1
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Tallan A, Kucinski J, Sunkel B, Taslim C, LaHaye S, Liu Q, Qi J, Wang M, Kendall GC, Stanton BZ. Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603283. [PMID: 39071412 PMCID: PMC11275836 DOI: 10.1101/2024.07.12.603283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
We report a universal strategy for 2D chromatin sequencing, to increase uniform data analyses and sharing across labs, and to facilitate highly quantitative comparisons across experimental conditions. Within our system, we provide wetlab and drylab tools for researchers to establish and analyze protein-genome binding data with PerCell ChIP-seq. Our methodology is virtually no cost and flexible, enabling rapid, quantitative, internally normalized chromatin sequencing to catalyze project development in a variety of systems, including in vivo zebrafish epigenomics and cancer cell epigenomics. While we highlight utility in these key areas, our methodology is flexible enough such that rapid comparisons of cellular spike-in versus non spike-in are possible, and generalizability to nuclease-based 2D chromatin sequencing would also be possible within the framework of our pipeline. Through the use of well-defined cellular ratios containing orthologous species' chromatin, we enable cross-species comparative epigenomics and highly quantitative low-cost chromatin sequencing with utility across a range of disciplines.
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2
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Kucinski J, Tallan A, Taslim C, Wang M, Cannon MV, Silvius KM, Stanton BZ, Kendall GC. Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603270. [PMID: 39071299 PMCID: PMC11275748 DOI: 10.1101/2024.07.12.603270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer molecularly characterized by arrested myogenesis. The defining genetic driver, PAX3::FOXO1, functions as a chimeric gain-of-function transcription factor. An incomplete understanding of PAX3::FOXO1's in vivo epigenetic mechanisms has hindered therapeutic development. Here, we establish a PAX3::FOXO1 zebrafish injection model and semi-automated ChIP-seq normalization strategy to evaluate how PAX3::FOXO1 initially interfaces with chromatin in a developmental context. We investigated PAX3::FOXO1's recognition of chromatin and subsequent transcriptional consequences. We find that PAX3::FOXO1 interacts with inaccessible chromatin through partial/homeobox motif recognition consistent with pioneering activity. However, PAX3::FOXO1-genome binding through a composite paired-box/homeobox motif alters chromatin accessibility and redistributes H3K27ac to activate neural transcriptional programs. We uncover neural signatures that are highly representative of clinical rhabdomyosarcoma gene expression programs that are enriched following chemotherapy. Overall, we identify partial/homeobox motif recognition as a new mode for PAX3::FOXO1 pioneer function and identify neural signatures as a potentially critical PAX3::FOXO1 tumor initiation event.
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3
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Wang Y, Zhai Y, Zhang M, Song C, Zhang Y, Zhang G. Escaping from CRISPR-Cas-mediated knockout: the facts, mechanisms, and applications. Cell Mol Biol Lett 2024; 29:48. [PMID: 38589794 PMCID: PMC11003099 DOI: 10.1186/s11658-024-00565-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats and associated Cas protein (CRISPR-Cas), a powerful genome editing tool, has revolutionized gene function investigation and exhibits huge potential for clinical applications. CRISPR-Cas-mediated gene knockout has already become a routine method in research laboratories. However, in the last few years, accumulating evidences have demonstrated that genes knocked out by CRISPR-Cas may not be truly silenced. Functional residual proteins could be generated in such knockout organisms to compensate the putative loss of function, termed herein knockout escaping. In line with this, several CRISPR-Cas-mediated knockout screenings have discovered much less abnormal phenotypes than expected. How does knockout escaping happen and how often does it happen have not been systematically reviewed yet. Without knowing this, knockout results could easily be misinterpreted. In this review, we summarize these evidences and propose two main mechanisms allowing knockout escaping. To avoid the confusion caused by knockout escaping, several strategies are discussed as well as their advantages and disadvantages. On the other hand, knockout escaping also provides convenient tools for studying essential genes and treating monogenic disorders such as Duchenne muscular dystrophy, which are discussed in the end.
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Affiliation(s)
- Ying Wang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Yujing Zhai
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Mingzhe Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Chunlin Song
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yuqing Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Gang Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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4
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Prykhozhij SV, Berman JN. Mutation Knock-in Methods Using Single-Stranded DNA and Gene Editing Tools in Zebrafish. Methods Mol Biol 2024; 2707:279-303. [PMID: 37668920 DOI: 10.1007/978-1-0716-3401-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Introduction or knock-in of precise genomic modifications remains one of the most important applications of CRISPR/Cas9 in all model systems including zebrafish. The most widely used type of donor template containing the desired modification is single-stranded DNA (ssDNA), either in the form of single-stranded oligodeoxynucleotides (ssODN) (<150 nucleotides (nt)) or as long ssDNA (lssDNA) molecules (up to about 2000 nt). Despite the challenges posed by DNA repair after DNA double-strand breaks, knock-in of precise mutations is relatively straightforward in zebrafish. Knock-in efficiency can be enhanced by careful donor template design, using lssDNA as template or tethering the donor template DNA to the Cas9-guide RNA complex. Other point mutation methods such as base editing and prime editing are starting to be applied in zebrafish and many other model systems. However, these methods may not always be sufficiently accessible or may have limited capacity to perform all desired mutation knock-ins which are possible with ssDNA-based knock-in methods. Thus, it is likely that there will be complementarity in the technologies used for generating precise mutants. Here, we review and describe a suite of CRISPR/Cas9 knock-in procedures utilizing ssDNA as the donor template in zebrafish, point out the potential challenges and suggest possible approaches for their solution ultimately leading to successful generation of precise mutant lines.
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Affiliation(s)
- Sergey V Prykhozhij
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Jason N Berman
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
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5
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Hernández-Bejarano M, Gestri G, Monfries C, Tucker L, Dragomir EI, Bianco IH, Bovolenta P, Wilson SW, Cavodeassi F. Foxd1-dependent induction of a temporal retinal character is required for visual function. Development 2022; 149:285946. [PMID: 36520654 PMCID: PMC9845753 DOI: 10.1242/dev.200938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022]
Abstract
Appropriate patterning of the retina during embryonic development is assumed to underlie the establishment of spatially localised specialisations that mediate the perception of specific visual features. For example, in zebrafish, an area involved in high acuity vision (HAA) is thought to be present in the ventro-temporal retina. Here, we show that the interplay of the transcription factor Rx3 with Fibroblast Growth Factor and Hedgehog signals initiates and restricts foxd1 expression to the prospective temporal retina, initiating naso-temporal regionalisation of the retina. Abrogation of Foxd1 results in the loss of temporal and expansion of nasal retinal character, and consequent absence of the HAA. These structural defects correlate with severe visual defects, as assessed in optokinetic and optomotor response assays. In contrast, optokinetic responses are unaffected in the opposite condition, in which nasal retinal character is lost at the expense of expanded temporal character. Our study indicates that the establishment of temporal retinal character during early retinal development is required for the specification of the HAA, and suggests a prominent role of the temporal retina in controlling specific visual functions.
