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Sieliwonczyk E, Vandendriessche B, Claes C, Mayeur E, Alaerts M, Holmgren P, Canter Cremers T, Snyders D, Loeys B, Schepers D. Improved selection of zebrafish CRISPR editing by early next-generation sequencing based genotyping. Sci Rep 2023; 13:1491. [PMID: 36707549 PMCID: PMC9883431 DOI: 10.1038/s41598-023-27503-9] [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: 09/29/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023] Open
Abstract
Despite numerous prior attempts to improve knock-in (KI) efficiency, the introduction of precise base pair substitutions by the CRISPR-Cas9 technique in zebrafish remains challenging. In our efforts to generate KI zebrafish models of human CACNA1C mutations, we have tested the effect of several CRISPR determinants on KI efficiency across two sites in a single gene and developed a novel method for early selection to ameliorate KI efficiency. We identified optimal KI conditions for Cas9 protein and non-target asymmetric PAM-distal single stranded deoxynucleotide repair templates at both cacna1c sites. An effect of distance to the cut site on the KI efficiency was only observed for a single repair template conformation at one of the two sites. By combining minimally invasive early genotyping with the zebrafish embryo genotyper (ZEG) device and next-generation sequencing, we were able to obtain an almost 17-fold increase in somatic editing efficiency. The added benefit of the early selection procedure was particularly evident for alleles with lower somatic editing efficiencies. We further explored the potential of the ZEG selection procedure for the improvement of germline transmission by demonstrating germline transmission events in three groups of pre-selected embryos.
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Affiliation(s)
- Ewa Sieliwonczyk
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
| | - Bert Vandendriessche
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Charlotte Claes
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Evy Mayeur
- Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Maaike Alaerts
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Philip Holmgren
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Tycho Canter Cremers
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dirk Snyders
- Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Bart Loeys
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dorien Schepers
- Faculty of Medicine and Health Sciences, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Zhang T, Peterson RT. Modeling Lysosomal Storage Diseases in the Zebrafish. Front Mol Biosci 2020; 7:82. [PMID: 32435656 PMCID: PMC7218095 DOI: 10.3389/fmolb.2020.00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a family of 70 metabolic disorders characterized by mutations in lysosomal proteins that lead to storage material accumulation, multiple-organ pathologies that often involve neurodegeneration, and early mortality in a significant number of patients. Along with the necessity for more effective therapies, there exists an unmet need for further understanding of disease etiology, which could uncover novel pathways and drug targets. Over the past few decades, the growth in knowledge of disease-associated pathways has been facilitated by studies in model organisms, as advancements in mutagenesis techniques markedly improved the efficiency of model generation in mammalian and non-mammalian systems. In this review we highlight non-mammalian models of LSDs, focusing specifically on the zebrafish, a vertebrate model organism that shares remarkable genetic and metabolic similarities with mammals while also conferring unique advantages such as optical transparency and amenability toward high-throughput applications. We examine published zebrafish LSD models and their reported phenotypes, address organism-specific advantages and limitations, and discuss recent technological innovations that could provide potential solutions.
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Affiliation(s)
- T Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, United States
| | - R T Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, United States
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Abstract
Most current methods for genotyping zebrafish embryos require sacrifice or raising the animal to at least 1 month of age for fin amputation. These limitations restrict the use of zebrafish and increase time and costs for experiments. This article introduces an innovative method for genotyping live zebrafish embryos. The method utilizes enzyme to extract a small amount of genetic material from the skin tissue of the embryo. Then, using conventional polymerase chain reaction (PCR) strategy, the embryo is genotyped. This approach was successful >95% of the time while maintaining high viability (>90%) of the embryo. This effective method can facilitate high-throughput screening and other applications in zebrafish.
