromosomes. We designed an attB-targeting vector that was integrated efficiently and precisely into the attP-landing site, and with which the DNA of interest was efficiently transmitted to germline cells. Extraneous sequences in the integrants derived from the bacterial backbone of the attB-targeting vector as well as a transgenic fluorescence marker present in the attP-landing site were removable through flippase-mediated recombination. Further, an advanced targeting vector with a heart-specific recombination marker served as a useful tool for easily screening phiC31 integrase-mediated recombinant G0 embryos, leading to the efficient establishment of transgenic strains. Thus, our resources advance genetic research in medaka.
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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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35
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Kibat C, Krishnan S, Ramaswamy M, Baker BJ, Jesuthasan S. Imaging voltage in zebrafish as a route to characterizing a vertebrate functional connectome: promises and pitfalls of genetically encoded indicators. J Neurogenet 2017; 30:80-8. [PMID: 27328843 DOI: 10.1080/01677063.2016.1180384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Neural circuits are non-linear dynamical systems that transform information based on the pattern of input, current state and functional connectivity. To understand how a given stimulus is processed, one would ideally record neural activity across the entire brain of a behaving animal, at cellular or even subcellular resolution, in addition to characterizing anatomical connectivity. Given their transparency and relatively small size, larval zebrafish provide a powerful system for brain-wide monitoring of neural activity. Genetically encoded calcium indicators have been used for this purpose, but cannot directly report hyperpolarization or sub-threshold activity. Voltage indicators, in contrast, have this capability. Here, we test whether two different genetically encoded voltage reporters, ASAP1 and Bongwoori, can be expressed and report activity in the zebrafish brain, using widefield, two-photon and light sheet microscopy. We were unable to express ASAP1 in neurons. Bongwoori, in contrast expressed well, and because of its membrane localization, allowed visualization of axon trajectories in 3D. Bongwoori displayed stimulus-evoked changes in fluorescence, which could be detected in single trials. However, under high laser illumination, puncta on neural membranes underwent spontaneous fluctuations in intensity, suggesting that the probe is susceptible to blinking artefacts. These data indicate that larval zebrafish can be used to image electrical activity in the brain of an intact vertebrate at high resolution, although care is needed in imaging and analysis. Recording activity across the whole brain will benefit from further developments in imaging hardware and indicators.
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Affiliation(s)
- Caroline Kibat
- a Neural Circuitry and Behaviour Lab , Institute of Molecular and Cell Biology , Singapore , Singapore
| | - Seetha Krishnan
- b NUS Graduate School for Integrative Sciences and Engineering , Singapore , Singapore
| | - Mahathi Ramaswamy
- b NUS Graduate School for Integrative Sciences and Engineering , Singapore , Singapore
| | - Bradley J Baker
- c Center for Functional Connectomics , Korea Institute of Science and Technology , Seoul , South Korea
| | - Suresh Jesuthasan
- a Neural Circuitry and Behaviour Lab , Institute of Molecular and Cell Biology , Singapore , Singapore ;,d Program in Neuroscience and Behavioural Disorders , Duke-NUS Graduate School of Medicine , Singapore , Singapore ;,e Department of Physiology , National University of Singapore , Singapore , Singapore
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36
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Pant S, Duan Y, Xiong F, Chen N. Augmented line-scan focal modulation microscopy for multi-dimensional imaging of zebrafish heart in vivo. BIOMEDICAL OPTICS EXPRESS 2017; 8:5698-5707. [PMID: 29296498 PMCID: PMC5745113 DOI: 10.1364/boe.8.005698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 05/18/2023]
Abstract
Multi-dimensional fluorescence imaging of live animal models demands strong optical sectioning, high spatial resolution, fast image acquisition, and minimal photobleaching. While conventional laser scanning microscopes are capable of deep penetration and sub-cellular resolution, they are generally too slow and causing excessive photobleaching for volumetric or time-lapse imaging. We demonstrate the performance of an augmented line-scan focal modulation microscope (aLSFMM), a high-speed imaging platform that affords above video-rate imaging speed by the use of line scanning. Exceptional background rejection is accomplished by combining a confocal slit with focal modulation. The image quality is further improved by merging the information from simultaneously acquired focal modulation and confocal images. Such a hybrid imaging scheme makes it possible to use very low power excitation light in high-speed imaging, and therefore leads to reduced photobleaching that is desirable for three-dimensional (3D) and four-dimensional (4D) in vivo image acquisition.