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Affiliation(s)
| | - Gaia Gestri
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK,Authors for correspondence (; )
| | - Clinton Monfries
- St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Lisa Tucker
- St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Elena I. Dragomir
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Isaac H. Bianco
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK,Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, UK
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain,CIBER de Enfermedades Raras (CIBERER), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Stephen W. Wilson
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Florencia Cavodeassi
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain,St George's University of London, Cranmer Terrace, London SW17 0RE, UK,Authors for correspondence (; )
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6
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Sun Y, Kumar SR, Wong CED, Tian Z, Bai H, Crump JG, Bajpai R, Lien CL. Craniofacial and cardiac defects in chd7 zebrafish mutants mimic CHARGE syndrome. Front Cell Dev Biol 2022; 10:1030587. [PMID: 36568983 PMCID: PMC9768498 DOI: 10.3389/fcell.2022.1030587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022] Open
Abstract
Congenital heart defects occur in almost 80% of patients with CHARGE syndrome, a sporadically occurring disease causing craniofacial and other abnormalities due to mutations in the CHD7 gene. Animal models have been generated to mimic CHARGE syndrome; however, heart defects are not extensively described in zebrafish disease models of CHARGE using morpholino injections or genetic mutants. Here, we describe the co-occurrence of craniofacial abnormalities and heart defects in zebrafish chd7 mutants. These mutant phenotypes are enhanced in the maternal zygotic mutant background. In the chd7 mutant fish, we found shortened craniofacial cartilages and extra cartilage formation. Furthermore, the length of the ventral aorta is altered in chd7 mutants. Many CHARGE patients have aortic arch anomalies. It should be noted that the aberrant branching of the first branchial arch artery is observed for the first time in chd7 fish mutants. To understand the cellular mechanism of CHARGE syndrome, neural crest cells (NCCs), that contribute to craniofacial and cardiovascular tissues, are examined using sox10:Cre lineage tracing. In contrast to its function in cranial NCCs, we found that the cardiac NCC-derived mural cells along the ventral aorta and aortic arch arteries are not affected in chd7 mutant fish. The chd7 fish mutants we generated recapitulate some of the craniofacial and cardiovascular phenotypes found in CHARGE patients and can be used to further determine the roles of CHD7.
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Affiliation(s)
- Yuhan Sun
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, United States
| | - S. Ram Kumar
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Chee Ern David Wong
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Zhiyu Tian
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Haipeng Bai
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - J. Gage Crump
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ruchi Bajpai
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, United States,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ching Ling Lien
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States,*Correspondence: Ching Ling Lien,
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7
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Carrington B, Bishop K, Sood R. A Comprehensive Review of Indel Detection Methods for Identification of Zebrafish Knockout Mutants Generated by Genome-Editing Nucleases. Genes (Basel) 2022; 13:857. [PMID: 35627242 PMCID: PMC9141975 DOI: 10.3390/genes13050857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
The use of zebrafish in functional genomics and disease modeling has become popular due to the ease of targeted mutagenesis with genome editing nucleases, i.e., zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These nucleases, specifically CRISPR/Cas9, are routinely used to generate gene knockout mutants by causing a double stranded break at the desired site in the target gene and selecting for frameshift insertions or deletions (indels) caused by the errors during the repair process. Thus, a variety of methods have been developed to identify fish with indels during the process of mutant generation and phenotypic analysis. These methods range from PCR and gel-based low-throughput methods to high-throughput methods requiring specific reagents and/or equipment. Here, we provide a comprehensive review of currently used indel detection methods in zebrafish. By discussing the molecular basis for each method as well as their pros and cons, we hope that this review will serve as a comprehensive resource for zebrafish researchers, allowing them to choose the most appropriate method depending upon their budget, access to required equipment and the throughput needs of the projects.
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Affiliation(s)
| | | | - Raman Sood
- Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.C.); (K.B.)
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8
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Wang L, Wang Y, Makhmoudova A, Nitschke F, Tetlow IJ, Emes MJ. CRISPR-Cas9-mediated editing of starch branching enzymes results in altered starch structure in Brassica napus. PLANT PHYSIOLOGY 2022; 188:1866-1886. [PMID: 34850950 PMCID: PMC8968267 DOI: 10.1093/plphys/kiab535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/20/2021] [Indexed: 05/24/2023]
Abstract
Starch branching enzymes (SBEs) are one of the major classes of enzymes that catalyze starch biosynthesis in plants. Here, we utilized the clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9)-mediated gene editing system to investigate the effects of SBE mutation on starch structure and turnover in the oilseed crop Brassica napus. Multiple single-guide RNA (sgRNA) expression cassettes were assembled into a binary vector and two rounds of transformation were employed to edit all six BnaSBE genes. All mutations were heterozygous monoallelic or biallelic, and no chimeric mutations were detected from a total of 216 editing events. Previously unannotated gene duplication events associated with two BnaSBE genes were characterized through analysis of DNA sequencing chromatograms, reflecting the complexity of genetic information in B. napus. Five Cas9-free homozygous mutant lines carrying two to six mutations of BnaSBE were obtained, allowing us to compare the effect of editing different BnaSBE isoforms. We also found that in the sextuple sbe mutant, although indels were introduced at the genomic DNA level, an alternate transcript of one BnaSBE2.1 gene bypassed the indel-induced frame shift and was translated to a modified full-length protein. Subsequent analyses showed that the sextuple mutant possesses much lower SBE enzyme activity and starch branching frequency, higher starch-bound phosphate content, and altered pattern of amylopectin chain length distribution relative to wild-type (WT) plants. In the sextuple mutant, irregular starch granules and a slower rate of starch degradation during darkness were observed in rosette leaves. At the pod-filling stage, the sextuple mutant was distinguishable from WT plants by its thick main stem. This work demonstrates the applicability of the CRISPR-Cas9 system for the study of multi-gene families and for investigation of gene-dosage effects in the oil crop B. napus. It also highlights the need for rigorous analysis of CRISPR-Cas9-mutated plants, particularly with higher levels of ploidy, to ensure detection of gene duplications.
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Affiliation(s)
| | - You Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Amina Makhmoudova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Felix Nitschke
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ian J Tetlow
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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9
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Değirmenci L, Geiger D, Rogé Ferreira FL, Keller A, Krischke B, Beye M, Steffan-Dewenter I, Scheiner R. CRISPR/Cas 9-Mediated Mutations as a New Tool for Studying Taste in Honeybees. Chem Senses 2021; 45:655-666. [PMID: 32968780 DOI: 10.1093/chemse/bjaa063] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Honeybees rely on nectar as their main source of carbohydrates. Sucrose, glucose, and fructose are the main components of plant nectars. Intriguingly, honeybees express only 3 putative sugar receptors (AmGr1, AmGr2, and AmGr3), which is in stark contrast to many other insects and vertebrates. The sugar receptors are only partially characterized. AmGr1 detects different sugars including sucrose and glucose. AmGr2 is assumed to act as a co-receptor only, while AmGr3 is assumedly a fructose receptor. We show that honeybee gustatory receptor AmGr3 is highly specialized for fructose perception when expressed in Xenopus oocytes. When we introduced nonsense mutations to the respective AmGr3 gene using CRISPR/Cas9 in eggs of female workers, the resulting mutants displayed almost a complete loss of responsiveness to fructose. In contrast, responses to sucrose were normal. Nonsense mutations introduced by CRISPR/Cas9 in honeybees can thus induce a measurable behavioral change and serve to characterize the function of taste receptors in vivo. CRISPR/Cas9 is an excellent novel tool for characterizing honeybee taste receptors in vivo. Biophysical receptor characterization in Xenopus oocytes and nonsense mutation of AmGr3 in honeybees unequivocally demonstrate that this receptor is highly specific for fructose.
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Affiliation(s)
- Laura Değirmenci
- Behavioral Physiology and Sociobiology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
| | - Dietmar Geiger
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Fábio Luiz Rogé Ferreira
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Alexander Keller
- Department of Bioinformatics, Biocenter, Am Hubland, Würzburg, Germany
| | - Beate Krischke
- Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
| | - Martin Beye
- Evolutionary Genetics, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ingolf Steffan-Dewenter
- Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
| | - Ricarda Scheiner
- Behavioral Physiology and Sociobiology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
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10
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Abstract
The zebrafish has emerged as a valuable and important model organism for studying vascular development and vascular biology. Here, we discuss some of the approaches used to study vessels in fish, including loss-of-function tools such as morpholinos and genetic mutants, along with methods and considerations for assessing vascular phenotypes. We also provide detailed protocols for methods used for vital imaging of the zebrafish vasculature, including microangiography and long-term time-lapse imaging. The methods we describe, and the considerations we suggest using for assessing phenotypes observed using these methods, will help ensure reliable, valid conclusions when assessing vascular phenotypes following genetic or experimental manipulation of zebrafish.
