101
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Kossack ME, Draper BW. Genetic regulation of sex determination and maintenance in zebrafish (Danio rerio). Curr Top Dev Biol 2019; 134:119-149. [PMID: 30999973 DOI: 10.1016/bs.ctdb.2019.02.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Over the last several decades zebrafish (Danio rerio) has become a major model organism for the study of vertebrate development and physiology. Given this, it may be surprising how little is known about the mechanism that zebrafish use to determine sex. While zebrafish are a gonochoristic species (having two sexes) that do not switch sex as adults, it was appreciated early on that sex ratios obtained from breeding lab domesticated lines were not typically a 1:1 ratio of male and female, suggesting that sex was not determined by a strict chromosomal mechanism. Here we will review the recent progress toward defining the genetic mechanism for sex determination in both wild and domesticated zebrafish.
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Affiliation(s)
- Michelle E Kossack
- Molecular and Cellular Biology, University of California, Davis, CA, United States
| | - Bruce W Draper
- Molecular and Cellular Biology, University of California, Davis, CA, United States.
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102
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Parsons KJ, Son YH, Crespel A, Thambithurai D, Killen S, Harris MP, Albertson RC. Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability. Proc Biol Sci 2019; 285:rspb.2017.2671. [PMID: 29669899 DOI: 10.1098/rspb.2017.2671] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/27/2018] [Indexed: 01/06/2023] Open
Abstract
Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis and its temporal dynamics over generations. To address these open questions, we compared patterns of craniofacial modularity among laboratory strains, defined mutant lines and a wild population of zebrafish (Danio rerio). Our findings suggest that relatively simple genetic changes can have profound effects on covariance, without greatly affecting craniofacial shape. Moreover, we show that instead of completely deconstructing the covariance structure among sets of traits, mutations cause shifts among seemingly latent patterns of modularity suggesting that the skull may be predisposed towards a limited number of phenotypes. This new insight may serve to greatly increase the evolvability of a population by providing a range of 'preset' patterns of modularity that can appear readily and allow for rapid evolution.
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Affiliation(s)
- Kevin J Parsons
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Young H Son
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Amelie Crespel
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Davide Thambithurai
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Shaun Killen
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Orthopaedic Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - R Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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103
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Wei N, Zhang X, Hong Q, Jiang Y, Zhang Q, Guo X, Chi X, Tong M, Liu Q. The sonic hedgehog signaling pathway is suppressed following PCB 1254 exposure during retinal development. ENVIRONMENTAL TOXICOLOGY 2019; 34:340-347. [PMID: 30578594 DOI: 10.1002/tox.22689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/16/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
Polychlorinated biphenyl (PCB) has been reported to have detrimental effects on retinal development. In order to explore the role of Shh signaling in retinal development after PCB1254 exposure in vivo and in vitro, zebrafish and RGC-5 retinal cell line were used. Compared with the controls, PCB exposure inhibited proliferation and increased the apoptosis levels. The expression of Shh mRNA decreased in the PCB1254 -treated groups both in vivo and in vitro compared with that of the controls. The ptch2 mRNA expression increased in the experimental groups. The expression of gli2 mRNA decreased in the PCB1254 -treated groups. Immunofluorescence and western blotting assays confirmed that the expression of Shh proteins decreased in PCB1254 -treated groups compared with control groups. Moreover, ptch2 protein levels increased in the PCB1254 -treated groups as well as the decreased protein expressions of gli1 and gli2. These results demonstrated that Shh signaling pathway may participate in the damage of retinal development caused by PCB1254 exposure, providing evidence that eye diseases could be caused by environmental pollutants.
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Affiliation(s)
- Ning Wei
- Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital affiliated to Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital affiliated to Nanjing Medical University, Nanjing, China
- Department of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Qin Hong
- Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital affiliated to Nanjing Medical University, Nanjing, China
- Department of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- Department of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Qingyu Zhang
- Department of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Xirong Guo
- Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital affiliated to Nanjing Medical University, Nanjing, China
- Department of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Xia Chi
- Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital affiliated to Nanjing Medical University, Nanjing, China
- Department of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Meiling Tong
- Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital affiliated to Nanjing Medical University, Nanjing, China
- Department of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Qinghuai Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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104
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Shao Y, Xiao H, Di Paolo C, Deutschmann B, Brack W, Hollert H, Seiler TB. Integrated zebrafish-based tests as an investigation strategy for water quality assessment. WATER RESEARCH 2019; 150:252-260. [PMID: 30528920 DOI: 10.1016/j.watres.2018.11.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/30/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Water pollution risks to human health and the environment are emerging as serious concerns in the European Union and worldwide. With the aim to achieve good ecological and chemical status of all European water bodies, the "European Water Framework Directive" (WFD) was enacted. With the framework, bioanalytical techniques have been recognized as an important aspect. However, there are limitations to the application of bioassays directly for water quality assessment. Such approaches often fail to identify pollutants of concern, since the defined priority and monitored pollutants often fail to explain the observed toxicity. In this study, we integrated an effect-based risk assessment with a zebrafish-based investigation strategy to evaluate water sample extracts and fractions collected from the Danube. Four tiered bioassays were implemented, namely RNA-level gene expression assay, protein-level ethoxyresorufin-O-deethylase (EROD) assay, cell-level micronucleus assay and organism-level fish embryo test (FET). The results show that teratogenicity and lethality during embryonic development might be induced by molecular or cellular damages mediated by the aryl hydrocarbon receptor (AhR) -mediated activity, estrogenic activity and genotoxic activity. With the combination of high-throughput fractionation, this effect-based strategy elucidated the major responsible mixtures of each specific toxic response. In particularly, the most toxic mixture in faction F4, covering a log Kow range from 2.83 to 3.42, was composed by 12 chemicals, which were then evaluated as a designed mixture. Our study applied tiered bioassays with zebrafish to avoid interspecies differences and highlights effect-based approaches to address toxic mixtures in water samples. This strategy can be applied for large throughput screenings to support the main toxic compounds identification in water quality assessment.
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Affiliation(s)
- Ying Shao
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany; UFZ - Helmholtz Centre for Environmental Research GmbH, Department of Cell Toxicology, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Hongxia Xiao
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Carolina Di Paolo
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Björn Deutschmann
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Werner Brack
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany; UFZ - Helmholtz Centre for Environmental Research GmbH, Department for Effect-Directed Analysis, Permoserstraße 15, 04318, Leipzig, Germany
| | - Henner Hollert
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany; College of Resources and Environmental Science, Chongqing University, 174 Shazheng Road Shapingba, 400044, Chongqing, China; College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping Road, 200092, Shanghai, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 200023, Nanjing, China
| | - Thomas Benjamin Seiler
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
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105
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Giardoglou P, Beis D. On Zebrafish Disease Models and Matters of the Heart. Biomedicines 2019; 7:E15. [PMID: 30823496 PMCID: PMC6466020 DOI: 10.3390/biomedicines7010015] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/23/2019] [Accepted: 02/26/2019] [Indexed: 12/18/2022] Open
Abstract
Coronary artery disease (CAD) is the leading form of cardiovascular disease (CVD), which is the primary cause of mortality worldwide. It is a complex disease with genetic and environmental risk factor contributions. Reports in human and mammalian models elucidate age-associated changes in cardiac function. The diverse mechanisms involved in cardiac diseases remain at the center of the research interest to identify novel strategies for prevention and therapy. Zebrafish (Danio rerio) have emerged as a valuable vertebrate model to study cardiovascular development over the last few decades. The facile genetic manipulation via forward and reverse genetic approaches combined with noninvasive, high-resolution imaging and phenotype-based screening has provided new insights to molecular pathways that orchestrate cardiac development. Zebrafish can recapitulate human cardiac pathophysiology due to gene and regulatory pathways conservation, similar heart rate and cardiac morphology and function. Thus, generations of zebrafish models utilize the functional analysis of genes involved in CAD, which are derived from large-scale human population analysis. Here, we highlight recent studies conducted on cardiovascular research focusing on the benefits of the combination of genome-wide association studies (GWAS) with functional genomic analysis in zebrafish. We further summarize the knowledge obtained from zebrafish studies that have demonstrated the architecture of the fundamental mechanisms underlying heart development, homeostasis and regeneration at the cellular and molecular levels.
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Affiliation(s)
- Panagiota Giardoglou
- Zebrafish Disease Models Lab, Center for Clinical Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, 11527 Athens, Greece.
- School of Health Science and Education, Harokopio University, 17676 Athens, Greece.
| | - Dimitris Beis
- Zebrafish Disease Models Lab, Center for Clinical Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, 11527 Athens, Greece.
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106
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Johnson CA. Obituary: Jarema Malicki (1965-2019). Development 2019. [DOI: 10.1242/dev.176677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Jarema Malicki, a pioneer in developmental studies of the vertebrate retina, died on 4th January 2019, shortly after being diagnosed with cancer. Here, I reflect on Jarema's life and work, with a particular focus on his research interests in zebrafish as a model organism for vertebrate retinogenesis and human ciliopathies.
