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Niu M, Whang H, Wu Z, Jiang S, Chen L. Deletion of Asb15b gene can lead to a significant decrease in zebrafish intermuscular bone. Gene 2024; 923:148561. [PMID: 38754570 DOI: 10.1016/j.gene.2024.148561] [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] [Received: 02/06/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Intermuscular bones, which are present in numerous economically significant fish species, have a negative impact on the development of aquaculture. The Asb15b gene, primarily expressed in skeletal muscle, plays a crucial role in regulating protein turnover and the development of muscle fibers. It stimulates protein synthesis and controls the differentiation of muscle fibers. In this study, we employed CRISPR/Cas9 technology to generate homozygous zebrafish strains with 7 bp and 49 bp deletions in the Asb15b gene. Subsequent analyses using skeleton staining demonstrated a substantial reduction in the number of intermuscular bones in adult Asb15b-/- -7 bp and Asb15b-/- -49 bp mutants compared to the wild-type zebrafish, with decreases of 30 % (P < 0.001) and 40 % (P < 0.0001), respectively. Histological experiments further revealed that the diameter and number of muscle fibers in adult Asb15b-/- mutants did not exhibit significant changes when compared to wild-type zebrafish. Moreover, qRT-PCR experiments demonstrated significant differences in the expression of bmp6 and runx2b genes, which are key regulators of intermuscular bone development, during different stages of intermuscular bone development in Asb15b-/- mutants. This study strongly suggests that the Asb15b gene plays a crucial role in regulating intermuscular bone development in fish and lays the groundwork for further exploration of the role of the Asb15b gene in zebrafish intermuscular bone development.
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Affiliation(s)
- Minghui Niu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Huamin Whang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Zhichao Wu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Shouwen Jiang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Liangbiao Chen
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China.
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2
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Uribe-Salazar JM, Kaya G, Weyenberg K, Radke B, Hino K, Soto DC, Shiu JL, Zhang W, Ingamells C, Haghani NK, Xu E, Rosas J, Simó S, Miesfeld J, Glaser T, Baraban SC, Jao LE, Dennis MY. Zebrafish models of human-duplicated gene SRGAP2 reveal novel functions in microglia and visual system development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612570. [PMID: 39314374 PMCID: PMC11418993 DOI: 10.1101/2024.09.11.612570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Recent expansion of duplicated genes unique in the Homo lineage likely contributed to brain evolution and other human-specific traits. One hallmark example is the expansion of the human SRGAP2 family, resulting in a human-specific paralog SRGAP2C . Introduction of SRGAP2C in mouse models is associated with altering cortical neuronal migration, axon guidance, synaptogenesis, and sensory-task performance. Truncated, human-specific SRGAP2C heterodimerizes with the full-length ancestral gene product SRGAP2A and antagonizes its functions. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we showed that srgap2 knockout results in viable offspring that phenocopy "humanized" SRGAP2C larvae. Specifically, human SRGAP2C protein interacts with zebrafish Srgap2, demonstrating similar Srgap2 functional antagonism observed in mice. Shared traits between knockout and humanized zebrafish larvae include altered morphometric features (i.e., reduced body length and inter-eye distance) and differential expression of synapse-, axogenesis-, vision-related genes. Through single-cell transcriptome analysis, we further observed a skewed balance of excitatory and inhibitory neurons that likely contributes to increased susceptibility to seizures displayed by Srgap2 mutant larvae, a phenotype resembling SRGAP2 loss-of-function in a child with early infantile epileptic encephalopathy. Single-cell data also pointed to strong microglia expression of srgap2 with mutants exhibiting altered membrane dynamics and likely delayed maturation of microglial cells. srgap2 -expressing microglia cells were also detected in the developing eye together with altered expression of genes related to axogenesis and synaptogenesis in mutant retinal cells. Consistent with the perturbed gene expression in the retina, we found that SRGAP2 mutant larvae exhibited increased sensitivity to broad and fine visual cues. Finally, comparing the transcriptomes of relevant cell types between human (+ SRGAP2C ) and non-human primates (- SRGAP2C ) revealed significant overlaps of gene alterations with mutant cells in our zebrafish models; this suggests that SRGAP2C plays similar roles altering microglia and the visual system in modern humans. Together, our functional characterization of zebrafish Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features.
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Goumenaki P, Günther S, Kikhi K, Looso M, Marín-Juez R, Stainier DYR. The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration. NATURE CARDIOVASCULAR RESEARCH 2024; 3:1158-1176. [PMID: 39271818 PMCID: PMC11399109 DOI: 10.1038/s44161-024-00538-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 08/06/2024] [Indexed: 09/15/2024]
Abstract
The innate immune response is triggered rapidly after injury and its spatiotemporal dynamics are critical for regeneration; however, many questions remain about its exact role. Here we show that MyD88, a key component of the innate immune response, controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88-/- ventricles a significant reduction in neutrophil and macrophage numbers and the expansion of a collagen-rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88-/- endocardium and increased myofibroblasts and scarring. Notably, endothelial-specific overexpression of myd88 reverses these neutrophil, fibrotic and scarring phenotypes. Mechanistically, we identify the endocardial-derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway, and using loss-of-function and gain-of-function tools, we show that it controls neutrophil recruitment. Altogether, these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration.
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Affiliation(s)
- Pinelopi Goumenaki
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Stefan Günther
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Khrievono Kikhi
- Flow Cytometry Service Group, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Rubén Marín-Juez
- Centre Hospitalier Universitaire Sainte-Justine Research Centre, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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4
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Shah AN, Leesch F, Lorenzo-Orts L, Grundmann L, Novatchkova M, Haselbach D, Calo E, Pauli A. A dual ribosomal system in the zebrafish soma and germline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610041. [PMID: 39257781 PMCID: PMC11383705 DOI: 10.1101/2024.08.29.610041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Protein synthesis during vertebrate embryogenesis is driven by ribosomes of two distinct origins: maternal ribosomes synthesized during oogenesis and stored in the egg, and somatic ribosomes, produced by the developing embryo after zygotic genome activation (ZGA). In zebrafish, these two ribosome types are expressed from different genomic loci and also differ in their ribosomal RNA (rRNA) sequence. To characterize this dual ribosome system further, we examined the expression patterns of maternal and somatic rRNAs during embryogenesis and in adult tissues. We found that maternal rRNAs are not only expressed during oogenesis but are continuously produced in the zebrafish germline. Proteomic analyses of maternal and somatic ribosomes unveiled differences in core ribosomal protein composition. Most nucleotide differences between maternal and somatic rRNAs are located in the flexible, structurally not resolved expansion segments. Our in vivo data demonstrated that both maternal and somatic ribosomes can be translationally active in the embryo. Using transgenically tagged maternal or somatic ribosome subunits, we experimentally confirm the presence of hybrid 80S ribosomes composed of 40S and 60S subunits from both origins and demonstrate the preferential in vivo association of maternal ribosomes with germline-specific transcripts. Our study identifies a distinct type of ribosomes in the zebrafish germline and thus presents a foundation for future explorations into possible regulatory mechanisms and functional roles of heterogeneous ribosomes.
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Affiliation(s)
- Arish N Shah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Friederike Leesch
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Laura Lorenzo-Orts
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Lorenz Grundmann
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Andrea Pauli
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
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Belleville AE, Thomas JD, Tonnies J, Gabel AM, Borrero Rossi A, Singh P, Queitsch C, Bradley RK. An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth. PLoS Genet 2024; 20:e1011363. [PMID: 39150991 PMCID: PMC11357089 DOI: 10.1371/journal.pgen.1011363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 08/28/2024] [Accepted: 07/08/2024] [Indexed: 08/18/2024] Open
Abstract
Many of the most highly conserved elements in the human genome are "poison exons," alternatively spliced exons that contain premature termination codons and permit post-transcriptional regulation of mRNA abundance through induction of nonsense-mediated mRNA decay (NMD). Poison exons are widely assumed to be highly conserved due to their presumed importance for organismal fitness, but this functional importance has never been tested in the context of a whole organism. Here, we report that a poison exon in Smndc1 is conserved across mammals and plants and plays a molecular autoregulatory function in both kingdoms. We generated mouse and A. thaliana models lacking this poison exon to find its loss leads to deregulation of SMNDC1 protein levels, pervasive alterations in mRNA processing, and organismal size restriction. Together, these models demonstrate the importance of poison exons for both molecular and organismal phenotypes that likely explain their extraordinary conservation.
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Affiliation(s)
- Andrea E. Belleville
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - James D. Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Graduate Program in Biology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Andrea Borrero Rossi
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Priti Singh
- Preclinical Modeling Core, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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6
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Bi D, Van Hal A, Aschmann D, Shen M, Zhang H, Su L, Arias-Alpizar G, Kros A, Barz M, Bussmann J. Deconvolving Passive and Active Targeting of Liposomes Bearing LDL Receptor Binding Peptides Using the Zebrafish Embryo Model. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310781. [PMID: 38488770 DOI: 10.1002/smll.202310781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/20/2024] [Indexed: 08/09/2024]
Abstract
Improving target versus off-target ratio in nanomedicine remains a major challenge for increasing drug bioavailability and reducing toxicity. Active targeting using ligands on nanoparticle surfaces is a key approach but has limited clinical success. A potential issue is the integration of targeting ligands also changes the physicochemical properties of nanoparticles (passive targeting). Direct studies to understand the mechanisms of active targeting and off-targeting in vivo are limited by the lack of suitable tools. Here, the biodistribution of a representative active targeting liposome is analyzed, modified with an apolipoprotein E (ApoE) peptide that binds to the low-density lipoprotein receptor (LDLR), using zebrafish embryos. The ApoE liposomes demonstrated the expected liver targeting effect but also accumulated in the kidney glomerulus. The ldlra-/- zebrafish is developed to explore the LDLR-specificity of ApoE liposomes. Interestingly, liver targeting depends on the LDLR-specific interaction, while glomerular accumulation is independent of LDLR and peptide sequence. It is found that cationic charges of peptides and the size of liposomes govern glomerular targeting. Increasing the size of ApoE liposomes can avoid this off-targeting. Taken together, the study shows the potential of the zebrafish embryo model for understanding active and passive targeting mechanisms, that can be used to optimize the design of nanoparticles.
