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Labusch M, Thetiot M, Than-Trong E, Morizet D, Coolen M, Varet H, Legendre R, Ortica S, Mancini L, Bally-Cuif L. Prosaposin maintains adult neural stem cells in a state associated with deep quiescence. Stem Cell Reports 2024; 19:515-528. [PMID: 38518783 PMCID: PMC11096431 DOI: 10.1016/j.stemcr.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/24/2024] Open
Abstract
In most vertebrates, adult neural stem cells (NSCs) continuously give rise to neurons in discrete brain regions. A critical process for maintaining NSC pools over long periods of time in the adult brain is NSC quiescence, a reversible and tightly regulated state of cell-cycle arrest. Recently, lysosomes were identified to regulate the NSC quiescence-proliferation balance. However, it remains controversial whether lysosomal activity promotes NSC proliferation or quiescence, and a finer influence of lysosomal activity on NSC quiescence duration or depth remains unexplored. Using RNA sequencing and pharmacological manipulations, we show that lysosomes are necessary for NSC quiescence maintenance. In addition, we reveal that expression of psap, encoding the lysosomal regulator Prosaposin, is enriched in quiescent NSCs (qNSCs) that reside upstream in the NSC lineage and display a deep/long quiescence phase in the adult zebrafish telencephalon. We show that shRNA-mediated psap knockdown increases the proportion of activated NSCs (aNSCs) as well as NSCs that reside in shallower quiescence states (signed by ascl1a and deltaA expression). Collectively, our results identify the lysosomal protein Psap as a (direct or indirect) quiescence regulator and unfold the interplay between lysosomal function and NSC quiescence heterogeneities.
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Affiliation(s)
- Miriam Labusch
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France; Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Melina Thetiot
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - Emmanuel Than-Trong
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - David Morizet
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France; Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Marion Coolen
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Platform Biomics, 75015 Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Platform Biomics, 75015 Paris, France
| | - Sara Ortica
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - Laure Mancini
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France; Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Laure Bally-Cuif
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France.
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2
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Gonzalez D, Vásquez-Doorman C, Luna A, Allende ML. Modeling Spinal Muscular Atrophy in Zebrafish: Current Advances and Future Perspectives. Int J Mol Sci 2024; 25:1962. [PMID: 38396640 PMCID: PMC10888324 DOI: 10.3390/ijms25041962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 02/25/2024] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease characterized by degeneration of lower motor neurons (LMNs), causing muscle weakness, atrophy, and paralysis. SMA is caused by mutations in the Survival Motor Neuron 1 (SMN1) gene and can be classified into four subgroups, depending on its severity. Even though the genetic component of SMA is well known, the precise mechanisms underlying its pathophysiology remain elusive. Thus far, there are three FDA-approved drugs for treating SMA. While these treatments have shown promising results, their costs are extremely high and unaffordable for most patients. Thus, more efforts are needed in order to identify novel therapeutic targets. In this context, zebrafish (Danio rerio) stands out as an ideal animal model for investigating neurodegenerative diseases like SMA. Its well-defined motor neuron circuits and straightforward neuromuscular structure offer distinct advantages. The zebrafish's suitability arises from its low-cost genetic manipulation and optical transparency exhibited during larval stages, which facilitates in vivo microscopy. This review explores advancements in SMA research over the past two decades, beginning with the creation of the first zebrafish model. Our review focuses on the findings using different SMA zebrafish models generated to date, including potential therapeutic targets such as U snRNPs, Etv5b, PLS3, CORO1C, Pgrn, Cpg15, Uba1, Necdin, and Pgk1, among others. Lastly, we conclude our review by emphasizing the future perspectives in the field, namely exploiting zebrafish capacity for high-throughput screening. Zebrafish, with its unique attributes, proves to be an ideal model for studying motor neuron diseases and unraveling the complexity of neuromuscular defects.
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Affiliation(s)
- David Gonzalez
- Millennium Institute Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, RM, Chile
- Departamento de Ciencias Químicas y Biológicas, Facultad de Ciencias de la Salud, Universidad Bernardo O'Higgins, Santiago 8370854, RM, Chile
| | - Constanza Vásquez-Doorman
- Millennium Institute Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, RM, Chile
- Departamento de Ciencias Químicas y Biológicas, Facultad de Ciencias de la Salud, Universidad Bernardo O'Higgins, Santiago 8370854, RM, Chile
| | - Adolfo Luna
- Departamento de Ciencias Químicas y Biológicas, Facultad de Ciencias de la Salud, Universidad Bernardo O'Higgins, Santiago 8370854, RM, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, RM, Chile
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Singh J, Pan YE, Patten SA. NMJ Analyser: a novel method to quantify neuromuscular junction morphology in zebrafish. Bioinformatics 2023; 39:btad720. [PMID: 38058204 PMCID: PMC10713120 DOI: 10.1093/bioinformatics/btad720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
MOTIVATION Neuromuscular junction (NMJ) structural integrity is crucial for transducing motor neuron signals that initiate skeletal muscle contraction. Zebrafish has emerged as a simple and efficient model to study NMJ structural morphology and function in the context of developmental neurobiology and neuromuscular diseases. However, methods to quantify NMJ morphology from voluminous data of NMJ confocal images accurately, rapidly, and reproducibly are lacking. RESULTS We developed an ImageJ macro called "NMJ Analyser" to automatically and unbiasedly analyse NMJ morphology in zebrafish. From the Z-stack of a zebrafish hemisomite, both presynaptic and postsynaptic fluorescently labeled termini at NMJs are extracted from background signal, with larger clusters of termini being segmented into individual termini using an unbiased algorithm. The program then determines whether each presynaptic terminus is co-localized with a postsynaptic terminus and vice versa, or whether it is orphaned, and tabulates the number of orphan and co-localized pre- and postsynaptic termini. The usefulness of this ImageJ macro plugin will be helpful to quantify NMJ parameters in zebrafish, particularly during development and in disease models of neuromuscular diseases. It can enable high-throughput NMJ phenotypic screens in the drug discovery process for neuromuscular diseases. It could also be further applied to the investigation of NMJ of other developmental systems. AVAILABILITY AND IMPLEMENTATION NMJ Analyser is available for download at https://github.com/PattenLab/NMJ-Analyser.git.
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Affiliation(s)
- Jaskaran Singh
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Yingzhou Edward Pan
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Shunmoogum A Patten
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
- Département de Neurosciences, Université de Montréal, Montreal, QC, Canada
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4
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Tromp A, Wang H, Hall TE, Mowry B, Giacomotto J. Optimising the zebrafish Cre/Lox toolbox. Codon improved iCre, new gateway tools, Cre protein and guidelines. Front Physiol 2023; 14:1221310. [PMID: 37601640 PMCID: PMC10433388 DOI: 10.3389/fphys.2023.1221310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
We recently introduced the Cre/Lox technology in our laboratory for both transient (mRNA injections) and stable/transgenic experiments. We experienced significant issues such as silencing, mosaicism, and partial recombination using both approaches. Reviewing the literature gave us the impression that these issues are common among the zebrafish community using the Cre/Lox system. While some researchers took advantage of these problems for specific applications, such as cell and lineage tracing using the Zebrabow construct, we tried here to improve the efficiency and reliability of this system by constituting and testing a new set of tools for zebrafish genetics. First, we implemented a codon-improved Cre version (iCre) designed for rodent studies to counteract some of the aforementioned problems. This eukaryotic-like iCre version was engineered to i) reduce silencing, ii) increase mRNA stability, iii) enhance translational efficiency, and iv) improve nuclear translocation. Second, we established a new set of tol2-kit compatible vectors to facilitate the generation of either iCre-mRNA or iCre-transgenes for transient and transgenic experiments, respectively. We then validated the use of this material and are providing tips for users. Interestingly, during the validation steps, we found that maternal iCRE-mRNA and/or protein deposition from female transgenics systematically led to complete/homogeneous conversion of all tested Lox-responder-transgenes, as opposed to some residual imperfect conversion when using males-drivers or mRNA injections. Considering that we did not find any evidence of Cre-protein soaking and injections in the literature as it is usually conducted with cells, we tested these approaches. While soaking of cell-permeant CRE-protein did not lead to any detectable Lox-conversion, 1ng-10 ng protein injections led to robust and homogeneous Lox-recombination, suggesting that the use of protein could be a robust option for exogenous delivery. This approach may be particularly useful to manipulate housekeeping genes involved in development, sex determination and reproduction which are difficult to investigate with traditional knockout approaches. All in all, we are providing here a new set of tools that should be useful in the field.
