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He J, Blazeski A, Nilanthi U, Menéndez J, Pirani SC, Levic DS, Bagnat M, Singh MK, Raya JG, García-Cardeña G, Torres-Vázquez J. Plxnd1-mediated mechanosensing of blood flow controls the caliber of the Dorsal Aorta via the transcription factor Klf2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.576555. [PMID: 38328196 PMCID: PMC10849625 DOI: 10.1101/2024.01.24.576555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The cardiovascular system generates and responds to mechanical forces. The heartbeat pumps blood through a network of vascular tubes, which adjust their caliber in response to the hemodynamic environment. However, how endothelial cells in the developing vascular system integrate inputs from circulatory forces into signaling pathways to define vessel caliber is poorly understood. Using vertebrate embryos and in vitro-assembled microvascular networks of human endothelial cells as models, flow and genetic manipulations, and custom software, we reveal that Plexin-D1, an endothelial Semaphorin receptor critical for angiogenic guidance, employs its mechanosensing activity to serve as a crucial positive regulator of the Dorsal Aorta's (DA) caliber. We also uncover that the flow-responsive transcription factor KLF2 acts as a paramount mechanosensitive effector of Plexin-D1 that enlarges endothelial cells to widen the vessel. These findings illuminate the molecular and cellular mechanisms orchestrating the interplay between cardiovascular development and hemodynamic forces.
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Affiliation(s)
- Jia He
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Adriana Blazeski
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA and Harvard Medical School, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Uthayanan Nilanthi
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857
| | - Javier Menéndez
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Samuel C. Pirani
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Manvendra K. Singh
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857
- National Heart Research Institute Singapore, National Heart Centre Singapore, 5 Hospital Drive, Singapore, 169609
| | - José G Raya
- Department of Radiology, New York University School of Medicine, New York, NY 10016, USA
| | - Guillermo García-Cardeña
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA and Harvard Medical School, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jesús Torres-Vázquez
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
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2
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Nanjappa DP, De Saffel H, Kalladka K, Arjuna S, Babu N, Prasad K, Sips P, Chakraborty A. Poly (A)-specific ribonuclease deficiency impacts oogenesis in zebrafish. Sci Rep 2023; 13:10026. [PMID: 37340076 DOI: 10.1038/s41598-023-37226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/18/2023] [Indexed: 06/22/2023] Open
Abstract
Poly (A)-specific ribonuclease (PARN) is the most important 3'-5'exonuclease involved in the process of deadenylation, the removal of poly (A) tails of mRNAs. Although PARN is primarily known for its role in mRNA stability, recent studies suggest several other functions of PARN including a role in telomere biology, non-coding RNA maturation, trimming of miRNAs, ribosome biogenesis and TP53 function. Moreover, PARN expression is de-regulated in many cancers, including solid tumours and hematopoietic malignancies. To better understand the in vivo role of PARN, we used a zebrafish model to study the physiological consequences of Parn loss-of-function. Exon 19 of the gene, which partially codes for the RNA binding domain of the protein, was targeted for CRISPR-Cas9-directed genome editing. Contrary to the expectations, no developmental defects were observed in the zebrafish with a parn nonsense mutation. Intriguingly, the parn null mutants were viable and fertile, but turned out to only develop into males. Histological analysis of the gonads in the mutants and their wild type siblings revealed a defective maturation of gonadal cells in the parn null mutants. The results of this study highlight yet another emerging function of Parn, i.e., its role in oogenesis.
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Affiliation(s)
- Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Hanna De Saffel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Krithika Kalladka
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Kishan Prasad
- Department of Pathology, KS Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India.
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3
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Li Y, Chen L, Li Y, Yang C, Gui B, Li Y, Liao L, Zhu Z, Huang R, Wang Y. Krüppel-like factor 2a (KLF2A) suppresses GCRV replication by upregulating serpinc1 expression in Ctenopharyngodon idellus kidney (CIK) cells. FISH & SHELLFISH IMMUNOLOGY 2022; 131:1118-1124. [PMID: 36400369 DOI: 10.1016/j.fsi.2022.11.017] [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: 08/05/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Krüppel-like factor 2a (KLF2A), a transcription factor of the krüppel-like family, is involved in regulating the immune molecules and is associated with viral infection. However, the function of KLF2A during viral infections in fish remains unclear. In this study, grass carp (Ctenopharyngodon idellus) was used to predict the target genes regulated by KLF2A. The results showed that the candidate target genes included four members of the serpin gene family (serpinb1l2, serpinc1, serpinh1a, and serpinh1b). Dual-luciferase experiments showed that klf2a positively regulates serpinc1 expression. Dose-dependent klf2a overexpression in C. idellus kidney (CIK) cells significantly upregulated the expression of serpinc1. Overexpressing klf2a or serpinc1 in CIK cells activated interferon responses and suppressed grass carp reovirus (GCRV) replication. Klf2a and serpinc1 co-expression inhibited GCRV replication. These results show that klf2a upregulates serpinc1 mRNA expression, promotes type 1 interferon responses, and suppresses GCRV infection. This study provides insights into the regulatory role and biological functions of KLF2A in host-virus interactions in fish.
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Affiliation(s)
- Yangyu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangming Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangyang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Bin Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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4
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Rouf MA, Wen L, Mahendra Y, Wang J, Zhang K, Liang S, Wang Y, Li Z, Wang Y, Wang G. The recent advances and future perspectives of genetic compensation studies in the zebrafish model. Genes Dis 2022; 10:468-479. [DOI: 10.1016/j.gendis.2021.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 11/08/2021] [Accepted: 12/01/2021] [Indexed: 10/19/2022] Open
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5
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Derrick CJ, Pollitt EJG, Sanchez Sevilla Uruchurtu A, Hussein F, Grierson AJ, Noël ES. Lamb1a regulates atrial growth by limiting second heart field addition during zebrafish heart development. Development 2021; 148:272294. [PMID: 34568948 DOI: 10.1242/dev.199691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/19/2021] [Indexed: 12/20/2022]
Abstract
During early vertebrate heart development, the heart transitions from a linear tube to a complex asymmetric structure, a morphogenetic process that occurs simultaneously with growth of the heart. Cardiac growth during early heart morphogenesis is driven by deployment of cells from the second heart field (SHF) into both poles of the heart. Laminin is a core component of the extracellular matrix and, although mutations in laminin subunits are linked with cardiac abnormalities, no role for laminin has been identified in early vertebrate heart morphogenesis. We identified tissue-specific expression of laminin genes in the developing zebrafish heart, supporting a role for laminins in heart morphogenesis. Analysis of heart development in lamb1a zebrafish mutant embryos reveals mild morphogenetic defects and progressive cardiomegaly, and that Lamb1a functions to limit heart size during cardiac development by restricting SHF addition. lamb1a mutants exhibit hallmarks of altered haemodynamics, and blocking cardiac contractility in lamb1a mutants rescues heart size and atrial SHF addition. Together, these results suggest that laminin mediates interactions between SHF deployment and cardiac biomechanics during heart morphogenesis and growth in the developing embryo.