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Affiliation(s)
- Colin A. Johnson
- Leeds Institute of Medical Research, The University of Leeds, Wellcome Trust Brenner Building, Beckett Street, Leeds LS9 7TF, UK
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107
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Bisht S, Feldmann G. Animal models for modeling pancreatic cancer and novel drug discovery. Expert Opin Drug Discov 2019; 14:127-142. [DOI: 10.1080/17460441.2019.1566319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Savita Bisht
- Department of Internal Medicine 3, University Hospital of Bonn, Bonn, Germany
| | - Georg Feldmann
- Department of Internal Medicine 3, University Hospital of Bonn, Bonn, Germany
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108
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Goudarzi M, Berg K, Pieper LM, Schier AF. Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility. eLife 2019; 8:40815. [PMID: 30620332 PMCID: PMC6347452 DOI: 10.7554/elife.40815] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 01/08/2019] [Indexed: 12/28/2022] Open
Abstract
Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyrano and squint) and other conserved lncRNAs (gas5 and lnc-setd1ba) were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs have no overt roles in embryogenesis, viability and fertility.
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Affiliation(s)
- Mehdi Goudarzi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Kathryn Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Lindsey M Pieper
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Center for Brain Science, Harvard University, Cambridge, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, United States.,Biozentrum, University of Basel, Basel, Switzerland
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109
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Genome Editing in Zebrafish Using CRISPR-Cas9: Applications for Developmental Toxicology. Methods Mol Biol 2019; 1965:235-250. [PMID: 31069679 DOI: 10.1007/978-1-4939-9182-2_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Environment-gene interactions have a powerful impact on embryo development. The ability to precisely edit the genome makes it possible to address questions concerning the specific roles that genes or variants play in modulating the response to environmental challenges. In this chapter, we provide a simplified protocol using CRISPR-Cas9 ribonucleoproteins for genome editing in the zebrafish model organism. The genetic manipulation can then be coupled with chemical screens to identify and understand the mechanism behind toxicants or compounds that modulate development.
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110
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Experimental Manipulation of Ploidy in Zebrafish Embryos and Its Application in Genetic Screens. Methods Mol Biol 2019; 1920:111-128. [PMID: 30737689 DOI: 10.1007/978-1-4939-9009-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Metazoan animals are typically diploid, possessing two sets of a chromosome in the somatic cells of an organism. In naturally diploid species, alteration from the endogenous diploid state is usually embryonic lethal. However, the ability to experimentally manipulate ploidy of animal embryos has fundamental as well as applied biology advantages. In this chapter we describe experimental procedures to convert normally diploid zebrafish embryos into haploid or tetraploid states. We also describe methodologies to verify the ploidy of embryos and the utility of ploidy manipulation in expediting the isolation of mutations using both forward and reverse genetic strategies in zebrafish.
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111
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Zebrafish disease models in hematology: Highlights on biological and translational impact. Biochim Biophys Acta Mol Basis Dis 2018; 1865:620-633. [PMID: 30593895 DOI: 10.1016/j.bbadis.2018.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023]
Abstract
Zebrafish (Danio rerio) has proven to be a versatile and reliable in vivo experimental model to study human hematopoiesis and hematological malignancies. As vertebrates, zebrafish has significant anatomical and biological similarities to humans, including the hematopoietic system. The powerful genome editing and genome-wide forward genetic screening tools have generated models that recapitulate human malignant hematopoietic pathologies in zebrafish and unravel cellular mechanisms involved in these diseases. Moreover, the use of zebrafish models in large-scale chemical screens has allowed the identification of new molecular targets and the design of alternative therapies. In this review we summarize the recent achievements in hematological research that highlight the power of the zebrafish model for discovery of new therapeutic molecules. We believe that the model is ready to give an immediate translational impact into the clinic.
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112
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Mukherjee K, Liao EC. Generation and characterization of a zebrafish muscle specific inducible Cre line. Transgenic Res 2018; 27:559-569. [PMID: 30353407 PMCID: PMC6364321 DOI: 10.1007/s11248-018-0098-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/01/2018] [Indexed: 01/18/2023]
Abstract
Zebrafish transgenic lines provide valuable insights into gene functions, cell lineages and cell behaviors during development. Spatiotemporal control over transgene expression is a critical need in many experimental approaches, with applications in loss- and gain-of-function expression, ectopic expression and lineage tracing experiments. The Cre/loxP recombination system is a powerful tool to provide this control and the demand for validated Cre and loxP zebrafish transgenics is high. One of the major challenges to widespread application of Cre/loxP technology in zebrafish is comparatively small numbers of established tissue-specific Cre or CreERT2 lines. We used Tol2-mediated transgenesis to generate Tg(CrymCherry;-1.9mylz2:CreERT2) which provides an inducible CreERT2 source driven by muscle-specific mylz2 promoter. The transgenic specifically labels the trunk and tail skeletal muscles. We assessed the temporal responsiveness of the transgenic by screening with a validated loxP reporter transgenic ubi:Switch. Further, we evaluated the recombination efficiency in the transgenic with varying concentrations of 4-OHT, for different induction time periods and at different stages of embryogenesis and observed that higher recombination efficiency is achieved when embryos are induced with 10 μM 4-OHT from 10-somites or 24 hpf till 48 or 72 hpf. The transgenic is an addition to currently available zebrafish transgenesis toolbox and a significant tool to advance muscle biology studies in zebrafish.
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Affiliation(s)
- Kusumika Mukherjee
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
| | - Eric C Liao
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA.
- Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA.
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113
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Fuentes R, Letelier J, Tajer B, Valdivia LE, Mullins MC. Fishing forward and reverse: Advances in zebrafish phenomics. Mech Dev 2018; 154:296-308. [PMID: 30130581 PMCID: PMC6289646 DOI: 10.1016/j.mod.2018.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/06/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022]
Abstract
Understanding how the genome instructs the phenotypic characteristics of an organism is one of the major scientific endeavors of our time. Advances in genetics have progressively deciphered the inheritance, identity and biological relevance of genetically encoded information, contributing to the rise of several, complementary omic disciplines. One of them is phenomics, an emergent area of biology dedicated to the systematic multi-scale analysis of phenotypic traits. This discipline provides valuable gene function information to the rapidly evolving field of genetics. Current molecular tools enable genome-wide analyses that link gene sequence to function in multi-cellular organisms, illuminating the genome-phenome relationship. Among vertebrates, zebrafish has emerged as an outstanding model organism for high-throughput phenotyping and modeling of human disorders. Advances in both systematic mutagenesis and phenotypic analyses of embryonic and post-embryonic stages in zebrafish have revealed the function of a valuable collection of genes and the general structure of several complex traits. In this review, we summarize multiple large-scale genetic efforts addressing parental, embryonic, and adult phenotyping in the zebrafish. The genetic and quantitative tools available in the zebrafish model, coupled with the broad spectrum of phenotypes that can be assayed, make it a powerful model for phenomics, well suited for the dissection of genotype-phenotype associations in development, physiology, health and disease.
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Affiliation(s)
- Ricardo Fuentes
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joaquín Letelier
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Seville, Spain; Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Benjamin Tajer
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonardo E Valdivia
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
| | - Mary C Mullins
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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114
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Menon T, Nair S. Transient window of resilience during early development minimizes teratogenic effects of heat in zebrafish embryos. Dev Dyn 2018; 247:992-1004. [PMID: 29806169 PMCID: PMC6099245 DOI: 10.1002/dvdy.24640] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 03/13/2018] [Accepted: 05/12/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Transient heat shock during early development is an established experimental paradigm for doubling the genome of the zebrafish zygote, which has practical applications in expedited identification of recessive mutations in genetic screens. Despite the simplicity of the strategy and the genetic tractability of zebrafish, heat shock has not been used for genome doubling since the proof‐of‐principle experiments done in the 1980s. This is because of poor survival of embryos that ensue from transient heat shocks and gross developmental abnormalities in the few survivors, which is incompatible with phenotype driven screens. Results: We show that heat shocks during early zebrafish development uncouple the second cycle of DNA and centrosome duplication. Interestingly, the developmental time of the heat shock that triggers the dissociation between DNA and centrosome duplication cycles significantly affect the potential of embryos to survive and attain normal morphology. The potential to develop normally after a heat shock alters in a developmental time span of 2 min in zebrafish embryos, a phenomenon that has not been reported in any species. Conclusions: The existence of heat resilient developmental windows and reduced heat teratogenicity during these windows could be an effective step forward in practical application of transient heat for experimental manipulation of ploidy in zebrafish. More broadly, heat resilience before zygotic genome activation suggests that metazoan embryos may possess innate protective features against heat beyond the canonical heat shock response. Developmental Dynamics 247:992–1004, 2018. © 2018 Wiley Periodicals, Inc. Zebrafish embryos at the end of pronuclear fusion and before initiation of zygotic mitosis are resistant to teratogenic effects of heat. The teratogenic heat resilient window exists transiently during the maternally controlled phase of development. Heat shock during the teratogenic heat resilient window enables generation of morphologically normal zebrafish tetraploids. Diploidization of haploids by transient heat shocks during the teratogenic heat resilient windows aids in effective generation of gynogenic diploids.