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Affiliation(s)
- Alisha Tromp
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Haitao Wang
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Thomas E. Hall
- Institute for Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Bryan Mowry
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
- Queensland Centre for Mental Health Research, Wacol, QLD, Australia
| | - Jean Giacomotto
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
- Centre for Cellular Phenomics, School of Environment and Science, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
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5
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Singh J, Patten SA. Modeling neuromuscular diseases in zebrafish. Front Mol Neurosci 2022; 15:1054573. [PMID: 36583079 PMCID: PMC9794147 DOI: 10.3389/fnmol.2022.1054573] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Neuromuscular diseases are a diverse group of conditions that affect the motor system and present some overlapping as well as distinct clinical manifestations. Although individually rare, the combined prevalence of NMDs is similar to Parkinson's. Over the past decade, new genetic mutations have been discovered through whole exome/genome sequencing, but the pathogenesis of most NMDs remains largely unexplored. Little information on the molecular mechanism governing the progression and development of NMDs accounts for the continual failure of therapies in clinical trials. Different aspects of the diseases are typically investigated using different models from cells to animals. Zebrafish emerges as an excellent model for studying genetics and pathogenesis and for developing therapeutic interventions for most NMDs. In this review, we describe the generation of different zebrafish genetic models mimicking NMDs and how they are used for drug discovery and therapy development.
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Affiliation(s)
- Jaskaran Singh
- INRS – Centre Armand Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Shunmoogum A. Patten
- INRS – Centre Armand Frappier Santé Biotechnologie, Laval, QC, Canada,Departement de Neurosciences, Université de Montréal, Montréal, QC, Canada,Centre d'Excellence en Recherche sur les Maladies Orphelines – Fondation Courtois (CERMO-FC), Université du Québec à Montréal (UQAM), Montréal, QC, Canada,*Correspondence: Shunmoogum A. Patten,
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6
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Jiang L, Zhang T, Lu K, Qi S. The progress in C9orf72 research: ALS/FTD pathogenesis, functions and structure. Small GTPases 2022; 13:56-76. [PMID: 33663328 PMCID: PMC9707547 DOI: 10.1080/21541248.2021.1892443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The hexanucleotide repeat (GGGGCC) expansion in C9orf72 is accounted for a large proportion of the genetic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The hypotheses of how the massive G4C2 repeats in C9orf72 destroy the neurons and lead to ALS/FTD are raised and improving. As a multirole player, C9orf72 exerts critical roles in many cellular processes, including autophagy, membrane trafficking, immune response, and so on. Notably, the partners of C9orf72, through which C9orf72 participates in the cell activities, have been identified. Notably, the structures of the C9orf72-SMCR8-WDR41 complex shed light on its activity as GTPase activating proteins (GAP). In this manuscript, we reviewed the latest research progress in the C9orf72-mediated ALS/FTD, the physiological functions of C9orf72, and the putative function models of C9orf72/C9orf72-containing complex.
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Affiliation(s)
- Lan Jiang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tizhong Zhang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kefeng Lu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China,CONTACT Shiqian Qi Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China.
These authors contributed equally to this work.
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7
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Lo HP, Lim YW, Xiong Z, Martel N, Ferguson C, Ariotti N, Giacomotto J, Rae J, Floetenmeyer M, Moradi SV, Gao Y, Tillu VA, Xia D, Wang H, Rahnama S, Nixon SJ, Bastiani M, Day RD, Smith KA, Palpant NJ, Johnston WA, Alexandrov K, Collins BM, Hall TE, Parton RG. Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle. J Cell Biol 2021; 220:e201905065. [PMID: 34633413 PMCID: PMC8513623 DOI: 10.1083/jcb.201905065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/02/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022] Open
Abstract
The cavin proteins are essential for caveola biogenesis and function. Here, we identify a role for the muscle-specific component, Cavin4, in skeletal muscle T-tubule development by analyzing two vertebrate systems, mouse and zebrafish. In both models, Cavin4 localized to T-tubules, and loss of Cavin4 resulted in aberrant T-tubule maturation. In zebrafish, which possess duplicated cavin4 paralogs, Cavin4b was shown to directly interact with the T-tubule-associated BAR domain protein Bin1. Loss of both Cavin4a and Cavin4b caused aberrant accumulation of interconnected caveolae within the T-tubules, a fragmented T-tubule network enriched in Caveolin-3, and an impaired Ca2+ response upon mechanical stimulation. We propose a role for Cavin4 in remodeling the T-tubule membrane early in development by recycling caveolar components from the T-tubule to the sarcolemma. This generates a stable T-tubule domain lacking caveolae that is essential for T-tubule function.
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Affiliation(s)
- Harriet P. Lo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ye-Wheen Lim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Zherui Xiong
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nick Martel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Charles Ferguson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Jean Giacomotto
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service and University of Queensland, Brisbane, Queensland, Australia
| | - James Rae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthias Floetenmeyer
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Shayli Varasteh Moradi
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Ya Gao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Vikas A. Tillu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Di Xia
- Genome Innovation Hub, The University of Queensland, Brisbane, Queensland, Australia
| | - Huang Wang
- Translational Research Institute, Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Samira Rahnama
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Susan J. Nixon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Michele Bastiani
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ryan D. Day
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Kelly A. Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nathan J. Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Wayne A. Johnston
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kirill Alexandrov
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas E. Hall
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
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Tay SH, Ellieyana EN, Le Y, Sarusie MV, Grimm C, Ohmer J, Mathuru A, Fischer U, Winkler C. A novel zebrafish model for intermediate type spinal muscular atrophy demonstrates importance of Smn for maintenance of mature motor neurons. Hum Mol Genet 2021; 30:2488-2502. [PMID: 34302176 DOI: 10.1093/hmg/ddab212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
A deficiency in Survival Motor Neuron (SMN) protein results in motor neuron loss in spinal muscular atrophy (SMA) patients. Human SMN is encoded by SMN1 and SMN2 that differ by a single C6T transition in a splice regulatory region of exon 7. In SMN2, exon 7 is skipped leading to an unstable protein, which cannot compensate for SMN1 loss in SMA patients. The disease severity of human SMA (Types 1 to 4) depends on the levels of SMN protein, with intermediate levels leading to delayed disease onset and extended life expectancy in Type 2 patients. We used homology directed repair (HDR) to generate a zebrafish mutant with intermediate Smn levels, to mimic intermediate, hSMN2 dependent forms of SMA. In the obtained smnA6Tind27 mutant zebrafish, Smn protein formed oligomers but protein levels dropped significantly at juvenile stages. Motor neurons and neuromuscular junctions (NMJ) also formed normally initially but motor neuron loss and locomotor deficiencies became evident at 21 days. Subsequent muscle wasting and early adult lethality also phenocopied intermediate forms of human SMA. Together, our findings are consistent with the interpretation that Smn is required for neuromuscular maintenance, and establish the smnA6Tind27 zebrafish mutant as a novel model for intermediate types of SMA. As this mutant allows studying the effect of late Smn loss on motor neurons, neuromuscular junctions, and muscle at advanced stages of the disease, it will be a valuable resource for testing new drugs targeted towards treating intermediate forms of SMA.