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Affiliation(s)
| | - Eric J G Pollitt
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | | | - Farah Hussein
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Andrew J Grierson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Emily S Noël
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
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6
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Paolini A, Fontana F, Pham VC, Rödel CJ, Abdelilah-Seyfried S. Mechanosensitive Notch-Dll4 and Klf2-Wnt9 signaling pathways intersect in guiding valvulogenesis in zebrafish. Cell Rep 2021; 37:109782. [PMID: 34610316 PMCID: PMC8511505 DOI: 10.1016/j.celrep.2021.109782] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/27/2022] Open
Abstract
In the zebrafish embryo, the onset of blood flow generates fluid shear stress on endocardial cells, which are specialized endothelial cells that line the interior of the heart. High levels of fluid shear stress activate both Notch and Klf2 signaling, which play crucial roles in atrioventricular valvulogenesis. However, it remains unclear why only individual endocardial cells ingress into the cardiac jelly and initiate valvulogenesis. Here, we show that lateral inhibition between endocardial cells, mediated by Notch, singles out Delta-like-4-positive endocardial cells. These cells ingress into the cardiac jelly, where they form an abluminal cell population. Delta-like-4-positive cells ingress in response to Wnt9a, which is produced in parallel through an Erk5-Klf2-Wnt9a signaling cascade also activated by blood flow. Hence, mechanical stimulation activates parallel mechanosensitive signaling pathways that produce binary effects by driving endocardial cells toward either luminal or abluminal fates. Ultimately, these cell fate decisions sculpt cardiac valve leaflets.
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Affiliation(s)
- Alessio Paolini
- Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany
| | - Federica Fontana
- Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany
| | - Van-Cuong Pham
- Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany
| | - Claudia Jasmin Rödel
- Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany
| | - Salim Abdelilah-Seyfried
- Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany; Institute of Molecular Biology, Hannover Medical School, 30625 Hannover, Germany.
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7
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Sugden WW, North TE. Making Blood from the Vessel: Extrinsic and Environmental Cues Guiding the Endothelial-to-Hematopoietic Transition. Life (Basel) 2021; 11:life11101027. [PMID: 34685398 PMCID: PMC8539454 DOI: 10.3390/life11101027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023] Open
Abstract
It is increasingly recognized that specialized subsets of endothelial cells carry out unique functions in specific organs and regions of the vascular tree. Perhaps the most striking example of this specialization is the ability to contribute to the generation of the blood system, in which a distinct population of “hemogenic” endothelial cells in the embryo transforms irreversibly into hematopoietic stem and progenitor cells that produce circulating erythroid, myeloid and lymphoid cells for the lifetime of an animal. This review will focus on recent advances made in the zebrafish model organism uncovering the extrinsic and environmental factors that facilitate hemogenic commitment and the process of endothelial-to-hematopoietic transition that produces blood stem cells. We highlight in particular biomechanical influences of hemodynamic forces and the extracellular matrix, metabolic and sterile inflammatory cues present during this developmental stage, and outline new avenues opened by transcriptomic-based approaches to decipher cell–cell communication mechanisms as examples of key signals in the embryonic niche that regulate hematopoiesis.
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Affiliation(s)
- Wade W. Sugden
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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8
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Jakutis G, Stainier DYR. Genotype-Phenotype Relationships in the Context of Transcriptional Adaptation and Genetic Robustness. Annu Rev Genet 2021; 55:71-91. [PMID: 34314597 DOI: 10.1146/annurev-genet-071719-020342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic manipulations with a robust and predictable outcome are critical to investigate gene function, as well as for therapeutic genome engineering. For many years, knockdown approaches and reagents including RNA interference and antisense oligonucleotides dominated functional studies; however, with the advent of precise genome editing technologies, CRISPR-based knockout systems have become the state-of-the-art tools for such studies. These technologies have helped decipher the role of thousands of genes in development and disease. Their use has also revealed how limited our understanding of genotype-phenotype relationships is. The recent discovery that certain mutations can trigger the transcriptional modulation of other genes, a phenomenon called transcriptional adaptation, has provided an additional explanation for the contradicting phenotypes observed in knockdown versus knockout models and increased awareness about the use of each of these approaches. In this review, we first cover the strengths and limitations of different gene perturbation strategies. Then we highlight the diverse ways in which the genotype-phenotype relationship can be discordant between these different strategies. Finally, we review the genetic robustness mechanisms that can lead to such discrepancies, paying special attention to the recently discovered phenomenon of transcriptional adaptation. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gabrielius Jakutis
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany;
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; .,German Centre for Cardiovascular Research (DZHK), Partner site Rhine-Main, 60590 Frankfurt am Main, Germany.,Excellence Cluster Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
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9
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Shi X, Guan K, Peng X, Xu B, Zhou X, Wang S, Xu S, Zheng M, Huang J, Wan X, Guan W, Su KP, Ye M, Gao X, Yin Z, Li X. Ghrelin modulates dopaminergic neuron formation and attention deficit hyperactivity disorder-like behaviors: From animals to human models. Brain Behav Immun 2021; 94:327-337. [PMID: 33412253 DOI: 10.1016/j.bbi.2020.12.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022] Open
Abstract
Attention deficit hyperactivity disorder (ADHD) is one of the most prevalent psychiatric disorders in children. The orexigenic hormone ghrelin is important in neuroprotection and neurodevelopment, which may play an important role in psychopathogenesis of ADHD. This study aimed to systematically investigate the genomic and pharmacological manipulations of ghrelin functioning in ADHD-like symptoms in zebrafish models and validated the effects of ghrelin polymorphisms in human subjects with ADHD. We firstly generated ghrelinΔ/Δ zebrafish mutant, which displayed hyperactive, attention deficit-like and impulsive-like behaviors, as well as endophenotypes, mimicking human ADHD. GhrelinΔ/Δ zebrafish exhibited downregulated expression levels of wnt1, wnt3a, wnt5a that are critical for dopaminergic neuron development to possibly regulate their number and spatial organization. Pharmacological blockade of wnt signaling with XAV939 induced a reduced moving activity and less dopaminergic neurons; whereas, wnt agonist SB415286 rescued hyperactivity and dopaminergic neuron loss in ghrelinΔ/Δ zebrafish. In addition, we further identified and validated a SNP, rs696217, on orexigenic hormone preproghrelin/ghrelin (T408T, Met72Met) to be associated with a higher risk of ADHD in a case-controlled association study with 248 subjects with ADHD and 208 subjects of healthy controls. Together, our results reveal a novel endogenous role for orexigenic hormone ghrelin in ADHD, which provides insights into genetic regulation and drug screens for the identification of novel treatments of ADHD.