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Affiliation(s)
- Dongdong Bi
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Anneke Van Hal
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Dennis Aschmann
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333, The Netherlands
| | - Mengjie Shen
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333, The Netherlands
| | - Heyang Zhang
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Lu Su
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Gabriela Arias-Alpizar
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Alexander Kros
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333, The Netherlands
| | - Matthias Barz
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Jeroen Bussmann
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
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Lesport E, Commeau L, Genet M, Baulieu EE, Tawk M, Giustiniani J. A decrease in Fkbp52 alters autophagosome maturation and A152T-tau clearance in vivo. Front Cell Neurosci 2024; 18:1425222. [PMID: 39119047 PMCID: PMC11306173 DOI: 10.3389/fncel.2024.1425222] [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: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024] Open
Abstract
The failure of the autophagy-lysosomal pathway to clear the pathogenic forms of Tau exacerbates the pathogenesis of tauopathies. We have previously shown that the immunophilin FKBP52 interacts both physically and functionally with Tau, and that a decrease in FKBP52 protein levels is associated with Tau deposition in affected human brains. We have also shown that FKBP52 is physiologically present within the lysosomal system in healthy human neurons and that a decrease in FKBP52 expression alters perinuclear lysosomal positioning and Tau clearance during Tau-induced proteotoxic stress in vitro. In this study, we generate a zebrafish fkbp4 loss of function mutant and show that axonal retrograde trafficking of Lamp1 vesicles is altered in this mutant. Moreover, using our transgenic HuC::mCherry-EGFP-LC3 line, we demonstrate that the autophagic flux is impaired in fkbp4 mutant embryos, suggesting a role for Fkbp52 in the maturation of autophagic vesicles. Alterations in both axonal transport and autophagic flux are more evident in heterozygous rather than homozygous fkbp4 mutants. Finally, taking advantage of the previously described A152T-Tau transgenic fish, we show that the clearance of pathogenic A152T-Tau mutant proteins is slower in fkbp4 +/- mutants in comparison to fkbp4 +/+ larvae. Altogether, these results indicate that Fkbp52 is required for the normal trafficking and maturation of lysosomes and autophagic vacuoles along axons, and that its decrease is sufficient to hinder the clearance of pathogenic Tau in vivo.
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Affiliation(s)
- Emilie Lesport
- Institut Professeur Baulieu, INSERM U1195, Kremlin-Bicêtre, France
- INSERM U1195, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Lucie Commeau
- Institut Professeur Baulieu, INSERM U1195, Kremlin-Bicêtre, France
| | - Mélanie Genet
- Institut Professeur Baulieu, INSERM U1195, Kremlin-Bicêtre, France
| | - Etienne-Emile Baulieu
- Institut Professeur Baulieu, INSERM U1195, Kremlin-Bicêtre, France
- INSERM U1195, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Marcel Tawk
- INSERM U1195, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Julien Giustiniani
- Institut Professeur Baulieu, INSERM U1195, Kremlin-Bicêtre, France
- INSERM U1195, Université Paris-Saclay, Kremlin-Bicêtre, France
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8
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Perlee S, Ma Y, Hunter MV, Swanson JB, Ming Z, Xia J, Lionnet T, McGrail M, White RM. Identifying in vivo genetic dependencies of melanocyte and melanoma development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586101. [PMID: 38562693 PMCID: PMC10983904 DOI: 10.1101/2024.03.22.586101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The advent of large-scale sequencing in both development and disease has identified large numbers of candidate genes that may be linked to important phenotypes. Validating the function of these candidates in vivo is challenging, due to low efficiency and low throughput of most model systems. We have developed a rapid, scalable system for assessing the role of candidate genes using zebrafish. We generated transgenic zebrafish in which Cas9 was knocked-in to the endogenous mitfa locus, a master transcription factor of the melanocyte lineage. We used this system to identify both cell-autonomous and non-cell autonomous regulators of normal melanocyte development. We then applied this to the melanoma setting to demonstrate that loss of genes required for melanocyte survival can paradoxically promote more aggressive phenotypes, highlighting that in vitro screens can mask in vivo phenotypes. Our high-efficiency genetic approach offers a versatile tool for exploring developmental processes and disease mechanisms that can readily be applied to other cell lineages.
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Apolínová K, Pérez FA, Dyballa S, Coppe B, Mercader Huber N, Terriente J, Di Donato V. ZebraReg-a novel platform for discovering regulators of cardiac regeneration using zebrafish. Front Cell Dev Biol 2024; 12:1384423. [PMID: 38799508 PMCID: PMC11116629 DOI: 10.3389/fcell.2024.1384423] [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: 02/09/2024] [Accepted: 04/25/2024] [Indexed: 05/29/2024] Open
Abstract
Cardiovascular disease is the leading cause of death worldwide with myocardial infarction being the most prevalent. Currently, no cure is available to either prevent or revert the massive death of cardiomyocytes that occurs after a myocardial infarction. Adult mammalian hearts display a limited regeneration capacity, but it is insufficient to allow complete myocardial recovery. In contrast, the injured zebrafish heart muscle regenerates efficiently through robust proliferation of pre-existing myocardial cells. Thus, zebrafish allows its exploitation for studying the genetic programs behind cardiac regeneration, which may be present, albeit dormant, in the adult human heart. To this end, we have established ZebraReg, a novel and versatile automated platform for studying heart regeneration kinetics after the specific ablation of cardiomyocytes in zebrafish larvae. In combination with automated heart imaging, the platform can be integrated with genetic or pharmacological approaches and used for medium-throughput screening of presumed modulators of heart regeneration. We demonstrate the versatility of the platform by identifying both anti- and pro-regenerative effects of genes and drugs. In conclusion, we present a tool which may be utilised to streamline the process of target validation of novel gene regulators of regeneration, and the discovery of new drug therapies to regenerate the heart after myocardial infarction.
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Affiliation(s)
- Kateřina Apolínová
- ZeClinics SL, Barcelona, Spain
- Biomedicine, Department of Medicine and Life Sciences, Faculty of Health and Life Sciences, Pompeu Fabra University, Barcelona, Spain
| | | | | | - Benedetta Coppe
- Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland
- Department for Biomedical Research DBMR, University of Bern, Bern, Switzerland
| | - Nadia Mercader Huber
- Developmental Biology and Regeneration, Institute of Anatomy, University of Bern, Bern, Switzerland
- Department for Biomedical Research DBMR, University of Bern, Bern, Switzerland
- Centro Nacional de Investigaciones Cardiovasculares CNIC, Madrid, Spain
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10
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Jin L, Liyanage R, Duan D, Chen SJ. Machine learning-inferred and energy landscape-guided analyses reveal kinetic determinants of CRISPR/Cas9 gene editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591525. [PMID: 38746227 PMCID: PMC11092603 DOI: 10.1101/2024.04.30.591525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The CRISPR/Cas nucleases system is widely considered the most important tool in genome engineering. However, current methods for predicting on/off-target effects and designing guide RNA (gRNA) rely on purely data-driven approaches or focus solely on the system's thermal equilibrium properties. Nonetheless, experimental evidence suggests that the process is kinetically controlled rather than being in equilibrium. In this study, we utilized a vast amount of available data and combined random forest, a supervised ensemble learning algorithm, and free energy landscape analysis to investigate the kinetic pathways of R-loop formation in the CRISPR/Cas9 system and the intricate molecular interactions between DNA and the Cas9 RuvC and HNH domains. The study revealed (a) a novel three-state kinetic mechanism, (b) the unfolding of the activation state of the R-loop being the most crucial kinetic determinant and the key predictor for on- and off-target cleavage efficiencies, and (c) the nucleotides from positions +13 to +16 being the kinetically critical nucleotides. The results provide a biophysical rationale for the design of a kinetic strategy for enhancing CRISPR/Cas9 gene editing accuracy and efficiency.
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11
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Barriga FM, Lowe SW. Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements). Nat Protoc 2024; 19:1381-1399. [PMID: 38326496 DOI: 10.1038/s41596-024-00953-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/21/2023] [Indexed: 02/09/2024]
Abstract
The elimination of large genomic regions has been enabled by the advent of site-specific nucleases. However, as the intended deletions get larger, the efficiency of successful engineering decreases to a point where it is not feasible to retrieve edited cells due to the rarity of on-target events. To address this issue, we developed a system called molecular alteration of chromosomes with engineered tandem elements (MACHETE). MACHETE is a CRISPR-Cas9-based system involving two stages: the initial insertion of a bicistronic positive/negative selection cassette to the locus of interest. This is followed by the introduction of single-guide RNAs flanking the knockin cassette to engineer the intended deletion, where only cells that have lost the locus survive the negative selection. In contrast to other approaches optimizing the activity of sequence-specific nucleases, MACHETE selects for the deletion event itself, thus greatly enriching for cells with the engineered alteration. The procedure routinely takes 4-6 weeks from design to selection of polyclonal populations bearing the deletion of interest. We have successfully deployed MACHETE to engineer deletions of up to 45 Mb, as well as the rapid creation of allelic series to map the relevant activities within a locus. This protocol details the design and step-by-step procedure to engineer megabase-sized deletions in cells of interest, with potential application for cancer genetics, transcriptional regulation, genome architecture and beyond.
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Affiliation(s)
- Francisco M Barriga
- Systems Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
| | - Scott W Lowe
- Cancer Biology and Genetics Program and Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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12
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Iglesias Gonzalez AB, Koning HK, Tuz-Sasik MU, van Osselen I, Manuel R, Boije H. Perturbed development of calb2b expressing dI6 interneurons and motor neurons underlies locomotor defects observed in calretinin knock-down zebrafish larvae. Dev Biol 2024; 508:77-87. [PMID: 38278086 DOI: 10.1016/j.ydbio.2024.01.001] [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] [Received: 01/20/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024]
Abstract
Calcium binding proteins are essential for neural development and cellular activity. Calretinin, encoded by calb2a and calb2b, plays a role during early zebrafish development and has been proposed as a marker for distinct neuronal populations within the locomotor network. We generated a calb2b:hs:eGFP transgenic reporter line to characterize calretinin expressing cells in the developing spinal cord and describe morphological and behavioral defects in calretinin knock-down larvae. eGFP was detected in primary and secondary motor neurons, as well as in dI6 and V0v interneurons. Knock-down of calretinin lead to disturbed development of motor neurons and dI6 interneurons, revealing a crucial role during early development of the locomotor network. Primary motor neurons showed delayed axon outgrowth and the distinct inhibitory CoLo neurons, originating from the dI6 lineage, were absent. These observations explain the locomotor defects we observed in calretinin knock-down animals where the velocity, acceleration and coordination were affected during escapes. Altogether, our analysis suggests an essential role for calretinin during the development of the circuits regulating escape responses and fast movements within the locomotor network.
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Affiliation(s)
| | - Harmen Kornelis Koning
- Department of Immunology, Genetics and Pathology, Uppsala University, S-75108, Uppsala, Sweden
| | - Melek Umay Tuz-Sasik
- Department of Immunology, Genetics and Pathology, Uppsala University, S-75108, Uppsala, Sweden
| | - Ilse van Osselen
- Department of Immunology, Genetics and Pathology, Uppsala University, S-75108, Uppsala, Sweden
| | - Remy Manuel
- Department of Immunology, Genetics and Pathology, Uppsala University, S-75108, Uppsala, Sweden
| | - Henrik Boije
- Department of Immunology, Genetics and Pathology, Uppsala University, S-75108, Uppsala, Sweden.