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Affiliation(s)
- Shermaine Huiping Tay
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Erna Nur Ellieyana
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yao Le
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Menachem Viktor Sarusie
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Clemens Grimm
- Department of Biochemistry, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Jürgen Ohmer
- Department of Biochemistry, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Ajay Mathuru
- Yale-NUS College, 12 College Avenue West, Singapore 138527, Singapore.,Institute of Molecular and Cell Biology, Singapore 138673, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Utz Fischer
- Department of Biochemistry, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
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9
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Butti Z, Pan YE, Giacomotto J, Patten SA. Reduced C9orf72 function leads to defective synaptic vesicle release and neuromuscular dysfunction in zebrafish. Commun Biol 2021; 4:792. [PMID: 34172817 PMCID: PMC8233344 DOI: 10.1038/s42003-021-02302-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
The most common genetic cause of amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD) is a hexanucleotide repeat expansion within the C9orf72 gene. Reduced levels of C9orf72 mRNA and protein have been found in ALS/FTD patients, but the role of this protein in disease pathogenesis is still poorly understood. Here, we report the generation and characterization of a stable C9orf72 loss-of-function (LOF) model in the zebrafish. We show that reduced C9orf72 function leads to motor defects, muscle atrophy, motor neuron loss and mortality in early larval and adult stages. Analysis of the structure and function of the neuromuscular junctions (NMJs) of the larvae, reveal a marked reduction in the number of presynaptic and postsynaptic structures and an impaired release of quantal synaptic vesicles at the NMJ. Strikingly, we demonstrate a downregulation of SV2a upon C9orf72-LOF and a reduced rate of synaptic vesicle cycling. Furthermore, we show a reduced number and size of Rab3a-postive synaptic puncta at NMJs. Altogether, these results reveal a key function for C9orf72 in the control of presynaptic vesicle trafficking and release at the zebrafish larval NMJ. Our study demonstrates an important role for C9orf72 in ALS/FTD pathogenesis, where it regulates synaptic vesicle release and neuromuscular functions. Butti et al. generate a C9orf72 loss-of-function model in zebrafish. They find that that C9orf72 is required for presynaptic vesicle trafficking and release at the zebrafish larval neuromuscular junctions. This study provides functional insights into the pathogenesis of amyotrophic lateral sclerosis and fronto-temporal dementia.
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Affiliation(s)
- Zoé Butti
- INRS- Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | | | - Jean Giacomotto
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia.,Queensland Centre for Mental Health Research, Brisbane, QLD, Australia
| | - Shunmoogum A Patten
- INRS- Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada. .,Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal (UQAM), Montréal, QC, Canada.
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10
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Garcia A, Dunoyer-Geindre S, Fish RJ, Neerman-Arbez M, Reny JL, Fontana P. Methods to Investigate miRNA Function: Focus on Platelet Reactivity. Thromb Haemost 2021; 121:409-421. [PMID: 33124028 PMCID: PMC8263142 DOI: 10.1055/s-0040-1718730] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs modulating protein production. They are key players in regulation of cell function and are considered as biomarkers in several diseases. The identification of the proteins they regulate, and their impact on cell physiology, may delineate their role as diagnostic or prognostic markers and identify new therapeutic strategies. During the last 3 decades, development of a large panel of techniques has given rise to multiple models dedicated to the study of miRNAs. Since plasma samples are easily accessible, circulating miRNAs can be studied in clinical trials. To quantify miRNAs in numerous plasma samples, the choice of extraction and purification techniques, as well as normalization procedures, are important for comparisons of miRNA levels in populations and over time. Recent advances in bioinformatics provide tools to identify putative miRNAs targets that can then be validated with dedicated assays. In vitro and in vivo approaches aim to functionally validate candidate miRNAs from correlations and to understand their impact on cellular processes. This review describes the advantages and pitfalls of the available techniques for translational research to study miRNAs with a focus on their role in regulating platelet reactivity.
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Affiliation(s)
- Alix Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Richard J. Fish
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics in Geneva, Geneva, Switzerland
| | - Jean-Luc Reny
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of General Internal Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Pierre Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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11
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Tromp A, Mowry B, Giacomotto J. Neurexins in autism and schizophrenia-a review of patient mutations, mouse models and potential future directions. Mol Psychiatry 2021; 26:747-760. [PMID: 33191396 DOI: 10.1038/s41380-020-00944-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 01/29/2023]
Abstract
Mutations in the family of neurexins (NRXN1, NRXN2 and NRXN3) have been repeatedly identified in patients with autism spectrum disorder (ASD) and schizophrenia (SCZ). However, it remains unclear how these DNA variants affect neurexin functions and thereby predispose to these neurodevelopmental disorders. Understanding both the wild-type and pathologic roles of these genes in the brain could help unveil biological mechanisms underlying mental disorders. In this regard, numerous studies have focused on generating relevant loss-of-function (LOF) mammalian models. Although this has increased our knowledge about their normal functions, the potential pathologic role(s) of these human variants remains elusive. Indeed, after reviewing the literature, it seems apparent that a traditional LOF-genetic approach based on complete LOF might not be sufficient to unveil the role of these human mutations. First, these genes present a very complex transcriptome and total-LOF of all isoforms may not be the cause of toxicity in patients, particularly given evidence that causative variants act through haploinsufficiency. Moreover, human DNA variants may not all lead to LOF but potentially to intricate transcriptome changes that could also include the generation of aberrant isoforms acting as a gain-of-function (GOF). Furthermore, their transcriptomic complexity most likely renders them prone to genetic compensation when one tries to manipulate them using traditional site-directed mutagenesis approaches, and this could act differently from model to model leading to heterogeneous and conflicting phenotypes. This review compiles the relevant literature on variants identified in human studies and on the mouse models currently deployed, and offers suggestions for future research.
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Affiliation(s)
- Alisha Tromp
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
| | - Bryan Mowry
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia.
- Queensland Centre for Mental Health Research, Brisbane, QLD, Australia.
| | - Jean Giacomotto
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia.
- Queensland Centre for Mental Health Research, Brisbane, QLD, Australia.
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12
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Modular transient nanoclustering of activated β2-adrenergic receptors revealed by single-molecule tracking of conformation-specific nanobodies. Proc Natl Acad Sci U S A 2020; 117:30476-30487. [PMID: 33214152 DOI: 10.1073/pnas.2007443117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
None of the current superresolution microscopy techniques can reliably image the changes in endogenous protein nanoclustering dynamics associated with specific conformations in live cells. Single-domain nanobodies have been invaluable tools to isolate defined conformational states of proteins, and we reasoned that expressing these nanobodies coupled to single-molecule imaging-amenable tags could allow superresolution analysis of endogenous proteins in discrete conformational states. Here, we used anti-GFP nanobodies tagged with photoconvertible mEos expressed as intrabodies, as a proof-of-concept to perform single-particle tracking on a range of GFP proteins expressed in live cells, neurons, and small organisms. We next expressed highly specialized nanobodies that target conformation-specific endogenous β2-adrenoreceptor (β2-AR) in neurosecretory cells, unveiling real-time mobility behaviors of activated and inactivated endogenous conformers during agonist treatment in living cells. We showed that activated β2-AR (Nb80) is highly immobile and organized in nanoclusters. The Gαs-GPCR complex detected with Nb37 displayed higher mobility with surprisingly similar nanoclustering dynamics to that of Nb80. Activated conformers are highly sensitive to dynamin inhibition, suggesting selective targeting for endocytosis. Inactivated β2-AR (Nb60) molecules are also largely immobile but relatively less sensitive to endocytic blockade. Expression of single-domain nanobodies therefore provides a unique opportunity to capture highly transient changes in the dynamic nanoscale organization of endogenous proteins.