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Affiliation(s)
- Xue Zhang
- Model Animal Research Centre, Nanjing University, Nanjing, China
| | - Zhaojunjie Zhang
- Model Animal Research Centre, Nanjing University, Nanjing, China
| | - Qinshun Zhao
- Model Animal Research Centre, Nanjing University, Nanjing, China
| | - Xin Lou
- Model Animal Research Centre, Nanjing University, Nanjing, China
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Lambert CJ, Freshner BC, Chung A, Stevenson TJ, Bowles DM, Samuel R, Gale BK, Bonkowsky JL. An automated system for rapid cellular extraction from live zebrafish embryos and larvae: Development and application to genotyping. PLoS One 2018; 13:e0193180. [PMID: 29543903 PMCID: PMC5854293 DOI: 10.1371/journal.pone.0193180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/06/2018] [Indexed: 01/31/2023] Open
Abstract
Zebrafish are a valuable model organism in biomedical research. Their rapid development, ability to model human diseases, utility for testing genetic variants identified from next-generation sequencing, amenity to CRISPR mutagenesis, and potential for therapeutic compound screening, has led to their wide-spread adoption in diverse fields of study. However, their power for large-scale screens is limited by the absence of automated genotyping tools for live animals. This constrains potential drug screen options, limits analysis of embryonic and larval phenotypes, and requires raising additional animals to adulthood to ensure obtaining an animal of the desired genotype. Our objective was to develop an automated system that would rapidly obtain cells and DNA from zebrafish embryos and larvae for genotyping, and that would keep the animals alive. We describe the development, testing, and validation of a zebrafish embryonic genotyping device, termed “ZEG” (Zebrafish Embryo Genotyper). Using microfluidic harmonic oscillation of the animal on a roughened glass surface, the ZEG is able to obtain genetic material (cells and DNA) for use in genotyping, from 24 embryos or larvae simultaneously in less than 10 minutes. Loading and unloading of the ZEG is performed manually with a standard pipette tip or transfer pipette. The obtained genetic material is amplified by PCR and can be used for subsequent analysis including sequencing, gel electrophoresis, or high-resolution melt-analysis. Sensitivity of genotyping and survival of animals are both greater than 90%. There are no apparent effects on body morphology, development, or motor behavior tests. In summary, the ZEG device enables rapid genotyping of live zebrafish embryos and larvae, and animals are available for downstream applications, testing, or raising.
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Affiliation(s)
- Christopher J Lambert
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah, United States of America
| | - Briana C Freshner
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Arlen Chung
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah, United States of America
| | - Tamara J Stevenson
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - D Miranda Bowles
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Raheel Samuel
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah, United States of America.,Nanonc Inc., Salt Lake City, Utah, United States of America
| | - Bruce K Gale
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah, United States of America.,Nanonc Inc., Salt Lake City, Utah, United States of America
| | - Joshua L Bonkowsky
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
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Yang F, Gao C, Wang P, Zhang GJ, Chen Z. Fish-on-a-chip: microfluidics for zebrafish research. LAB ON A CHIP 2016; 16:1106-25. [PMID: 26923141 DOI: 10.1039/c6lc00044d] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-efficiency zebrafish (embryo) handling platforms are crucially needed to facilitate the deciphering of the increasingly expanding vertebrate-organism model values. However, the manipulation platforms for zebrafish are scarce and rely mainly on the conventional "static" microtiter plates or glass slides with rigid gel, which limits the dynamic, three-dimensional (3D), tissue/organ-oriented information acquisition from the intact larva with normal developmental dynamics. In addition, these routine platforms are not amenable to high-throughput handling of such swimming multicellular biological entities at the single-organism level and incapable of precisely controlling the growth microenvironment by delivering stimuli in a well-defined spatiotemporal fashion. Recently, microfluidics has been developed to address these technical challenges via tailor-engineered microscale structures or structured arrays, which integrate with or interface to functional components (e.g. imaging systems), allowing quantitative readouts of small objects (zebrafish larvae and embryos) under normal physiological conditions. Here, we critically review the recent progress on zebrafish manipulation, imaging and phenotype readouts of external stimuli using these microfluidic tools and discuss the challenges that confront these promising "fish-on-a-chip" technologies. We also provide an outlook on future potential trends in this field by combining with bionanoprobes and biosensors.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
| | - Chuan Gao
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
| | - Ping Wang
- School of Basic Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
| | - Zuanguang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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