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Affiliation(s)
- Triveni Menon
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Sreelaja Nair
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
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115
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Burg L, Palmer N, Kikhi K, Miroshnik ES, Rueckert H, Gaddy E, MacPherson Cunningham C, Mattonet K, Lai SL, Marín-Juez R, Waring RB, Stainier DYR, Balciunas D. Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish. PLoS Genet 2018; 14:e1007754. [PMID: 30427827 PMCID: PMC6261631 DOI: 10.1371/journal.pgen.1007754] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 11/28/2018] [Accepted: 10/10/2018] [Indexed: 02/07/2023] Open
Abstract
Many eukaryotic genes play essential roles in multiple biological processes in several different tissues. Conditional mutants are needed to analyze genes with such pleiotropic functions. In vertebrates, conditional gene inactivation has only been feasible in the mouse, leaving other model systems to rely on surrogate experimental approaches such as overexpression of dominant negative proteins and antisense-based tools. Here, we have developed a simple and straightforward method to integrate loxP sequences at specific sites in the zebrafish genome using the CRISPR/Cas9 technology and oligonucleotide templates for homology directed repair. We engineered conditional (floxed) mutants of tbx20 and fleer, and demonstrate excision of exons flanked by loxP sites using tamoxifen-inducible CreERT2 recombinase. To demonstrate broad applicability of our method, we also integrated loxP sites into two additional genes, aldh1a2 and tcf21. The ease of this approach will further expand the use of zebrafish to study various aspects of vertebrate biology, especially post-embryonic processes such as regeneration. Some genes are expressed and function in a single tissue, and the effect of their loss on that tissue can be readily determined. Frequently, however, genes that are necessary for the development or maintenance of one tissue are also important for other tissues or cell types. Genes of the latter type are difficult to analyze because of the complications resulting from an organism having multiple defects in different tissues. The solution pioneered by mouse geneticists is to inactivate the gene of interest in only one tissue at a time. This elegant approach requires the ability to make specific edits to the genome, a technology that was not readily available to zebrafish researchers until recently. Using the CRISPR/Cas9 genome editing tool, we have developed a simple, reliable, and efficient method to insert DNA sequences into the zebrafish genome that enable conditional gene inactivation. Our methodology will be useful not only for the study of genes that play important roles in multiple tissues, but also for the genetic analysis of biological processes which occur in adult animals.
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Affiliation(s)
- Leonard Burg
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Nicholas Palmer
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Khrievono Kikhi
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Evgeniya S. Miroshnik
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Helen Rueckert
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Eleanor Gaddy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Carlee MacPherson Cunningham
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Kenny Mattonet
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Shih-Lei Lai
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Rubén Marín-Juez
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Richard B. Waring
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Darius Balciunas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Jiang H, Newman M, Lardelli M. The zebrafish orthologue of familial Alzheimer's disease gene PRESENILIN 2 is required for normal adult melanotic skin pigmentation. PLoS One 2018; 13:e0206155. [PMID: 30359395 PMCID: PMC6201934 DOI: 10.1371/journal.pone.0206155] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/07/2018] [Indexed: 12/25/2022] Open
Abstract
Alzheimer's disease is the most common form of age-related dementia. At least 15 mutations in the human gene PRESENILIN 2 (PSEN2) have been found to cause familial Alzheimer's disease (fAD). Zebrafish possess an orthologous gene, psen2, and present opportunities for investigation of PRESENILIN function related to Alzheimer's disease. The most prevalent and best characterized fAD mutation in PSEN2 is N141I. The equivalent codon in zebrafish psen2 is N140. We used genome editing technology in zebrafish to target generation of mutations to the N140 codon. We isolated two mutations: psen2N140fs, (hereafter "N140fs"), causing truncation of the coding sequence, and psen2T141_L142delinsMISLISV, (hereafter "T141_L142delinsMISLISV"), that deletes the two codons immediately downstream of N140 and replaces them with seven codons coding for amino acid residues MISLISV. Thus, like almost every fAD mutation in the PRESENILIN genes, this latter mutation does not truncate the gene's open reading frame. Both mutations are homozygous viable although N140fs transcripts are subject to nonsense-mediated decay and lack any possibility of coding for an active γ-secretase enzyme. N140fs homozygous larvae initially show grossly normal melanotic skin pigmentation but subsequently lose this as they grow while retaining pigmentation in the retinal pigmented epithelium. T141_L142delinsMISLISV homozygotes retain faint skin melanotic pigmentation as adults, most likely indicating that the protein encoded by this allele retains weak γ-secretase activity. Null mutations in the human PRESENILIN genes do not cause Alzheimer's disease so these two mutations may be useful for future investigation of the differential effects of null and fAD-like PRESENILIN mutations on brain aging.
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Affiliation(s)
- Haowei Jiang
- University of Adelaide, School of Biological Sciences, Alzheimer’s Disease Genetics Laboratory, North Terrace, Adelaide, South Australia, Australia
| | - Morgan Newman
- University of Adelaide, School of Biological Sciences, Alzheimer’s Disease Genetics Laboratory, North Terrace, Adelaide, South Australia, Australia
| | - Michael Lardelli
- University of Adelaide, School of Biological Sciences, Alzheimer’s Disease Genetics Laboratory, North Terrace, Adelaide, South Australia, Australia
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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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Lee W, Kim EA, Um JH, Kang N, Oh JY, Park SY, Han EJ, Cheong SH, Chang KJ, Kim SH, Ahn CB, Jeon YJ, Ahn G. Protective Effects of Xylose-Taurine Reduced against Damages Caused by Oxidative Stress in Zebrafish Embryos In Vivo Model. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 975 Pt 1:643-653. [PMID: 28849488 DOI: 10.1007/978-94-024-1079-2_50] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The zebrafish (Danio rerio) is useful and convenient vertebrate models in various studies in human disease and drug discovery. In this present study, we first evaluated whether Xylose-Taurine reduced (X-T-R), a taurine derivate protects zebrafish embryos against oxidative stress caused by AAPH (2,2'-Azobis(2-amidinopropane) dihydrochloride). First of all, we selected the concentration of X-T-R showing no toxicity in zebrafish embryos. We identified that X-T-R significantly increased the survival of zebrafish embryo reduced by treatment of AAPH. Also, X-T-R effectively inhibited the productions of reactive oxygen species (ROS) and nitric oxide (NO) as well as the formation of cell death in zebrafish embryos. Moreover, X-T-R down-regulated the expression levels of Bax, caspase-3, caspase-9 and p53 known as pro-apoptotic molecules, whereas up-regulated those of Bcl-2, an anti-apoptotic molecule in AAPH-treated zebrafish embryos. From these results, this study reveals that X-T-R, a taurine derivate might be a potential protector against various damages caused by oxidative stress.
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Affiliation(s)
- WonWoo Lee
- Department of Marine Life Science, Jeju National University, Jeju, Republic of Korea
| | - Eun-A Kim
- Jeju International Marine Science Center for Research and Education, Korea Institute of Ocean Science & Technology (KIOST), Jeju, Republic of Korea
| | - Ju Hyung Um
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu, Republic of Korea
| | - Nalae Kang
- Department of Marine Bio-Food Sciences, Chonnam National University, Yeosu, Republic of Korea
| | - Jae Young Oh
- Department of Marine Life Science, Jeju National University, Jeju, Republic of Korea
| | - Soo Yeon Park
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu, Republic of Korea
| | - Eui Jeong Han
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu, Republic of Korea
| | - Sun Hee Cheong
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu, Republic of Korea
- Department of Marine Bio-Food Sciences, Chonnam National University, Yeosu, Republic of Korea
| | - Kyung Ja Chang
- Department of Food and Nutrition, Inha University, Incheon, Republic of Korea
| | - Sung Hoon Kim
- Department of Chemistry, Konkuk University, Seoul, Republic of Korea
| | - Chang-Bum Ahn
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu, Republic of Korea
| | - You-Jin Jeon
- Department of Marine Life Science, Jeju National University, Jeju, Republic of Korea.
| | - Ginnae Ahn
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu, Republic of Korea.
- Department of Marine Bio-Food Sciences, Chonnam National University, Yeosu, Republic of Korea.
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119
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How Surrogate and Chemical Genetics in Model Organisms Can Suggest Therapies for Human Genetic Diseases. Genetics 2018; 208:833-851. [PMID: 29487144 PMCID: PMC5844338 DOI: 10.1534/genetics.117.300124] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/26/2017] [Indexed: 12/12/2022] Open
Abstract
Genetic diseases are both inherited and acquired. Many genetic diseases fall under the paradigm of orphan diseases, a disease found in < 1 in 2000 persons. With rapid and cost-effective genome sequencing becoming the norm, many causal mutations for genetic diseases are being rapidly determined. In this regard, model organisms are playing an important role in validating if specific mutations identified in patients drive the observed phenotype. An emerging challenge for model organism researchers is the application of genetic and chemical genetic platforms to discover drug targets and drugs/drug-like molecules for potential treatment options for patients with genetic disease. This review provides an overview of how model organisms have contributed to our understanding of genetic disease, with a focus on the roles of yeast and zebrafish in gene discovery and the identification of compounds that could potentially treat human genetic diseases.
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120
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Rayani K, Lin E, Craig C, Lamothe M, Shafaattalab S, Gunawan M, Li AY, Hove-Madsen L, Tibbits GF. Zebrafish as a model of mammalian cardiac function: Optically mapping the interplay of temperature and rate on voltage and calcium dynamics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 138:69-90. [DOI: 10.1016/j.pbiomolbio.2018.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/27/2022]
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Bhattacharya M, Ghosh S, Malick RC, Patra BC, Das BK. Therapeutic applications of zebrafish (Danio rerio) miRNAs linked with human diseases: A prospective review. Gene 2018; 679:202-211. [PMID: 30201335 DOI: 10.1016/j.gene.2018.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/31/2018] [Accepted: 09/06/2018] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are the class of small, non-coding RNAs that are produced from precursor transcripts by subsequent processing steps mediated by members of the RNaseIII family, Dicer and Drosha protein within cell. The importance of zebrafish miRNAs in regulation of normal cellular development and support to various kinds of metabolism process. Although the zebrafish model provides a fundamental platform for the study of developmental biology but recent work with zebrafish model has expanded its appliance to a broad range of experimental studies relevant to different kind of human diseases. Presently, the zebrafish model is used for the study of cardiovascular disease, schizophrenia, bipolar I disorder in eyes, psoriasis, spinal cord injury, cancer and diabetes that showing in some selected miRNAs are regulate these diseases in molecular levels. Here, a superior drive performed to depict the fundamental utilization of the zebrafish miRNAs that targeted to several clinical diseases connected to human. This review aims to provide a summary of understanding of the cellular mechanism which is responsible for selected diseases and suggests some therapeutic application for inhibition of miRNA functions.