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13
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Sarti S, De Paolo R, Ippolito C, Pucci A, Pitto L, Poliseno L. Inducible modulation of miR-204 levels in a zebrafish melanoma model. Biol Open 2020; 9:bio053785. [PMID: 33037013 PMCID: PMC7657466 DOI: 10.1242/bio.053785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022] Open
Abstract
Here, we present miniCoopR-I, an inducible upgrade of the constitutive miniCoopR vector. We developed miniCoopR-I-sponge-204 and miniCoopR-I-pre-miR-204 vectors and we successfully tested them for their ability to achieve time- (embryo/juvenile/adult) and space- (melanocytic lineage) restricted inhibition/overexpression of miR-204, a positive modulator of pigmentation previously discovered by us. Furthermore, melanoma-free survival curves performed on induced fish at the adult stage indicate that miR-204 overexpression accelerates the development of BRAFV600E-driven melanoma. miniCoopR-I allows study of the impact that coding and non-coding modulators of pigmentation exert on melanomagenesis in adult zebrafish, uncoupling it from the impact that they exert on melanogenesis during embryonic development.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Samanta Sarti
- Oncogenomics Unit, CRL-ISPRO, Pisa 56124, Italy
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
| | - Raffaella De Paolo
- Oncogenomics Unit, CRL-ISPRO, Pisa 56124, Italy
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
- University of Siena, Siena 53100, Italy
| | - Chiara Ippolito
- Unit of Histology and Human Embryology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa 56126, Italy
| | - Angela Pucci
- Histopathology Department, Pisa University Hospital, Pisa 56126, Italy
| | - Letizia Pitto
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
| | - Laura Poliseno
- Oncogenomics Unit, CRL-ISPRO, Pisa 56124, Italy
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
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14
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Lawrence EA, Hammond CL, Blain EJ. Potential of zebrafish as a model to characterise MicroRNA profiles in mechanically mediated joint degeneration. Histochem Cell Biol 2020; 154:521-531. [PMID: 32935147 PMCID: PMC7609428 DOI: 10.1007/s00418-020-01918-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2020] [Indexed: 12/19/2022]
Abstract
Mechanically mediated joint degeneration and cartilage dyshomeostasis is implicated in highly prevalent diseases such as osteoarthritis. Increasingly, MicroRNAs are being associated with maintaining the normal state of cartilage, making them an exciting and potentially key contributor to joint health and disease onset. Here, we present a summary of current in vitro and in vivo models which can be used to study the role of mechanical load and MicroRNAs in joint degeneration, including: non-invasive murine models of PTOA, surgical models which involve ligament transection, and unloading models based around immobilisation of joints or removal of load from the joint through suspension. We also discuss how zebrafish could be used to advance this field, namely through the availability of transgenic lines relevant to cartilage homeostasis and the ability to accurately map strain through the cartilage, enabling the response of downstream MicroRNA targets to be followed dynamically at a cellular level in areas of high and low strain.
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Affiliation(s)
- Elizabeth A Lawrence
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK.
| | - Chrissy L Hammond
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Emma J Blain
- Biomechanics and Bioengineering Centre Versus Arthritis, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
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15
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Fortier G, Butti Z, Patten SA. Modelling C9orf72-Related Amyotrophic Lateral Sclerosis in Zebrafish. Biomedicines 2020; 8:E440. [PMID: 33096681 PMCID: PMC7589578 DOI: 10.3390/biomedicines8100440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 12/12/2022] Open
Abstract
A hexanucleotide repeat expansion within the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and its discovery has revolutionized our understanding of this devastating disease. Model systems are a valuable tool for studying ALS pathobiology and potential therapies. The zebrafish (Danio rerio) has particularly become a useful model organism to study neurological diseases, including ALS, due to high genetic and physiological homology to mammals, and sensitivity to various genetic and pharmacological manipulations. In this review we summarize the zebrafish models that have been used to study the pathology of C9orf72-related ALS. We discuss their value in providing mechanistic insights and their potential use for drug discovery.
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Affiliation(s)
- Gabrielle Fortier
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC H7V 1B7, Canada; (G.F.); (Z.B.)
| | - Zoé Butti
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC H7V 1B7, Canada; (G.F.); (Z.B.)
| | - Shunmoogum A. Patten
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC H7V 1B7, Canada; (G.F.); (Z.B.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal (UQAM), Montréal, QC H2X 3Y7, Canada
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16
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Oprişoreanu AM, Smith HL, Arya S, Webster R, Zhong Z, Eaton-Hart C, Wehner D, Cardozo MJ, Becker T, Talbot K, Becker CG. Interaction of Axonal Chondrolectin with Collagen XIXa1 Is Necessary for Precise Neuromuscular Junction Formation. Cell Rep 2020; 29:1082-1098.e10. [PMID: 31665626 DOI: 10.1016/j.celrep.2019.09.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/13/2019] [Accepted: 09/12/2019] [Indexed: 01/05/2023] Open
Abstract
Chondrolectin (Chodl) is needed for motor axon extension in zebrafish and is dysregulated in mouse models of spinal muscular atrophy (SMA). However, the mechanistic basis of Chodl function is not known. Here, we use Chodl-deficient zebrafish and mouse mutants to show that the absence of Chodl leads to anatomical and functional defects of the neuromuscular synapse. In zebrafish, the growth of an identified motor axon beyond an "en passant" synapse and later axon branching from synaptic points are impaired, leading to functional deficits. Mechanistically, motor-neuron-autonomous Chodl function depends on its intracellular domain and on binding muscle-derived collagen XIXa1 by its extracellular C-type lectin domain. Our data support evolutionarily conserved roles of Chodl in synaptogenesis and provide evidence for a "synapse-first" scenario of motor axon growth in zebrafish.
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Affiliation(s)
- Ana-Maria Oprişoreanu
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Hannah L Smith
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Sukrat Arya
- Nuffield Department of Clinical Neurosciences, West Wing, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Richard Webster
- Nuffield Department of Clinical Neurosciences, West Wing, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Zhen Zhong
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Charlotte Eaton-Hart
- Nuffield Department of Clinical Neurosciences, West Wing, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Daniel Wehner
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Marcos J Cardozo
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Thomas Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK.
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, West Wing, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
| | - Catherina G Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK.
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17
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Stanford BC, Clake DJ, Morris MR, Rogers SM. The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. Evol Appl 2020; 13:1166-1182. [PMID: 32684953 PMCID: PMC7359838 DOI: 10.1111/eva.12935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Rapid environmental changes impact the global distribution and abundance of species, highlighting the urgency to understand and predict how populations will respond. The analysis of differentially expressed genes has elucidated areas of the genome involved in adaptive divergence to past and present environmental change. Such studies however have been hampered by large numbers of differentially expressed genes and limited knowledge of how these genes work in conjunction with each other. Recent methods (broadly termed "pathway analyses") have emerged that aim to group genes that behave in a coordinated fashion to a factor of interest. These methods aid in functional annotation and uncovering biological pathways, thereby collapsing complex datasets into more manageable units, providing more nuanced understandings of both the organism-level effects of modified gene expression, and the targets of adaptive divergence. Here, we reanalyze a dataset that investigated temperature-induced changes in gene expression in marine-adapted and freshwater-adapted threespine stickleback (Gasterosteus aculeatus), using Weighted Gene Co-expression Network Analysis (WGCNA) with PANTHER Gene Ontology (GO)-Slim overrepresentation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Six modules exhibited a conserved response and six a divergent response between marine and freshwater stickleback when acclimated to 7°C or 22°C. One divergent module showed freshwater-specific response to temperature, and the remaining divergent modules showed differences in height of reaction norms. PPARAa, a transcription factor that regulates fatty acid metabolism and has been implicated in adaptive divergence, was located in a module that had higher expression at 7°C and in freshwater stickleback. This updated methodology revealed patterns that were not found in the original publication. Although such methods hold promise toward predicting population response to environmental stressors, many limitations remain, particularly with regard to module expression representation, database resources, and cross-database integration.