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11
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Song J, Zhang J, Xu J, Garcia-Barrio M, Chen YE, Yang D. Genome engineering technologies in rabbits. J Biomed Res 2021; 35:135-147. [PMID: 32934190 PMCID: PMC8038526 DOI: 10.7555/jbr.34.20190133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The rabbit has been recognized as a valuable model in various biomedical and biological research fields because of its intermediate size and phylogenetic proximity to primates. However, the technology for precise genome manipulations in rabbit has been stalled for decades, severely limiting its applications in biomedical research. Novel genome editing technologies, especially CRISPR/Cas9, have remarkably enhanced precise genome manipulation in rabbits, and shown their superiority and promise for generating rabbit models of human genetic diseases. In this review, we summarize the brief history of transgenic rabbit technology and the development of novel genome editing technologies in rabbits.
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Affiliation(s)
- Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Minerva Garcia-Barrio
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Y Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
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12
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Jin Y, Datsomor AK, Olsen RE, Vik JO, Torgersen JS, Edvardsen RB, Wargelius A, Winge P, Grammes F. Targeted mutagenesis of ∆5 and ∆6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar). BMC Genomics 2020; 21:805. [PMID: 33213387 PMCID: PMC7678299 DOI: 10.1186/s12864-020-07218-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background With declining wild fish populations, farmed salmon has gained popularity as a source for healthy long-chain highly unsaturated fatty acids (LC-HUFA). However, the introduction of plant oil in farmed salmon feeds has reduced the content of these beneficial LC-HUFA. The synthetic capability for LC-HUFAs depends upon the dietary precursor fatty acids and the genetic potential, thus there is a need for in-depth understanding of LC-HUFA synthetic genes and their interactions with other genes involved in lipid metabolism. Several key genes of LC-HUFA synthesis in salmon belong to the fatty acid desaturases 2 (fads2) family. The present study applied whole transcriptome analysis on two CRISPR-mutated salmon strains (crispants), 1) Δ6abc/5Mt with mutations in Δ5fads2, Δ6fads2-a, Δ6fads2-b and Δ6fads2-c genes, and 2) Δ6bcMt with mutations in Δ6fads2-b and Δ6fads2-c genes. Our purpose is to evaluate the genetic effect fads2 mutations have on other lipid metabolism pathways in fish, as well as to investigate mosaicism in a commercial species with a very long embryonal period. Results Both Δ6abc/5Mt and Δ6bcMt crispants demonstrated high percentage of indels within all intended target genes, though different indel types and percentage were observed between individuals. The Δ6abc/5Mt fish displayed several disruptive indels which resulted in over 100 differentially expressed genes (DEGs) enriched in lipid metabolism pathways in liver. This includes up-regulation of srebp1 genes which are known key transcription regulators of lipid metabolism as well as a number of down-stream genes involved in fatty acid de-novo synthesis, fatty acid β-oxidation and lipogenesis. Both elovl5 and elovl2 genes were not changed, suggesting that the genes were not targeted by Srebp1. The mutation of Δ6bcMt surprisingly resulted in over 3000 DEGs which were enriched in factors encoding genes involved in mRNA regulation and stability. Conclusions CRISPR-Cas9 can efficiently mutate multiple fads2 genes simultaneously in salmon. The results of the present study have provided new information on the transcriptional regulations of lipid metabolism genes after reduction of LC-HUFA synthesis pathways in salmon. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07218-1.
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Affiliation(s)
- Yang Jin
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432, Aas, Norway
| | - Alex K Datsomor
- Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Rolf E Olsen
- Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Jon Olav Vik
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432, Aas, Norway
| | | | | | | | - Per Winge
- Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Fabian Grammes
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432, Aas, Norway. .,AquaGen AS, Post box 1240, Torgard, N-7462, Trondheim, Norway.
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13
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Ichino N, Serres MR, Urban RM, Urban MD, Treichel AJ, Schaefbauer KJ, Greif LE, Varshney GK, Skuster KJ, McNulty MS, Daby CL, Wang Y, Liao HK, El-Rass S, Ding Y, Liu W, Anderson JL, Wishman MD, Sabharwal A, Schimmenti LA, Sivasubbu S, Balciunas D, Hammerschmidt M, Farber SA, Wen XY, Xu X, McGrail M, Essner JJ, Burgess SM, Clark KJ, Ekker SC. Building the vertebrate codex using the gene breaking protein trap library. eLife 2020; 9:54572. [PMID: 32779569 PMCID: PMC7486118 DOI: 10.7554/elife.54572] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b, fras1, tnnt2a, edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated genes with 40 as potential new disease models. Severely reduced skeletal muscle Ca2+ transients in GBT ryr1b homozygous animals validated the ability to explore molecular mechanisms of genetic diseases. This GBT system facilitates novel functional genome annotation towards understanding cellular and molecular underpinnings of vertebrate biology and human disease.
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Affiliation(s)
- Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - MaKayla R Serres
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Rhianna M Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Mark D Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Anthony J Treichel
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Kyle J Schaefbauer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Lauren E Greif
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States.,Functional & Chemical Genomics Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Kimberly J Skuster
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Melissa S McNulty
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Camden L Daby
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Ying Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Hsin-Kai Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Suzan El-Rass
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Weibin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Mark D Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Lisa A Schimmenti
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Clinical Genomics, Mayo Clinic, Rochester, United States.,Department of Otorhinolaryngology, Mayo Clinic, Rochester, United States
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Darius Balciunas
- Department of Biology, Temple University, Philadelphia, United States
| | - Matthias Hammerschmidt
- Institute of Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
| | - Steven Arthur Farber
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
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14
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McElderry J, Carrington B, Bishop K, Kim E, Pei W, Chen Z, Ramanagoudr-Bhojappa R, Prakash A, Burgess SM, Liu PP, Sood R. Splicing factor DHX15 affects tp53 and mdm2 expression via alternate splicing and promoter usage. Hum Mol Genet 2020; 28:4173-4185. [PMID: 31691804 DOI: 10.1093/hmg/ddz261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/18/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022] Open
Abstract
DHX15, a DEAH box containing RNA helicase, is a splicing factor required for the last step of splicing. Recent studies identified a recurrent mutational hotspot, R222G, in DHX15 in ∼ 6% of acute myeloid leukemia (AML) patients that carry the fusion protein RUNX1-RUNX1T1 produced by t (8;21) (q22;q22). Studies using yeast mutants showed that substitution of G for the residue equivalent to R222 leads to loss of its helicase function, suggesting that it is a loss-of-function mutation. To elucidate the role of DHX15 during development, we established the first vertebrate knockout model with CRISPR/Cas9 in zebrafish. Our data showed that dhx15 expression is enriched in the brain, eyes, pectoral fin primordia, liver and intestinal bulb during embryonic development. Dhx15 deficiency leads to pleiotropic morphological phenotypes in homozygous mutant embryos starting at 3 days post fertilization (dpf) that result in lethality by 7 dpf, revealing an essential role during embryonic development. RNA-seq analysis suggested important roles of Dhx15 in chromatin and nucleosome assembly and regulation of the Mdm2-p53 pathway. Interestingly, exons corresponding to the alternate transcriptional start sites for tp53 and mdm2 were preferentially expressed in the mutant embryos, leading to significant upregulation of their alternate isoforms, Δ113p53 (orthologous to Δ133p53 isoform in human) and mdm2-P2 (isoform using distal promoter P2), respectively. We speculate that these alterations in the Mdm2-p53 pathway contribute to the development of AML in patients with t(8;21) and somatically mutated DHX15.