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Affiliation(s)
- Xulai Shi
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Kaiyu Guan
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Xuyan Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, PR China
| | - Bingru Xu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Xianyong Zhou
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Shao Wang
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Shengnan Xu
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Miaomiao Zheng
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Jing Huang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Xiaoyang Wan
- Institute of Infectious Liver Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Wanchun Guan
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Kuan-Pin Su
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; An-Nan Hospital, China Medical University, Tainan, Taiwan
| | - Minjie Ye
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China
| | - Xiang Gao
- Central Laboratory, Scientific Research Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, PR China.
| | - Xi Li
- The Affiliated Kangning Hospital of Wenzhou Medical University, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, PR China.
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10
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Fontana F, Haack T, Reichenbach M, Knaus P, Puceat M, Abdelilah-Seyfried S. Antagonistic Activities of Vegfr3/Flt4 and Notch1b Fine-tune Mechanosensitive Signaling during Zebrafish Cardiac Valvulogenesis. Cell Rep 2021; 32:107883. [PMID: 32668254 DOI: 10.1016/j.celrep.2020.107883] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/10/2020] [Accepted: 06/17/2020] [Indexed: 12/22/2022] Open
Abstract
The formation of cardiac valves depends on mechanical forces exerted by blood flow. Endocardial cells lining the interior of the heart are sensitive to these stimuli and respond by rearranging into luminal cells subjected to shear stress and abluminal cells not exposed to it. The mechanisms by which endocardial cells sense these dynamic biomechanical stimuli and how they evoke different cellular responses are largely unknown. Here, we show that blood flow activates two parallel mechanosensitive pathways, one mediated by Notch and the other by Klf2a. Both pathways negatively regulate the angiogenesis receptor Vegfr3/Flt4, which becomes restricted to abluminal endocardial cells. Its loss disrupts valve morphogenesis and results in the occurrence of Notch signaling within abluminal endocardial cells. Our work explains how antagonistic activities by Vegfr3/Flt4 on the abluminal side and by Notch on the luminal side shape cardiac valve leaflets by triggering unique differences in the fates of endocardial cells.
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Affiliation(s)
- Federica Fontana
- Institute of Biochemistry and Biology, Potsdam University, D-14476 Potsdam, Germany
| | - Timm Haack
- Institute of Molecular Biology, Hannover Medical School, D-30625 Hannover, Germany
| | - Maria Reichenbach
- Institute of Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Petra Knaus
- Institute of Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Michel Puceat
- INSERM U-1251, MMG, Aix-Marseille University, 13885 Marseille, France
| | - Salim Abdelilah-Seyfried
- Institute of Biochemistry and Biology, Potsdam University, D-14476 Potsdam, Germany; Institute of Molecular Biology, Hannover Medical School, D-30625 Hannover, Germany.
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11
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Cunningham CM, Bellipanni G, Habas R, Balciunas D. Deletion of morpholino binding sites (DeMOBS) to assess specificity of morphant phenotypes. Sci Rep 2020; 10:15366. [PMID: 32958829 PMCID: PMC7506532 DOI: 10.1038/s41598-020-71708-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/13/2020] [Indexed: 01/05/2023] Open
Abstract
Two complimentary approaches are widely used to study gene function in zebrafish: induction of genetic mutations, usually using targeted nucleases such as CRISPR/Cas9, and suppression of gene expression, typically using Morpholino oligomers. Neither method is perfect. Morpholinos (MOs) sometimes produce off-target or toxicity-related effects that can be mistaken for true phenotypes. Conversely, genetic mutants can be subject to compensation, or may fail to yield a null phenotype due to leakiness (e.g. use of cryptic splice sites or downstream AUGs). When discrepancy between mutant and morpholino-induced (morphant) phenotypes is observed, experimental validation of such phenotypes becomes very labor intensive. We have developed a simple genetic method to differentiate between genuine morphant phenotypes and those produced due to off-target effects. We speculated that indels within 5' untranslated regions would be unlikely to have a significant negative effect on gene expression. Mutations induced within a MO target site would result in a Morpholino-refractive allele thus suppressing true MO phenotypes whilst non-specific phenotypes would remain. We tested this hypothesis on one gene with an exclusively zygotic function, tbx5a, and one gene with strong maternal effect, ctnnb2. We found that indels within the Morpholino binding site are indeed able to suppress both zygotic and maternal morphant phenotypes. We also observed that the ability of such indels to suppress morpholino phenotypes does depend on the size and the location of the deletion. Nonetheless, mutating the morpholino binding sites in both maternal and zygotic genes can ascertain the specificity of morphant phenotypes.
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Affiliation(s)
| | - Gianfranco Bellipanni
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Raymond Habas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Darius Balciunas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA.
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12
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Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease. PLoS One 2020; 15:e0230566. [PMID: 32208444 PMCID: PMC7092968 DOI: 10.1371/journal.pone.0230566] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/03/2020] [Indexed: 12/22/2022] Open
Abstract
A phenomenon of genetic compensation is commonly observed when an organism with a disease-bearing mutation shows incomplete penetrance of the disease phenotype. Such incomplete phenotypic penetrance, or genetic compensation, is more commonly found in stable knockout models, rather than transient knockdown models. As such, these incidents present a challenge for the disease modeling field, although a deeper understanding of genetic compensation may also hold the key for novel therapeutic interventions. In our study we created a knockout model of slc25a46 gene, which is a recently discovered important player in mitochondrial dynamics, and deleterious mutations in which are known to cause peripheral neuropathy, optic atrophy and cerebellar ataxia. We report a case of genetic compensation in a stable slc25a46 homozygous zebrafish mutant (hereafter referred as “mutant”), in contrast to a penetrant disease phenotype in the first generation (F0) slc25a46 mosaic mutant (hereafter referred as “crispant”), generated with CRISPR/Cas-9 technology. We show that the crispant phenotype is specific and rescuable. By performing mRNA sequencing, we define significant changes in slc25a46 mutant’s gene expression profile, which are largely absent in crispants. We find that among the most significantly altered mRNAs, anxa6 gene stands out as a functionally relevant player in mitochondrial dynamics. We also find that our genetic compensation case does not arise from mechanisms driven by mutant mRNA decay. Our study contributes to the growing evidence of the genetic compensation phenomenon and presents novel insights about Slc25a46 function. Furthermore, our study provides the evidence for the efficiency of F0 CRISPR screens for disease candidate genes, which may be used to advance the field of functional genetics.
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Li Q, Qin Z, Wang Q, Xu T, Yang Y, He Z. Applications of Genome Editing Technology in Animal Disease Modeling and Gene Therapy. Comput Struct Biotechnol J 2019; 17:689-698. [PMID: 31303973 PMCID: PMC6603303 DOI: 10.1016/j.csbj.2019.05.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 02/05/2023] Open
Abstract
Genome editing technology is a technique for targeted genetic modifications, enabling the knockout and addition of specific DNA fragments. This technology has been widely used in various types of biomedical research, clinics and agriculture. In terms of disease research, constructing appropriate animal models is necessary. Combining reproductive technology with genome editing, many animal disease models have been generated for basic and clinical research. In addition, precisely targeted modifications allow genome editing to flourish in the field of gene therapy. Many mutations refractory to traditional gene therapy could be permanently corrected at the DNA level. Thus, genome editing is undoubtedly a promising technology for gene therapy. In this review, we mainly introduce the applications of genome editing in constructing animal disease models and gene therapies, as well as its future prospects and challenges.