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Affiliation(s)
| | - Danielle J. Clake
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
| | | | - Sean M. Rogers
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
- Bamfield Marine Sciences CentreBamfieldBCCanada
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18
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Characterisation of d-Conotoxin TxVIA as a Mammalian T-Type Calcium Channel Modulator. Mar Drugs 2020; 18:md18070343. [PMID: 32629781 PMCID: PMC7401249 DOI: 10.3390/md18070343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022] Open
Abstract
The 27-amino acid (aa)-long d-conotoxin TxVIA, originally isolated from the mollusc-hunting cone snail Conus textile, slows voltage-gated sodium (NaV) channel inactivation in molluscan neurons, but its mammalian ion channel targets remain undetermined. In this study, we confirmed that TxVIA was inactive on mammalian NaV1.2 and NaV1.7 even at high concentrations (10 µM). Given the fact that invertebrate NaV channel and T-type calcium channels (CaV3.x) are evolutionarily related, we examined the possibility that TxVIA may act on CaV3.x. Electrophysiological characterisation of the native TxVIA on CaV3.1, 3.2 and 3.3 revealed that TxVIA preferentially inhibits CaV3.2 current (IC50 = 0.24 mM) and enhances CaV3.1 current at higher concentrations. In fish bioassays TxVIA showed little effect on zebrafish behaviours when injected intramuscular at 250 ng/100 mg fish. The binding sites for TxVIA at NaV1.7 and CaV3.1 revealed that their channel binding sites contained a common epitope.
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19
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Zapilko V, Fish RJ, Garcia A, Reny JL, Dunoyer-Geindre S, Lecompte T, Neerman-Arbez M, Fontana P. MicroRNA-126 is a regulator of platelet-supported thrombin generation. Platelets 2020; 31:746-755. [DOI: 10.1080/09537104.2020.1775804] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Veronika Zapilko
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Richard J. Fish
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Alix Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Reny
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of General Internal Medicine, Geneva University Hospitals, Geneva, Switzerland
| | | | - Thomas Lecompte
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Pierre Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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20
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Cheresiz SV, Volgin AD, Kokorina Evsyukova A, Bashirzade AAO, Demin KA, de Abreu MS, Amstislavskaya TG, Kalueff AV. Understanding neurobehavioral genetics of zebrafish. J Neurogenet 2020; 34:203-215. [PMID: 31902276 DOI: 10.1080/01677063.2019.1698565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Due to its fully sequenced genome, high genetic homology to humans, external fertilization, fast development, transparency of embryos, low cost and active reproduction, the zebrafish (Danio rerio) has become a novel promising model organism in biomedicine. Zebrafish are a useful tool in genetic and neuroscience research, including linking various genetic mutations to brain mechanisms using forward and reverse genetics. These approaches have produced novel models of rare genetic CNS disorders and common brain illnesses, such as addiction, aggression, anxiety and depression. Genetically modified zebrafish also foster neuroanatomical studies, manipulating neural circuits and linking them to different behaviors. Here, we discuss recent advances in neurogenetics of zebrafish, and evaluate their unique strengths, inherent limitations and the rapidly growing potential for elucidating the conserved roles of genes in neuropsychiatric disorders.
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Affiliation(s)
- Sergey V Cheresiz
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Andrey D Volgin
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Alexandra Kokorina Evsyukova
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Alim A O Bashirzade
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia
| | - Konstantin A Demin
- Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil.,The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Tamara G Amstislavskaya
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,Institute of Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia.,The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China.,Ural Federal University, Ekaterinburg, Russia.,Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.,Russian Scientific Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
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21
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The α 1-adrenoceptor inhibitor ρ-TIA facilitates net hunting in piscivorous Conus tulipa. Sci Rep 2019; 9:17841. [PMID: 31780714 PMCID: PMC6882899 DOI: 10.1038/s41598-019-54186-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/07/2019] [Indexed: 11/08/2022] Open
Abstract
Cone snails use separately evolved venoms for prey capture and defence. While most use a harpoon for prey capture, the Gastridium clade that includes the well-studied Conus geographus and Conus tulipa, have developed a net hunting strategy to catch fish. This unique feeding behaviour requires secretion of "nirvana cabal" peptides to dampen the escape response of targeted fish allowing for their capture directly by mouth. However, the active components of the nirvana cabal remain poorly defined. In this study, we evaluated the behavioural effects of likely nirvana cabal peptides on the teleost model, Danio rerio (zebrafish). Surprisingly, the conantokins (NMDA receptor antagonists) and/or conopressins (vasopressin receptor agonists and antagonists) found in C. geographus and C. tulipa venom failed to produce a nirvana cabal-like effect in zebrafish. In contrast, low concentrations of the non-competitive adrenoceptor antagonist ρ-TIA found in C. tulipa venom (EC50 = 190 nM) dramatically reduced the escape response of zebrafish larvae when added directly to aquarium water. ρ-TIA inhibited the zebrafish α1-adrenoceptor, confirming ρ-TIA has the potential to reverse the known stimulating effects of norepinephrine on fish behaviour. ρ-TIA may act alone and not as part of a cabal, since it did not synergise with conopressins and/or conantokins. This study highlights the importance of using ecologically relevant animal behaviour models to decipher the complex neurobiology underlying the prey capture and defensive strategies of cone snails.
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22
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Chudinova AV, Rossel M, Vergunst A, Le-Masson G, Camu W, Raoul C, Lumbroso S, Mouzat K. Theme 4 In vivo experimental models. Amyotroph Lateral Scler Frontotemporal Degener 2019; 20:160-187. [PMID: 31702459 DOI: 10.1080/21678421.2019.1646992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: In 90% of Amyotrophic Lateral Sclerosis (ALS) cases, the disease is sporadic, the remaining 10% being familial. Many genes have been associated with the disease. The use of next generation sequencing has allowed increasing the number of genes analysed in routine diagnostics. However, this increase raises the issue of genetic variants interpretation within a growing number of ALS-associated-genes. Variant classification is based on a combinatory analysis of multiple factors. Among them, functional analyses provide strong arguments on pathogenicity interpretation.Objectives: We developed a simple animal model, the Zebrafish, for the functional analysis of candidate variants pathogenicity identified by routine genetic testing.Methods: Transient overexpression of different ALS associated genetic variants has been performed by mRNA injection in 1-cell stage zebrafish eggs. Validation of protein overexpression has been done by western blot. Embryos mortality, developmental delay and morphological abnormalities have been assessed within the first two days of development. Cellular phenotype has been investigated by the analysis of axonal length of 2-days old larvae with confocal microscopy. Motor phenotype of 5-days old larvae has been explored by touched-evoked response assay.Results: The model has been validated by the analysis of well-described ALS mutations, SOD1-Gly93Ala and OPTN Glu478Gly. Overexpression of this mutated protein was shown to provoke a shortening of axons and a premature axonal branching, as well as an impairment of motor performances as expected. We did not observe these aberrations in SOD1-WT injected fishes. Two candidate variants observed in ALS-patients have been explored with our model: SOD1 NM_000454.4:c.400_402del, p.Glu134del and OPTN NM_021980.4:c.1475T > G, p. Leu492Arg. Overexpression of both variants induced morphological abnormalities and motor impairment, suggesting a pathogenic involvement of these variants in ALS-patients.Discussion and conclusions: We developed for the first time a simple animal model, the Zebrafish, useful for the functional analysis of variant pathogenicity in order to assist ALS molecular diagnosis. Our model has been used to assess the pathogenicity of SOD1 and OPTN candidate variants, allowing to improve genetic testing interpretation.