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Affiliation(s)
- John McElderry
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erika Kim
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zelin Chen
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anupam Prakash
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - P Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Prykhozhij SV, Cordeiro-Santanach A, Caceres L, Berman JN. Genome Editing in Zebrafish Using High-Fidelity Cas9 Nucleases: Choosing the Right Nuclease for the Task. Methods Mol Biol 2020; 2115:385-405. [PMID: 32006412 DOI: 10.1007/978-1-0716-0290-4_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Shortly after the development of the CRISPR/Cas9 system, it was recognized that it is prone to induce off-target mutations at significant frequencies. Therefore, there is a strong motivation to develop Cas9 enzymes with reduced off-target activity. Multiple rational design or selection approaches have been applied to develop several Cas9 versions with reduced off-target activities (high fidelity). To make these high-fidelity Cas9s available for model systems other than human cells and bacterial strains, as, for example, in zebrafish, new specialized expression vectors need to be developed. In this chapter, we focused on the HypaCas9 and HiFi Cas9 high-fidelity enzymes and incorporated the mutations of these Cas9 versions into a codon-optimized zebrafish Cas9 vector. This optimized vector was further improved by introducing an artificial polyadenine insert (A71) since polyadenylation is known to enhance mRNA translational efficiency. The Hypa-nCas9n and HiFi-nCas9n vectors were produced by single-site mutagenesis from pT3TS-nCas9n-A71 vector. We then tested the polyadenylated mRNAs for nCas9n, Hypa-nCas9n, HiFi-nCas9n, and HiFi-Cas9 protein for editing efficiency in five genome editing strategies and found that these high-fidelity Cas9 versions had different performances ranging from activity at 2-4 sites, where the wild-type nCas9n is active, indicating that these Cas9 versions have different sgRNA preferences. In summary, the developed new high-fidelity Cas9 vectors will enable researchers to perform much more accurate genome editing.
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16
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Hoshijima K, Jurynec MJ, Klatt Shaw D, Jacobi AM, Behlke MA, Grunwald DJ. Highly Efficient CRISPR-Cas9-Based Methods for Generating Deletion Mutations and F0 Embryos that Lack Gene Function in Zebrafish. Dev Cell 2019; 51:645-657.e4. [PMID: 31708433 DOI: 10.1016/j.devcel.2019.10.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/13/2019] [Accepted: 10/03/2019] [Indexed: 11/24/2022]
Abstract
Inconsistent activity limits the use of CRISPR-Cas9 in zebrafish. We show supernumerary guanine nucleotides at the 5' ends of single guide RNAs (sgRNAs) account for diminished CRISPR-Cas9 activity in zebrafish embryos. Genomic sequences can be targeted consistently with extremely high efficiency using Cas9 ribonucleoproteins (RNPs) containing either a sgRNA molecule or a synthetic crRNA:tracrRNA duplex that perfectly matches the protospacer target site. Following injection of zebrafish eggs with such RNPs, virtually every copy of a targeted locus harbors an induced indel mutation. Loss of gene function is often complete, as F0 embryos closely resemble true null mutants without detectable non-specific effects. Mosaicism is sufficiently low in F0 embryos that cell non-autonomous gene functions can be probed effectively and redundant activities of genes can be uncovered when two genes are targeted simultaneously. Finally, heritable deletion mutations of at least 50 kbp can be readily induced using pairs of duplex guide RNPs targeted to a single chromosome.
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Affiliation(s)
- Kazuyuki Hoshijima
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael J Jurynec
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Department of Orthopaedics, University of Utah, Salt Lake City, UT 84112, USA
| | - Dana Klatt Shaw
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Ashley M Jacobi
- Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - Mark A Behlke
- Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - David Jonah Grunwald
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
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17
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Tracking genome-editing and associated molecular perturbations by SWATH mass spectrometry. Sci Rep 2019; 9:15240. [PMID: 31645615 PMCID: PMC6811567 DOI: 10.1038/s41598-019-51612-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022] Open
Abstract
Advances in gene editing now allow reverse genetics to be applied to a broad range of biological systems. Ultimately, any modification to coding sequences requires confirmation at the protein level, although immunoblotting is often hampered by antibody quality or availability especially in non-model species. Sequential Window Acquisition of All Theoretical Spectra (SWATH), a mass spectrometry (MS) technology with exceptional quantitative reproducibility and accuracy, offers an ideal alternative for protein-based confirmation. Here, using genome edits in mouse, zebrafish and Bicyclus anynana butterflies produced using either homologous recombination or targeted nucleases, we demonstrate absence of the targeted proteins using SWATH, thus confirming successful editing. We show that SWATH is a robust antibody-independent alternative for monitoring gene editing at the protein level and broadly applicable across diverse organisms and targeted genome manipulation techniques. Moreover, SWATH concomitantly defines the global proteome response in the edited organism, which may provide pertinent biological insights.
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18
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Konantz M, Schürch C, Hanns P, Müller JS, Sauteur L, Lengerke C. Modeling hematopoietic disorders in zebrafish. Dis Model Mech 2019; 12:12/9/dmm040360. [PMID: 31519693 PMCID: PMC6765189 DOI: 10.1242/dmm.040360] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Zebrafish offer a powerful vertebrate model for studies of development and disease. The major advantages of this model include the possibilities of conducting reverse and forward genetic screens and of observing cellular processes by in vivo imaging of single cells. Moreover, pathways regulating blood development are highly conserved between zebrafish and mammals, and several discoveries made in fish were later translated to murine and human models. This review and accompanying poster provide an overview of zebrafish hematopoiesis and discuss the existing zebrafish models of blood disorders, such as myeloid and lymphoid malignancies, bone marrow failure syndromes and immunodeficiencies, with a focus on how these models were generated and how they can be applied for translational research. Summary: This At A Glance article and poster summarize the last 20 years of research in zebrafish models for hematopoietic disorders, highlighting how these models were created and are being applied for translational research.
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Affiliation(s)
- Martina Konantz
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel 4031, Switzerland
| | - Christoph Schürch
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel 4031, Switzerland
| | - Pauline Hanns
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel 4031, Switzerland
| | - Joëlle S Müller
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel 4031, Switzerland
| | - Loïc Sauteur
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel 4031, Switzerland
| | - Claudia Lengerke
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel 4031, Switzerland.,Division of Hematology, University of Basel and University Hospital Basel, Basel 4031, Switzerland
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19
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Geng Y, Peterson RT. The zebrafish subcortical social brain as a model for studying social behavior disorders. Dis Model Mech 2019; 12:dmm039446. [PMID: 31413047 PMCID: PMC6737945 DOI: 10.1242/dmm.039446] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Social behaviors are essential for the survival and reproduction of social species. Many, if not most, neuropsychiatric disorders in humans are either associated with underlying social deficits or are accompanied by social dysfunctions. Traditionally, rodent models have been used to model these behavioral impairments. However, rodent assays are often difficult to scale up and adapt to high-throughput formats, which severely limits their use for systems-level science. In recent years, an increasing number of studies have used zebrafish (Danio rerio) as a model system to study social behavior. These studies have demonstrated clear potential in overcoming some of the limitations of rodent models. In this Review, we explore the evolutionary conservation of a subcortical social brain between teleosts and mammals as the biological basis for using zebrafish to model human social behavior disorders, while summarizing relevant experimental tools and assays. We then discuss the recent advances gleaned from zebrafish social behavior assays, the applications of these assays to studying related disorders, and the opportunities and challenges that lie ahead.
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Affiliation(s)
- Yijie Geng
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, 30 S. 2000 East, Salt Lake City, UT 84112, USA
| | - Randall T Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, 30 S. 2000 East, Salt Lake City, UT 84112, USA
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20
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Demireva EY, Xie H, Flood ED, Thompson JM, Seitz BM, Watts SW. Creation of the 5-hydroxytryptamine receptor 7 knockout rat as a tool for cardiovascular research. Physiol Genomics 2019; 51:290-301. [PMID: 31125290 PMCID: PMC6689730 DOI: 10.1152/physiolgenomics.00030.2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/13/2019] [Accepted: 05/21/2019] [Indexed: 11/22/2022] Open
Abstract
Using CRISPR-Cas9 technology, we created a 5-HT7 receptor global knockout (KO) rat, on a Sprague-Dawley background, for use in cardiovascular physiology studies focused on blood pressure regulation. A stable line carrying indels in exons 1 and 2 of the rat Htr7 locus was established and validated. Surprisingly, 5-HT7 receptor mRNA was still present in the KO rat. However, extensive cDNA and genomic sequencing of KO tissues confirmed an 11 bp deletion in exon 1 and 4 bp deletion in exon 2. The exon 1 deletion resulted in a frameshifted mRNA sequence coding for a nonfunctional protein. While the Htr1B locus was a potential off-target for the guide RNAs designed for exon 2 of Htr7, there were no off-target sequence changes at this locus in the originating founder. When the F2 generation of KO was compared with wild-type (WT) counterparts, neither the male nor female KO rats were different in body size, fat weights, or mass of organs (kidney, heart, and brain) important to blood pressure. Females were smaller in mass than their counterpart males. Clinical measures of plasma from nonfasted rats revealed largely similar values, comparing WT and KO, of glucose, blood urea nitrogen, creatinine, phosphate, calcium, and albumin to name a few. Loss of a functional 5-HT7 receptor was validated by the complete loss of relaxation to the 5-HT1/7 receptor agonist 5-carboxamidotryptamine in the isolated abdominal vena cava. This newly created 5-HT7 receptor KO rat will be of use to investigate the importance of the 5-HT7 receptor in blood pressure regulation.