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Affiliation(s)
- Qian Li
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China
| | - Zhou Qin
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China.,Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China
| | - Qingnan Wang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China
| | - Ting Xu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China.,Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China
| | - Zhiyao He
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China.,Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, Sichuan 610041, China
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Zimmer AM, Pan YK, Chandrapalan T, Kwong RWM, Perry SF. Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? ACTA ACUST UNITED AC 2019; 222:222/7/jeb175737. [PMID: 30948498 DOI: 10.1242/jeb.175737] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).
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Affiliation(s)
- Alex M Zimmer
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yihang K Pan
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | | | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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15
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Abstract
Heart formation involves a complex series of tissue rearrangements, during which regions of the developing organ expand, bend, converge, and protrude in order to create the specific shapes of important cardiac components. Much of this morphogenesis takes place while cardiac function is underway, with blood flowing through the rapidly contracting chambers. Fluid forces are therefore likely to influence the regulation of cardiac morphogenesis, but it is not yet clear how these biomechanical cues direct specific cellular behaviors. In recent years, the optical accessibility and genetic amenability of zebrafish embryos have facilitated unique opportunities to integrate the analysis of flow parameters with the molecular and cellular dynamics underlying cardiogenesis. Consequently, we are making progress toward a comprehensive view of the biomechanical regulation of cardiac chamber emergence, atrioventricular canal differentiation, and ventricular trabeculation. In this review, we highlight a series of studies in zebrafish that have provided new insight into how cardiac function can shape cardiac morphology, with a particular focus on how hemodynamics can impact cardiac cell behavior. Over the long-term, this knowledge will undoubtedly guide our consideration of the potential causes of congenital heart disease.
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Affiliation(s)
- Pragya Sidhwani
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Deborah Yelon
- Division of Biological Sciences, University of California, San Diego, CA, United States.
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Rasouli SJ, El-Brolosy M, Tsedeke AT, Bensimon-Brito A, Ghanbari P, Maischein HM, Kuenne C, Stainier DY. The flow responsive transcription factor Klf2 is required for myocardial wall integrity by modulating Fgf signaling. eLife 2018; 7:e38889. [PMID: 30592462 PMCID: PMC6329608 DOI: 10.7554/elife.38889] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 12/24/2018] [Indexed: 12/17/2022] Open
Abstract
Complex interplay between cardiac tissues is crucial for their integrity. The flow responsive transcription factor KLF2, which is expressed in the endocardium, is vital for cardiovascular development but its exact role remains to be defined. To this end, we mutated both klf2 paralogues in zebrafish, and while single mutants exhibit no obvious phenotype, double mutants display a novel phenotype of cardiomyocyte extrusion towards the abluminal side. This extrusion requires cardiac contractility and correlates with the mislocalization of N-cadherin from the lateral to the apical side of cardiomyocytes. Transgenic rescue data show that klf2 expression in endothelium, but not myocardium, prevents this cardiomyocyte extrusion phenotype. Transcriptome analysis of klf2 mutant hearts reveals that Fgf signaling is affected, and accordingly, we find that inhibition of Fgf signaling in wild-type animals can lead to abluminal cardiomyocyte extrusion. These studies provide new insights into how Klf2 regulates cardiovascular development and specifically myocardial wall integrity.
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Affiliation(s)
- Seyed Javad Rasouli
- Department of Developmental GeneticsMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Mohamed El-Brolosy
- Department of Developmental GeneticsMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Ayele Taddese Tsedeke
- Department of Developmental GeneticsMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Anabela Bensimon-Brito
- Department of Developmental GeneticsMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Parisa Ghanbari
- Department of Cardiac Development and RemodelingMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Hans-Martin Maischein
- Department of Developmental GeneticsMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Carsten Kuenne
- Bioinformatics Core UnitMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Didier Y Stainier
- Department of Developmental GeneticsMax Planck Institute for Heart and Lung ResearchBad NauheimGermany
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Bickers C, Española SD, Grainger S, Pouget C, Traver D. Zebrafish snai2 mutants fail to phenocopy morphant phenotypes. PLoS One 2018; 13:e0202747. [PMID: 30208064 PMCID: PMC6135377 DOI: 10.1371/journal.pone.0202747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/07/2018] [Indexed: 11/24/2022] Open
Abstract
Snail2 is a zinc-finger transcription factor best known to repress expression of genes encoding cell adherence proteins to facilitate induction of the epithelial-to-mesenchymal transition. While this role has been best documented in the developmental migration of the neural crest and mesoderm, here we expand on previously reported preliminary findings that morpholino knock-down of snai2 impairs the generation of hematopoietic stem cells (HSCs) during zebrafish development. We demonstrate that snai2 morphants fail to initiate HSC specification and show defects in the somitic niche of migrating HSC precursors. These defects include a reduction in sclerotome markers as well as in the Notch ligands dlc and dld, which are known to be essential components of HSC specification. Accordingly, enforced expression of the Notch1-intracellular domain was capable of rescuing HSC specification in snai2 morphants. To parallel our approach, we obtained two mutant alleles of snai2. In contrast to the morphants, homozygous mutant embryos displayed no defects in HSC specification or in sclerotome development, and mutant fish survive into adulthood. However, when these homozygous mutants were injected with snai2 morpholino, HSCs were improperly specified. In summary, our morpholino data support a role for Snai2 in HSC development, whereas our mutant data suggest that Snai2 is dispensable for this process. Together, these findings further support the need for careful consideration of both morpholino and mutant phenotypes in studies of gene function.
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Affiliation(s)
- Cara Bickers
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Sophia D. Española
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Stephanie Grainger
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Claire Pouget
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - David Traver
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America
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Zheng SS, Han RY, Xiang L, Zhuang YY, Jin ZB. Versatile Genome Engineering Techniques Advance Human Ocular Disease Researches in Zebrafish. Front Cell Dev Biol 2018; 6:75. [PMID: 30050903 PMCID: PMC6052052 DOI: 10.3389/fcell.2018.00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Over recent decades, zebrafish has been established as a sophisticated vertebrate model for studying human ocular diseases due to its high fecundity, short generation time and genetic tractability. With the invention of morpholino (MO) technology, it became possible to study the genetic basis and relevant genes of ocular diseases in vivo. Many genes have been shown to be related to ocular diseases. However, the issue of specificity is the major concern in defining gene functions with MO technology. The emergence of the first- and second-generation genetic modification tools zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs), respectively, eliminated the potential phenotypic risk induced by MOs. Nevertheless, the efficiency of these nucleases remained relatively low until the third technique, the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, was discovered. This review highlights the application of multiple genome engineering techniques, especially the CRISPR/Cas9 system, in the study of human ocular diseases in zebrafish.