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13
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Dixit S, Kumar A, Srinivasan K, Vincent PMDR, Ramu Krishnan N. Advancing genome editing with artificial intelligence: opportunities, challenges, and future directions. Front Bioeng Biotechnol 2024; 11:1335901. [PMID: 38260726 PMCID: PMC10800897 DOI: 10.3389/fbioe.2023.1335901] [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: 11/09/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-based genome editing (GED) technologies have unlocked exciting possibilities for understanding genes and improving medical treatments. On the other hand, Artificial intelligence (AI) helps genome editing achieve more precision, efficiency, and affordability in tackling various diseases, like Sickle cell anemia or Thalassemia. AI models have been in use for designing guide RNAs (gRNAs) for CRISPR-Cas systems. Tools like DeepCRISPR, CRISTA, and DeepHF have the capability to predict optimal guide RNAs (gRNAs) for a specified target sequence. These predictions take into account multiple factors, including genomic context, Cas protein type, desired mutation type, on-target/off-target scores, potential off-target sites, and the potential impacts of genome editing on gene function and cell phenotype. These models aid in optimizing different genome editing technologies, such as base, prime, and epigenome editing, which are advanced techniques to introduce precise and programmable changes to DNA sequences without relying on the homology-directed repair pathway or donor DNA templates. Furthermore, AI, in collaboration with genome editing and precision medicine, enables personalized treatments based on genetic profiles. AI analyzes patients' genomic data to identify mutations, variations, and biomarkers associated with different diseases like Cancer, Diabetes, Alzheimer's, etc. However, several challenges persist, including high costs, off-target editing, suitable delivery methods for CRISPR cargoes, improving editing efficiency, and ensuring safety in clinical applications. This review explores AI's contribution to improving CRISPR-based genome editing technologies and addresses existing challenges. It also discusses potential areas for future research in AI-driven CRISPR-based genome editing technologies. The integration of AI and genome editing opens up new possibilities for genetics, biomedicine, and healthcare, with significant implications for human health.
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Affiliation(s)
- Shriniket Dixit
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - Anant Kumar
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| | - Kathiravan Srinivasan
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - P. M. Durai Raj Vincent
- School of Computer Science Engineering and Information Systems, Vellore Institute of Technology, Vellore, India
| | - Nadesh Ramu Krishnan
- School of Computer Science Engineering and Information Systems, Vellore Institute of Technology, Vellore, India
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14
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Keating M, Hagle R, Osorio-Méndez D, Rodriguez-Parks A, Almutawa SI, Kang J. A robust knock-in approach using a minimal promoter and a minicircle. Dev Biol 2024; 505:24-33. [PMID: 37839785 PMCID: PMC10841522 DOI: 10.1016/j.ydbio.2023.10.002] [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: 06/09/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
Knock-in reporter (KI) animals are essential tools in biomedical research to study gene expression impacting diverse biological events. While CRISPR/Cas9-mediated genome editing allows for the successful generation of KI animals, several factors should be considered, such as low expression of the target gene, prevention of bacterial DNA integration, and in-frame editing. To circumvent these challenges, we developed a new strategy that utilizes minicircle technology and introduces a minimal promoter. We demonstrated that minicircles serve as an efficient donor DNA in zebrafish, significantly enhancing KI events compared to plasmids containing bacterial backbones. In an attempt to generate a KI reporter for scn8ab, we precisely integrated a fluorescence gene at the start codon. However, the seamlessly integrated reporter was unable to direct expression that recapitulates endogenous scn8ab expression. To overcome this obstacle, we introduced the hsp70 minimal promoter to provide an ectopic transcription initiation site and succeeded in establishing stable KI transgenic reporters for scn8ab. This strategy also created a fgf20b KI reporter line with a high success rate. Furthermore, our data revealed that an unexpectedly edited genome can inappropriately influence the integrated reporter gene expression, highlighting the importance of selecting a proper KI line. Overall, our approach utilizing a minicircle and an ectopic promoter establishes a robust and efficient strategy for KI generation, expanding our capacity to create KI animals.
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Affiliation(s)
- Margaret Keating
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Ryan Hagle
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Anjelica Rodriguez-Parks
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Sarah I Almutawa
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA; UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA.
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15
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Parvez S, Zhang T, Peterson RT. Scalable CRISPR Screens in Zebrafish Using MIC-Drop. Methods Mol Biol 2024; 2707:319-334. [PMID: 37668922 DOI: 10.1007/978-1-0716-3401-1_21] [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
CRISPR-Cas9 is a powerful tool to interrogate gene function in a targeted and systematic manner. Although the technology has been scaled up for large-scale genetic screens in cell culture, similar scale screens in vivo have been extremely challenging due to the cost, labor, and time required to generate and keep track of thousands of mutant animals. We reported the development of Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform that makes large-scale reverse genetic screens possible in zebrafish. In this chapter, we provide a detailed protocol to conduct large-scale genetic screens using this novel platform.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, University of Utah, Salt Lake City, UT, USA
| | - Tejia Zhang
- Department of Pharmacology & Toxicology, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, University of Utah, Salt Lake City, UT, USA.
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16
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Zapilko V, Moisio S, Parikka M, Heinäniemi M, Lohi O. Generation of a Zebrafish Knock-In Model Recapitulating Childhood ETV6::RUNX1-Positive B-Cell Precursor Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:5821. [PMID: 38136366 PMCID: PMC10871125 DOI: 10.3390/cancers15245821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Approximately 25% of children with B-cell precursor acute lymphoblastic leukemia (pB-ALL) harbor the t(12;21)(p13;q22) translocation, leading to the ETV6::RUNX1 (E::R) fusion gene. This translocation occurs in utero, but the disease is much less common than the prevalence of the fusion in newborns, suggesting that secondary mutations are required for overt leukemia. The role of these secondary mutations remains unclear and may contribute to treatment resistance and disease recurrence. We developed a zebrafish model for E::R leukemia using CRISPR/Cas9 to introduce the human RUNX1 gene into zebrafish etv6 intron 5, resulting in E::R fusion gene expression controlled by the endogenous etv6 promoter. As seen by GFP fluorescence at a single-cell level, the model correctly expressed the fusion protein in the right places in zebrafish embryos. The E::R fusion expression induced an expansion of the progenitor cell pool and led to a low 2% frequency of leukemia. The introduction of targeted pax5 and cdkn2a/b gene mutations, mimicking secondary mutations, in the E::R line significantly increased the incidence in leukemia. Transcriptomics revealed that the E::R;pax5mut leukemias exclusively represented B-lineage disease. This novel E::R zebrafish model faithfully recapitulates human disease and offers a valuable tool for a more detailed analysis of disease biology in this subtype.
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Affiliation(s)
- Veronika Zapilko
- Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland;
| | - Sanni Moisio
- The Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland; (S.M.); (M.H.)
| | - Mataleena Parikka
- Laboratory of Infection Biology, Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland;
| | - Merja Heinäniemi
- The Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland; (S.M.); (M.H.)
| | - Olli Lohi
- Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland;
- Department of Pediatrics and Tays Cancer Center, Tampere University Hospital, Wellbeing Services County of Pirkanmaa, 33520 Tampere, Finland
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17
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Zhong Z, Li Z, Yang J, Wang Q. Unified Model to Predict gRNA Efficiency across Diverse Cell Lines and CRISPR-Cas9 Systems. J Chem Inf Model 2023; 63:7320-7329. [PMID: 37983481 DOI: 10.1021/acs.jcim.3c01339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Computationally predicting the efficiency of a guide RNA (gRNA) from its sequence is crucial to designing the CRISPR-Cas9 system. Currently, machine learning (ML)-based models are widely used for such predictions. However, these ML models often show performance imbalance when applied to multiple data sets from diverse sources, hindering the practical utilization of these tools. To address this issue, we propose a Michaelis-Menten theoretical framework that integrates information from multiple data sets. We demonstrate that the binding free energy can serve as a useful invariant that bridges the data from different experimental setups. Building upon this framework, we develop a new ML model called Uni-deepSG. This model exhibits broad applicability on 27 data sets with different cell types, Cas9 variants, and gRNA designs. Our work confirms the existence of a generalized model for predicting gRNA efficiency and lays the theoretical groundwork necessary to finalize such a model.
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Affiliation(s)
- Zhicheng Zhong
- Department of Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Zeying Li
- Department of Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qian Wang
- Department of Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
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18
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Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
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Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
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19
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Nagorska A, Zaucker A, Lambert F, Inman A, Toral-Perez S, Gorodkin J, Wan Y, Smutny M, Sampath K. Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function. Development 2023; 150:dev201657. [PMID: 38032088 PMCID: PMC10730018 DOI: 10.1242/dev.201657] [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: 01/30/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Heart development is a complex process that requires asymmetric positioning of the heart, cardiac growth and valve morphogenesis. The mechanisms controlling heart morphogenesis and valve formation are not fully understood. The pro-convertase FurinA functions in heart development across vertebrates. How FurinA activity is regulated during heart development is unknown. Through computational analysis of the zebrafish transcriptome, we identified an RNA motif in a variant FurinA transcript harbouring a long 3' untranslated region (3'UTR). The alternative 3'UTR furina isoform is expressed prior to organ positioning. Somatic deletions in the furina 3'UTR lead to embryonic left-right patterning defects. Reporter localisation and RNA-binding assays show that the furina 3'UTR forms complexes with the conserved RNA-binding translational repressor, Ybx1. Conditional ybx1 mutant embryos show premature and increased Furin reporter expression, abnormal cardiac morphogenesis and looping defects. Mutant ybx1 hearts have an expanded atrioventricular canal, abnormal sino-atrial valves and retrograde blood flow from the ventricle to the atrium. This is similar to observations in humans with heart valve regurgitation. Thus, the furina 3'UTR element/Ybx1 regulon is important for translational repression of FurinA and regulation of heart development.
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Affiliation(s)
- Agnieszka Nagorska
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Andreas Zaucker
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Finnlay Lambert
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Angus Inman
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Sara Toral-Perez
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jan Gorodkin
- Center for non-coding RNAs in Technology and Health, Department of Veterinary and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Grønnega °rdsvej 3, 1870 Frederiksberg C, Denmark
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore 138672
| | - Michael Smutny
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Karuna Sampath
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Early Life, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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20
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Tuz-Sasik MU, Manuel R, Boije H. Efferent axons in the zebrafish lateral line degenerate following sensory hair cell ablation. Mol Cell Neurosci 2023; 127:103900. [PMID: 37714280 DOI: 10.1016/j.mcn.2023.103900] [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] [Received: 07/06/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023] Open
Abstract
The zebrafish lateral line is a frequently used model to study the mechanisms behind peripheral neuronal innervation of sensory organs and the regeneration thereof. The lateral line system consists of neuromasts, a cluster of protruding hair cells, which are innervated by sensory afferent and modulatory efferent neurons. These flow-sensing hair cells are similar to the hair cells in the mammalian ear. Though, while hair cell loss in humans is irreversible, the zebrafish neuromasts are regarded as the fastest regenerating structure in vertebrates, making them an ideal model to study regeneration. However, one component of the lateral line system, the efferent projections, has largely been omitted in regenerative studies. Here, for the first time, we bring insights into the fate of efferent axons during ablation and regeneration of the hair cells in the zebrafish lateral line. Our behavioral analysis showed functional recovery of hair cells and sensory transmission within 48 h and their regeneration were in line with previous studies. Analysis of the inhibitory efferent projections revealed that in approximately half the cases the inhibitory efferent axons degenerated, which was never observed for the sensory afferent axons. Quantification of hair cells following ablation suggests that the presence of mature hair cells in the neuromast may prevent axon degeneration. Within 120 h, degenerated efferent axons regenerated along the axonal tract of the lateral line. Reanalysis of published single cell neuromast data hinted to a role for Bdnf in the survival of efferent axons. However, sequestering Bdnf, blocking the Trk-receptors, and inhibiting the downstream ERK-signaling, did not induce axon degeneration, indicating that efferent survival is not mediated through neurotrophic factors. To further explore the relation between hair cells and efferent projections, we generated atoh1a mutants, where mature hair cells never form. In larvae lacking hair cells, inhibitory efferent projections were still present, following the tract of the sensory afferent without displaying any innervation. Our study reveal the fate of efferent innervation following hair cell ablation and provide insights into the inherent differences in regeneration between neurons in the peripheral and central nervous system.