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Affiliation(s)
- Manojit Bhattacharya
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Soumendu Ghosh
- Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Ramesh Chandra Malick
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Bidhan Chandra Patra
- Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700 120, West Bengal, India.
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122
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Demin KA, Meshalkina DA, Kysil EV, Antonova KA, Volgin AD, Yakovlev OA, Alekseeva PA, Firuleva MM, Lakstygal AM, de Abreu MS, Barcellos LJG, Bao W, Friend AJ, Amstislavskaya TG, Rosemberg DB, Musienko PE, Song C, Kalueff AV. Zebrafish models relevant to studying central opioid and endocannabinoid systems. Prog Neuropsychopharmacol Biol Psychiatry 2018; 86:301-312. [PMID: 29604314 DOI: 10.1016/j.pnpbp.2018.03.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 12/19/2022]
Abstract
The endocannabinoid and opioid systems are two interplaying neurotransmitter systems that modulate drug abuse, anxiety, pain, cognition, neurogenesis and immune activity. Although they are involved in such critical functions, our understanding of endocannabinoid and opioid physiology remains limited, necessitating further studies, novel models and new model organisms in this field. Zebrafish (Danio rerio) is rapidly emerging as one of the most effective translational models in neuroscience and biological psychiatry. Due to their high physiological and genetic homology to humans, zebrafish may be effectively used to study the endocannabinoid and opioid systems. Here, we discuss current models used to target the endocannabinoid and opioid systems in zebrafish, and their potential use in future translational research and high-throughput drug screening. Emphasizing the high degree of conservation of the endocannabinoid and opioid systems in zebrafish and mammals, we suggest zebrafish as an excellent model organism to study these systems and to search for the new drugs and therapies targeting their evolutionarily conserved mechanisms.
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Affiliation(s)
- Konstantin A Demin
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia; Laboratory of Preclinical Bioscreening, Russian Research Center for Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia
| | - Darya A Meshalkina
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia; Laboratory of Preclinical Bioscreening, Russian Research Center for Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia
| | - Elana V Kysil
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Kristina A Antonova
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey D Volgin
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Medical Military Academy, St. Petersburg, Russia
| | - Oleg A Yakovlev
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Medical Military Academy, St. Petersburg, Russia
| | - Polina A Alekseeva
- Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Maria M Firuleva
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton M Lakstygal
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo (UPF), Passo Fundo, RS, Brazil; Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Leonardo J G Barcellos
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Brazil; Graduate Programs in Environmental Sciences, and Bio-Experimentation, University of Passo Fundo (UPF), Passo Fundo, Brazil; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Wandong Bao
- School of Pharmacy, Southwest University, Chongqing, China
| | - Ashton J Friend
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Tamara G Amstislavskaya
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Laboratory of Translational Biopsychiatry, Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; Neuroscience Department, Novosibirsk State University, Novosibirsk, Russia
| | - Denis B Rosemberg
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Pavel E Musienko
- Laboratory of Neuroprosthetics, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Laboratory of Motor Physiology, Pavlov Institute of Physiology RAS, St. Petersburg, Russia; Laboratory of Neurophysiology and Experimental Neurorehabilitation, St. Petersburg State Research Institute of Phthysiopulmonology, Ministry of Health, St. Petersburg, Russia; Russian Research Center of Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia
| | - Cai Song
- Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, China; Marine Medicine Research and Development Center, Shenzhen Institute of Guangdong Ocean University, Shenzhen, China
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China; Laboratory of Translational Biopsychiatry, Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; Neuroscience Department, Novosibirsk State University, Novosibirsk, Russia; ZENEREI Research Center, Slidell, LA, USA; Russian Research Center of Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia; Ural Federal University, Ekaterinburg, Russia; Aquatic Laboratory, Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia.
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123
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Unal Eroglu A, Mulligan TS, Zhang L, White DT, Sengupta S, Nie C, Lu NY, Qian J, Xu L, Pei W, Burgess SM, Saxena MT, Mumm JS. Multiplexed CRISPR/Cas9 Targeting of Genes Implicated in Retinal Regeneration and Degeneration. Front Cell Dev Biol 2018; 6:88. [PMID: 30186835 PMCID: PMC6111214 DOI: 10.3389/fcell.2018.00088] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/25/2018] [Indexed: 01/28/2023] Open
Abstract
Thousands of genes have been implicated in retinal regeneration, but only a few have been shown to impact the regenerative capacity of Müller glia—an adult retinal stem cell with untapped therapeutic potential. Similarly, among nearly 300 genetic loci associated with human retinal disease, the majority remain untested in animal models. To address the large-scale nature of these problems, we are applying CRISPR/Cas9-based genome modification strategies in zebrafish to target over 300 genes implicated in retinal regeneration or degeneration. Our intent is to enable large-scale reverse genetic screens by applying a multiplexed gene disruption strategy that markedly increases the efficiency of the screening process. To facilitate large-scale phenotyping, we incorporate an automated reporter quantification-based assay to identify cellular degeneration and regeneration-deficient phenotypes in transgenic fish. Multiplexed gene targeting strategies can address mismatches in scale between “big data” bioinformatics and wet lab experimental capacities, a critical shortfall limiting comprehensive functional analyses of factors implicated in ever-expanding multiomics datasets. This report details the progress we have made to date with a multiplexed CRISPR/Cas9-based gene targeting strategy and discusses how the methodologies applied can further our understanding of the genes that predispose to retinal degenerative disease and which control the regenerative capacity of retinal Müller glia cells.
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Affiliation(s)
- Arife Unal Eroglu
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David T White
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sumitra Sengupta
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cathy Nie
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Noela Y Lu
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lisha Xu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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124
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Dupret B, Völkel P, Follet P, Le Bourhis X, Angrand PO. Combining genotypic and phenotypic analyses on single mutant zebrafish larvae. MethodsX 2018; 5:244-256. [PMID: 30090702 PMCID: PMC6078847 DOI: 10.1016/j.mex.2018.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/09/2018] [Indexed: 01/22/2023] Open
Abstract
Zebrafish is a powerful animal model used to study vertebrate embryogenesis, organ development and diseases (Gut et al., 2017) [1]. The usefulness of the model was established as a result of various large forward genetic screens identifying mutants in almost every organ or cell type (Driever et al., 1996; Haffter et al., 1996) [[2], [3]]. More recently, the advent of genome editing methodologies, including TALENs (Sander et al., 2011) [4] and the CRISPR/Cas9 technology (Hwang et al., 2013) [5], led to an increase in the production of zebrafish mutants. A number of these mutations are homozygous lethal at the embryonic or larval stages preventing the generation of homozygous mutant zebrafish lines. Here, we present a method allowing both genotyping and phenotype analyses of mutant zebrafish larvae from heterozygous zebrafish incrosses. The procedure is based on the genotyping of the larval tail after transection, whereas phenotypic studies are performed on the anterior part of the zebrafish larvae. The method includes (i) a protocol for genotyping, (ii) protocols for paraffin embedding and histological analyses, (iii) protocols for protein and histone extraction and characterization by Western blot, (iv) protocols for RNA extraction and characterization by RT-PCR, and (v) protocols to study caudal spinal cord regeneration. The technique is optimized in order to be applied on single zebrafish embryos and larvae.
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Affiliation(s)
- Barbara Dupret
- Inserm U908, Cell Plasticity & Cancer, Lille, France
- University of Lille, Lille, France
| | - Pamela Völkel
- Inserm U908, Cell Plasticity & Cancer, Lille, France
- University of Lille, Lille, France
- CNRS, Lille, France
| | - Pauline Follet
- Inserm U908, Cell Plasticity & Cancer, Lille, France
- University of Lille, Lille, France
- FRABio, CNRS FR3688, Lille, France
- SIRIC ONCOLille, Lille, France
| | - Xuefen Le Bourhis
- Inserm U908, Cell Plasticity & Cancer, Lille, France
- University of Lille, Lille, France
| | - Pierre-Olivier Angrand
- Inserm U908, Cell Plasticity & Cancer, Lille, France
- University of Lille, Lille, France
- Corresponding author at: Cell Plasticity & Cancer, Inserm U908/University of Lille, Bâtiment SN3, Cité Scientifique, F-59655 Villeneuve d’Ascq, France.