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Affiliation(s)
- Aleksandra V Chudinova
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nîmes et Université de Montpellier, Nimes, France.,INSERM UMR1051, Institut des Neurosciences de Montpellier, Hôpital Saint Eloi, Montpellier, France
| | - Mireille Rossel
- 3MMDN, Univ. Montpellier, EPHE, INSERM, U1198, PSL Research University, Montpellier, France
| | | | - Gwendal Le-Masson
- Department of Neurology, Nerve-Muscle Unit and Centre de Référence Des Pathologies Neuromusculaires CHU Bordeaux (Groupe Hospitalier Pellegrin), University of Bordeaux, Bordeaux, France
| | - William Camu
- INSERM UMR1051, Institut des Neurosciences de Montpellier, Hôpital Saint Eloi, Montpellier, France.,ALS Center, Département de Neurologie, CHU Gui de Chauliac, Montpellier, France
| | - Cédric Raoul
- INSERM UMR1051, Institut des Neurosciences de Montpellier, Hôpital Saint Eloi, Montpellier, France
| | - Serge Lumbroso
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nîmes et Université de Montpellier, Nimes, France.,INSERM UMR1051, Institut des Neurosciences de Montpellier, Hôpital Saint Eloi, Montpellier, France
| | - Kevin Mouzat
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nîmes et Université de Montpellier, Nimes, France.,INSERM UMR1051, Institut des Neurosciences de Montpellier, Hôpital Saint Eloi, Montpellier, France
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23
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Periyasamy S, John S, Padmavati R, Rajendren P, Thirunavukkarasu P, Gratten J, Vinkhuyzen A, McRae A, Holliday EG, Nyholt DR, Nancarrow D, Bakshi A, Hemani G, Nertney D, Smith H, Filippich C, Patel K, Fowdar J, McLean D, Tirupati S, Nagasundaram A, Gundugurti PR, Selvaraj K, Jegadeesan J, Jorde LB, Wray NR, Brown MA, Suetani R, Giacomotto J, Thara R, Mowry BJ. Association of Schizophrenia Risk With Disordered Niacin Metabolism in an Indian Genome-wide Association Study. JAMA Psychiatry 2019; 76:1026-1034. [PMID: 31268507 PMCID: PMC6613304 DOI: 10.1001/jamapsychiatry.2019.1335] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Importance Genome-wide association studies (GWASs) in European populations have identified more than 100 schizophrenia-associated loci. A schizophrenia GWAS in a unique Indian population offers novel findings. Objective To discover and functionally evaluate genetic loci for schizophrenia in a GWAS of a unique Indian population. Design, Setting, and Participants This GWAS included a sample of affected individuals, family members, and unrelated cases and controls. Three thousand ninety-two individuals were recruited and diagnostically ascertained via medical records, hospitals, clinics, and clinical networks in Chennai and surrounding regions. Affected participants fulfilled DSM-IV diagnostic criteria for schizophrenia. Unrelated control participants had no personal or family history of psychotic disorder. Recruitment, genotyping, and analysis occurred in consecutive phases beginning January 1, 2001. Recruitment was completed on February 28, 2018, and genotyping and analysis are ongoing. Main Outcomes and Measures Associations of single-nucleotide polymorphisms and gene expression with schizophrenia. Results The study population included 1321 participants with schizophrenia, 885 family controls, and 886 unrelated controls. Among participants with schizophrenia, mean (SD) age was 39.1 (11.4) years, and 52.7% were male. This sample demonstrated uniform ethnicity, a degree of inbreeding, and negligible rates of substance abuse. A novel genome-wide significant association was observed between schizophrenia and a chromosome 8q24.3 locus (rs10866912, allele A; odds ratio [OR], 1.27 [95% CI, 1.17-1.38]; P = 4.35 × 10-8) that attracted support in the schizophrenia Psychiatric Genomics Consortium 2 data (rs10866912, allele A; OR, 1.04 [95% CI, 1.02-1.06]; P = 7.56 × 10-4). This locus has undergone natural selection, with the risk allele A declining in frequency from India (approximately 72%) to Europe (approximately 43%). rs10866912 directly modifies the abundance of the nicotinate phosphoribosyltransferase gene (NAPRT1) transcript in brain cortex (normalized effect size, 0.79; 95% CI, 0.6-1.0; P = 5.8 × 10-13). NAPRT1 encodes a key enzyme for niacin metabolism. In Indian lymphoblastoid cell lines, (risk) allele A of rs10866912 was associated with NAPRT1 downregulation (AA: 0.74, n = 21; CC: 1.56, n = 17; P = .004). Preliminary zebrafish data further suggest that partial loss of function of NAPRT1 leads to abnormal brain development. Conclusions and Relevance Bioinformatic analyses and cellular and zebrafish gene expression studies implicate NAPRT1 as a novel susceptibility gene. Given this gene's role in niacin metabolism and the evidence for niacin deficiency provoking schizophrenialike symptoms in neuropsychiatric diseases such as pellagra and Hartnup disease, these results suggest that the rs10866912 genotype and niacin status may have implications for schizophrenia susceptibility and treatment.
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Affiliation(s)
- Sathish Periyasamy
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Sujit John
- Schizophrenia Research Foundation, Chennai, India
| | | | | | | | - Jacob Gratten
- Mater Research Institute and University of Queensland, Translational Research Institute, Brisbane, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Anna Vinkhuyzen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Allan McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Dale R Nyholt
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Biomedical Sciences and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | | | - Andrew Bakshi
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Gibran Hemani
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Deborah Nertney
- Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Heather Smith
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Cheryl Filippich
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Kalpana Patel
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Javed Fowdar
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Duncan McLean
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Srinivasan Tirupati
- Psychiatric Rehabilitation Service, Hunter New England Mental Health, Newcastle, Australia
| | | | | | | | | | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Translational Research Institute, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Australia
| | - Rachel Suetani
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Jean Giacomotto
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | | | - Bryan J Mowry
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
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Lin CY, Lee HC, Wu JH, Tsai HJ. Short fish-origin DNA elements served as flanking sequences in a knockdown cloning vector enabling the generation of a functional siRNA molecule in mammalian cells and fish embryos. Biochem Biophys Res Commun 2018; 505:850-857. [PMID: 30301529 DOI: 10.1016/j.bbrc.2018.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022]
Abstract
Improving the quality of a siRNA-knockdown cloning vector requires simpler, shorter, and more effective flanking sequences. In this study, we designed such flanking sequences based on those found in zebrafish pre-miR3906, namely, internal element (IE) 1 and IE2. We engineered a vegf-shRNA fragment flanked by an 80-bp IE1/IE2 and then inserted into the 3' UTR of GFP reporter cDNA driven by a cytomegalovirus promoter to obtain a plasmid containing gfp-IE-vegf-shRNA-polA. Upon microinjection of this plasmid into zebrafish embryos, we found that IE flanking sequences could effectively induce the production of vegf-shRNA fragment, which was then processed into a functional siRNA to silence the target vegf121 gene. Northern blot showed that the vegf-shRNA fragment was cleaved from gfp-IE-vegf-shRNA-polA, resulting in the loss of polyA tails, subsequently degrading the remaining RNA-containing GFP. Moreover, Western blot revealed that addition of IE-based vegf-shRNA fragment could markedly decrease the expression of VEGF. Finally, to facilitate a more versatile application of the IE-based knockdown vector, we generated an inducible expression vector in which IE-vegf-shRNA was constructed downstream in a Tet-on system to generate a Tet-on-IE-vegf-shRNA construct. After doxycycline induction, the protein level of VEGF in SW620 cells harboring the Tet-on-IE-vegf-shRNA construct was decreased 77%. Interestingly, when SW620 cells harboring Tet-on-IE-vegf-shRNA cells were induced and transplanted into zebrafish embryos, we found that abnormal branch of the sub-intestinal vessels was reduced in the recipient embryos, suggesting that vegf-shRNA cleaved from Tet-on-IE-vegf-shRNA-polA was processed into a functional vegf-siRNA in embryos suppressing endogenous VEGF and reducing tumor angiogenesis. Therefore, we conclude that fish-origin IEs are flanking sequences with short, simple, and effective DNA elements. This IE-based knockdown cloning vector provides a new alternative material to facilitate the generation of functional siRNA with which to perform loss-of-function experiments, both in vitro (mammalian cells) and in vivo (zebrafish embryos).