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Affiliation(s)
- Elena Y Demireva
- Transgenic and Genome Editing Facility, and Institute for Quantitative Health Science and Engineering, Michigan State University , East Lansing, Michigan
| | - Huirong Xie
- Transgenic and Genome Editing Facility, and Institute for Quantitative Health Science and Engineering, Michigan State University , East Lansing, Michigan
| | - Emma D Flood
- Department of Pharmacology and Toxicology, Michigan State University , East Lansing, Michigan
| | - Janice M Thompson
- Department of Pharmacology and Toxicology, Michigan State University , East Lansing, Michigan
| | - Bridget M Seitz
- Department of Pharmacology and Toxicology, Michigan State University , East Lansing, Michigan
| | - Stephanie W Watts
- Department of Pharmacology and Toxicology, Michigan State University , East Lansing, Michigan
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21
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Patton EE, Tobin DM. Spotlight on zebrafish: the next wave of translational research. Dis Model Mech 2019; 12:12/3/dmm039370. [PMID: 30858282 PMCID: PMC6451428 DOI: 10.1242/dmm.039370] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Five years after the launch of the Disease Models & Mechanisms (DMM) Special Issue on zebrafish as a disease model, the field has progressed significantly. Zebrafish have been used to precisely model human genetic variants, to unpick the mechanisms of metabolic and other diseases, to study infection, inflammation and cancer, and to develop and test new therapeutic approaches. In this Editorial, we highlight recent research published in DMM that uses zebrafish to develop new experimental tools and to provide new insight into disease mechanism and therapy. The broad spectrum of subjects and approaches covered in these articles underscores the versatility of zebrafish in translational research. Further, it highlights the zebrafish community's ethos of creativity and collaboration in translating basic biological research into clinically relevant advances affecting how we understand and treat human disease. Summary: Zebrafish are a highly versatile and relevant organism for human disease modelling. This Editorial highlights the recent zebrafish research published in DMM.
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Affiliation(s)
- E Elizabeth Patton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - David M Tobin
- Departments of Molecular Genetics and Microbiology, and Immunology, Box 3020, Duke University School of Medicine, Durham, NC 27710, USA
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22
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Monk BC, Sagatova AA, Hosseini P, Ruma YN, Wilson RK, Keniya MV. Fungal Lanosterol 14α-demethylase: A target for next-generation antifungal design. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140206. [PMID: 30851431 DOI: 10.1016/j.bbapap.2019.02.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 12/19/2022]
Abstract
The cytochrome P450 enzyme lanosterol 14α-demethylase (LDM) is the target of the azole antifungals used widely in medicine and agriculture as prophylaxis or treatments of infections or diseases caused by fungal pathogens. These drugs and agrochemicals contain an imidazole, triazole or tetrazole substituent, with one of the nitrogens in the azole ring coordinating as the sixth axial ligand to the LDM heme iron. Structural studies show that this membrane bound enzyme contains a relatively rigid ligand binding pocket comprised of a deeply buried heme-containing active site together with a substrate entry channel and putative product exit channel that reach to the membrane. Within the ligand binding pocket the azole antifungals have additional affinity determining interactions with hydrophobic side-chains, the polypeptide backbone and via water-mediated hydrogen bond networks. This review will describe the tools that can be used to identify and characterise the next generation of antifungals targeting LDM, with the goal of obtaining highly potent broad-spectrum fungicides that will be able to avoid target and drug efflux mediated antifungal resistance.
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Affiliation(s)
- Brian C Monk
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Alia A Sagatova
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Parham Hosseini
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Yasmeen N Ruma
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Rajni K Wilson
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Mikhail V Keniya
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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23
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Moravec CE, Pelegri FJ. An Accessible Protocol for the Generation of CRISPR-Cas9 Knockouts Using INDELs in Zebrafish. Methods Mol Biol 2019; 1920:377-392. [PMID: 30737704 DOI: 10.1007/978-1-4939-9009-2_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ability to create targeted mutations in specific genes, and therefore a loss-of-function condition, provides essential information about their endogenous functions during development and homeostasis. The discovery that CRISPR-Cas9 can target specific sequences according to base-pair complementarity and readily create knockouts in a desired gene has elevated the implementation of genetic analysis in numerous organisms. As CRISPR-Cas9 has become a powerful tool in a number of species, multiple methods for designing, creating, and screening editing efficiencies have been published, each of which has unique benefits. This chapter presents a cost-efficient, accessible protocol for creating knockout mutants in zebrafish using insertions/deletions (INDELS), from target site selection to mutant propagation, using basic laboratory supplies. The presented approach can be adapted to other systems, including any vertebrate species.
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Affiliation(s)
- Cara E Moravec
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
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24
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Ramanagoudr-Bhojappa R, Carrington B, Ramaswami M, Bishop K, Robbins GM, Jones M, Harper U, Frederickson SC, Kimble DC, Sood R, Chandrasekharappa SC. Multiplexed CRISPR/Cas9-mediated knockout of 19 Fanconi anemia pathway genes in zebrafish revealed their roles in growth, sexual development and fertility. PLoS Genet 2018; 14:e1007821. [PMID: 30540754 PMCID: PMC6328202 DOI: 10.1371/journal.pgen.1007821] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 01/10/2019] [Accepted: 11/08/2018] [Indexed: 11/28/2022] Open
Abstract
Fanconi Anemia (FA) is a genomic instability syndrome resulting in aplastic anemia, developmental abnormalities, and predisposition to hematological and other solid organ malignancies. Mutations in genes that encode proteins of the FA pathway fail to orchestrate the repair of DNA damage caused by DNA interstrand crosslinks. Zebrafish harbor homologs for nearly all known FA genes. We used multiplexed CRISPR/Cas9-mediated mutagenesis to generate loss-of-function mutants for 17 FA genes: fanca, fancb, fancc, fancd1/brca2, fancd2, fance, fancf, fancg, fanci, fancj/brip1, fancl, fancm, fancn/palb2, fanco/rad51c, fancp/slx4, fancq/ercc4, fanct/ube2t, and two genes encoding FA-associated proteins: faap100 and faap24. We selected two indel mutations predicted to cause premature truncations for all but two of the genes, and a total of 36 mutant lines were generated for 19 genes. Generating two independent mutant lines for each gene was important to validate their phenotypic consequences. RT-PCR from homozygous mutant fish confirmed the presence of transcripts with indels in all genes. Interestingly, 4 of the indel mutations led to aberrant splicing, which may produce a different protein than predicted from the genomic sequence. Analysis of RNA is thus critical in proper evaluation of the consequences of the mutations introduced in zebrafish genome. We used fluorescent reporter assay, and western blots to confirm loss-of-function for several mutants. Additionally, we developed a DEB treatment assay by evaluating morphological changes in embryos and confirmed that homozygous mutants from all the FA genes that could be tested (11/17), displayed hypersensitivity and thus were indeed null alleles. Our multiplexing strategy helped us to evaluate 11 multiple gene knockout combinations without additional breeding. Homozygous zebrafish for all 19 single and 11 multi-gene knockouts were adult viable, indicating FA genes in zebrafish are generally not essential for early development. None of the mutant fish displayed gross developmental abnormalities except for fancp-/- fish, which were significantly smaller in length than their wildtype clutch mates. Complete female-to-male sex reversal was observed in knockouts for 12/17 FA genes, while partial sex reversal was seen for the other five gene knockouts. All adult females were fertile, and among the adult males, all were fertile except for the fancd1 mutants and one of the fancj mutants. We report here generation and characterization of zebrafish knockout mutants for 17 FA disease-causing genes, providing an integral resource for understanding the pathophysiology associated with the disrupted FA pathway. Deficiencies in repair of DNA damage can cause diseases such as Fanconi anemia (FA), which is characterized by birth defects, bone marrow failure, anemia, leukemia and other cancers. A set of proteins constitute the FA pathway and together orchestrate the DNA repair process. Inactivation of one or more gene(s) encoding the proteins of the DNA repair pathway in an animal model would enable us to study the functions of these proteins in maintenance of normal cellular functions and the overall health of an individual in the absence of function. We systematically targeted the FA pathway in zebrafish using CRISPR/Cas9. We generated 36 fish lines with loss-of-function mutations in 19 FA pathway genes and showed that all survive to adulthood. We did not notice obvious morphological changes except in fancp gene-inactivated fish, which were smaller in length. However, all mutant fish were either exclusively or in majority male. Unlike reduced fertility among FA patients, all adult mutant fish were fertile, except for the fancd1 and fancj knockout males. These mutant zebrafish will serve as a huge resource for the scientific community to study the role of FA proteins in fish development, DNA repair, and as models for FA disease.