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125
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Nowak-Sliwinska P, Alitalo K, Allen E, Anisimov A, Aplin AC, Auerbach R, Augustin HG, Bates DO, van Beijnum JR, Bender RHF, Bergers G, Bikfalvi A, Bischoff J, Böck BC, Brooks PC, Bussolino F, Cakir B, Carmeliet P, Castranova D, Cimpean AM, Cleaver O, Coukos G, Davis GE, De Palma M, Dimberg A, Dings RPM, Djonov V, Dudley AC, Dufton NP, Fendt SM, Ferrara N, Fruttiger M, Fukumura D, Ghesquière B, Gong Y, Griffin RJ, Harris AL, Hughes CCW, Hultgren NW, Iruela-Arispe ML, Irving M, Jain RK, Kalluri R, Kalucka J, Kerbel RS, Kitajewski J, Klaassen I, Kleinmann HK, Koolwijk P, Kuczynski E, Kwak BR, Marien K, Melero-Martin JM, Munn LL, Nicosia RF, Noel A, Nurro J, Olsson AK, Petrova TV, Pietras K, Pili R, Pollard JW, Post MJ, Quax PHA, Rabinovich GA, Raica M, Randi AM, Ribatti D, Ruegg C, Schlingemann RO, Schulte-Merker S, Smith LEH, Song JW, Stacker SA, Stalin J, Stratman AN, Van de Velde M, van Hinsbergh VWM, Vermeulen PB, Waltenberger J, Weinstein BM, Xin H, Yetkin-Arik B, Yla-Herttuala S, Yoder MC, Griffioen AW. Consensus guidelines for the use and interpretation of angiogenesis assays. Angiogenesis 2018; 21:425-532. [PMID: 29766399 PMCID: PMC6237663 DOI: 10.1007/s10456-018-9613-x] [Citation(s) in RCA: 419] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference.
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Affiliation(s)
- Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, Faculty of Sciences, University of Geneva, University of Lausanne, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland.
- Translational Research Center in Oncohaematology, University of Geneva, Geneva, Switzerland.
| | - Kari Alitalo
- Wihuri Research Institute and Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Elizabeth Allen
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, Department of Oncology, VIB-Center for Cancer Biology, KU Leuven, Louvain, Belgium
| | - Andrey Anisimov
- Wihuri Research Institute and Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Alfred C Aplin
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Hellmut G Augustin
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - David O Bates
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Judy R van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - R Hugh F Bender
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Gabriele Bergers
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, Department of Oncology, VIB-Center for Cancer Biology, KU Leuven, Louvain, Belgium
- Department of Neurological Surgery, Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Andreas Bikfalvi
- Angiogenesis and Tumor Microenvironment Laboratory (INSERM U1029), University Bordeaux, Pessac, France
| | - Joyce Bischoff
- Vascular Biology Program and Department of Surgery, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Barbara C Böck
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Peter C Brooks
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME, USA
| | - Federico Bussolino
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO-IRCCS, 10060, Candiolo, Italy
| | - Bertan Cakir
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Daniel Castranova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anca M Cimpean
- Department of Microscopic Morphology/Histology, Angiogenesis Research Center, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Ondine Cleaver
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - George E Davis
- Department of Medical Pharmacology and Physiology, University of Missouri, School of Medicine and Dalton Cardiovascular Center, Columbia, MO, USA
| | - Michele De Palma
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ruud P M Dings
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Andrew C Dudley
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA
- Emily Couric Cancer Center, The University of Virginia, Charlottesville, VA, USA
| | - Neil P Dufton
- Vascular Sciences, Imperial Centre for Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute, Leuven, Belgium
| | | | - Marcus Fruttiger
- Institute of Ophthalmology, University College London, London, UK
| | - Dai Fukumura
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, Metabolomics Expertise Center, KU Leuven, Leuven, Belgium
| | - Yan Gong
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Robert J Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Adrian L Harris
- Molecular Oncology Laboratories, Oxford University Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Christopher C W Hughes
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Nan W Hultgren
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | | | - Melita Irving
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Rakesh K Jain
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Robert S Kerbel
- Department of Medical Biophysics, Biological Sciences Platform, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Jan Kitajewski
- Department of Physiology and Biophysics, University of Illinois, Chicago, IL, USA
| | - Ingeborg Klaassen
- Ocular Angiogenesis Group, Departments of Ophthalmology and Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hynda K Kleinmann
- The George Washington University School of Medicine, Washington, DC, USA
| | - Pieter Koolwijk
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Elisabeth Kuczynski
- Department of Medical Biophysics, Biological Sciences Platform, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Brenda R Kwak
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | | | - Juan M Melero-Martin
- Department of Cardiac Surgery, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Lance L Munn
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Roberto F Nicosia
- Department of Pathology, University of Washington, Seattle, WA, USA
- Pathology and Laboratory Medicine Service, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Agnes Noel
- Laboratory of Tumor and Developmental Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Jussi Nurro
- Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Anna-Karin Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Tatiana V Petrova
- Department of oncology UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund, Sweden
| | - Roberto Pili
- Genitourinary Program, Indiana University-Simon Cancer Center, Indianapolis, IN, USA
| | - Jeffrey W Pollard
- Medical Research Council Centre for Reproductive Health, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Mark J Post
- Department of Physiology, Maastricht University, Maastricht, The Netherlands
| | - Paul H A Quax
- Einthoven Laboratory for Experimental Vascular Medicine, Department Surgery, LUMC, Leiden, The Netherlands
| | - Gabriel A Rabinovich
- Laboratory of Immunopathology, Institute of Biology and Experimental Medicine, National Council of Scientific and Technical Investigations (CONICET), Buenos Aires, Argentina
| | - Marius Raica
- Department of Microscopic Morphology/Histology, Angiogenesis Research Center, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Anna M Randi
- Vascular Sciences, Imperial Centre for Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Medical School, Bari, Italy
- National Cancer Institute "Giovanni Paolo II", Bari, Italy
| | - Curzio Ruegg
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Reinier O Schlingemann
- Ocular Angiogenesis Group, Departments of Ophthalmology and Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Stefan Schulte-Merker
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU, Münster, Germany
| | - Lois E H Smith
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan W Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Steven A Stacker
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre and The Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jimmy Stalin
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU, Münster, Germany
| | - Amber N Stratman
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Maureen Van de Velde
- Laboratory of Tumor and Developmental Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Victor W M van Hinsbergh
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Peter B Vermeulen
- HistoGeneX, Antwerp, Belgium
- Translational Cancer Research Unit, GZA Hospitals, Sint-Augustinus & University of Antwerp, Antwerp, Belgium
| | - Johannes Waltenberger
- Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, Münster, Germany
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Hong Xin
- University of California, San Diego, La Jolla, CA, USA
| | - Bahar Yetkin-Arik
- Ocular Angiogenesis Group, Departments of Ophthalmology and Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Seppo Yla-Herttuala
- Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mervin C Yoder
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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Naert T, Vleminckx K. CRISPR/Cas9 disease models in zebrafish and Xenopus: The genetic renaissance of fish and frogs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 28:41-52. [PMID: 30205880 DOI: 10.1016/j.ddtec.2018.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 12/11/2022]
Abstract
The speed by which clinical genomics is currently identifying novel potentially pathogenic variants is outperforming the speed by which these can be functionally (genotype-phenotype) annotated in animal disease models. However, over the past few years the emergence of CRISPR/Cas9 as a straight-forward genome editing technology has revolutionized disease modeling in vertebrate non-mammalian model organisms such as zebrafish, medaka and Xenopus. It is now finally possible, by CRISPR/Cas9, to rapidly establish clinically relevant disease models in these organisms. Interestingly, these can provide both cost-effective genotype-phenotype correlations for gene-(variants) and genomic rearrangements obtained from clinical practice, as well as be exploited to perform translational research to improve prospects of disease afflicted patients. In this review, we show an extensive overview of these new CRISPR/Cas9-mediated disease models and provide future prospects that will allow increasingly accurate modeling of human disease in zebrafish, medaka and Xenopus.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Center for Medical Genetics, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium.
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127
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Rafferty SA, Quinn TA. A beginner's guide to understanding and implementing the genetic modification of zebrafish. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 138:3-19. [PMID: 30032905 DOI: 10.1016/j.pbiomolbio.2018.07.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/07/2018] [Accepted: 07/10/2018] [Indexed: 02/05/2023]
Abstract
Zebrafish are a relevant and useful vertebrate model species to study normal- and patho-physiology, including that of the heart, due to conservation of protein-coding genes, organ system organisation and function, and efficient breeding and housing. Their amenability to genetic modification, particularly compared to other vertebrate species, is another great advantage, and is the focus of this review. A vast number of genetically engineered zebrafish lines and methods for their creation exist, but their incorporation into research programs is hindered by the overwhelming amount of technical details. The purpose of this paper is to provide a simplified guide to the fundamental information required by the uninitiated researcher for the thorough understanding, critical evaluation, and effective implementation of genetic approaches in the zebrafish. First, an overview of existing zebrafish lines generated through large scale chemical mutagenesis, retroviral insertional mutagenesis, and gene and enhancer trap screens is presented. Second, descriptions of commonly-used genetic modification methods are provided including Tol2 transposon, TALENs (transcription activator-like effector nucleases), and CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9). Lastly, design features of genetic modification strategies such as promoters, fluorescent reporters, and conditional transgenesis, are summarised. As a comprehensive resource containing both background information and technical notes of how to obtain or generate zebrafish, this review compliments existing resources to facilitate the use of genetically-modified zebrafish by researchers who are new to the field.
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Affiliation(s)
- Sara A Rafferty
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada
| | - T Alexander Quinn
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada; School of Biomedical Engineering, Dalhousie University, Halifax, Canada.
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128
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Kithcart AP, MacRae CA. Zebrafish assay development for cardiovascular disease mechanism and drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 138:126-131. [PMID: 30518489 DOI: 10.1016/j.pbiomolbio.2018.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/26/2018] [Accepted: 07/01/2018] [Indexed: 12/15/2022]
Affiliation(s)
| | - Calum A MacRae
- Brigham and Women's Hospital, Harvard Medical School, USA.