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Affiliation(s)
- Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Hung-Chieh Lee
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Ju-Hui Wu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan.
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25
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Zhao Y, Liu Y, Sun J, Sha H, Yang Y, Ye Q, Yang Q, Huang B, Yu Y, Huang H. Acute toxic responses of embryo-larval zebrafish to zinc pyrithione (ZPT) reveal embryological and developmental toxicity. CHEMOSPHERE 2018; 205:62-70. [PMID: 29684692 DOI: 10.1016/j.chemosphere.2018.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Zinc pyrithione (ZPT) is widely used in industrial and human daily life, due to its broad antimicrobial spectrum activity. Persistent accumulation of ZTP in the aquatic environment and bioaccumulation in the living organisms attracts more and more attention. However, only very limited information is available so far for the evaluation of systematic toxicity effects of ZPT on multiple organs development. This study intends to deepen our knowledge about the potential toxicity elicited by ZPT by assessing its acute effects on zebrafish (Danio rerio) through morphological, histological and molecular investigations. It has been verified that ZPT exhibits a broad spectrum of toxicity which causes growth retardation and tissue pathological and physiology alternations in heart, liver, eye, notochord, kidney and other organisms of zebrafish. The acute toxicity values of LC50 (95% CI) 96-h is calculated as 0.073 μM. Furthermore, the organ toxicity was verified due to up-regulation of expression of biomarker genes related to organ function and development. In sum, this study demonstrats systematic acute embryological and developmental toxicity of the ZPT on zebrafish embryos/larvae.
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Affiliation(s)
- Ye Zhao
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 211800, China.
| | - Yuyang Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China
| | - Jing Sun
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China
| | - Hongtao Sha
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China
| | - Yu Yang
- College of Environmental Sciences, Nanjing Tech University, Nanjing, 211800, China
| | - Qian Ye
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Qi Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Baoqi Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Yadong Yu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, China.
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 211800, China.
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26
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Boyd PJ, Tu WY, Shorrock HK, Groen EJN, Carter RN, Powis RA, Thomson SR, Thomson D, Graham LC, Motyl AAL, Wishart TM, Highley JR, Morton NM, Becker T, Becker CG, Heath PR, Gillingwater TH. Bioenergetic status modulates motor neuron vulnerability and pathogenesis in a zebrafish model of spinal muscular atrophy. PLoS Genet 2017; 13:e1006744. [PMID: 28426667 PMCID: PMC5417717 DOI: 10.1371/journal.pgen.1006744] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/04/2017] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
Degeneration and loss of lower motor neurons is the major pathological hallmark of spinal muscular atrophy (SMA), resulting from low levels of ubiquitously-expressed survival motor neuron (SMN) protein. One remarkable, yet unresolved, feature of SMA is that not all motor neurons are equally affected, with some populations displaying a robust resistance to the disease. Here, we demonstrate that selective vulnerability of distinct motor neuron pools arises from fundamental modifications to their basal molecular profiles. Comparative gene expression profiling of motor neurons innervating the extensor digitorum longus (disease-resistant), gastrocnemius (intermediate vulnerability), and tibialis anterior (vulnerable) muscles in mice revealed that disease susceptibility correlates strongly with a modified bioenergetic profile. Targeting of identified bioenergetic pathways by enhancing mitochondrial biogenesis rescued motor axon defects in SMA zebrafish. Moreover, targeting of a single bioenergetic protein, phosphoglycerate kinase 1 (Pgk1), was found to modulate motor neuron vulnerability in vivo. Knockdown of pgk1 alone was sufficient to partially mimic the SMA phenotype in wild-type zebrafish. Conversely, Pgk1 overexpression, or treatment with terazosin (an FDA-approved small molecule that binds and activates Pgk1), rescued motor axon phenotypes in SMA zebrafish. We conclude that global bioenergetics pathways can be therapeutically manipulated to ameliorate SMA motor neuron phenotypes in vivo.
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Affiliation(s)
- Penelope J. Boyd
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Wen-Yo Tu
- Sheffield Institute for Translation Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Hannah K. Shorrock
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ewout J. N. Groen
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Roderick N. Carter
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queens Medical Research Institute, Edinburgh, United Kingdom
| | - Rachael A. Powis
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sophie R. Thomson
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Derek Thomson
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura C. Graham
- Division of Neurobiology, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna A. L. Motyl
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas M. Wishart
- Division of Neurobiology, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Robin Highley
- Sheffield Institute for Translation Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Nicholas M. Morton
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queens Medical Research Institute, Edinburgh, United Kingdom
| | - Thomas Becker
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Neuroregeneration, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Catherina G. Becker
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Neuroregeneration, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul R. Heath
- Sheffield Institute for Translation Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Thomas H. Gillingwater
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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27
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Farrar MA, Park SB, Vucic S, Carey KA, Turner BJ, Gillingwater TH, Swoboda KJ, Kiernan MC. Emerging therapies and challenges in spinal muscular atrophy. Ann Neurol 2017; 81:355-368. [PMID: 28026041 PMCID: PMC5396275 DOI: 10.1002/ana.24864] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/13/2016] [Accepted: 12/18/2016] [Indexed: 12/14/2022]
Abstract
Spinal muscular atrophy (SMA) is a hereditary neurodegenerative disease with severity ranging from progressive infantile paralysis and premature death (type I) to limited motor neuron loss and normal life expectancy (type IV). Without disease‐modifying therapies, the impact is profound for patients and their families. Improved understanding of the molecular basis of SMA, disease pathogenesis, natural history, and recognition of the impact of standardized care on outcomes has yielded progress toward the development of novel therapeutic strategies and are summarized. Therapeutic strategies in the pipeline are appraised, ranging from SMN1 gene replacement to modulation of SMN2 encoded transcripts, to neuroprotection, to an expanding repertoire of peripheral targets, including muscle. With the advent of preliminary trial data, it can be reasonably anticipated that the SMA treatment landscape will transform significantly. Advancement in presymptomatic diagnosis and screening programs will be critical, with pilot newborn screening studies underway to facilitate preclinical diagnosis. The development of disease‐modifying therapies will necessitate monitoring programs to determine the long‐term impact, careful evaluation of combined treatments, and further acceleration of improvements in supportive care. In advance of upcoming clinical trial results, we consider the challenges and controversies related to the implementation of novel therapies for all patients and set the scene as the field prepares to enter an era of novel therapies. Ann Neurol 2017;81:355–368
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Affiliation(s)
- Michelle A Farrar
- Discipline of Paediatrics, School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, Australia
| | - Susanna B Park
- Brain & Mind Centre and Sydney Medical School, University of Sydney, Sydney, Australia
| | - Steve Vucic
- Department of Neurology, Westmead Hospital and Western Clinical School, University of Sydney, Sydney, Australia
| | - Kate A Carey
- Discipline of Paediatrics, School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, Australia
| | - Bradley J Turner
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Australia
| | - Thomas H Gillingwater
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburg, Edinburg, United Kingdom
| | - Kathryn J Swoboda
- Center for Human Genetics Research, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Matthew C Kiernan
- Brain & Mind Centre and Sydney Medical School, University of Sydney, Sydney, Australia
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Neuronal sFlt1 and Vegfaa determine venous sprouting and spinal cord vascularization. Nat Commun 2017; 8:13991. [PMID: 28071661 PMCID: PMC5234075 DOI: 10.1038/ncomms13991] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
Formation of organ-specific vasculatures requires cross-talk between developing tissue and specialized endothelial cells. Here we show how developing zebrafish spinal cord neurons coordinate vessel growth through balancing of neuron-derived Vegfaa, with neuronal sFlt1 restricting Vegfaa-Kdrl mediated angiogenesis at the neurovascular interface. Neuron-specific loss of flt1 or increased neuronal vegfaa expression promotes angiogenesis and peri-neural tube vascular network formation. Combining loss of neuronal flt1 with gain of vegfaa promotes sprout invasion into the neural tube. On loss of neuronal flt1, ectopic sprouts emanate from veins involving special angiogenic cell behaviours including nuclear positioning and a molecular signature distinct from primary arterial or secondary venous sprouting. Manipulation of arteriovenous identity or Notch signalling established that ectopic sprouting in flt1 mutants requires venous endothelium. Conceptually, our data suggest that spinal cord vascularization proceeds from veins involving two-tiered regulation of neuronal sFlt1 and Vegfaa via a novel sprouting mode. The generation of vasculature in organs is regulated by cross-talk between the developing tissue and specialized endothelial cells. Here, the authors show that vessel growth feeding the zebrafish spinal cord is coordinated by balancing neuron-derived pro-angiogenic ligand Vegfaa and its receptor, sFlt1.