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Affiliation(s)
- Melek Umay Tuz-Sasik
- Department of Immunology, Genetics and Pathology, Cell and Neurobiology, Uppsala University, Uppsala, Sweden
| | - Remy Manuel
- Department of Immunology, Genetics and Pathology, Cell and Neurobiology, Uppsala University, Uppsala, Sweden
| | - Henrik Boije
- Department of Immunology, Genetics and Pathology, Cell and Neurobiology, Uppsala University, Uppsala, Sweden.
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21
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Ben-Zvi I, Karasik D, Ackert-Bicknell CL. Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies. Curr Osteoporos Rep 2023; 21:650-659. [PMID: 37971665 DOI: 10.1007/s11914-023-00831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW GWAS, as a largely correlational analysis, requires in vitro or in vivo validation. Zebrafish (Danio rerio) have many advantages for studying the genetics of human diseases. Since gene editing in zebrafish has been highly valuable for studying embryonic skeletal developmental processes that are prenatally or perinatally lethal in mammalian models, we are reviewing pros and cons of this model. RECENT FINDINGS The true power for the use of zebrafish is the ease by which the genome can be edited, especially using the CRISPR/Cas9 system. Gene editing, followed by phenotyping, for complex traits such as BMD, is beneficial, but the major physiological differences between the fish and mammals must be considered. Like mammals, zebrafish do have main bone cells; thus, both in vivo stem cell analyses and in vivo imaging are doable. Yet, the "long" bones of fish are peculiar, and their bone cavities do not contain bone marrow. Partial duplication of the zebrafish genome should be taken into account. Overall, small fish toolkit can provide unmatched opportunities for genetic modifications and morphological investigation as a follow-up to human-first discovery.
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Affiliation(s)
- Inbar Ben-Zvi
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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22
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Mirzaei F, Eslahi A, Karimi S, Alizadeh F, Salmaninejad A, Rezaei M, Mozaffari S, Hamzehloei T, Pasdar A, Mojarrad M. Generation of Zebrafish Models of Human Retinitis Pigmentosa Diseases Using CRISPR/Cas9-Mediated Gene Editing System. Mol Biotechnol 2023:10.1007/s12033-023-00907-8. [PMID: 37980693 DOI: 10.1007/s12033-023-00907-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/14/2023] [Indexed: 11/21/2023]
Abstract
Generating animal models can explore the role of new candidate genes in causing diseases and the pathogenicity of a specific mutation in the underlying genes. These animals can be used to identify new pharmaceutical or genetic therapeutic methods. In the present experiment, we developed a rpe65a knock out (KO) zebrafish as a retinitis pigmentosa (RP) disease model. Using the CRISPR/Cas9 system, the rpe65a gene was KO in zebrafish. Two specific single-guide RNAs (sgRNAs) were designed for the zebrafish rpe65a gene. SgRNAs were cloned into the DR274 plasmid and synthesized using in vitro transcription method. The efficiency of Ribonucleoprotein (synthesized sgRNA and recombinant Cas9) was evaluated by in vitro digestion experiment. Ribonucleoprotein complexes were microinjected into one to four-celled eggs of the TU zebrafish strain. The effectiveness of sgRNAs in KO the target gene was determined using the Heteroduplex mobility assay (HMA) and Sanger sequencing. Online software was used to determine the percent of mosaicism in the sequenced samples. By examining the sequences of the larvae that showed a mobility shift in the HMA method, the presence of indels in the binding region of sgRNAs was confirmed, so the zebrafish model for RP disease established. Zebrafish is an ideal animal model for the functional study of various diseases involving different genes and mutations and used for evaluating different therapeutic approaches in human diseases. This study presents the production of rpe65a gene KO zebrafish models using CRISPR/Cas9 technology. This model can be used in RP pathophysiology studies and preclinical gene therapy experiments.
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Affiliation(s)
- Farzaneh Mirzaei
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atiyeh Eslahi
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sareh Karimi
- Department of Anatomy and Cell Biology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzaneh Alizadeh
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arash Salmaninejad
- Regenerative Medicine, Organ Procurement and Transplantation Multi-Disciplinary Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Rezaei
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sina Mozaffari
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tayebeh Hamzehloei
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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23
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Wang Y, Bo J, Zhao Z, Han Y, Zhang Q, Liu L. Depletion of Igfbp7 alleviates zebrafish NAFLD progression through inhibiting hepatic ferroptosis. Life Sci 2023; 332:122086. [PMID: 37714372 DOI: 10.1016/j.lfs.2023.122086] [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] [Received: 04/17/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
AIMS The global increased expression of Insulin-like growth factor binding protein 7 (IGFBP7) has been detected in non-alcoholic fatty liver disease (NAFLD) patients, however, its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. MAIN METHODS The igfbp7-/- null zebrafish mutant and the Igfbp7 liver overexpressed (LOE) transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique, respectively. The zebrafish NAFLD models in wildtypes, igfbp7-/- mutants and Igfbp7 LOE fishes have been established by high-fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification. KEY FINDINGS High Igfbp7 levels in NASH and fibrosis stages have been detected in liver tissues of both human NAFLD patients and zebrafish models. Depletion of Igfbp7 significantly alleviated liver steatosis, inflammation, and fibrosis, whereas liver specific Igfbp7 overexpression dramatically exacerbated liver fibrosis in zebrafish NAFLD model. The hepatic iron deposition, lipid peroxidation products, and ferroptosis-related index were also significantly reduced at the NASH stage in the absence of Igfbp7. Igfbp7 promotes NAFLD progression through regulating ferroptosis, and Ncoa4-mediated ferritinophagy may be the pathway of Igfbp7-regulated ferroptosis. SIGNIFICANCE Igfbp7 is confirmed as an important regulator in NAFLD progression. Depleting Igfbp7 effectively alleviates zebrafish NAFLD progression by inhibiting hepatic ferroptosis, suggesting a novel potential target for NAFLD treatment.
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Affiliation(s)
- Yanqin Wang
- Department of Gastroenterology and Hepatology, The First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Jiaqi Bo
- Department of Gastroenterology and Hepatology, The First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Zhonghua Zhao
- Institutes of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Shanxi University, Taiyuan 030006, China
| | - Yuhang Han
- Department of Gastroenterology and Hepatology, The First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Qianqian Zhang
- Department of Gastroenterology and Hepatology, The First Hospital of Shanxi Medical University, Taiyuan 030001, China; Experimental Center of Science and Research, The First Hospital of Shanxi Medical University, Taiyuan 030001, China; Key Laboratory of Prevention and Treatment of Liver Injury and Digestive System Neoplasms, Provincial Committee of the Medical and Health, Taiyuan 030001, China
| | - Lixin Liu
- Department of Gastroenterology and Hepatology, The First Hospital of Shanxi Medical University, Taiyuan 030001, China; Experimental Center of Science and Research, The First Hospital of Shanxi Medical University, Taiyuan 030001, China; Key Laboratory of Prevention and Treatment of Liver Injury and Digestive System Neoplasms, Provincial Committee of the Medical and Health, Taiyuan 030001, China.
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24
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Liu Y, Fan R, Yi J, Cui Q, Cui C. A fusion framework of deep learning and machine learning for predicting sgRNA cleavage efficiency. Comput Biol Med 2023; 165:107476. [PMID: 37696181 DOI: 10.1016/j.compbiomed.2023.107476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
CRISPR/Cas9 system is a powerful tool for genome editing. Numerous studies have shown that sgRNAs can strongly affect the efficiency of editing. However, it is still not clear what rules should be followed for designing sgRNA with high cleavage efficiency. At present, several machine learning or deep learning methods have been developed to predict the cleavage efficiency of sgRNAs, however, the prediction accuracy of these tools is still not satisfactory. Here we propose a fusion framework of deep learning and machine learning, which first deals with the primary sequence and secondary structure features of the sgRNAs using both convolutional neural network (CNN) and recurrent neural network (RNN), and then uses the features extracted by the deep neural network to train a conventional machine learning model with LGBM. As a result, the new approach overwhelmed previous methods. The Spearman's correlation coefficient between predicted and measured sgRNA cleavage efficiency of our model (0.917) is improved by over 5% compared with the most advanced method (0.865), and the mean square error reduces from 7.89 × 10-3 to 4.75 × 10-3. Finally, we developed an online tool, CRISep (http://www.cuilab.cn/CRISep), to evaluate the availability of sgRNAs based on our models.
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Affiliation(s)
- Yu Liu
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Rui Fan
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Jingkun Yi
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qinghua Cui
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China.
| | - Chunmei Cui
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China.
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25
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Madushani KP, Shanaka KASN, Jung S, Kim MJ, Lee J. Ablation of myd88 alters the immune gene expression and immune cell recruitment during VHSV infection in zebrafish. FISH & SHELLFISH IMMUNOLOGY 2023; 141:109006. [PMID: 37598733 DOI: 10.1016/j.fsi.2023.109006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Myeloid differentiation primary response protein-88 (MYD88) is an essential adaptor molecule in pathogen-related pattern recognition signaling pathways. Toll-like and interleukin receptors recognize numerous signals and are funneled through MyD88 to express genes responsible for the innate and adaptive immune systems. In the present study, the relevance of MyD88 in viral hemorrhagic septicemia virus (VHSV) was investigated by generating myd88-/- zebrafish. The model was challenged with VHSV, and viral propagation was quantified by evaluating clinical symptoms, mortality, and VHSV copy number. The infected fish showed abnormal morphologies, such as subcutaneous hemorrhages, abdominal swelling, and bulging eyes, which were comparatively more intense in myd88-/- fish than in the wild-type. An injury infection experiment conducted in zebrafish larvae indicated a substantial spread of VHSV in the wound site. The number of neutrophils and macrophages recruited to the wounded area were markedly reduced in myd88-/- fish. According to gene expression analysis, VHSV NP gene expression was considerably upregulated in myd88-/- fish. Substantial gene expression and immune cell marker modulation were observed in the mutant model compared to that in the wild-type. These results suggest that the lack of a significant adaptor protein for immune signal transduction results in enhanced VHSV replication.