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129
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Ghosh P, Maurer JM, Sagerström CG. Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish. Neural Dev 2018; 13:13. [PMID: 29945667 PMCID: PMC6020313 DOI: 10.1186/s13064-018-0112-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous work aimed at understanding the gene regulatory networks (GRNs) governing caudal hindbrain formation identified morphogens such as Retinoic Acid (RA) and Fibroblast growth factors (FGFs), as well as transcription factors like hoxb1b, hoxb1a, hnf1ba, and valentino as being required for rhombomere (r) r4-r6 formation in zebrafish. Considering that the caudal hindbrain is relatively complex - for instance, unique sets of neurons are formed in each rhombomere segment - it is likely that additional essential genes remain to be identified and integrated into the caudal hindbrain GRN. METHODS By taking advantage of gene expression data available in the Zebrafish Information Network (ZFIN), we identified 84 uncharacterized genes that are expressed in r4-r6. We selected a representative set of 22 genes and assayed their expression patterns in hoxb1b, hoxb1a, hnf1b, and valentino mutants with the goal of positioning them in the caudal hindbrain GRN. We also investigated the effects of RA and FGF on the expression of this gene set. To examine whether these genes are necessary for r4-r6 development, we analyzed germline mutants for six of the genes (gas6, gbx1, sall4, eglf6, celf2, and greb1l) for defects in hindbrain development. RESULTS Our results reveal that r4 gene expression is unaffected by the individual loss of hoxb1b, hoxb1a or RA, but is under the combinatorial regulation of RA together with hoxb1b. In contrast, r5/r6 gene expression is dependent on RA, FGF, hnf1ba and valentino - as individual loss of these factors abolishes r5/r6 gene expression. Our analysis of six mutant lines did not reveal rhombomere or neuronal defects, but transcriptome analysis of one line (gas6 mutant) identified expression changes for genes involved in several developmental processes - suggesting that these genes may have subtle roles in hindbrain development. CONCLUSION We conclude that r4-r6 formation is relatively robust, such that very few genes are absolutely required for this process. However, there are mechanistic differences in r4 versus r5/r6, such that no single factor is required for r4 development while several genes are individually required for r5/r6 formation.
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Affiliation(s)
- Priyanjali Ghosh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA
| | - Jennifer M Maurer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA.
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Affiliation(s)
- Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United Staes of America
- * E-mail:
| | - Robert Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States America
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
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131
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Compound K Inhibits the Lipopolysaccharide-Induced Inflammatory Responses in Raw 264.7 Cell Line and Zebrafish. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8060924] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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132
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Paone C, Diofano F, Park DD, Rottbauer W, Just S. Genetics of Cardiovascular Disease: Fishing for Causality. Front Cardiovasc Med 2018; 5:60. [PMID: 29911105 PMCID: PMC5992778 DOI: 10.3389/fcvm.2018.00060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/15/2018] [Indexed: 01/08/2023] Open
Abstract
Cardiovascular disease (CVD) is still the leading cause of death in all western world countries and genetic predisposition in combination with traditional risk factors frequently mediates their manifestation. Genome-wide association (GWA) studies revealed numerous potentially disease modifying genetic loci often including several SNPs and associated genes. However, pure genetic association does not prove direct or indirect relevance of the modifier region on pathogenesis, nor does it define within the associated region the exact genetic driver of the disease. Therefore, the relevance of the identified genetic disease associations needs to be confirmed either in monogenic traits or in experimental in vivo model system by functional genomic studies. In this review, we focus on the use of functional genomic approaches such as gene knock-down or CRISPR/Cas9-mediated genome editing in the zebrafish model to validate disease-associated genomic loci and to identify novel cardiovascular disease genes. We summarize the benefits of the zebrafish for cardiovascular research and highlight examples demonstrating the successful combination of GWA studies and functional genomics in zebrafish to broaden our knowledge on the genetic and molecular underpinnings of cardiovascular diseases.
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Affiliation(s)
- Christoph Paone
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Federica Diofano
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Deung-Dae Park
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | | | - Steffen Just
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
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133
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Zebrafish Models of Rare Hereditary Pediatric Diseases. Diseases 2018; 6:diseases6020043. [PMID: 29789451 PMCID: PMC6023479 DOI: 10.3390/diseases6020043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 12/12/2022] Open
Abstract
Recent advances in sequencing technologies have made it significantly easier to find the genetic roots of rare hereditary pediatric diseases. These novel methods are not panaceas, however, and they often give ambiguous results, highlighting multiple possible causative mutations in affected patients. Furthermore, even when the mapping results are unambiguous, the affected gene might be of unknown function. In these cases, understanding how a particular genotype can result in a phenotype also needs carefully designed experimental work. Model organism genetics can offer a straightforward experimental setup for hypothesis testing. Containing orthologs for over 80% of the genes involved in human diseases, zebrafish (Danio rerio) has emerged as one of the top disease models over the past decade. A plethora of genetic tools makes it easy to create mutations in almost any gene of the zebrafish genome and these mutant strains can be used in high-throughput preclinical screens for active molecules. As this small vertebrate species offers several other advantages as well, its popularity in biomedical research is bound to increase, with “aquarium to bedside” drug development pipelines taking a more prevalent role in the near future.
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134
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Berrun A, Harris E, Stachura DL. Isthmin 1 (ism1) is required for normal hematopoiesis in developing zebrafish. PLoS One 2018; 13:e0196872. [PMID: 29758043 PMCID: PMC5951578 DOI: 10.1371/journal.pone.0196872] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/20/2018] [Indexed: 02/06/2023] Open
Abstract
Hematopoiesis is an essential and highly regulated biological process that begins with hematopoietic stem cells (HSCs). In healthy organisms, HSCs are responsible for generating a multitude of mature blood cells every day, yet the molecular pathways that instruct HSCs to self-renew and differentiate into post-mitotic blood cells are not fully known. To understand these molecular pathways, we investigated novel genes expressed in hematopoietic-supportive cell lines from the zebrafish (Danio rerio), a model system increasingly utilized to uncover molecular pathways important in the development of other vertebrate species. We performed RNA sequencing of the transcriptome of three stromal cell lines derived from different stages of embryonic and adult zebrafish and identified hundreds of highly expressed transcripts. For our studies, we focused on isthmin 1 (ism1) due to its shared synteny with its human gene ortholog and because it is a secreted protein. To characterize ism1, we performed loss-of-function experiments to identify if mature blood cell production was disrupted. Myeloid and erythroid lineages were visualized and scored with transgenic zebrafish expressing lineage-specific markers. ism1 knockdown led to reduced numbers of neutrophils, macrophages, and erythrocytes. Analysis of clonal methylcellulose assays from ism1 morphants also showed a reduction in total hematopoietic stem and progenitor cells (HSPCs). Overall, we demonstrate that ism1 is required for normal generation of HSPCs and their downstream progeny during zebrafish hematopoiesis. Further investigation into ism1 and its importance in hematopoiesis may elucidate evolutionarily conserved processes in blood formation that can be further investigated for potential clinical utility.
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Affiliation(s)
- Arturo Berrun
- Department of Biological Sciences, California State University Chico, Chico, CA, United States of America
| | - Elena Harris
- Department of Computer Sciences, California State University Chico, Chico, CA, United States of America
| | - David L Stachura
- Department of Biological Sciences, California State University Chico, Chico, CA, United States of America
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135
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Zebrafish heart failure models: opportunities and challenges. Amino Acids 2018; 50:787-798. [DOI: 10.1007/s00726-018-2578-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/24/2018] [Indexed: 01/03/2023]
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136
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Delomas TA, Dabrowski K. Larval rearing of zebrafish at suboptimal temperatures. J Therm Biol 2018; 74:170-173. [DOI: 10.1016/j.jtherbio.2018.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/02/2018] [Accepted: 03/18/2018] [Indexed: 10/17/2022]
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137
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Völkel P, Dupret B, Le Bourhis X, Angrand PO. [The zebrafish model in oncology]. Med Sci (Paris) 2018; 34:345-353. [PMID: 29658479 DOI: 10.1051/medsci/20183404016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although cell culture and mouse models will remain a cornerstone of cancer research, the unique capabilities of the zebrafish outline the potential of this model for shedding light on cancer biology in vivo. Zebrafish develops cancers spontaneously, after chemical mutagenesis or through genetic manipulations. Furthermore, zebrafish cancers are similar to human tumors at the histological and molecular levels allowing the study of tumor initiation, progression and heterogeneity. Xenotransplantation of human cancer cells in embryos or adult zebrafish presents the advantage of following cancer cell behavior in vivo. Finally, zebrafish embryos are used in molecule screens and contribute to the identification of novel anti-cancer therapeutic strategies. Here, we review different involvements of the zebrafish model in cancer research.
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Affiliation(s)
- Pamela Völkel
- CNRS Lille, Inserm U908, Université de Lille, Bâtiment SN3, Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - Babara Dupret
- Inserm U908, Université de Lille, Bâtiment SN3, Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - Xuefen Le Bourhis
- Inserm U908, Université de Lille, Bâtiment SN3, Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - Pierre-Olivier Angrand
- Inserm U908, Université de Lille, Bâtiment SN3, Cité Scientifique, 59655 Villeneuve d'Ascq, France
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Calzia D, Garbarino G, Caicci F, Pestarino M, Manni L, Traverso CE, Panfoli I, Candiani S. Evidence of Oxidative Phosphorylation in Zebrafish Photoreceptor Outer Segments at Different Larval Stages. J Histochem Cytochem 2018; 66:497-509. [PMID: 29547350 DOI: 10.1369/0022155418762389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Previous studies on purified bovine rod outer segments (OS) disks pointed to Oxidative Phosphorylation (OXPHOS) as being the most likely mechanism involved in ATP production, as yet not fully understood, to support the first phototransduction steps. Bovine and murine rod OS disks, devoid of mitochondria, would house respiratory chain complexes I to IV and ATP synthase, similar to mitochondria. Zebrafish ( Danio rerio) is a well-suited animal model to study vertebrate embryogenesis as well as the retina, morphologically and functionally similar to its human counterpart. The present article reports fluorescence and Transmission Electron Microscopy colocalization analyses of respiratory complexes I and IV and ATP synthase with zpr3, the rod OS marker, in adult and larval zebrafish retinas. MitoTracker Deep Red 633 staining and assays of complexes I and III-IV activity suggest that those proteins are active in OS. Results show that an extramitochondrial aerobic metabolism is active in the zebrafish OS at 4 and 10 days of larval development, as well as in adults, suggesting that it is probably maintained during embryogenesis. Data support the hypothesis of an extramitochondrial aerobic metabolism in the OS of zebrafish.