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Affiliation(s)
- Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mukundhan Ramaswami
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gabrielle M. Robbins
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - MaryPat Jones
- Genomics Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ursula Harper
- Genomics Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen C. Frederickson
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Danielle C. Kimble
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Settara C. Chandrasekharappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Genomics Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Sarasamma S, Lai YH, Liang ST, Liu K, Hsiao CD. The Power of Fish Models to Elucidate Skin Cancer Pathogenesis and Impact the Discovery of New Therapeutic Opportunities. Int J Mol Sci 2018; 19:E3929. [PMID: 30544544 PMCID: PMC6321611 DOI: 10.3390/ijms19123929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/21/2023] Open
Abstract
Animal models play important roles in investigating the pathobiology of cancer, identifying relevant pathways, and developing novel therapeutic tools. Despite rapid progress in the understanding of disease mechanisms and technological advancement in drug discovery, negative trial outcomes are the most frequent incidences during a Phase III trial. Skin cancer is a potential life-threatening disease in humans and might be medically futile when tumors metastasize. This explains the low success rate of melanoma therapy amongst other malignancies. In the past decades, a number of skin cancer models in fish that showed a parallel development to the disease in humans have provided important insights into the fundamental biology of skin cancer and future treatment methods. With the diversity and breadth of advanced molecular genetic tools available in fish biology, fish skin cancer models will continue to be refined and expanded to keep pace with the rapid development of skin cancer research. This review begins with a brief introduction of molecular characteristics of skin cancers, followed by an overview of teleost models that have been used in the last decades in melanoma research. Next, we will detail the importance of the zebrafish (Danio rerio) animal model and other emerging fish models including platyfish (Xiphophorus sp.), and medaka (Oryzias latipes) in future cutaneous malignancy studies. The last part of this review provides the recent development and genome editing applications of skin cancer models in zebrafish and the progress in small molecule screening.
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Affiliation(s)
- Sreeja Sarasamma
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Yu-Heng Lai
- Department of Chemistry, Chinese Culture University, Taipei 11114, Taiwan.
| | - Sung-Tzu Liang
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China.
| | - Chung-Der Hsiao
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Taiwan Center for Biomedical Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
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26
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Li C, Fu Z, Yang Y, Yan J, Liu F, Zhao W, Zhang L, Wei L, Feng Z, Li D, Jiang LH. CRISPR/Cas9-mediated editing of GABRR2 gene in RGC-5 cells induces random exon deletion, exon splicing and new exon recruitment. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Sui T, Song Y, Liu Z, Chen M, Deng J, Xu Y, Lai L, Li Z. CRISPR-induced exon skipping is dependent on premature termination codon mutations. Genome Biol 2018; 19:164. [PMID: 30333044 PMCID: PMC6193291 DOI: 10.1186/s13059-018-1532-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/10/2018] [Indexed: 12/24/2022] Open
Abstract
In previous studies, CRISPR/Cas9 was shown to induce unexpected exon skipping; however, the mechanism by which this phenomenon is triggered is controversial. By analyzing 22 gene-edited rabbit lines generated using CRISPR/Cas9, we provide evidence of exon skipping at high frequency in premature termination codon-mutated rabbits but not in the rabbits with a premature termination codon mutation in exon 1 rabbits with non-frameshift or missense mutations. Our results suggest that CRISPR-mediated exon skipping depends on premature termination codon mutation-induced nonsense-associated altered splicing.
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Affiliation(s)
- Tingting Sui
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Yuning Song
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Zhiquan Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Yuanyuan Xu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China. .,Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China.
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
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28
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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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29
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Chen D, Tang JX, Li B, Hou L, Wang X, Kang L. CRISPR/Cas9-mediated genome editing induces exon skipping by complete or stochastic altering splicing in the migratory locust. BMC Biotechnol 2018; 18:60. [PMID: 30253761 PMCID: PMC6156852 DOI: 10.1186/s12896-018-0465-7] [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: 06/13/2018] [Accepted: 08/31/2018] [Indexed: 01/31/2023] Open
Abstract
Background The CRISPR/Cas9 system has been widely used to generate gene knockout/knockin models by inducing frameshift mutants in cell lines and organisms. Several recent studies have reported that such mutants can lead to in-frame exon skipping in cell lines. However, there was little research about post-transcriptional effect of CRISPR-mediated gene editing in vivo. Results We showed that frameshift indels also induced complete or stochastic exon skipping by deleting different regions to influence pre-mRNA splicing in vivo. In the migratory locust, the missing 55 bp at the boundary of intron 3 and exon 4 of an olfactory receptor gene, LmigOr35, resulted in complete exon 4 skipping, whereas the lacking 22 bp in exon 4 of LmigOr35 only resulted in stochastic exon 4 skipping. A single sgRNA induced small insertions or deletions at the boundary of intron and exon to disrupt the 3′ splicing site causing completely exon skipping, or alternatively induce small insertions or deletions in the exon to stochastic alter splicing causing the stochastic exon skipping. Conclusions These results indicated that complete or stochastic exon skipping could result from the CRISPR-mediated genome editing by deleting different regions of the gene. Although exon skipping caused by CRISPR-mediated editing was an unexpected outcome, this finding could be developed as a technology to investigate pre-mRNA splicing or to cure several human diseases caused by splicing mutations. Electronic supplementary material The online version of this article (10.1186/s12896-018-0465-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dafeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Xin Tang
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Beibei Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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30
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Argus: An open-source and flexible software application for automated quantification of behavior during social interaction in adult zebrafish. Behav Res Methods 2018; 51:727-746. [PMID: 30105442 DOI: 10.3758/s13428-018-1083-y] [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: 11/08/2022]
Abstract
Zebrafish show great potential for behavioral neuroscience. Promising lines of research, however, require the development and validation of software tools that will allow automated and cost-effective behavioral analysis. Building on our previous work with the RealFishTracker (in-house-developed tracking system), we present Argus, a data extraction and analysis tool built in the open-source R language for behavioral researchers without any expertise in R. Argus includes a new, user-friendly, and efficient graphical user interface, instead of a command-line interface, and offers simplicity and flexibility in measuring complex zebrafish behavior through customizable parameters. In this article, we compare Argus with Noldus EthoVision and Noldus The Observer, to validate this new system. All three software applications were originally designed to quantify the behavior of a single subject. We first also performed an analysis of the movement of individual fish and compared the performance of the three software applications. Next we computed and quantified the behavioral variables that characterize dyadic interactions between zebrafish. We found that Argus and EthoVision extract similar absolute values and patterns of changes in these values for several behavioral measures, including speed, freezing, erratic movement, and interindividual distance. In contrast, the manual coding of behavior in The Observer showed weaker correlations with the two tracking methods (EthoVision and Argus). Thus, Argus is a novel, cost-effective, and customizable method for the analysis of adult zebrafish behavior that may be utilized for the behavioral quantification of both single and dyadic interacting subjects, but further sophistication will be needed for the proper identification of complex motor patterns, measures that a human observers can easily detect.