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Affiliation(s)
- K P Madushani
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - K A S N Shanaka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Sumi Jung
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Myoung-Jin Kim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea; Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea.
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea.
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26
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Keating M, Hagle R, Osorio-Mendez D, Rodriguez-Parks A, Almutawa SI, Kang J. A robust knock-in approach using a minimal promoter and a minicircle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558008. [PMID: 37745465 PMCID: PMC10516040 DOI: 10.1101/2023.09.15.558008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Knock-in reporter (KI) animals are essential tools in biomedical research to study gene expression impacting diverse biological events. While CRISPR/Cas9-mediated genome editing allows for the successful generation of KI animals, several factors should be considered, such as low expression of the target gene, prevention of bacterial DNA integration, and in-frame editing. To circumvent these challenges, we developed a new strategy that utilizes minicircle technology and introduces a minimal promoter. We demonstrated that minicircles serve as an efficient donor DNA in zebrafish, significantly enhancing KI events compared to plasmids containing bacterial backbones. In an attempt to generate a KI reporter for scn8ab, we precisely integrated a fluorescence gene at the start codon. However, the seamlessly integrated reporter was unable to direct expression that recapitulates endogenous scn8ab expression. To overcome this obstacle, we introduced the hsp70 minimal promoter to provide an ectopic transcription initiation site and succeeded in establishing stable KI transgenic reporters for scn8ab. This strategy also created a fgf20b KI reporter line with a high success rate. Furthermore, our data revealed that an unexpectedly edited genome can inappropriately influence the integrated reporter gene expression, highlighting the importance of selecting a proper KI line. Overall, our approach utilizing a minicircle and an ectopic promoter establishes a robust and efficient strategy for KI generation, expanding our capacity to create KI animals.
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Affiliation(s)
- Margaret Keating
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Ryan Hagle
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Daniel Osorio-Mendez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Anjelica Rodriguez-Parks
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Sarah I Almutawa
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
- UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
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27
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Yu EPY, Saxena V, Perin S, Ekker M. Loss of dlx5a/ dlx6a Locus Alters Non-Canonical Wnt Signaling and Meckel's Cartilage Morphology. Biomolecules 2023; 13:1347. [PMID: 37759750 PMCID: PMC10526740 DOI: 10.3390/biom13091347] [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] [Received: 08/05/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The dlx genes encode transcription factors that establish a proximal-distal polarity within neural crest cells to bestow a regional identity during craniofacial development. The expression regions of dlx paralogs are overlapping yet distinct within the zebrafish pharyngeal arches and may also be involved in progressive morphologic changes and organization of chondrocytes of the face. However, how each dlx paralog of dlx1a, dlx2a, dlx5a and dlx6a affects craniofacial development is still largely unknown. We report here that the average lengths of the Meckel's, palatoquadrate and ceratohyal cartilages in different dlx mutants were altered. Mutants for dlx5a-/- and dlx5i6-/-, where the entire dlx5a/dlx6a locus was deleted, have the shortest lengths for all three structures at 5 days post fertilization (dpf). This phenotype was also observed in 14 dpf larvae. Loss of dlx5i6 also resulted in increased proliferation of neural crest cells and expression of chondrogenic markers. Additionally, altered expression and function of non-canonical Wnt signaling were observed in these mutants suggesting a novel interaction between dlx5i6 locus and non-canonical Wnt pathway regulating ventral cartilage morphogenesis.
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Affiliation(s)
| | | | | | - Marc Ekker
- Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 94A, Canada (S.P.)
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28
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Shin U, Lee Y. Unraveling DNA Repair Processes In Vivo: Insights from Zebrafish Studies. Int J Mol Sci 2023; 24:13120. [PMID: 37685935 PMCID: PMC10487404 DOI: 10.3390/ijms241713120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The critical role of the DNA repair system in preserving the health and survival of living organisms is widely recognized as dysfunction within this system can result in a broad range of severe conditions, including neurodegenerative diseases, blood disorders, infertility, and cancer. Despite comprehensive research on the molecular and cellular mechanisms of DNA repair pathways, there remains a significant knowledge gap concerning these processes at an organismal level. The teleost zebrafish has emerged as a powerful model organism for investigating these intricate DNA repair mechanisms. Their utility arises from a combination of their well-characterized genomic information, the ability to visualize specific phenotype outcomes in distinct cells and tissues, and the availability of diverse genetic experimental approaches. In this review, we provide an in-depth overview of recent advancements in our understanding of the in vivo roles of DNA repair pathways. We cover a variety of critical biological processes including neurogenesis, hematopoiesis, germ cell development, tumorigenesis, and aging, with a specific emphasis on findings obtained from the use of zebrafish as a model system. Our comprehensive review highlights the importance of zebrafish in enhancing our understanding of the functions of DNA repair systems at the organismal level and paves the way for future investigations in this field.
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Affiliation(s)
- Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yoonsung Lee
- Clinical Research Institute, Kyung Hee University Hospital at Gangdong, School of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea
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29
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Coogan M, Xing D, Su B, Alston V, Johnson A, Khan M, Khalil K, Elaswad A, Li S, Wang J, Lu C, Wang W, Hettiarachchi D, Shang M, Hasin T, Qin Z, Cone R, Butts IAE, Dunham RA. CRISPR/Cas9-mediated knock-in of masu salmon (Oncorhyncus masou) elongase gene in the melanocortin-4 (mc4r) coding region of channel catfish (Ictalurus punctatus) genome. Transgenic Res 2023; 32:251-264. [PMID: 37468714 DOI: 10.1007/s11248-023-00346-w] [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] [Received: 07/08/2022] [Accepted: 03/24/2023] [Indexed: 07/21/2023]
Abstract
Channel catfish, Ictalurus punctatus, have limited ability to synthesize Ω-3 fatty acids. The ccβA-msElovl2 transgene containing masu salmon, Oncorhynchus masou, elongase gene driven by the common carp, Cyprinus carpio, β-actin promoter was inserted into the channel catfish melanocortin-4 receptor (mc4r) gene site using the two-hit two-oligo with plasmid (2H2OP) method. The best performing sgRNA resulted in a knockout mutation rate of 92%, a knock-in rate of 54% and a simultaneous knockout/knock-in rate of 49%. Fish containing both the ccβA-msElovl2 transgene knock-in and mc4r knockout (Elovl2) were 41.8% larger than controls at 6 months post-hatch (p = 0.005). Mean eicosapentaenoic acid (EPA, C20:5n-3) levels in Elov2 mutants and mc4r knockout mutants (MC4R) were 121.6% and 94.1% higher than in controls, respectively (p = 0.045; p = 0.025). Observed mean docosahexaenoic acid (DHA, C22:6n-3) and total EPA + DHA content was 32.8% and 45.1% higher, respectively, in Elovl2 transgenic channel catfish than controls (p = 0.368; p = 0.025). To our knowledge this is the first example of genome engineering to simultaneously target transgenesis and knock-out a gene in a commercially important aquaculture species for multiple improved performance traits. With a high transgene integration rate, improved growth, and higher omega-3 fatty acid content, the use of Elovl2 transgenic channel catfish appears beneficial for application on commercial farms.
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Affiliation(s)
- Michael Coogan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - De Xing
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Veronica Alston
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Andrew Johnson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohd Khan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shangjia Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Cuiyu Lu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wenwen Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Darshika Hettiarachchi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tasnuba Hasin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhenkui Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Cone
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ian A E Butts
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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30
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Huang L, Wang D, Chen H, Hu J, Dai X, Liu C, Li A, Shen X, Qi C, Sun H, Zhang D, Chen T, Jiang Y. CRISPR-detector: fast and accurate detection, visualization, and annotation of genome-wide mutations induced by genome editing events. J Genet Genomics 2023; 50:563-572. [PMID: 37003351 DOI: 10.1016/j.jgg.2023.03.010] [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] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023]
Abstract
The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome editing. To track on/off-target events with emerging new editing techniques, improved bioinformatic tools are indispensable. Existing tools suffer from limitations in speed and scalability, especially with whole-genome sequencing (WGS) data analysis. To address these limitations, we have developed a comprehensive tool called CRISPR-detector, a web-based and locally deployable pipeline for genome editing sequence analysis. The core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline, with additional novel annotation and visualization modules designed to fit CRISPR applications. Co-analysis of the treated and control samples is performed to remove existing background variants prior to genome editing. CRISPR-detector offers optimized scalability, enabling WGS data analysis beyond Browser Extensible Data file-defined regions, with improved accuracy due to haplotype-based variant calling to handle sequencing errors. In addition, the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by users. These advantages facilitate rapid and efficient detection of mutations induced by genome editing events, especially for datasets generated from WGS. The web-based version of CRISPR-detector is available at https://db.cngb.org/crispr-detector, and the locally deployable version is available at https://github.com/hlcas/CRISPR-detector.
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Affiliation(s)
- Lei Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Dan Wang
- BNU-HKBU United International College, Zhuhai, Guangdong 519087, China.
| | | | - Jinnan Hu
- Sentieon Inc, San Jose, CA 94042, USA
| | - Xuechen Dai
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Chuan Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Anduo Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xuechun Shen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Chen Qi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixi Sun
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Tong Chen
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yuan Jiang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China.
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31
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Simpson CL, Kimble DC, Chandrasekharappa SC, Alqosayer K, Holzinger E, Carrington B, McElderry J, Sood R, Al‐Souqi G, Albacha‐Hejazi H, Bailey‐Wilson JE. A novel de novo TP63 mutation in whole-exome sequencing of a Syrian family with Oral cleft and ectrodactyly. Mol Genet Genomic Med 2023; 11:e2179. [PMID: 37070724 PMCID: PMC10422068 DOI: 10.1002/mgg3.2179] [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: 03/03/2022] [Revised: 03/06/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Oral clefts and ectrodactyly are common, heterogeneous birth defects. We performed whole-exome sequencing (WES) analysis in a Syrian family. The proband presented with both orofacial clefting and ectrodactyly but not ectodermal dysplasia as typically seen in ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome-3. A paternal uncle with only an oral cleft was deceased and unavailable for analysis. METHODS Variant annotation, Mendelian inconsistencies, and novel variants in known cleft genes were examined. Candidate variants were validated using Sanger sequencing, and pathogenicity assessed by knocking out the tp63 gene in zebrafish to evaluate its role during zebrafish development. RESULTS Twenty-eight candidate de novo events were identified, one of which is in a known oral cleft and ectrodactyly gene, TP63 (c.956G > T, p.Arg319Leu), and confirmed by Sanger sequencing. CONCLUSION TP63 mutations are associated with multiple autosomal dominant orofacial clefting and limb malformation disorders. The p.Arg319Leu mutation seen in this patient is de novo but also novel. Two known mutations in the same codon (c.956G > A, p.(Arg319His; rs121908839, c.955C > T), p.Arg319Cys) cause ectrodactyly, providing evidence that mutating this codon is deleterious. While this TP63 mutation is the best candidate for the patient's clinical presentation, whether it is responsible for the entire phenotype is unclear. Generation and characterization of tp63 knockout zebrafish showed necrosis and rupture of the head at 3 days post-fertilization (dpf). The embryonic phenotype could not be rescued by injection of zebrafish or human messenger RNA (mRNA). Further functional analysis is needed to determine what proportion of the phenotype is due to this mutation.