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Affiliation(s)
- Daniela Calzia
- Department of Pharmacy-DIFAR-Biochemistry and Physiology Lab, University of Genoa, Genova, Italy
| | - Greta Garbarino
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita (DISTAV), University of Genoa, Genova, Italy
| | | | - Mario Pestarino
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita (DISTAV), University of Genoa, Genova, Italy
| | - Lucia Manni
- Department of Biology, Università di Padova, Padova, Italy
| | - Carlo Enrico Traverso
- Clinica Oculistica, (Di.N.O.G.M.I.), University of Genoa, IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genova, Italy
| | - Isabella Panfoli
- Department of Pharmacy-DIFAR-Biochemistry and Physiology Lab, University of Genoa, Genova, Italy
| | - Simona Candiani
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita (DISTAV), University of Genoa, Genova, Italy
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139
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Meshalkina DA, Kysil EV, Warnick JE, Demin KA, Kalueff AV. Adult zebrafish in CNS disease modeling: a tank that's half-full, not half-empty, and still filling. Lab Anim (NY) 2018; 46:378-387. [PMID: 28984854 DOI: 10.1038/laban.1345] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/18/2017] [Indexed: 01/17/2023]
Abstract
The zebrafish (Danio rerio) is increasingly used in a broad array of biomedical studies, from cancer research to drug screening. Zebrafish also represent an emerging model organism for studying complex brain diseases. The number of zebrafish neuroscience studies is exponentially growing, significantly outpacing those conducted with rodents or other model organisms. Yet, there is still a substantial amount of resistance in adopting zebrafish as a first-choice model system. Studies of the repertoire of zebrafish neural and behavioral functions continue to reveal new opportunities for understanding the pathobiology of various CNS deficits. Although some of these models are well established in zebrafish, including models for anxiety, depression, and addiction, others are less recognized, for example, models of autism and obsessive-compulsive states. However, mounting data indicate that a wide spectrum of CNS diseases can be modeled in adult zebrafish. Here, we summarize recent findings using zebrafish CNS assays, discuss model limitations and the existing challenges, as well as outline future directions of research in this field.
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Affiliation(s)
- Darya A Meshalkina
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.,The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, Louisiana, USA
| | - Elana V Kysil
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Jason E Warnick
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, Louisiana, USA.,Department of Behavioral Sciences, Arkansas Tech University, Russellville, Arkansas, USA
| | - Konstantin A Demin
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.,The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, Louisiana, USA
| | - Allan V Kalueff
- School of Pharmaceutical Sciences, Southwest University, Chongqing, China.,Laboratory of Biological Psychiatry, ITBM, St. Petersburg State University, St. Petersburg, Russia.,Ural Federal University, Ekaterinburg, Russia.,ZENEREI Research Center, Slidell, Louisiana, USA
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140
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Das TK, Cagan RL. Non-mammalian models of multiple endocrine neoplasia type 2. Endocr Relat Cancer 2018; 25:T91-T104. [PMID: 29348307 PMCID: PMC5935467 DOI: 10.1530/erc-17-0411] [Citation(s) in RCA: 6] [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: 11/22/2017] [Accepted: 12/06/2017] [Indexed: 12/14/2022]
Abstract
Twenty-five years ago, RET was identified as the primary driver of multiple endocrine neoplasia type 2 (MEN2) syndrome. MEN2 is characterized by several transformation events including pheochromocytoma, parathyroid adenoma and, especially penetrant, medullary thyroid carcinoma (MTC). Overall, MTC is a rare but aggressive type of thyroid cancer for which no effective treatment currently exists. Surgery, radiation, radioisotope treatment and chemotherapeutics have all shown limited success, and none of these approaches have proven durable in advanced disease. Non-mammalian models that incorporate the oncogenic RET isoforms associated with MEN2 and other RET-associated diseases have been useful in delineating mechanisms underlying disease progression. These models have also identified novel targeted therapies as single agents and as combinations. These studies highlight the importance of modeling disease in the context of the whole animal, accounting for the complex interplay between tumor and normal cells in controlling disease progression as well as response to therapy. With convenient access to whole genome sequencing data from expanded thyroid cancer patient cohorts, non-mammalian models will become more complex, sophisticated and continue to complement future mammalian studies. In this review, we explore the contributions of non-mammalian models to our understanding of thyroid cancer including MTC, with a focus on Danio rerio and Drosophila melanogaster (fish and fly) models.
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Affiliation(s)
- Tirtha K Das
- Department of Cell Developmental and Regenerative Biology, School of Biomedical Sciences, Icahn School of Medicine, New York, New York, USA
| | - Ross L Cagan
- Department of Cell Developmental and Regenerative Biology, School of Biomedical Sciences, Icahn School of Medicine, New York, New York, USA
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141
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Rashid D, Puettmann P, Roy E, Bradley RS. Neural crest development in Xenopus requires Protocadherin 7 at the lateral neural crest border. Mech Dev 2018; 149:41-52. [PMID: 29366801 PMCID: PMC5820198 DOI: 10.1016/j.mod.2018.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/04/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022]
Abstract
In vertebrates, the neural crest is a unique population of pluripotent cells whose development is dependent on signaling from neighboring tissues. Cadherin family members, including protocadherins, are emerging as major players in neural crest development, largely through their roles in cell adhesion and sorting in embryonic tissues. Here, we show that Protocadherin 7 (Pcdh7), previously shown to function in sensorial layer integrity and neural tube closure in Xenopus, is also involved in neural crest specification and survival. Pcdh7 expression partly overlaps the neural crest domain at the lateral neural crest border. Pcdh7 knockdown in embryos does not alter neural crest induction; however, neural crest specification markers, including Snail2 and Sox9, are lost, due to apoptosis of the neural crest starting after stage 13. Pcdh7 knockdown also results in downregulation of Wnt11b; both of which are co-expressed in the sensorial layer lateral to the neural crest, suggestive of a role for Wnt11b in the neural crest apoptosis. Confirming this role, apoptosis, Snail2 expression and the developmental fate of the neural crest can be partially rescued by ectopic expression of Wnt11b. These results indicate that Pcdh7 plays an important role in maintaining the sensorial layer at the lateral neural crest border, which is necessary for the secretion of survival factors, including Wnt11b.
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Affiliation(s)
- Dana Rashid
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717
| | - Paul Puettmann
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717
| | - Ethan Roy
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717
| | - Roger S. Bradley
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717
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142
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Torraca V, Mostowy S. Zebrafish Infection: From Pathogenesis to Cell Biology. Trends Cell Biol 2018; 28:143-156. [PMID: 29173800 PMCID: PMC5777827 DOI: 10.1016/j.tcb.2017.10.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022]
Abstract
The study of host-pathogen interactions has illuminated fundamental research avenues in both infection and cell biology. Zebrafish (Danio rerio) larvae are genetically tractable, optically accessible, and present a fully functional innate immune system with macrophages and neutrophils that mimic their mammalian counterparts. A wide variety of pathogenic bacteria have been investigated using zebrafish models, providing unprecedented resolution of the cellular response to infection in vivo. In this review, we illustrate how zebrafish models have contributed to our understanding of cellular microbiology by providing an in vivo platform to study host-pathogen interactions from the single cell to whole animal level. We also highlight discoveries made from zebrafish infection that hold great promise for translation into novel therapies for humans.
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Affiliation(s)
- Vincenzo Torraca
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Serge Mostowy
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
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143
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Li S, Wang M, Qu X, Xu Z, Yang Y, Su Q, Wu H. SUMOylation of PES1 upregulates its stability and function via inhibiting its ubiquitination. Oncotarget 2018; 7:50522-50534. [PMID: 27409667 PMCID: PMC5226600 DOI: 10.18632/oncotarget.10494] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 06/15/2016] [Indexed: 12/21/2022] Open
Abstract
PES1 is a component of the PeBoW complex, which is required for the maturation of 28S and 5.8S ribosomal RNAs, as well as for the formation of the 60S ribosome. Deregulation of ribosomal biogenesis can contribute to carcinogenesis. In this study, we showed that PES1 could be modified by the small ubiquitin-like modifier (SUMO) SUMO-1, SUMO-2 and SUMO-3, and SUMOylation of PES1 was stimulated by estrogen (E2). One major SUMOylation site (K517) was identified in the C-terminal Glu-rich domain of PES1. Substitution of K517 with arginine abolished the SUMOylation of PES1. SUMOylation also stabilized PES1 through inhibiting its ubiquitination. In addition, PES1 SUMOylation positively regulated the estrogen signaling pathway. SUMOylation enhanced the ability of PES1 to promote estrogen receptor α (ERα)-mediated transcription by increasing the stability of ERα, both in the presence and absence of E2. Moreover, SUMOylation of PES1 also increased the proportion of S-phase cells in the cell cycle and promoted the proliferation of breast cancer cells both in vitro and in vivo. These findings showed that posttranslational modification of PES1 by SUMOylation may serve as a key factor that regulates the function of PES1 in vivo.