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37
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Abstract
The zebrafish (Danio rerio) possesses a vertebrate-type retina that is extraordinarily conserved in evolution. This well-organized and anatomically easily accessible part of the central nervous system has been widely investigated in zebrafish, promoting general understanding of retinal development, morphology, function and associated diseases. Over the recent years, genome and protein engineering as well as imaging techniques have experienced revolutionary advances and innovations, creating new possibilities and methods to study zebrafish development and function. In this review, we focus on some of these emerging technologies and how they may impact retinal research in the future. We place an emphasis on genetic techniques, such as transgenic approaches and the revolutionizing new possibilities in genome editing.
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Affiliation(s)
- Stephanie Niklaus
- a Institute of Molecular Life Sciences , University of Zurich , Zurich , Switzerland.,b Life Science Zurich Graduate Program - Neuroscience , Zurich , Switzerland
| | - Stephan C F Neuhauss
- a Institute of Molecular Life Sciences , University of Zurich , Zurich , Switzerland
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38
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Chen J, Xia L, Bruchas MR, Solnica-Krezel L. Imaging early embryonic calcium activity with GCaMP6s transgenic zebrafish. Dev Biol 2017; 430:385-396. [PMID: 28322738 PMCID: PMC5835148 DOI: 10.1016/j.ydbio.2017.03.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/12/2017] [Accepted: 03/11/2017] [Indexed: 12/02/2022]
Abstract
Intracellular Ca2+ signaling regulates cellular activities during embryogenesis and in adult organisms. We generated stable Tg[βactin2:GCaMP6s]stl351 and Tg[ubi:GCaMP6s]stl352 transgenic lines that combine the ubiquitously-expressed Ca2+ indicator GCaMP6s with the transparent characteristics of zebrafish embryos to achieve superior in vivo Ca2+ imaging. Using the Tg[βactin2:GCaMP6s]stl351 line featuring strong GCaMP6s expression from cleavage through gastrula stages, we detected higher frequency of Ca2+ transients in the superficial blastomeres during the blastula stages preceding the midblastula transition. Additionally, GCaMP6s also revealed that dorsal-biased Ca2+ signaling that follows the midblastula transition persisted longer during gastrulation, compared with earlier studies. We observed that dorsal-biased Ca2+ signaling is diminished in ventralized ichabod/β-catenin2 mutant embryos and ectopically induced in embryos dorsalized by excess β-catenin. During gastrulation, we directly visualized Ca2+ signaling in the dorsal forerunner cells, which form in a Nodal signaling dependent manner and later give rise to the laterality organ. We found that excess Nodal increases the number and the duration of Ca2+ transients specifically in the dorsal forerunner cells. The GCaMP6s transgenic lines described here enable unprecedented visualization of dynamic Ca2+ events from embryogenesis through adulthood, augmenting the zebrafish toolbox.