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Affiliation(s)
- Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland21224USA
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennessee38163USA
| | - Danielle C. Kimble
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20814USA
| | - Settara C. Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20814USA
| | | | | | - Emily Holzinger
- Computational and Statistical Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland21224USA
| | - Blake Carrington
- Zebrafish Core, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20892USA
| | - John McElderry
- Zebrafish Core, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20892USA
| | - Raman Sood
- Zebrafish Core, National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland20892USA
| | | | | | - Joan E. Bailey‐Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland21224USA
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32
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Yang S, Huang L, Liang H, Guo J, Liu L, Chen S, Cao M. Loss of flrt2 gene leads to microphthalmia in zebrafish. Biol Open 2023; 12:bio059784. [PMID: 37259881 PMCID: PMC10281255 DOI: 10.1242/bio.059784] [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: 12/08/2022] [Accepted: 05/25/2023] [Indexed: 06/02/2023] Open
Abstract
As a member of the fibronectin leucine-rich transmembrane (flrt) gene family, fibronectin leucine-rich transmembrane 2 (flrt2) is strongly expressed in a subset of sclerotome cells, and the resultant protein interacts with FGFR1 in the FGF signaling pathway during development. Studies on flrt2 have focused mainly on its roles in the brain, heart and chondrogenesis. However, reports on its expression and function in the zebrafish retina are lacking. Here, we detected the high expression of flrt2 in zebrafish retina using in situ hybridization technique and developed an flrt2-knockout (KO) zebrafish line using CRISPR/Cas9 genome editing. Quantitative real-time PCR was used to measure the expression levels of flrt2, which results in an approximately 60% mRNA reduction. The flrt2-KO zebrafish eyes' altered morphological, cellular, and molecular events were identified using BrdU labeling, TUNEL assay, immunofluorescent staining, fluorescent dye injection and RNA sequencing. Abnormal eye development, known as microphthalmia, was found in flrt2-KO larvae, and the retinal progenitor cells exhibited increased apoptosis, perhaps owing to the combined effects of crx, neurod4, atoh7, and pcdh8 downregulation and Casp3a and Caspbl upregulation. In contrast, the retinal neural development, as well as retinal progenitor cell differentiation and proliferation, were not affected by the flrt2 deletion. Thus, flrt2 appears to play important roles in retinal development and function, which may provide the basis for further investigations into the molecular mechanisms of retinal development and evolution.
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Affiliation(s)
- Siyu Yang
- Department of Ophthalmology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, China
| | - Lianggui Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Huiling Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jingyi Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Liyue Liu
- China Zebrafish Resource Center, National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shuyi Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Mingzhe Cao
- Department of Ophthalmology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, China
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33
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Parvez S, Brandt ZJ, Peterson RT. Large-scale F0 CRISPR screens in vivo using MIC-Drop. Nat Protoc 2023; 18:1841-1865. [PMID: 37069311 PMCID: PMC10419324 DOI: 10.1038/s41596-023-00821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale in vivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR-Cas9 has recently gained prominence as the tool of choice for genetic manipulation in zebrafish. However, scaling up the technique for high-throughput in vivo functional genetics has been a challenge. We recently developed a method, Multiplexed Intermixed CRISPR Droplets (MIC-Drop), that makes large-scale CRISPR screening in zebrafish possible. Here, we outline the step-by-step protocol for performing functional genetic screens in zebrafish by using MIC-Drop. MIC-Drop uses multiplexed single-guide RNAs to generate biallelic mutations in injected zebrafish embryos, allowing genetic screens to be performed in F0 animals. Combining microfluidics and DNA barcoding enables simultaneous targeting of tens to hundreds of genes from a single injection needle, while also enabling retrospective and rapid identification of the genotype responsible for an observed phenotype. The primary target audiences for MIC-Drop are developmental biologists, zebrafish geneticists, and researchers interested in performing in vivo functional genetic screens in a vertebrate model system. MIC-Drop will also prove useful in the hands of chemical biologists seeking to identify targets of small molecules that cause phenotypic changes in zebrafish. By using MIC-Drop, a typical screen of 100 genes can be conducted within 2-3 weeks by a single user.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Zachary J Brandt
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
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Zhou J, Liu A, He F, Zhang Y, Shen L, Yu J, Zhang X. Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:501-514. [PMID: 36470576 PMCID: PMC10787021 DOI: 10.1016/j.gpb.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
The white-blotched river stingray (Potamotrygon leopoldi) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available, P. leopoldi provides the evolutionary details in fish phylogeny, niche adaptation, and skeleton formation. In this study, we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds, with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size. Our analysis shows that P. leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago. Moreover, two gene families related to the immune system (immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes) exhibit expansion in P. leopoldi only. We also identified the Hox gene clusters in P. leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P. leopoldi. The RNA sequencing data from P. leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals. Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes (both P. leopoldi and Callorhinchus milii) could partly explain the absence of hard bone in their endoskeleton. Overall, this genome resource provides new insights into the niche adaptation, body plan, and skeleton formation of P. leopoldi, as well as the genome evolution in cartilaginous fishes.
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Affiliation(s)
- Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Funan He
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Yunbin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Libing Shen
- International Human Phenome Institutes (Shanghai), Shanghai 200433, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiang Zhang
- Shanghai Nanmulin Biotechnology Company Limited, Shanghai 200031, China.
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state. J Clin Invest 2023; 133:e166919. [PMID: 37183825 PMCID: PMC10178836 DOI: 10.1172/jci166919] [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: 11/09/2022] [Accepted: 03/14/2023] [Indexed: 05/16/2023] Open
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like mesenchymal cell state and a more differentiated sympathetic adrenergic cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional cofactor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism, G/T, that affects a GATA motif in the first intron of LMO1. Here, we showed that WT zebrafish with the GATA genotype developed adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduced the penetrance of MYCN-driven tumors, which were restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrated that TATA/TATA tumors also exhibited a mesenchymal cell state and were low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduced the neuroblastoma-initiation rate by preventing formation of the adrenergic cell state. This mechanism was conserved over 400 million years of evolution, separating zebrafish and humans.
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Affiliation(s)
- Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Hui Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam D. Durbin
- Department of Oncology and Comprehensive Cancer Center, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brian J. Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mark W. Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota, USA
| | - Andrew C. Wood
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J. Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Biology Department, MIT, Cambridge, Massachusetts, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
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Boezio GLM, Zhao S, Gollin J, Priya R, Mansingh S, Guenther S, Fukuda N, Gunawan F, Stainier DYR. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 2023; 16:dmm049571. [PMID: 36172839 PMCID: PMC9612869 DOI: 10.1242/dmm.049571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/13/2022] [Indexed: 11/20/2022] Open
Abstract
The epicardium, the outermost layer of the heart, is an important regulator of cardiac regeneration. However, a detailed understanding of the crosstalk between the epicardium and myocardium during development requires further investigation. Here, we generated three models of epicardial impairment in zebrafish by mutating the transcription factor genes tcf21 and wt1a, and ablating tcf21+ epicardial cells. Notably, all three epicardial impairment models exhibited smaller ventricles. We identified the initial cause of this phenotype as defective cardiomyocyte growth, resulting in reduced cell surface and volume. This failure of cardiomyocyte growth was followed by decreased proliferation and increased abluminal extrusion. By temporally manipulating its ablation, we show that the epicardium is required to support cardiomyocyte growth mainly during early cardiac morphogenesis. By transcriptomic profiling of sorted epicardial cells, we identified reduced expression of FGF and VEGF ligand genes in tcf21-/- hearts, and pharmacological inhibition of these signaling pathways in wild type partially recapitulated the ventricular growth defects. Taken together, these data reveal distinct roles of the epicardium during cardiac morphogenesis and signaling pathways underlying epicardial-myocardial crosstalk.
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Affiliation(s)
- Giulia L. M. Boezio
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Shengnan Zhao
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Josephine Gollin
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Rashmi Priya
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Shivani Mansingh
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Stefan Guenther
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Nana Fukuda
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Felix Gunawan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
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Kocere A, Lalonde RL, Mosimann C, Burger A. Lateral thinking in syndromic congenital cardiovascular disease. Dis Model Mech 2023; 16:dmm049735. [PMID: 37125615 PMCID: PMC10184679 DOI: 10.1242/dmm.049735] [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] [Indexed: 05/02/2023] Open
Abstract
Syndromic birth defects are rare diseases that can present with seemingly pleiotropic comorbidities. Prime examples are rare congenital heart and cardiovascular anomalies that can be accompanied by forelimb defects, kidney disorders and more. Whether such multi-organ defects share a developmental link remains a key question with relevance to the diagnosis, therapeutic intervention and long-term care of affected patients. The heart, endothelial and blood lineages develop together from the lateral plate mesoderm (LPM), which also harbors the progenitor cells for limb connective tissue, kidneys, mesothelia and smooth muscle. This developmental plasticity of the LPM, which founds on multi-lineage progenitor cells and shared transcription factor expression across different descendant lineages, has the potential to explain the seemingly disparate syndromic defects in rare congenital diseases. Combining patient genome-sequencing data with model organism studies has already provided a wealth of insights into complex LPM-associated birth defects, such as heart-hand syndromes. Here, we summarize developmental and known disease-causing mechanisms in early LPM patterning, address how defects in these processes drive multi-organ comorbidities, and outline how several cardiovascular and hematopoietic birth defects with complex comorbidities may be LPM-associated diseases. We also discuss strategies to integrate patient sequencing, data-aggregating resources and model organism studies to mechanistically decode congenital defects, including potentially LPM-associated orphan diseases. Eventually, linking complex congenital phenotypes to a common LPM origin provides a framework to discover developmental mechanisms and to anticipate comorbidities in congenital diseases affecting the cardiovascular system and beyond.