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Affiliation(s)
- Shujing Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Miao Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Xinjian Qu
- School of Life Science and Medicine, Dalian University of Technology, Panjin, China
| | - Zhaowei Xu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yangyang Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Qiming Su
- School of Life Science and Medicine, Dalian University of Technology, Panjin, China
| | - Huijian Wu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.,School of Life Science and Medicine, Dalian University of Technology, Panjin, China
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144
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Gehrig J, Pandey G, Westhoff JH. Zebrafish as a Model for Drug Screening in Genetic Kidney Diseases. Front Pediatr 2018; 6:183. [PMID: 30003073 PMCID: PMC6031734 DOI: 10.3389/fped.2018.00183] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
Genetic disorders account for a wide range of renal diseases emerging during childhood and adolescence. Due to the utilization of modern biochemical and biomedical techniques, the number of identified disease-associated genes is increasing rapidly. Modeling of congenital human disease in animals is key to our understanding of the biological mechanism underlying pathological processes and thus developing novel potential treatment options. The zebrafish (Danio rerio) has been established as a versatile small vertebrate organism that is widely used for studying human inherited diseases. Genetic accessibility in combination with elegant experimental methods in zebrafish permit modeling of human genetic diseases and dissecting the perturbation of underlying cellular networks and physiological processes. Beyond its utility for genetic analysis and pathophysiological and mechanistic studies, zebrafish embryos, and larvae are amenable for phenotypic screening approaches employing high-content and high-throughput experiments using automated microscopy. This includes large-scale chemical screening experiments using genetic models for searching for disease-modulating compounds. Phenotype-based approaches of drug discovery have been successfully performed in diverse zebrafish-based screening applications with various phenotypic readouts. As a result, these can lead to the identification of candidate substances that are further examined in preclinical and clinical trials. In this review, we discuss zebrafish models for inherited kidney disease as well as requirements and considerations for the technical realization of drug screening experiments in zebrafish.
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Affiliation(s)
- Jochen Gehrig
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
| | - Gunjan Pandey
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany.,Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Jens H Westhoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
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145
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Small molecule screen in embryonic zebrafish using modular variations to target segmentation. Nat Commun 2017; 8:1901. [PMID: 29196645 PMCID: PMC5711842 DOI: 10.1038/s41467-017-01469-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/19/2017] [Indexed: 01/19/2023] Open
Abstract
Small molecule in vivo phenotypic screening is used to identify drugs or biological activities by directly assessing effects in intact organisms. However, current screening designs may not exploit the full potential of chemical libraries due to false negatives. Here, we demonstrate a modular small molecule screen in embryonic zebrafish that varies concentration, genotype and timing to target segmentation disorders, birth defects that affect the spinal column. By testing each small molecule in multiple interrelated ways, this screen recovers compounds that a standard screening design would have missed, increasing the hit frequency from the chemical library three-fold. We identify molecular pathways and segmentation phenotypes, which we share in an open-access annotated database. These hits provide insight into human vertebral segmentation disorders and myopathies. This modular screening strategy is applicable to other developmental questions and disease models, highlighting the power of relatively small chemical libraries to accelerate gene discovery and disease study.
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146
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Kamel M, Ninov N. Catching new targets in metabolic disease with a zebrafish. Curr Opin Pharmacol 2017; 37:41-50. [DOI: 10.1016/j.coph.2017.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/04/2017] [Accepted: 08/11/2017] [Indexed: 12/12/2022]
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147
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Geurtzen K, Vernet A, Freidin A, Rauner M, Hofbauer LC, Schneider JE, Brand M, Knopf F. Immune Suppressive and Bone Inhibitory Effects of Prednisolone in Growing and Regenerating Zebrafish Tissues. J Bone Miner Res 2017; 32:2476-2488. [PMID: 28771888 DOI: 10.1002/jbmr.3231] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/19/2017] [Accepted: 07/31/2017] [Indexed: 01/15/2023]
Abstract
Glucocorticoids are widely used as therapeutic agents to treat immune-mediated diseases in humans because of their anti-inflammatory and immunosuppressive effects. However, glucocorticoids have various adverse effects, in particular rapid and pronounced bone loss associated with fractures in glucocorticoid-induced osteoporosis, a common form of secondary osteoporosis. In zebrafish, which are increasingly used to study processes of bone regeneration and disease, glucocorticoids show detrimental effects on bone tissue; however, the underlying cellular mechanisms are incompletely understood. Here, we show that treatment with the glucocorticoid prednisolone impacts on the number, activity and differentiation of osteoblasts, osteoclasts, and immune cells during ontogenetic growth, homeostasis, and regeneration of zebrafish bone. Macrophage numbers are reduced in both larval and adult tissues, correlating with decreased generation of myelomonocytes and enhanced apoptosis of these cells. In contrast, osteoblasts fail to proliferate, show decreased activity, and undergo incomplete differentiation. In addition, prednisolone treatment mitigates the number and recruitment of osteoclasts to sites of bone regeneration in adult fish. In combination, these effects delay bone growth and impair bone regeneration. Our study demonstrates the many-faceted effects of glucocorticoids in non-mammalian vertebrates and helps to further establish the zebrafish as a model to study glucocorticoid-induced osteoporosis. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Karina Geurtzen
- Center for Regenerative Therapies Dresden (CRTD) and Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Aude Vernet
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew Freidin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Martina Rauner
- Division of Endocrinology, Diabetes, and Bone Diseases, Department of Medicine III, Technische Universität Dresden, Dresden, Germany
- Center for Healthy Aging, Technische Universität Dresden, Dresden, Germany
| | - Lorenz C Hofbauer
- Center for Regenerative Therapies Dresden (CRTD) and Biotechnology Center, Technische Universität Dresden, Dresden, Germany
- Division of Endocrinology, Diabetes, and Bone Diseases, Department of Medicine III, Technische Universität Dresden, Dresden, Germany
- Center for Healthy Aging, Technische Universität Dresden, Dresden, Germany
| | - Jürgen E Schneider
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Michael Brand
- Center for Regenerative Therapies Dresden (CRTD) and Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Franziska Knopf
- Center for Regenerative Therapies Dresden (CRTD) and Biotechnology Center, Technische Universität Dresden, Dresden, Germany
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Center for Healthy Aging, Technische Universität Dresden, Dresden, Germany
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148
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White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife 2017; 6. [PMID: 29144233 PMCID: PMC5690287 DOI: 10.7554/elife.30860] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/04/2017] [Indexed: 12/18/2022] Open
Abstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
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Affiliation(s)
| | - John E Collins
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Zsofia Digby
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Matthew P Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anton J Enright
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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149
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Basta HA, Buzak AJ, McClure MA. Identification of Novel Retroid Agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis. Evol Bioinform Online 2017. [DOI: 10.1177/117693430700300018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Retroid agents are genomes that encode a reverse transcriptase (RT) and replicate or transpose by way of an RNA intermediate. The Genome Parsing Suite (GPS) is software created to identify and characterize Retroid agents in any genome database (McClure et al. 2005). The detailed analysis of all Retroid agents found by the GPS in Danio rerio (zebrafish), Oryzias latipes (medaka), Gasterosteus aculeatus (stickleback) and Tetraodon nigroviridis (spotted green pufferfish) reveals extensive Retroid agent diversity in the compact genomes of all four fish. Novel Retroid agents were identified by the GPS software: the telomerase reverse transcriptase (TERT) in O. latipes, G aculeatus and T. nigroviridis and a potential TERT in D. rerio, a retrotransposon in D. rerio, and multiple lineages of endogenous retroviruses (ERVs) in D. rerio, O. latipes and G aculeatus.
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Affiliation(s)
- Holly A. Basta
- Department of Microbiology and the Center for Computational Biology, Montana State University at Bozeman, 109 Lewis Hall, Bozeman, MT 59717, U.S.A
| | - Alex J. Buzak
- Department of Microbiology and the Center for Computational Biology, Montana State University at Bozeman, 109 Lewis Hall, Bozeman, MT 59717, U.S.A
| | - Marcella A. McClure
- Department of Microbiology and the Center for Computational Biology, Montana State University at Bozeman, 109 Lewis Hall, Bozeman, MT 59717, U.S.A
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150
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Gamse JT, Gorelick DA. Mixtures, Metabolites, and Mechanisms: Understanding Toxicology Using Zebrafish. Zebrafish 2017; 13:377-8. [PMID: 27618129 DOI: 10.1089/zeb.2016.1370] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
For more than 60 years, zebrafish have been used in toxicological studies. Due to their transparency, genetic tractability, and compatibility with high-throughput screens, zebrafish embryos are uniquely suited to study the effects of pharmaceuticals and environmental insults on embryonic development, organ formation and function, and reproductive success. This special issue of Zebrafish highlights the ways zebrafish are used to investigate the toxic effects of endocrine disruptors, pesticides, and heavy metals.
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Affiliation(s)
- Joshua T Gamse
- 1 Department of Reproductive Toxicology, Drug Safety Evaluation, Bristol-Myers Squibb , New Brunswick, New Jersey
| | - Daniel A Gorelick
- 2 Department of Pharmacology and Toxicology, University of Alabama at Birmingham , Birmingham, Alabama
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