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Affiliation(s)
- Jiakun Chen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Li Xia
- Department of Anesthesiology, Division of Basic Research, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St Louis, MO, 63105, USA
| | - Michael R Bruchas
- Department of Anesthesiology, Division of Basic Research, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St Louis, MO, 63105, USA; Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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39
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Baxendale S, van Eeden F, Wilkinson R. The Power of Zebrafish in Personalised Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:179-197. [PMID: 28840558 DOI: 10.1007/978-3-319-60733-7_10] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The goal of personalised medicine is to develop tailor-made therapies for patients in whom currently available therapeutics fail. This approach requires correlating individual patient genotype data to specific disease phenotype data and using these stratified data sets to identify bespoke therapeutics. Applications for personalised medicine include common complex diseases which may have multiple targets, as well as rare monogenic disorders, for which the target may be unknown. In both cases, whole genome sequence analysis (WGS) is discovering large numbers of disease associated mutations in new candidate genes and potential modifier genes. Currently, the main limiting factor is the determination of which mutated genes are important for disease progression and therefore represent potential targets for drug discovery. Zebrafish have gained popularity as a model organism for understanding developmental processes, disease mechanisms and more recently for drug discovery and toxicity testing. In this chapter, we will examine the diverse roles that zebrafish can make in the expanding field of personalised medicine, from generating humanised disease models to xenograft screening of different cancer cell lines, through to finding new drugs via in vivo phenotypic screens. We will discuss the tools available for zebrafish research and recent advances in techniques, highlighting the advantages and potential of using zebrafish for high throughput disease modeling and precision drug discovery.
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Affiliation(s)
- Sarah Baxendale
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Freek van Eeden
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Wilkinson
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.,Department of Infection, Immunity and Cardiovascular Disease, Medical School, Beech Hill Rd, University of Sheffield, Sheffield, S10 2RX, UK
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40
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Abstract
Tissue or cell transplantation is an invaluable technique with a multitude of applications including studying the developmental potential of certain cell populations, dissecting cell-environment interactions, and identifying stem cells. One key technical requirement for performing transplantation assays is the capability of distinguishing the transplanted donor cells from the endogenous host cells and tracing the donor cells over time. The zebrafish has emerged as an excellent model organism for performing transplantation assays, thanks in part to the transparency of embryos and even adults when pigment mutants are employed. Using transgenic techniques and fast-evolving imaging technology, fluorescence-labeled donor cells can be readily identified and studied during development in vivo. In this chapter, we will discuss the rationale of different types of zebrafish transplantation in both embryos and adults and then focus on four detailed methods of transplantation: blastula/gastrula transplantation for mosaic analysis, hematopoietic stem cell transplantation, chemical screening using a transplantation model, and tumor transplantation.
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Affiliation(s)
- J M Gansner
- Harvard Medical School, Boston, MA, United States
| | - M Dang
- Harvard Medical School, Boston, MA, United States
| | - M Ammerman
- Harvard Medical School, Boston, MA, United States
| | - L I Zon
- Harvard Medical School, Boston, MA, United States
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41
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Panser K, Tirian L, Schulze F, Villalba S, Jefferis GSXE, Bühler K, Straw AD. Automatic Segmentation of Drosophila Neural Compartments Using GAL4 Expression Data Reveals Novel Visual Pathways. Curr Biol 2016; 26:1943-1954. [PMID: 27426516 PMCID: PMC4985560 DOI: 10.1016/j.cub.2016.05.052] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/14/2016] [Accepted: 05/20/2016] [Indexed: 01/26/2023]
Abstract
Identifying distinct anatomical structures within the brain and developing genetic tools to target them are fundamental steps for understanding brain function. We hypothesize that enhancer expression patterns can be used to automatically identify functional units such as neuropils and fiber tracts. We used two recent, genome-scale Drosophila GAL4 libraries and associated confocal image datasets to segment large brain regions into smaller subvolumes. Our results (available at https://strawlab.org/braincode) support this hypothesis because regions with well-known anatomy, namely the antennal lobes and central complex, were automatically segmented into familiar compartments. The basis for the structural assignment is clustering of voxels based on patterns of enhancer expression. These initial clusters are agglomerated to make hierarchical predictions of structure. We applied the algorithm to central brain regions receiving input from the optic lobes. Based on the automated segmentation and manual validation, we can identify and provide promising driver lines for 11 previously identified and 14 novel types of visual projection neurons and their associated optic glomeruli. The same strategy can be used in other brain regions and likely other species, including vertebrates. Genome-scale enhancer expression patterns can be used to predict brain structure Automated clustering of images finds known structures such as olfactory glomeruli Results identify GAL4 lines with strong expression in the predicted structures We validate novel predictions to reveal previously undescribed optic glomeruli
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Affiliation(s)
- Karin Panser
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria
| | - Laszlo Tirian
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria
| | - Florian Schulze
- VRVis Zentrum für Virtual Reality und Visualisierung Forschungs, Donau-City-Strasse 1, 1220 Vienna, Austria
| | - Santiago Villalba
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria
| | - Gregory S X E Jefferis
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Katja Bühler
- VRVis Zentrum für Virtual Reality und Visualisierung Forschungs, Donau-City-Strasse 1, 1220 Vienna, Austria
| | - Andrew D Straw
- Research Institute of Molecular Pathology (IMP), Vienna Bio-Center, Doktor-Bohr-Gasse 7, 1030 Vienna, Austria; Department of Neurobiology and Behavior, Institute of Biology I, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany.