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Affiliation(s)
- Agnese Kocere
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
- Department of Molecular Life Science, University of Zurich, 8057 Zurich, Switzerland
| | - Robert L. Lalonde
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
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38
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Bernardo-Colón A, Dong L, Abu-Asab M, Brush RS, Agbaga MP, Becerra SP. Ablation of pigment epithelium-derived factor receptor (PEDF-R/Pnpla2) causes photoreceptor degeneration. J Lipid Res 2023; 64:100358. [PMID: 36934843 PMCID: PMC10233210 DOI: 10.1016/j.jlr.2023.100358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/19/2023] Open
Abstract
Photoreceptor cells express the patatin-like phospholipase domain-containing 2 (PNPLA2) gene that codes for pigment epithelium-derived factor receptor (PEDF-R) (also known as ATGL). PEDF-R exhibits phospholipase activity that mediates the neurotrophic action of its ligand PEDF. Because phospholipids are the most abundant lipid class in the retina, we investigated the role of PEDF-R in photoreceptors by generating CRISPR Pnpla2 knock-out mouse lines in a retinal degeneration-free background. Pnpla2-/- mice had undetectable retinal Pnpla2 gene expression and PEDF-R protein levels as assayed by RT-PCR and immunofluorescence, respectively. The photoreceptors of mice deficient in PEDF-R had deformities as examined by histology and transmission electron microscopy. Pnpla2 knockdown diminished the PLA2 enzymatic activity of PEDF-R in the retina. Lipidomic analyses revealed the accumulation of lysophosphatidyl choline-DHA and lysophosphatidyl ethanolamine-DHA in PEDF-R-deficient retinas, suggesting a possible causal link to photoreceptor dysfunction. Loss of PEDF-R decreased levels of rhodopsin, opsin, PKCα, and synaptophysin relative to controls. Pnpla2-/- photoreceptors had surface-exposed phosphatidylserine, and their nuclei were TUNEL positive and condensed, revealing an apoptotic onset. Paralleling its structural defects, PEDF-R deficiency compromised photoreceptor function in vivo as indicated by the attenuation of photoreceptor a- and b-waves in Pnpla2-/- and Pnpla2+/- mice relative to controls as determined by electroretinography. In conclusion, ablation of PEDF-R in mice caused alteration in phospholipid composition associated with malformation and malperformance of photoreceptors. These findings identify PEDF-R as an important component for photoreceptor structure and function, highlighting its role in phospholipid metabolism for retinal survival and its consequences.
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Affiliation(s)
- Alexandra Bernardo-Colón
- Section of Protein Structure and Function, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mones Abu-Asab
- Histopathology Core Facility, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard S Brush
- Department of Ophthalmology(,) and Dean A. McGee Eye Institute, Oklahoma City, OK, USA
| | - Martin-Paul Agbaga
- Department of Ophthalmology(,) and Dean A. McGee Eye Institute, Oklahoma City, OK, USA; Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - S Patricia Becerra
- Section of Protein Structure and Function, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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39
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Hageter J, Starkey J, Horstick EJ. Thalamic regulation of a visual critical period and motor behavior. Cell Rep 2023; 42:112287. [PMID: 36952349 PMCID: PMC10514242 DOI: 10.1016/j.celrep.2023.112287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/24/2023] Open
Abstract
During the visual critical period (CP), sensory experience refines the structure and function of visual circuits. The basis of this plasticity was long thought to be limited to cortical circuits, but recently described thalamic plasticity challenges this dogma and demonstrates greater complexity underlying visual plasticity. Yet how visual experience modulates thalamic neurons or how the thalamus modulates CP timing is incompletely understood. Using a larval zebrafish, thalamus-centric ocular dominance model, we show functional changes in the thalamus and a role of inhibitory signaling to establish CP timing using a combination of functional imaging, optogenetics, and pharmacology. Hemisphere-specific changes in genetically defined thalamic neurons correlate with changes in visuomotor behavior, establishing a role of thalamic plasticity in modulating motor performance. Our work demonstrates that visual plasticity is broadly conserved and that visual experience leads to neuron-level functional changes in the thalamus that require inhibitory signaling to establish critical period timing.
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Affiliation(s)
- John Hageter
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Jacob Starkey
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Eric J Horstick
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA; Department of Neuroscience, West Virginia University, Morgantown, WV 26506, USA.
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40
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Sherkatghanad Z, Abdar M, Charlier J, Makarenkov V. Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review. Brief Bioinform 2023; 24:7130974. [PMID: 37080758 DOI: 10.1093/bib/bbad131] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9) is a popular and effective two-component technology used for targeted genetic manipulation. It is currently the most versatile and accurate method of gene and genome editing, which benefits from a large variety of practical applications. For example, in biomedicine, it has been used in research related to cancer, virus infections, pathogen detection, and genetic diseases. Current CRISPR/Cas9 research is based on data-driven models for on- and off-target prediction as a cleavage may occur at non-target sequence locations. Nowadays, conventional machine learning and deep learning methods are applied on a regular basis to accurately predict on-target knockout efficacy and off-target profile of given single-guide RNAs (sgRNAs). In this paper, we present an overview and a comparative analysis of traditional machine learning and deep learning models used in CRISPR/Cas9. We highlight the key research challenges and directions associated with target activity prediction. We discuss recent advances in the sgRNA-DNA sequence encoding used in state-of-the-art on- and off-target prediction models. Furthermore, we present the most popular deep learning neural network architectures used in CRISPR/Cas9 prediction models. Finally, we summarize the existing challenges and discuss possible future investigations in the field of on- and off-target prediction. Our paper provides valuable support for academic and industrial researchers interested in the application of machine learning methods in the field of CRISPR/Cas9 genome editing.
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Affiliation(s)
- Zeinab Sherkatghanad
- Departement d'Informatique, Universite du Quebec a Montreal, H2X 3Y7, Montreal, QC, Canada
| | - Moloud Abdar
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, 3216, Geelong, VIC, Australia
| | - Jeremy Charlier
- Departement d'Informatique, Universite du Quebec a Montreal, H2X 3Y7, Montreal, QC, Canada
| | - Vladimir Makarenkov
- Departement d'Informatique, Universite du Quebec a Montreal, H2X 3Y7, Montreal, QC, Canada
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Naeem M, Alkhnbashi OS. Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects. Int J Mol Sci 2023; 24:ijms24076261. [PMID: 37047235 PMCID: PMC10094584 DOI: 10.3390/ijms24076261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
The CRISPR-Cas system has evolved into a cutting-edge technology that has transformed the field of biological sciences through precise genetic manipulation. CRISPR/Cas9 nuclease is evolving into a revolutionizing method to edit any gene of any species with desirable outcomes. The swift advancement of CRISPR-Cas technology is reflected in an ever-expanding ecosystem of bioinformatics tools designed to make CRISPR/Cas9 experiments easier. To assist researchers with efficient guide RNA designs with fewer off-target effects, nuclease target site selection, and experimental validation, bioinformaticians have built and developed a comprehensive set of tools. In this article, we will review the various computational tools available for the assessment of off-target effects, as well as the quantification of nuclease activity and specificity, including web-based search tools and experimental methods, and we will describe how these tools can be optimized for gene knock-out (KO) and gene knock-in (KI) for model organisms. We also discuss future directions in precision genome editing and its applications, as well as challenges in target selection, particularly in predicting off-target effects.
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42
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Susceptibility and Permissivity of Zebrafish (Danio rerio) Larvae to Cypriniviruses. Viruses 2023; 15:v15030768. [PMID: 36992477 PMCID: PMC10051318 DOI: 10.3390/v15030768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/19/2023] Open
Abstract
The zebrafish (Danio rerio) represents an increasingly important model organism in virology. We evaluated its utility in the study of economically important viruses from the genus Cyprinivirus (anguillid herpesvirus 1, cyprinid herpesvirus 2 and cyprinid herpesvirus 3 (CyHV-3)). This revealed that zebrafish larvae were not susceptible to these viruses after immersion in contaminated water, but that infections could be established using artificial infection models in vitro (zebrafish cell lines) and in vivo (microinjection of larvae). However, infections were transient, with rapid viral clearance associated with apoptosis-like death of infected cells. Transcriptomic analysis of CyHV-3-infected larvae revealed upregulation of interferon-stimulated genes, in particular those encoding nucleic acid sensors, mediators of programmed cell death and related genes. It was notable that uncharacterized non-coding RNA genes and retrotransposons were also among those most upregulated. CRISPR/Cas9 knockout of the zebrafish gene encoding protein kinase R (PKR) and a related gene encoding a protein kinase containing Z-DNA binding domains (PKZ) had no impact on CyHV-3 clearance in larvae. Our study strongly supports the importance of innate immunity-virus interactions in the adaptation of cypriniviruses to their natural hosts. It also highlights the potential of the CyHV-3-zebrafish model, versus the CyHV-3-carp model, for study of these interactions.
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43
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Verwilligen RAF, Mulder L, Araújo PM, Carneiro M, Bussmann J, Hoekstra M, Van Eck M. Zebrafish as outgroup model to study evolution of scavenger receptor class B type I functions. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159308. [PMID: 36931457 DOI: 10.1016/j.bbalip.2023.159308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/26/2023] [Accepted: 02/25/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND AND AIMS Scavenger receptor class B1 (SCARB1) - also known as the high-density lipoprotein (HDL) receptor - is a multi-ligand scavenger receptor that is primarily expressed in liver and steroidogenic organs. This receptor is known for its function in reverse cholesterol transport (RCT) in mammals and hence disruption leads to a massive increase in HDL cholesterol in these species. The extracellular domain of SCARB1 - which is important for cholesterol handling - is highly conserved across multiple vertebrates, except in zebrafish. METHODS To examine the functional conservation of SCARB1 among vertebrates, two stable scarb1 knockout zebrafish lines, scarb1 715delA (scarb1 -1 nt) and scarb1 715_716insGG (scarb1 +2 nt), were created using CRISPR-Cas9 technology. RESULTS We demonstrate that, in zebrafish, SCARB1 deficiency leads to disruption of carotenoid-based pigmentation, reduced fertility, and a decreased larvae survival rate, whereas steroidogenesis was unaltered. The observed reduced fertility is driven by defects in female fertility (-50 %, p < 0.001). Importantly, these alterations were independent of changes in free (wild-type 2.4 ± 0.2 μg/μl versus scarb1-/- 2.0 ± 0.1 μg/μl) as well as total (wild-type 4.2 ± 0.4 μg/μl versus scarb1-/- 4.0 ± 0.3 μg/μl) plasma cholesterol levels. Uptake of HDL in the liver of scarb1-/- zebrafish larvae was reduced (-86.7 %, p < 0.001), but this coincided with reduced perfusion of the liver. No effect was observed on lipoprotein uptake in the caudal vein. SCARB1 deficient canaries, which also lack carotenoids in their plumage, similarly as scarb1-/- zebrafish, failed to show an increase in plasma free- and total cholesterol levels. CONCLUSION Our findings suggest that the specific function of SCARB1 in maintaining plasma cholesterol could be an evolutionary novelty that became prominent in mammals, while other known functions were already present earlier during vertebrate evolution.