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Affiliation(s)
- Si-Si Zheng
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ru-Yi Han
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Lue Xiang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - You-Yuan Zhuang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
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Investigation of Islet2a function in zebrafish embryos: Mutants and morphants differ in morphologic phenotypes and gene expression. PLoS One 2018; 13:e0199233. [PMID: 29927984 PMCID: PMC6013100 DOI: 10.1371/journal.pone.0199233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
Zebrafish primary motor neurons differ from each other with respect to morphology, muscle targets and electrophysiological properties. For example, CaP has 2-3-fold larger densities of both inward and outward currents than do other motor neurons. We tested whether the transcription factor Islet2a, uniquely expressed in CaP, but not other primary motor neurons, plays a role in specifying its stereotypic electrophysiological properties. We used both TALEN-based gene editing and antisense morpholino approaches to disrupt Islet2a function. Our electrophysiology results do not support a specific role for Islet2a in determining CaP’s unique electrical properties. However, we also found that the morphological phenotypes of CaP and a later-born motor neuron differed between islet2a mutants and morphants. Using microarrays, we tested whether the gene expression profiles of whole embryo morphants, mutants and controls also differed. Morphants had 174 and 201 genes that were differentially expressed compared to mutants and controls, respectively. Further, islet2a was identified as a differentially expressed gene. To examine how mutation of islet2a affected islet gene expression specifically in CaPs, we performed RNA in situ hybridization. We detected no obvious differences in expression of islet1, islet2a, or islet2b in CaPs of mutant versus sibling control embryos. However, immunolabeling studies revealed that an Islet protein persisted in CaPs of mutants, albeit at a reduced level compared to controls. While we cannot exclude requirement for some Islet protein, we conclude that differentiation of the CaP’s stereotypic large inward and outward currents does not have a specific requirement for Islet2a.
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Paone C, Diofano F, Park DD, Rottbauer W, Just S. Genetics of Cardiovascular Disease: Fishing for Causality. Front Cardiovasc Med 2018; 5:60. [PMID: 29911105 PMCID: PMC5992778 DOI: 10.3389/fcvm.2018.00060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/15/2018] [Indexed: 01/08/2023] Open
Abstract
Cardiovascular disease (CVD) is still the leading cause of death in all western world countries and genetic predisposition in combination with traditional risk factors frequently mediates their manifestation. Genome-wide association (GWA) studies revealed numerous potentially disease modifying genetic loci often including several SNPs and associated genes. However, pure genetic association does not prove direct or indirect relevance of the modifier region on pathogenesis, nor does it define within the associated region the exact genetic driver of the disease. Therefore, the relevance of the identified genetic disease associations needs to be confirmed either in monogenic traits or in experimental in vivo model system by functional genomic studies. In this review, we focus on the use of functional genomic approaches such as gene knock-down or CRISPR/Cas9-mediated genome editing in the zebrafish model to validate disease-associated genomic loci and to identify novel cardiovascular disease genes. We summarize the benefits of the zebrafish for cardiovascular research and highlight examples demonstrating the successful combination of GWA studies and functional genomics in zebrafish to broaden our knowledge on the genetic and molecular underpinnings of cardiovascular diseases.
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Affiliation(s)
- Christoph Paone
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Federica Diofano
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Deung-Dae Park
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | | | - Steffen Just
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
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Making a Morpholino Experiment Work: Controls, Favoring Specificity, Improving Efficacy, Storage, and Dose. Methods Mol Biol 2018; 1565:17-29. [PMID: 28364230 DOI: 10.1007/978-1-4939-6817-6_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A good Morpholino experiment starts with oligos that have been carefully designed to minimize off-target RNA binding. Performing a successful, reproducible, and well-controlled Morpholino experiment requires oligos that are single stranded and in solution at a known concentration. The outcome of treatment with the oligo needs to be checked for specificity, that is, that the observed outcome is due to interaction with the intended RNA and not an interaction with an unexpected RNA. In this chapter, I will discuss Morpholino use mostly in the context of embryonic microinjection experiments, though many techniques and warnings will be applicable to cell culture or adult animal experiments as well. Controls are critical to a good experiment, but good techniques in designing, preparing, storing, and using the oligos can improve the strength and specificity of the knockdown. Finally, it is important to know the solution concentration of the oligo to ensure that the results are reproducible.
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22
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Zhu B, Ge W. Genome editing in fishes and their applications. Gen Comp Endocrinol 2018; 257:3-12. [PMID: 28919449 DOI: 10.1016/j.ygcen.2017.09.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 08/15/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022]
Abstract
There have been revolutionary progresses in genome engineering in the past few years. The newly-emerged genome editing technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats associated with Cas9 (CRISPR/Cas9) have enabled biological scientists to perform efficient and precise targeted genome editing in different species. Fish represent the largest group of vertebrates with many species having values for both scientific research and aquaculture industry. Genome editing technologies have found extensive applications in different fish species for basic functional studies as well asapplied research in such fields as disease modeling and aquaculture. This mini-review focuses on recent advancements and applications of the new generation of genome editing technologies in fish species, with particular emphasis on their applications in understanding reproductive functions because the reproductive axis has been most systematically and best studied among others and its function has been difficult to address with reverse genetics approach.
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Affiliation(s)
- Bo Zhu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.
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The Impact of CRISPR/Cas9 Technology on Cardiac Research: From Disease Modelling to Therapeutic Approaches. Stem Cells Int 2017; 2017:8960236. [PMID: 29434642 PMCID: PMC5757142 DOI: 10.1155/2017/8960236] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/16/2017] [Indexed: 12/19/2022] Open
Abstract
Genome-editing technology has emerged as a powerful method that enables the generation of genetically modified cells and organisms necessary to elucidate gene function and mechanisms of human diseases. The clustered regularly interspaced short palindromic repeats- (CRISPR-) associated 9 (Cas9) system has rapidly become one of the most popular approaches for genome editing in basic biomedical research over recent years because of its simplicity and adaptability. CRISPR/Cas9 genome editing has been used to correct DNA mutations ranging from a single base pair to large deletions in both in vitro and in vivo model systems. CRISPR/Cas9 has been used to increase the understanding of many aspects of cardiovascular disorders, including lipid metabolism, electrophysiology and genetic inheritance. The CRISPR/Cas9 technology has been proven to be effective in creating gene knockout (KO) or knockin in human cells and is particularly useful for editing induced pluripotent stem cells (iPSCs). Despite these progresses, some biological, technical, and ethical issues are limiting the therapeutic potential of genome editing in cardiovascular diseases. This review will focus on various applications of CRISPR/Cas9 genome editing in the cardiovascular field, for both disease research and the prospect of in vivo genome-editing therapies in the future.