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42
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Burger A, Lindsay H, Felker A, Hess C, Anders C, Chiavacci E, Zaugg J, Weber LM, Catena R, Jinek M, Robinson MD, Mosimann C. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 2016; 143:2025-37. [PMID: 27130213 DOI: 10.1242/dev.134809] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/12/2016] [Indexed: 12/14/2022]
Abstract
CRISPR-Cas9 enables efficient sequence-specific mutagenesis for creating somatic or germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-sgRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we apply in vitro assembled, fluorescent Cas9-sgRNA RNPs in solubilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. MiSeq-based sequence analysis of targeted loci in individual embryos using CrispRVariants, a customized software tool for mutagenesis quantification and visualization, reveals efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis exposes loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show that targeting of non-coding elements in gene regulatory regions using saturating mutagenesis uncovers functional control elements in transgenic reporters and endogenous genes in injected embryos. Our results establish that optimally solubilized, in vitro assembled fluorescent Cas9-sgRNA RNPs provide a reproducible reagent for direct and scalable loss-of-function studies and applications beyond zebrafish experiments that require maximal DNA cutting efficiency in vivo.
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Affiliation(s)
- Alexa Burger
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Helen Lindsay
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich 8057, Switzerland
| | - Anastasia Felker
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Christopher Hess
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Carolin Anders
- Institute of Biochemistry, University of Zürich, Zürich 8057, Switzerland
| | - Elena Chiavacci
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Jonas Zaugg
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Lukas M Weber
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich 8057, Switzerland
| | - Raul Catena
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Martin Jinek
- Institute of Biochemistry, University of Zürich, Zürich 8057, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich 8057, Switzerland
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
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43
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A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish. G3-GENES GENOMES GENETICS 2016; 6:829-34. [PMID: 26818072 PMCID: PMC4825653 DOI: 10.1534/g3.115.026344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Transgenesis of large DNA constructs is essential for gene function analysis. Recently, Tol2 transposase-mediated transgenesis has emerged as a powerful tool to insert bacterial artificial chromosome (BAC) DNA constructs into the genome of zebrafish. For efficient transgenesis, the genomic DNA piece in the BAC construct needs to be flanked by Tol2 transposon sites, and the constructs should contain a transgenesis marker for easy identification of transgenic animals. We report a set of plasmids that contain targeting cassettes that allow the insertion of Tol2 sites and different transgenesis markers into BACs. Using BACs containing these targeting cassettes, we show that transgenesis is as efficient as iTol2, that preselecting for expression of the transgenesis marker increases the transgenesis rate, and that BAC transgenics faithfully recapitulate the endogenous gene expression patterns and allow for the estimation of the endogenous gene expression levels.