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Affiliation(s)
- Robin A F Verwilligen
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands.
| | - Lindsay Mulder
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Pedro M Araújo
- University of Coimbra, MARE - Marine and Environmental Sciences Centre, Department Life Sciences, Coimbra, Portugal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jeroen Bussmann
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Menno Hoekstra
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Pharmacy Leiden, Leiden, the Netherlands
| | - Miranda Van Eck
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Pharmacy Leiden, Leiden, the Netherlands
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Lin B, Ma J, Fang Y, Lei P, Wang L, Qu L, Wu W, Jin L, Sun D. Advances in Zebrafish for Diabetes Mellitus with Wound Model. Bioengineering (Basel) 2023; 10:bioengineering10030330. [PMID: 36978721 PMCID: PMC10044998 DOI: 10.3390/bioengineering10030330] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Diabetic foot ulcers cause great suffering and are costly for the healthcare system. Normal wound healing involves hemostasis, inflammation, proliferation, and remodeling. However, the negative factors associated with diabetes, such as bacterial biofilms, persistent inflammation, impaired angiogenesis, inhibited cell proliferation, and pathological scarring, greatly interfere with the smooth progress of the entire healing process. It is this impaired wound healing that leads to diabetic foot ulcers and even amputations. Therefore, drug screening is challenging due to the complexity of damaged healing mechanisms. The establishment of a scientific and reasonable animal experimental model contributes significantly to the in-depth research of diabetic wound pathology, prevention, diagnosis, and treatment. In addition to the low cost and transparency of the embryo (for imaging transgene applications), zebrafish have a discrete wound healing process for the separate study of each stage, resulting in their potential as the ideal model animal for diabetic wound healing in the future. In this review, we examine the reasons behind the delayed healing of diabetic wounds, systematically review various studies using zebrafish as a diabetic wound model by different induction methods, as well as summarize the challenges and improvement strategies which provide references for establishing a more reasonable diabetic wound zebrafish model.
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Affiliation(s)
- Bangchang Lin
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310000, China
| | - Jiahui Ma
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Yimeng Fang
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Pengyu Lei
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Lei Wang
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Linkai Qu
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Wei Wu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, China
- Correspondence: (W.W.); (L.J.); (D.S.)
| | - Libo Jin
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
- Wenzhou City and WenZhouOuTai Medical Laboratory Co., Ltd. Joint Doctoral Innovation Station, Wenzhou Association for Science and Technology, Wenzhou 325000, China
- Correspondence: (W.W.); (L.J.); (D.S.)
| | - Da Sun
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
- Correspondence: (W.W.); (L.J.); (D.S.)
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530457. [PMID: 36909587 PMCID: PMC10002714 DOI: 10.1101/2023.02.28.530457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like "mesenchymal" cell state and a more differentiated sympathetic "adrenergic" cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional co-factor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism G/T that affects a G ATA motif in the first intron of LMO1. Here we show that wild-type zebrafish with the G ATA genotype develop adrenergic neuroblastoma, while knock-in of the protective T ATA allele at this locus reduces the penetrance of MYCN-driven tumors, which are restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrates that T ATA/ T ATA tumors also exhibit a mesenchymal cell state and are low risk at diagnosis. Thus, conversion of the regulatory G ATA to a T ATA allele in the first intron of LMO1 reduces the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that is conserved over 400 million years of evolution separating zebrafish and humans.
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Lu F, Leach LL, Gross JM. A CRISPR-Cas9-mediated F0 screen to identify pro-regenerative genes in the zebrafish retinal pigment epithelium. Sci Rep 2023; 13:3142. [PMID: 36823429 PMCID: PMC9950062 DOI: 10.1038/s41598-023-29046-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Ocular diseases resulting in death of the retinal pigment epithelium (RPE) lead to vision loss and blindness. There are currently no FDA-approved strategies to restore damaged RPE cells. Stimulating intrinsic regenerative responses within damaged tissues has gained traction as a possible mechanism for tissue repair. Zebrafish possess remarkable regenerative abilities, including within the RPE; however, our understanding of the underlying mechanisms remains limited. Here, we conducted an F0 in vivo CRISPR-Cas9-mediated screen of 27 candidate RPE regeneration genes. The screen involved injection of a ribonucleoprotein complex containing three highly mutagenic guide RNAs per target gene followed by PCR-based genotyping to identify large intragenic deletions and MATLAB-based automated quantification of RPE regeneration. Through this F0 screening pipeline, eight positive and seven negative regulators of RPE regeneration were identified. Further characterization of one candidate, cldn7b, revealed novel roles in regulating macrophage/microglia infiltration after RPE injury and in clearing RPE/pigment debris during late-phase RPE regeneration. Taken together, these data support the utility of targeted F0 screens for validating pro-regenerative factors and reveal novel factors that could regulate regenerative responses within the zebrafish RPE.
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Affiliation(s)
- Fangfang Lu
- grid.21925.3d0000 0004 1936 9000Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.452708.c0000 0004 1803 0208Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Lyndsay L. Leach
- grid.21925.3d0000 0004 1936 9000Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.89336.370000 0004 1936 9924Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Jeffrey M. Gross
- grid.21925.3d0000 0004 1936 9000Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.89336.370000 0004 1936 9924Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
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Hu H, Long Y, Song G, Chen S, Xu Z, Li Q, Wu Z. Dysfunction of Prkcaa Links Social Behavior Defects with Disturbed Circadian Rhythm in Zebrafish. Int J Mol Sci 2023; 24:ijms24043849. [PMID: 36835261 PMCID: PMC9961154 DOI: 10.3390/ijms24043849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Protein kinase Cα (PKCα/PRKCA) is a crucial regulator of circadian rhythm and is associated with human mental illnesses such as autism spectrum disorders and schizophrenia. However, the roles of PRKCA in modulating animal social behavior and the underlying mechanisms remain to be explored. Here we report the generation and characterization of prkcaa-deficient zebrafish (Danio rerio). The results of behavioral tests indicate that a deficiency in Prkcaa led to anxiety-like behavior and impaired social preference in zebrafish. RNA-sequencing analyses revealed the significant effects of the prkcaa mutation on the expression of the morning-preferring circadian genes. The representatives are the immediate early genes, including egr2a, egr4, fosaa, fosab and npas4a. The downregulation of these genes at night was attenuated by Prkcaa dysfunction. Consistently, the mutants demonstrated reversed day-night locomotor rhythm, which are more active at night than in the morning. Our data show the roles of PRKCA in regulating animal social interactions and link the social behavior defects with a disturbed circadian rhythm.
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Affiliation(s)
- Han Hu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Research Center of Fishery Resources and Environment, Southwest University, Chongqing 400715, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence: (Y.L.); (Z.W.); Tel.: +86-27-6878-0100 (Y.L.); +86-23-6836-6018 (Z.W.)
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shaoxiong Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Zhicheng Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Research Center of Fishery Resources and Environment, Southwest University, Chongqing 400715, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhengli Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Research Center of Fishery Resources and Environment, Southwest University, Chongqing 400715, China
- Correspondence: (Y.L.); (Z.W.); Tel.: +86-27-6878-0100 (Y.L.); +86-23-6836-6018 (Z.W.)
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Suzuki M, Iida M, Hayashi T, Suzuki KIT. CRISPR-Cas9-Based Functional Analysis in Amphibians: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. Methods Mol Biol 2023; 2637:341-357. [PMID: 36773159 DOI: 10.1007/978-1-0716-3016-7_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Amphibians have made many fundamental contributions to our knowledge, from basic biology to biomedical research on human diseases. Current genome editing tools based on the CRISPR-Cas system enable us to perform gene functional analysis in vivo, even in non-model organisms. We introduce here a highly efficient and easy protocol for gene knockout, which can be used in three different amphibians seamlessly: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. As it utilizes Cas9 ribonucleoprotein complex (RNP) for injection, this cloning-free method enables researchers to obtain founder embryos with a nearly complete knockout phenotype within a week. To evaluate somatic mutation rate and its correlation to the phenotype of a Cas9 RNP-injected embryo (crispant), we also present accurate and cost-effective genotyping methods using pooled amplicon-sequencing and a user-friendly web-based tool.
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Affiliation(s)
- Miyuki Suzuki
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Midori Iida
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Fukuoka, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Ken-Ichi T Suzuki
- Emerging Model Organisms Facility, Trans-scale Biology Center, National Institute for Basic Biology, Okazaki, Aichi, Japan.
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Voigt B, Minowa R, Gray RS. Screening Sperm for the Rapid Isolation of Germline Edits in Zebrafish. J Vis Exp 2023:10.3791/64686. [PMID: 36847371 PMCID: PMC10697136 DOI: 10.3791/64686] [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] [Indexed: 02/12/2023] Open
Abstract
The advent of targeted CRISPR-Cas nuclease technologies has revolutionized the ability to perform precise genome editing in both established and emerging model systems. CRISPR-Cas genome editing systems use a synthetic guide RNA (sgRNA) to target a CRISPR-associated (Cas) endonuclease to specific genomic DNA loci, where the Cas endonuclease generates a double-strand break. The repair of double-strand breaks by intrinsic error-prone mechanisms leads to insertions and/or deletions, disrupting the locus. Alternatively, the inclusion of double-stranded DNA donors or single-stranded DNA oligonucleotides in this process can elicit the inclusion of precise genome edits ranging from single nucleotide polymorphisms to small immunological tags or even large fluorescent protein constructs. However, a major bottleneck in this procedure can be finding and isolating the desired edit in the germline. This protocol outlines a robust method for screening and isolating germline mutations at specific loci in Danio rerio (zebrafish); however, these principles may be adaptable in any model where in vivo sperm collection is possible.
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Affiliation(s)
- Brittney Voigt
- Department of Molecular Biosciences, The University of Texas at Austin
| | - Ryoko Minowa
- Department of Nutritional Sciences, The University of Texas at Austin
| | - Ryan S Gray
- Department of Molecular Biosciences, The University of Texas at Austin; Department of Nutritional Sciences, The University of Texas at Austin;
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Richardson C, Kelsh RN, J. Richardson R. New advances in CRISPR/Cas-mediated precise gene-editing techniques. Dis Model Mech 2023; 16:dmm049874. [PMID: 36847161 PMCID: PMC10003097 DOI: 10.1242/dmm.049874] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutations in a variety of model organisms, from Escherichia coli to zebrafish, rodents and large mammals. CRISPR/Cas-based gene editing effectively generates insertions or deletions (indels), which allow for rapid gene disruption. However, a large proportion of human genetic diseases are caused by single-base-pair substitutions, which result in more subtle alterations to protein function, and which require more complex and precise editing to recreate in model systems. Precise genome editing (PGE) methods, however, typically have efficiencies of less than a tenth of those that generate less-specific indels, and so there has been a great deal of effort to improve PGE efficiency. Such optimisations include optimal guide RNA and mutation-bearing donor DNA template design, modulation of DNA repair pathways that underpin how edits result from Cas-induced cuts, and the development of Cas9 fusion proteins that introduce edits via alternative mechanisms. In this Review, we provide an overview of the recent progress in optimising PGE methods and their potential for generating models of human genetic disease.
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Affiliation(s)
- Chris Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Rebecca J. Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
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