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Abstract
PURPOSE OF REVIEW The opportunities afforded through the recent advent of genome-editing technologies have allowed investigators to more easily study a number of diseases. The advantages and limitations of the most prominent genome-editing technologies are described in this review, along with potential applications specifically focused on cardiovascular diseases. RECENT FINDINGS The recent genome-editing tools using programmable nucleases, such as zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), have rapidly been adapted to manipulate genes in a variety of cellular and animal models. A number of recent cardiovascular disease-related publications report cases in which specific mutations are introduced into disease models for functional characterization and for testing of therapeutic strategies. Recent advances in genome-editing technologies offer new approaches to understand and treat diseases. Here, we discuss genome editing strategies to easily characterize naturally occurring mutations and offer strategies with potential clinical relevance.
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Affiliation(s)
- Alexandra C Chadwick
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kiran Musunuru
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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25
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Eve AMJ, Smith JC. Knockdown of Laminin gamma-3 (Lamc3) impairs motoneuron guidance in the zebrafish embryo. Wellcome Open Res 2017; 2:111. [PMID: 29417095 PMCID: PMC5785718 DOI: 10.12688/wellcomeopenres.12394.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2017] [Indexed: 01/09/2023] Open
Abstract
Background: Previous work in the zebrafish embryo has shown that laminin γ-3 ( lamc3) is enriched in endothelial cells marked by expression of fli1a, but the role of Lamc3 has been unknown. Methods: We use antisense morpholino oligonucleotides, and CRISPR/Cas9 mutagenesis of F0 embryos, to create zebrafish embryos in which lamc3 expression is compromised. Transgenic imaging, immunofluorescence, and in situ hybridisation reveal that Lamc3 loss-of-function affects the development of muscle pioneers, endothelial cells, and motoneurons. Results: Lamc3 is enriched in endothelial cells during zebrafish development, but it is also expressed by other tissues. Depletion of Lamc3 by use of antisense morpholino oligonucleotides perturbs formation of the parachordal chain and subsequently the thoracic duct, but Lamc3 is not required for sprouting of the cardinal vein. F0 embryos in which lamc3 expression is perturbed by a CRISPR/Cas9 approach also fail to form a parachordal chain, but we were unable to establish a stable lamc3 null line. Lamc3 is dispensable for muscle pioneer specification and for the expression of netrin-1a in these cells. Lamc3 knockdown causes netrin-1a up-regulation in the neural tube and there is increased Netrin-1 protein throughout the trunk of the embryo. Axonal guidance of rostral primary motoneurons is defective in Lamc3 knockdown embryos. Conclusions: We suggest that knockdown of Lamc3 perturbs migration of rostral primary motoneurons at the level of the horizontal myoseptum, indicating that laminin γ3 plays a role in motoneuron guidance.
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Affiliation(s)
- Alexander M. J. Eve
- Developmental Biology Laboratory, Francis Crick Institute, London, NW1 1AT, UK
| | - James C. Smith
- Developmental Biology Laboratory, Francis Crick Institute, London, NW1 1AT, UK
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26
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Schwarzer S, Spieß S, Brand M, Hans S. Dlx3b/4b is required for early-born but not later-forming sensory hair cells during zebrafish inner ear development. Biol Open 2017; 6:1270-1278. [PMID: 28751305 PMCID: PMC5612237 DOI: 10.1242/bio.026211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Morpholino-mediated knockdown has shown that the homeodomain transcription factors Dlx3b and Dlx4b are essential for proper induction of the otic-epibranchial progenitor domain (OEPD), as well as subsequent formation of sensory hair cells in the developing zebrafish inner ear. However, increasing use of reverse genetic approaches has revealed poor correlation between morpholino-induced and mutant phenotypes. Using CRISPR/Cas9-mediated mutagenesis, we generated a defined deletion eliminating the entire open reading frames of dlx3b and dlx4b (dlx3b/4b) and investigated a potential phenotypic difference between mutants and morpholino-mediated knockdown. Consistent with previous findings obtained by morpholino-mediated knockdown of Dlx3b and Dlx4b, dlx3b/4b mutants display compromised otic induction, the development of smaller otic vesicles and an elimination of all indications of otic specification when combined with loss of foxi1, a second known OEPD competence factor in zebrafish. Furthermore, sensorigenesis is also affected in dlx3b/4b mutants. However, we find that only early-born sensory hair cells (tether cells), that seed and anchor the formation of otoliths, are affected. Later-forming sensory hair cells are present, indicating that two genetically distinct pathways control the development of early-born and later-forming sensory hair cells. Finally, impairment of early-born sensory hair cell formation in dlx3b/4b mutant embryos reverses the common temporal sequence of neuronal and sensory hair cell specification in zebrafish, resembling the order of cell specification in amniotes; Neurog1 expression before Atoh1 expression. We conclude that the Dlx3b/4b-dependent pathway has been either acquired newly in the fish lineage or lost in other vertebrate species during evolution, and that the events during early inner ear development are remarkably similar in fish and amniotes in the absence of this pathway. Summary: The transcription factors Dlx3b and Dlx4b control the formation of early-born sensory hair cells or tether cells in the developing zebrafish inner ear.
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Affiliation(s)
- Simone Schwarzer
- Technische Universität Dresden, Biotechnology Center and DFG-Center for Regenerative Therapies Dresden Cluster of Excellence, Tatzberg 47-49, 01307 Dresden, Germany
| | - Sandra Spieß
- Technische Universität Dresden, Biotechnology Center and DFG-Center for Regenerative Therapies Dresden Cluster of Excellence, Tatzberg 47-49, 01307 Dresden, Germany
| | - Michael Brand
- Technische Universität Dresden, Biotechnology Center and DFG-Center for Regenerative Therapies Dresden Cluster of Excellence, Tatzberg 47-49, 01307 Dresden, Germany
| | - Stefan Hans
- Technische Universität Dresden, Biotechnology Center and DFG-Center for Regenerative Therapies Dresden Cluster of Excellence, Tatzberg 47-49, 01307 Dresden, Germany
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Claudin5a is required for proper inflation of Kupffer's vesicle lumen and organ laterality. PLoS One 2017; 12:e0182047. [PMID: 28771527 PMCID: PMC5542556 DOI: 10.1371/journal.pone.0182047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/11/2017] [Indexed: 12/18/2022] Open
Abstract
Left-right asymmetric organ development is critical to establish a proper body plan of vertebrates. In zebrafish, the Kupffer’s vesicle (KV) is a fluid-filled sac which controls asymmetric organ development, and a properly inflated KV lumen by means of fluid influx is a prerequisite for the asymmetric signal transmission. However, little is known about the components that support the paracellular tightness between the KV luminal epithelial cells to sustain hydrostatic pressure during KV lumen expansion. Here, we identified that the claudin5a (cldn5a) is highly expressed at the apical surface of KV epithelial cells and tightly seals the KV lumen. Downregulation of cldn5a in zebrafish showed a failure in organ laterality that resulted from malformed KV. In addition, accelerated fluid influx into KV by combined treatment of forskolin and 3-isobutyl-1-methylxanthine failed to expand the partially-formed KV lumen in cldn5a morphants. However, malformed KV lumen and defective heart laterality in cldn5a morphants were significantly rescued by exogenous cldn5a mRNA, suggesting that the tightness between the luminal epithelial cells is important for KV lumen formation. Taken together, these findings suggest that cldn5a is required for KV lumen inflation and left-right asymmetric organ development.