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44
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Felker A, Mosimann C. Contemporary zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments. Methods Cell Biol 2016; 135:219-44. [PMID: 27443928 DOI: 10.1016/bs.mcb.2016.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Spatiotemporal transgene regulation by transgenic DNA recombinases is a central tool for reverse genetics in multicellular organisms, with excellent applications for misexpression and lineage tracing experiments. One of the most widespread technologies for this purpose is Cre recombinase-controlled lox site recombination that is attracting increasing interest in the zebrafish field. Tol2-mediated zebrafish transgenesis provides a stable platform to integrate lox cassette transgenes, while the amenability of the zebrafish embryo to drug treatments makes the model an ideal candidate for tamoxifen-inducible CreERT2 experiments. In addition, advanced transgenesis technologies such as phiC31 or CRISPR-Cas9-based knock-ins are even further promoting zebrafish transgenesis for Cre/lox applications. In this chapter, we will first introduce the basics of Cre/lox methodology, CreERT2 regulation by tamoxifen, as well as the utility of Tol2 and other contemporary transgenesis techniques for Cre/lox experiments. We will then outline in detail practical experimental steps for efficient transgenesis toward the creation of single-insertion transgenes and will introduce protocols for 4-hydroxytamoxifen-mediated CreERT2 induction to perform spatiotemporal lox transgene regulation experiments in zebrafish embryos. Last, we will discuss advanced experimental applications of Cre/lox beyond traditional lineage tracing approaches.
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Affiliation(s)
- A Felker
- University of Zürich, Zürich, Switzerland
| | - C Mosimann
- University of Zürich, Zürich, Switzerland
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45
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Mayrhofer M, Mione M. The Toolbox for Conditional Zebrafish Cancer Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:21-59. [PMID: 27165348 DOI: 10.1007/978-3-319-30654-4_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we describe the conditional zebrafish cancer toolbox, which allows for fine control of the expression of oncogenes or downregulation of tumor suppressors at the spatial and temporal level. Methods such as the Gal4/UAS or the Cre/lox systems paved the way to the development of elegant tumor models, which are now being used to study cancer cell biology, clonal evolution, identification of cancer stem cells and anti-cancer drug screening. Combination of these tools, as well as novel developments such as the promising genome editing system through CRISPR/Cas9 and clever application of light reactive proteins will enable the development of even more sophisticated zebrafish cancer models. Here, we introduce this growing toolbox of conditional transgenic approaches, discuss its current application in zebrafish cancer models and provide an outlook on future perspectives.
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Affiliation(s)
- Marie Mayrhofer
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
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46
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Erickson T, Nicolson T. Cell type-specific transcriptomic analysis by thiouracil tagging in zebrafish. Methods Cell Biol 2016; 135:309-28. [DOI: 10.1016/bs.mcb.2016.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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47
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Venken KJT, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:233-67. [PMID: 26447401 DOI: 10.1002/wdev.214] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 08/03/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
A central challenge in investigating biological phenomena is the development of techniques to modify genomic DNA with nucleotide precision that can be transmitted through the germ line. Recent years have brought a boon in these technologies, now collectively known as genome engineering. Defined genomic manipulations at the nucleotide level enable a variety of reverse engineering paradigms, providing new opportunities to interrogate diverse biological functions. These genetic modifications include controlled removal, insertion, and substitution of genetic fragments, both small and large. Small fragments up to a few kilobases (e.g., single nucleotide mutations, small deletions, or gene tagging at single or multiple gene loci) to large fragments up to megabase resolution can be manipulated at single loci to create deletions, duplications, inversions, or translocations of substantial sections of whole chromosome arms. A specialized substitution of chromosomal portions that presumably are functionally orthologous between different organisms through syntenic replacement, can provide proof of evolutionary conservation between regulatory sequences. Large transgenes containing endogenous or synthetic DNA can be integrated at defined genomic locations, permitting an alternative proof of evolutionary conservation, and sophisticated transgenes can be used to interrogate biological phenomena. Precision engineering can additionally