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31
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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: 404] [Impact Index Per Article: 67.3] [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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32
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Zebrafish Models of Rare Hereditary Pediatric Diseases. Diseases 2018; 6:diseases6020043. [PMID: 29789451 PMCID: PMC6023479 DOI: 10.3390/diseases6020043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 12/12/2022] Open
Abstract
Recent advances in sequencing technologies have made it significantly easier to find the genetic roots of rare hereditary pediatric diseases. These novel methods are not panaceas, however, and they often give ambiguous results, highlighting multiple possible causative mutations in affected patients. Furthermore, even when the mapping results are unambiguous, the affected gene might be of unknown function. In these cases, understanding how a particular genotype can result in a phenotype also needs carefully designed experimental work. Model organism genetics can offer a straightforward experimental setup for hypothesis testing. Containing orthologs for over 80% of the genes involved in human diseases, zebrafish (Danio rerio) has emerged as one of the top disease models over the past decade. A plethora of genetic tools makes it easy to create mutations in almost any gene of the zebrafish genome and these mutant strains can be used in high-throughput preclinical screens for active molecules. As this small vertebrate species offers several other advantages as well, its popularity in biomedical research is bound to increase, with “aquarium to bedside” drug development pipelines taking a more prevalent role in the near future.
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33
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Cloney K, Steele SL, Stoyek MR, Croll RP, Smith FM, Prykhozhij SV, Brown MM, Midgen C, Blake K, Berman JN. Etiology and functional validation of gastrointestinal motility dysfunction in a zebrafish model of CHARGE syndrome. FEBS J 2018; 285:2125-2140. [PMID: 29660852 DOI: 10.1111/febs.14473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 03/17/2018] [Accepted: 04/09/2018] [Indexed: 12/21/2022]
Abstract
CHARGE syndrome is linked to autosomal-dominant mutations in the CHD7 gene and results in a number of physiological and structural abnormalities, including heart defects, hearing and vision loss, and gastrointestinal (GI) problems. Of these challenges, GI problems have a profound impact throughout an individual's life, resulting in increased morbidity and mortality. A homolog of CHD7 has been identified in the zebrafish, the loss of which recapitulates many of the features of the human disease. Using a morpholino chd7 knockdown model complemented by a chd7 null mutant zebrafish line, we examined GI structure, innervation, and motility in larval zebrafish. Loss of chd7 resulted in physically smaller GI tracts with normal epithelial and muscular histology, but decreased and disorganized vagal projections, particularly in the foregut. chd7 morphant larvae had significantly less ability to empty their GI tract of gavaged fluorescent beads, and this condition was only minimally improved by the prokinetic agents, domperidone and erythromycin, in keeping with mixed responses to these agents in patients with CHARGE syndrome. The conserved genetics and transparency of the zebrafish have provided new insights into the consequences of chd7 gene dysfunction on the GI system and cranial nerve patterning. These findings highlight the opportunity of the zebrafish to serve as a preclinical model for studying compounds that may improve GI motility in individuals with CHARGE syndrome.
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Affiliation(s)
- Kellie Cloney
- Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, Canada
| | - Matthew R Stoyek
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada
| | - Roger P Croll
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada
| | - Frank M Smith
- Department of Medical Neuroscience, Dalhousie University, Halifax, Canada
| | | | - Mary M Brown
- Departments of Pediatrics and Obstetrics and Gynaecology, Dalhousie University, Halifax, Canada
| | - Craig Midgen
- Department of Pathology, Dalhousie University, Halifax, Canada
| | - Kim Blake
- Faculty of Medicine, Dalhousie University, Halifax, Canada.,Department of Pediatrics, Dalhousie University, Halifax, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, Canada.,Department of Pathology, Dalhousie University, Halifax, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
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34
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Ward R, Sundaramurthi H, Di Giacomo V, Kennedy BN. Enhancing Understanding of the Visual Cycle by Applying CRISPR/Cas9 Gene Editing in Zebrafish. Front Cell Dev Biol 2018; 6:37. [PMID: 29696141 PMCID: PMC5904205 DOI: 10.3389/fcell.2018.00037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/19/2018] [Indexed: 01/23/2023] Open
Abstract
During the vertebrate visual cycle, all-trans-retinal is exported from photoreceptors to the adjacent RPE or Müller glia wherein 11-cis-retinal is regenerated. The 11-cis chromophore is returned to photoreceptors, forming light-sensitive visual pigments with opsin GPCRs. Dysfunction of this process perturbs phototransduction because functional visual pigment cannot be generated. Mutations in visual cycle genes can result in monogenic inherited forms of blindness. Though key enzymatic processes are well characterized, questions remain as to the physiological role of visual cycle proteins in different retinal cell types, functional domains of these proteins in retinoid biochemistry and in vivo pathogenesis of disease mutations. Significant progress is needed to develop effective and accessible treatments for inherited blindness arising from mutations in visual cycle genes. Here, we review opportunities to apply gene editing technology to two crucial visual cycle components, RPE65 and CRALBP. Expressed exclusively in the human RPE, RPE65 enzymatically converts retinyl esters into 11-cis retinal. CRALBP is an 11-cis-retinal binding protein expressed in human RPE and Muller glia. Loss-of-function mutations in either protein results in autosomal recessive forms of blindness. Modeling these human conditions using RPE65 or CRALBP murine knockout models have enhanced our understanding of their biochemical function, associated disease pathogenesis and development of therapeutics. However, rod-dominated murine retinae provide a challenge to assess cone function. The cone-rich zebrafish model is amenable to cost-effective maintenance of a variety of strains. Interestingly, gene duplication in zebrafish resulted in three Rpe65 and two Cralbp isoforms with differential temporal and spatial expression patterns. Functional investigations of zebrafish Rpe65 and Cralbp were restricted to gene knockdown with morpholino oligonucleotides. However, transient silencing, off-target effects and discrepancies between knockdown and knockout models, highlight a need for more comprehensive alternatives for functional genomics. CRISPR/Cas9 in zebrafish has emerged as a formidable technology enabling targeted gene knockout, knock-in, activation, or silencing to single base-pair resolution. Effective, targeted gene editing by CRISPR/Cas9 in zebrafish enables unprecedented opportunities to create genetic research models. This review will discuss existing knowledge gaps regarding RPE65 and CRALBP. We explore the benefits of CRISPR/Cas9 to establish innovative zebrafish models to enhance knowledge of the visual cycle.
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Affiliation(s)
- Rebecca Ward
- UCD School of Biomolecular & Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Husvinee Sundaramurthi
- UCD School of Biomolecular & Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
- UCD School of Medicine, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Breandán N. Kennedy
- UCD School of Biomolecular & Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
- *Correspondence: Breandán N. Kennedy
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35
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Carreño Gutiérrez H, Vacca I, Pons AI, Norton WHJ. Automatic quantification of juvenile zebrafish aggression. J Neurosci Methods 2017; 296:23-31. [PMID: 29274793 DOI: 10.1016/j.jneumeth.2017.12.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/12/2017] [Accepted: 12/20/2017] [Indexed: 11/24/2022]
Abstract
BACKGROUND Although aggression is a common symptom of psychiatric disorders the drugs available to treat it are non-specific and can have unwanted side effects. The zebrafish is an ideal model for aggression research. Zebrafish are small, amenable to genetic and pharmacological manipulation, and agonistic behaviour can be measured reliably. NEW METHOD In this study we have established a novel setup to automatically quantify aggression and locomotion in one-month old juvenile zebrafish, a stage at which fish exhibit adult-like behaviour but are small so that one camera can film several animals. RESULTS We have validated our novel software by comparison to manual quantification of behaviour, characterised the aggression of one-month old fish, and demonstrated that we can detect alterations to aggression caused by mutation or drug application. COMPARISON WITH OTHER METHODS The ability to record up to 12 juvenile fish allows us to speed up and standardise data acquisition compared to studies of single fish. CONCLUSIONS This setup appears to be suitable to screen for drugs that decrease zebrafish aggression as a first step toward developing novel treatments for this behaviour.