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28
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Gut P, Reischauer S, Stainier DYR, Arnaout R. LITTLE FISH, BIG DATA: ZEBRAFISH AS A MODEL FOR CARDIOVASCULAR AND METABOLIC DISEASE. Physiol Rev 2017; 97:889-938. [PMID: 28468832 PMCID: PMC5817164 DOI: 10.1152/physrev.00038.2016] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/17/2022] Open
Abstract
The burden of cardiovascular and metabolic diseases worldwide is staggering. The emergence of systems approaches in biology promises new therapies, faster and cheaper diagnostics, and personalized medicine. However, a profound understanding of pathogenic mechanisms at the cellular and molecular levels remains a fundamental requirement for discovery and therapeutics. Animal models of human disease are cornerstones of drug discovery as they allow identification of novel pharmacological targets by linking gene function with pathogenesis. The zebrafish model has been used for decades to study development and pathophysiology. More than ever, the specific strengths of the zebrafish model make it a prime partner in an age of discovery transformed by big-data approaches to genomics and disease. Zebrafish share a largely conserved physiology and anatomy with mammals. They allow a wide range of genetic manipulations, including the latest genome engineering approaches. They can be bred and studied with remarkable speed, enabling a range of large-scale phenotypic screens. Finally, zebrafish demonstrate an impressive regenerative capacity scientists hope to unlock in humans. Here, we provide a comprehensive guide on applications of zebrafish to investigate cardiovascular and metabolic diseases. We delineate advantages and limitations of zebrafish models of human disease and summarize their most significant contributions to understanding disease progression to date.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sven Reischauer
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Didier Y R Stainier
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Rima Arnaout
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
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29
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Doetschman T, Georgieva T. Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease. Circ Res 2017; 120:876-894. [DOI: 10.1161/circresaha.116.309727] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 01/30/2017] [Accepted: 02/06/2017] [Indexed: 12/22/2022]
Abstract
Genetic engineering of model organisms and cultured cells has for decades provided important insights into the mechanisms underlying cardiovascular development and disease. In the past few years the development of several nuclease systems has broadened the range of model/cell systems that can be engineered. Of these, the CRISPR (clustered regularly interspersed short palindromic repeats)/Cas9 (CRISPR-associated protein 9) system has become the favorite for its ease of application. Here we will review this RNA-guided nuclease system for gene editing with respect to its usefulness for cardiovascular studies and with an eye toward potential therapy. Studies on its off-target activity, along with approaches to minimize this activity will be given. The advantages of gene editing versus gene targeting in embryonic stem cells, including the breadth of species and cell types to which it is applicable, will be discussed. We will also cover its use in iPSC for research and possible therapeutic purposes; and we will review its use in muscular dystrophy studies where considerable progress has been made toward dystrophin correction in mice. The CRISPR/Ca9s system is also being used for high-throughput screening of genes, gene regulatory regions, and long noncoding RNAs. In addition, the CRISPR system is being used for nongene-editing purposes such as activation and inhibition of gene expression, as well as for fluorescence tagging of chromosomal regions and individual mRNAs to track their cellular location. Finally, an approach to circumvent the inability of post-mitotic cells to support homologous recombination-based gene editing will be presented. In conclusion, applications of the CRISPR/Cas system are expanding at a breath-taking pace and are revolutionizing approaches to gain a better understanding of human diseases.
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Affiliation(s)
- Thomas Doetschman
- From the BIO5 Institute (T.D., T.G.) and Department of Cellular and Molecular Medicine (T.D.), University of Arizona, Tucson
| | - Teodora Georgieva
- From the BIO5 Institute (T.D., T.G.) and Department of Cellular and Molecular Medicine (T.D.), University of Arizona, Tucson
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30
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Comparison of Zebrafish tmem88a mutant and morpholino knockdown phenotypes. PLoS One 2017; 12:e0172227. [PMID: 28192479 PMCID: PMC5305201 DOI: 10.1371/journal.pone.0172227] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 02/01/2017] [Indexed: 01/13/2023] Open
Abstract
Tmem88a is a transmembrane protein that is thought to be a negative regulator of the Wnt signalling pathway. Several groups have used antisense morpholino oligonucleotides in an effort to characterise the role of tmem88a in zebrafish cardiovascular development, but they have not obtained consistent results. Here, we generate an 8 bp deletion in the coding region of the tmem88a locus using TALENs, and we have gone on to establish a viable homozygous tmem88aΔ8 mutant line. Although tmem88aΔ8 mutants have reduced expression of some key haematopoietic genes, differentiation of erythrocytes and neutrophils is unaffected, contradicting our previous study using antisense morpholino oligonucleotides. We find that expression of the tmem88a paralogue tmem88b is not significantly changed in tmem88aΔ8 mutants and injection of the tmem88a splice-blocking morpholino oligonucleotide into tmem88aΔ8 mutants recapitulates the reduction of erythrocytes observed in morphants using o-Dianisidine. This suggests that there is a partial, but inessential, requirement for tmem88a during haematopoiesis and that morpholino injection exacerbates this phenotype in tmem88a morpholino knockdown embryos.
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Baxendale S, van Eeden F, Wilkinson R. The Power of Zebrafish in Personalised Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:179-197. [PMID: 28840558 DOI: 10.1007/978-3-319-60733-7_10] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The goal of personalised medicine is to develop tailor-made therapies for patients in whom currently available therapeutics fail. This approach requires correlating individual patient genotype data to specific disease phenotype data and using these stratified data sets to identify bespoke therapeutics. Applications for personalised medicine include common complex diseases which may have multiple targets, as well as rare monogenic disorders, for which the target may be unknown. In both cases, whole genome sequence analysis (WGS) is discovering large numbers of disease associated mutations in new candidate genes and potential modifier genes. Currently, the main limiting factor is the determination of which mutated genes are important for disease progression and therefore represent potential targets for drug discovery. Zebrafish have gained popularity as a model organism for understanding developmental processes, disease mechanisms and more recently for drug discovery and toxicity testing. In this chapter, we will examine the diverse roles that zebrafish can make in the expanding field of personalised medicine, from generating humanised disease models to xenograft screening of different cancer cell lines, through to finding new drugs via in vivo phenotypic screens. We will discuss the tools available for zebrafish research and recent advances in techniques, highlighting the advantages and potential of using zebrafish for high throughput disease modeling and precision drug discovery.