be used to manipulate the genomes of organelles (e.g., mitochondria). Novel genome engineering paradigms are often accelerated in existing, easily genetically tractable model organisms, primarily because these paradigms can be integrated in a rigorous, existing technology foundation. The Drosophila melanogaster fly model is ideal for these types of studies. Due to its small genome size, having just four chromosomes, the vast amount of cutting-edge genetic technologies, and its short life-cycle and inexpensive maintenance requirements, the fly is exceptionally amenable to complex genetic analysis using advanced genome engineering. Thus, highly sophisticated methods developed in the fly model can be used in nearly any sequenced organism. Here, we summarize different ways to perform precise inheritable genome engineering using integrases, recombinases, and DNA nucleases in the D. melanogaster. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Koen J T Venken
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Paul J Vandeventer
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Audrey E Christiansen
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Kristi L Hoffman
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
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48
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Haghighat-Khah RE, Scaife S, Martins S, St John O, Matzen KJ, Morrison N, Alphey L. Site-specific cassette exchange systems in the Aedes aegypti mosquito and the Plutella xylostella moth. PLoS One 2015; 10:e0121097. [PMID: 25830287 PMCID: PMC4382291 DOI: 10.1371/journal.pone.0121097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/09/2015] [Indexed: 12/02/2022] Open
Abstract
Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests.
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Affiliation(s)
- Roya Elaine Haghighat-Khah
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | - Sara Martins
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | - Oliver St John
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | | | - Luke Alphey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
- * E-mail: (LA); (KJM)
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49
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Generating customized transgene landing sites and multi-transgene arrays in Drosophila using phiC31 integrase. Genetics 2015; 199:919-34. [PMID: 25680812 PMCID: PMC4391550 DOI: 10.1534/genetics.114.173187] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/09/2015] [Indexed: 01/05/2023] Open
Abstract
Transgenesis in numerous eukaryotes has been facilitated by the use of site-specific integrases to stably insert transgenes at predefined genomic positions (landing sites). However, the utility of integrase-mediated transgenesis in any system is constrained by the limited number and variable expression properties of available landing sites. By exploiting the nonstandard recombination activity exhibited by a phiC31 integrase mutant, we developed a rapid and inexpensive method for isolating landing sites that exhibit desired expression properties. Additionally, we devised a simple technique for constructing arrays of transgenes at a single landing site, thereby extending the utility of previously characterized landing sites. Using the fruit fly Drosophila melanogaster, we demonstrate the feasibility of these approaches by isolating new landing sites optimized to express transgenes in the nervous system and by building fluorescent reporter arrays at several landing sites. Because these strategies require the activity of only a single exogenous protein, we anticipate that they will be portable to species such as nonmodel organisms, in which genetic manipulation is more challenging, expediting the development of genetic resources in these systems.
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50
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Santoro MM. Zebrafish as a model to explore cell metabolism. Trends Endocrinol Metab 2014; 25:546-54. [PMID: 24997878 DOI: 10.1016/j.tem.2014.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/04/2014] [Accepted: 06/10/2014] [Indexed: 12/20/2022]
Abstract
Cell metabolism plays a key role in many essential biological processes. The recent availability of novel technologies and organisms to model cell metabolism in vivo is expanding current knowledge of cell metabolism. In this context, the zebrafish (Danio rerio) is emerging as a valuable model system to learn about the metabolic routes critical for cellular homeostasis. Here, the most recent methods and studies on cell metabolism are summarized, which support the overall value for the zebrafish model system not only to study metabolism but also metabolic disease states. It is envisioned that this small vertebrate system will help in the understanding of pathogenesis for numerous metabolic-related disorders in humans and in the identification of their therapeutic treatments.
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Affiliation(s)
- Massimo M Santoro
- Laboratory of Endothelial Molecular Biology, Vesalius Research Center, Department of Oncology, University of Leuven, Leuven, B-3000, Belgium; Laboratory of Endothelial Molecular Biology, Vesalius Research Center, VIB, Leuven, B-3000, Belgium.
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