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Affiliation(s)
- Héctor Carreño Gutiérrez
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, LE1 7RH, UK
| | - Irene Vacca
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, LE1 7RH, UK
| | - Anna Inguanzo Pons
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, LE1 7RH, UK
| | - William H J Norton
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, LE1 7RH, UK.
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36
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van Ravenswaaij-Arts C, Martin DM. New insights and advances in CHARGE syndrome: Diagnosis, etiologies, treatments, and research discoveries. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2017; 175:397-406. [PMID: 29171162 DOI: 10.1002/ajmg.c.31592] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 01/17/2023]
Abstract
CHARGE syndrome is a multiple congenital anomaly condition caused, in a majority of individuals, by loss of function pathogenic variants in the gene CHD7. In this special issue of the American Journal of Medical Genetics part C, authors of eleven manuscripts describe specific organ system features of CHARGE syndrome, with a focus on recent developments in diagnosis, etiologies, and treatments. Since 2004, when CHD7 was identified as the major causative gene in CHARGE, several animal models (mice, zebrafish, flies, and frog) and cell-based systems have been developed to explore the underlying pathophysiology of this condition. In this article, we summarize those advances, highlight opportunities for new discoveries, and encourage readers to explore specific organ systems in more detail in each individual article. We hope the excitement around innovative research and development in CHARGE syndrome will encourage others to join this effort, and will stimulate other investigators and professionals to engage with individuals diagnosed as having CHARGE syndrome, their families, and their care providers.
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Affiliation(s)
- Conny van Ravenswaaij-Arts
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Donna M Martin
- Departments of Human Genetics, The University of Michigan Medical School, Ann Arbor, Michigan.,Departments of Pediatrics, The University of Michigan Medical School, Ann Arbor, Michigan
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37
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Anderson JL, Mulligan TS, Shen MC, Wang H, Scahill CM, Tan FJ, Du SJ, Busch-Nentwich EM, Farber SA. mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay. PLoS Genet 2017; 13:e1007105. [PMID: 29161261 PMCID: PMC5716581 DOI: 10.1371/journal.pgen.1007105] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 12/05/2017] [Accepted: 11/07/2017] [Indexed: 12/26/2022] Open
Abstract
As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of adaptations that can occur may inform the strategies of mutant generation. The recent rise of reverse genetic, gene targeting methods has allowed researchers to readily generate mutations in any gene of interest with relative ease. Should these mutations have the predicted effect on the mRNA and encoded protein, we would expect many more abnormal phenotypes than are typically being seen in reverse genetic screens. Here we set out to explore some of the reasons for this discrepancy by studying seven separate mutations in zebrafish. We present evidence that thorough cDNA sequence analysis is a key step in assessing the likelihood that a given mutation will produce hypomorphic or null alleles. This study reveals that mRNA processing in the mutant background often produces transcripts that escape nonsense-mediated decay, thereby potentially preserving gene function. By understanding the ways that cells avoid the deleterious consequences of mutations, researchers can better design reverse genetic strategies to increase the likelihood of gene disruption.
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Affiliation(s)
- Jennifer L. Anderson
- Carnegie Institution for Science, Department of Embryology, Baltimore, Maryland, United States of America
| | - Timothy S. Mulligan
- Carnegie Institution for Science, Department of Embryology, Baltimore, Maryland, United States of America
| | - Meng-Chieh Shen
- Carnegie Institution for Science, Department of Embryology, Baltimore, Maryland, United States of America
| | - Hui Wang
- University of Maryland School of Medicine, Department of Biochemistry and Molecular Biology, Baltimore, Maryland, United States of America
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Catherine M. Scahill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Frederick J. Tan
- Carnegie Institution for Science, Department of Embryology, Baltimore, Maryland, United States of America
| | - Shao J. Du
- University of Maryland School of Medicine, Department of Biochemistry and Molecular Biology, Baltimore, Maryland, United States of America
| | - Elisabeth M. Busch-Nentwich
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Steven A. Farber
- Carnegie Institution for Science, Department of Embryology, Baltimore, Maryland, United States of America
- * E-mail:
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38
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Razaghi B, Steele SL, Prykhozhij SV, Stoyek MR, Hill JA, Cooper MD, McDonald L, Lin W, Daugaard M, Crapoulet N, Chacko S, Lewis SM, Scott IC, Sorensen PHB, Berman JN. hace1 Influences zebrafish cardiac development via ROS-dependent mechanisms. Dev Dyn 2017; 247:289-303. [PMID: 29024245 DOI: 10.1002/dvdy.24600] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/23/2017] [Accepted: 09/15/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In this study, we reveal a previously undescribed role of the HACE1 (HECT domain and Ankyrin repeat Containing E3 ubiquitin-protein ligase 1) tumor suppressor protein in normal vertebrate heart development using the zebrafish (Danio rerio) model. We examined the link between the cardiac phenotypes associated with hace1 loss of function to the expression of the Rho small family GTPase, rac1, which is a known target of HACE1 and promotes ROS production via its interaction with NADPH oxidase holoenzymes. RESULTS We demonstrate that loss of hace1 in zebrafish via morpholino knockdown results in cardiac deformities, specifically a looping defect, where the heart is either tubular or "inverted". Whole-mount in situ hybridization of cardiac markers shows distinct abnormalities in ventricular morphology and atrioventricular valve formation in the hearts of these morphants, as well as increased expression of rac1. Importantly, this phenotype appears to be directly related to Nox enzyme-dependent ROS production, as both genetic inhibition by nox1 and nox2 morpholinos or pharmacologic rescue using ROS scavenging agents restores normal cardiac structure. CONCLUSIONS Our study demonstrates that HACE1 is critical in the normal development and proper function of the vertebrate heart via a ROS-dependent mechanism. Developmental Dynamics 247:289-303, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Babak Razaghi
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew R Stoyek
- Department of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jessica A Hill
- Department of Marine Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew D Cooper
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lindsay McDonald
- Department of Emergency Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - William Lin
- Undergraduate Program, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mads Daugaard
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.,Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Simi Chacko
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Ian C Scott
- Department of Molecular Genetics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Poul H B Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada.,IWK Health Centre, Halifax, Nova Scotia, Canada
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39
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Stainier DYR, Raz E, Lawson ND, Ekker SC, Burdine RD, Eisen JS, Ingham PW, Schulte-Merker S, Yelon D, Weinstein BM, Mullins MC, Wilson SW, Ramakrishnan L, Amacher SL, Neuhauss SCF, Meng A, Mochizuki N, Panula P, Moens CB. Guidelines for morpholino use in zebrafish. PLoS Genet 2017; 13:e1007000. [PMID: 29049395 PMCID: PMC5648102 DOI: 10.1371/journal.pgen.1007000] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Erez Raz
- Institute of Cell Biology, ZBME, University of Münster, Münster, Germany
| | - Nathan D. Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | | | - Rebecca D. Burdine
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Judith S. Eisen
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Philip W. Ingham
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Stefan Schulte-Merker
- Institute of Cardiovascular Organogenesis and Regeneration, WWU Münster, Faculty of Medicine, Münster, Germany
| | - Deborah Yelon
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Brant M. Weinstein
- Division of Developmental Biology, NICHD, NIH, Bethesda, Maryland, United States of America
| | - Mary C. Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Stephen W. Wilson
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sharon L. Amacher
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, Ohio State University, Columbus, Ohio, United States of America
| | | | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Naoki Mochizuki
- National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Pertti Panula
- Department of Anatomy and Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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40
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Abstract
A new study finds that splicing disruption is a frequent consequence of mutations generated by CRISPR/Cas9 gene-editing technology, and alleles designed to be null can express aberrant proteins. This new information allows enhanced quality control procedures to select the best mutant alleles generated by CRISPR/Cas9. Please see related Method article: https://www.doi.org/10.1186/s13059-017-1237-8
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Affiliation(s)
- Joshua J Sharpe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
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