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Affiliation(s)
- Sarah Baxendale
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Freek van Eeden
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Wilkinson
- The Bateson Centre, Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.,Department of Infection, Immunity and Cardiovascular Disease, Medical School, Beech Hill Rd, University of Sheffield, Sheffield, S10 2RX, UK
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32
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Boer EF, Jette CA, Stewart RA. Neural Crest Migration and Survival Are Susceptible to Morpholino-Induced Artifacts. PLoS One 2016; 11:e0167278. [PMID: 28005909 PMCID: PMC5179070 DOI: 10.1371/journal.pone.0167278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023] Open
Abstract
The neural crest (NC) is a stem cell-like embryonic population that is essential for generating and patterning the vertebrate body, including the craniofacial skeleton and peripheral nervous system. Defects in NC development underlie many birth defects and contribute to formation of some of the most malignant cancers in humans, such as melanoma and neuroblastoma. For these reasons, significant research efforts have been expended to identify genes that control NC development, as it is expected to lead to a deeper understanding of the genetic mechanisms controlling vertebrate development and identify new treatments for NC-derived diseases and cancers. However, a number of inconsistencies regarding gene function during NC development have emerged from comparative analyses of gene function between mammalian and non-mammalian systems (chick, frog, zebrafish). This poses a significant barrier to identification of single genes and/or redundant pathways to target in NC diseases. Here, we determine whether technical differences, namely morpholino-based approaches used in non-mammalian systems, could contribute to these discrepancies, by examining the extent to which NC phenotypes in fascin1a (fscn1a) morphant embryos are similar to or different from fscn1a null mutants in zebrafish. Analysis of fscn1a morphants showed that they mimicked early NC phenotypes observed in fscn1a null mutants; however, these embryos also displayed NC migration and derivative phenotypes not observed in null mutants, including accumulation of p53-independent cell death. These data demonstrate that morpholinos can cause seemingly specific NC migration and derivative phenotypes, and thus have likely contributed to the inconsistencies surrounding NC gene function between species. We suggest that comparison of genetic mutants between different species is the most rigorous method for identifying conserved genetic mechanisms controlling NC development and is critical to identify new treatments for NC diseases.
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Affiliation(s)
- Elena F. Boer
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Cicely A. Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Zhao H, Yao P, Li L, Chen L. Apelin receptor signaling: a novel mechanism of endothelial cell polarization. Acta Biochim Biophys Sin (Shanghai) 2016; 48:1138-1139. [PMID: 27797720 DOI: 10.1093/abbs/gmw108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 12/24/2022] Open
Affiliation(s)
- Hong Zhao
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative innovation Center for Molecular Target New Drugs Study, University of South China, Hengyang 421001, China
| | - Pingbo Yao
- Intensive Care Units of the Affiliated Nanhua Hospital, University of South China, Hengyang 421002, China
| | - Lanfang Li
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative innovation Center for Molecular Target New Drugs Study, University of South China, Hengyang 421001, China
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative innovation Center for Molecular Target New Drugs Study, University of South China, Hengyang 421001, China
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34
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Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DYR, Seydoux G, Mohr SE, Zuber J, Perrimon N. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet 2016; 18:24-40. [PMID: 27795562 DOI: 10.1038/nrg.2016.118] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caused by these perturbations the wild-type function of genes can be elucidated. Although all LOF methods reduce gene activity, the choice of approach (for example, mutagenesis, CRISPR-based gene editing, RNA interference, morpholinos or pharmacological inhibition) can have a major effect on phenotypic outcomes. Interpretation of the LOF phenotype must take into account the biological process that is targeted by each method. The practicality and efficiency of LOF methods also vary considerably between model systems. We describe parameters for choosing the optimal combination of method and system, and for interpreting phenotypes within the constraints of each method.
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Affiliation(s)
- Benjamin E Housden
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Matthew Gemberling
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 43 Ludwigstrasse, Bad Nauheim 61231, Germany
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21218, USA.,Howard Hughes Medical Institute, 725 North Wolfe Street, Baltimore, Maryland 21218, USA
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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35
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Abstract
Genome-editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems, have emerged as an invaluable technology to achieve somatic and germline genomic manipulation in cells and model organisms for multiple applications, including the creation of knockout alleles, introducing desired mutations into genomic DNA, and inserting novel transgenes. Genome editing is being rapidly adopted into all fields of biomedical research, including the cardiovascular field, where it has facilitated a greater understanding of lipid metabolism, electrophysiology, cardiomyopathies, and other cardiovascular disorders, has helped to create a wider variety of cellular and animal models, and has opened the door to a new class of therapies. In this Review, we discuss the applications of genome-editing technology throughout cardiovascular disease research and the prospect of in vivo genome-editing therapies in the future. We also describe some of the existing limitations of genome-editing tools that will need to be addressed if cardiovascular genome editing is to achieve its full scientific and therapeutic potential.
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36
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Haack T, Abdelilah-Seyfried S. The force within: endocardial development, mechanotransduction and signalling during cardiac morphogenesis. Development 2016; 143:373-86. [PMID: 26839341 DOI: 10.1242/dev.131425] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Endocardial cells are cardiac endothelial cells that line the interior of the heart tube. Historically, their contribution to cardiac development has mainly been considered from a morphological perspective. However, recent studies have begun to define novel instructive roles of the endocardium, as a sensor and signal transducer of biophysical forces induced by blood flow, and as an angiocrine signalling centre that is involved in myocardial cellular morphogenesis, regeneration and reprogramming. In this Review, we discuss how the endocardium develops, how endocardial-myocardial interactions influence the developing embryonic heart, and how the dysregulation of blood flow-responsive endocardial signalling can result in pathophysiological changes.
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Affiliation(s)
- Timm Haack
- Institute of Molecular Biology, Hannover Medical School, Carl-Neuberg Straße 1, Hannover D-30625, Germany
| | - Salim Abdelilah-Seyfried
- Institute of Molecular Biology, Hannover Medical School, Carl-Neuberg Straße 1, Hannover D-30625, Germany Institute of Biochemistry and Biology, Potsdam University, Karl-Liebknecht-Straße 24-25, Potsdam D-14476, Germany
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37
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In vivo modulation of endothelial polarization by Apelin receptor signalling. Nat Commun 2016; 7:11805. [PMID: 27248505 PMCID: PMC4895482 DOI: 10.1038/ncomms11805] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/02/2016] [Indexed: 12/18/2022] Open
Abstract
Endothelial cells (ECs) respond to shear stress by aligning in the direction of flow. However, how ECs respond to flow in complex in vivo environments is less clear. Here we describe an endothelial-specific transgenic zebrafish line, whereby the Golgi apparatus is labelled to allow for in vivo analysis of endothelial polarization. We find that most ECs polarize within 4.5 h after the onset of vigorous blood flow and, by manipulating cardiac function, observe that flow-induced EC polarization is a dynamic and reversible process. Based on its role in EC migration, we analyse the role of Apelin signalling in EC polarization and find that it is critical for this process. Knocking down Apelin receptor function in human primary ECs also affects their polarization. Our study provides new tools to analyse the mechanisms of EC polarization in vivo and reveals an important role in this process for a signalling pathway implicated in cardiovascular disease.
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