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Abstract
Animal models have been an invaluable means to advance biomedical research as they provide experimental avenues for cellular and molecular investigations of disease pathology. The zebrafish (Danio rerio) is a good alternative to mammalian models that can be used to apply powerful genetic experimental methods normally used in invertebrates to answer questions about vertebrate development and disease. In the case of the kidney, the zebrafish has proven itself to be an applicable and versatile experimental system, mainly due to the simplicity of its pronephros, which contains two nephrons that possess conserved structural and physiological aspects with mammalian nephrons. Numerous genes that were not previously related to kidney conditions have now been linked to renal diseases by applying genetic screening with the zebrafish. In fact, a large collection of mutations that affect nephron formation and function were generated through phenotype-based forward screens. Complementary reverse genetic approaches have also been insightful, with methods spanning the use of antisense morpholino oligonucleotides to genome editing approaches such as the CRISPR/Cas9 system, to selectively knock down or knock out genes of interest to see if they produce kidney phenotypes. Acute kidney injury (AKI) has also been easily modeled in the zebrafish by injecting nephrotoxins, directly inducing damage through surgical intervention, or by generating transgenic lines that express compounds in a tissue-specific manner that when exposed to certain drugs promote an apoptotic response within cells. In this chapter, we provide an overview of these various approaches as well as discuss many of the contributions that have been achieved through the use of zebrafish to model kidney disease.
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Fowler DK, Stewart S, Seredick S, Eisen JS, Stankunas K, Washbourne P. A MultiSite Gateway Toolkit for Rapid Cloning of Vertebrate Expression Constructs with Diverse Research Applications. PLoS One 2016; 11:e0159277. [PMID: 27500400 PMCID: PMC4976983 DOI: 10.1371/journal.pone.0159277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022] Open
Abstract
Recombination-based cloning is a quick and efficient way to generate expression vectors. Recent advancements have provided powerful recombinant DNA methods for molecular manipulations. Here, we describe a novel collection of three-fragment MultiSite Gateway cloning system-compatible vectors providing expanded molecular tools for vertebrate research. The components of this toolkit encompass a broad range of uses such as fluorescent imaging, dual gene expression, RNA interference, tandem affinity purification, chemically-inducible dimerization and lentiviral production. We demonstrate examples highlighting the utility of this toolkit for producing multi-component vertebrate expression vectors with diverse primary research applications. The vectors presented here are compatible with other Gateway toolkits and collections, facilitating the rapid generation of a broad range of innovative DNA constructs for biological research.
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Affiliation(s)
- Daniel K. Fowler
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Scott Stewart
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Steve Seredick
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Judith S. Eisen
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Kryn Stankunas
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Philip Washbourne
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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31
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Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish. Sci Rep 2016; 6:27470. [PMID: 27273160 PMCID: PMC4895340 DOI: 10.1038/srep27470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/19/2016] [Indexed: 12/12/2022] Open
Abstract
An unresolved mystery in the field of spinal muscular atrophy (SMA) is why a reduction of the ubiquitously expressed Smn protein causes defects mostly in motoneurons. We addressed the possibility that this restricted vulnerability stems from elevated Smn expression in motoneurons. To explore this, we established an ex vivo zebrafish culture system of GFP-marked motoneurons to quantitatively measure Smn protein and smn mRNA levels as well as promoter activity in motoneurons versus other cell types. Importantly, we uncovered that Smn levels are elevated in motoneurons by means of transcriptional activation. In addition, we identified the ETS family transcription factor Etv5b to be responsible for increased smn transcription in motoneurons. Moreover, we established that the additional supply of Smn protein in motoneurons is necessary for proper axonogenesis in a cell-autonomous manner. These findings demonstrate the reliance of motoneurons on more Smn, thereby adding a novel piece of evidence for their increased vulnerability under SMA conditions.
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32
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Giacomotto J, Carroll AP, Rinkwitz S, Mowry B, Cairns MJ, Becker TS. Developmental suppression of schizophrenia-associated miR-137 alters sensorimotor function in zebrafish. Transl Psychiatry 2016; 6:e818. [PMID: 27219344 PMCID: PMC5070046 DOI: 10.1038/tp.2016.88] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 01/02/2023] Open
Abstract
The neurodevelopmentally regulated microRNA miR-137 was strongly implicated as risk locus for schizophrenia in the most recent genome wide association study coordinated by the Psychiatric Genome Consortium (PGC). This molecule is highly conserved in vertebrates enabling the investigation of its function in the developing zebrafish. We utilized this model system to achieve overexpression and suppression of miR-137, both transiently and stably through transgenesis. While miR-137 overexpression was not associated with an observable specific phenotype, downregulation by antisense morpholino and/or transgenic expression of miR-sponge RNA induced significant impairment of both embryonic and larval touch-sensitivity without compromising overall anatomical development. We observed miR-137 expression and activity in sensory neurons including Rohon-Beard neurons and dorsal root ganglia, two neuronal cell types that confer touch-sensitivity in normal zebrafish, suggesting a role of these cell types in the observed phenotype. The lack of obvious anatomical or histological pathology in these cells, however, suggested that subtle axonal network defects or a change in synaptic function and neural connectivity might be responsible for the behavioral phenotype rather than a change in the cellular morphology or neuroanatomy.
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Affiliation(s)
- J Giacomotto
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia,Psychiatric Genomics Group, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia,Brain and Mind Research Institute, Sydney Medical School, University of Sydney, 94 Mallet Street, Camperdown, NSW 2050, Australia. E-mail: or or
| | - A P Carroll
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
| | - S Rinkwitz
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - B Mowry
- Psychiatric Genomics Group, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia,Queensland Centre for Mental Health Research, University of Queensland, Brisbane, QLD, Australia
| | - M J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia,Schizophrenia Research Institute, Sydney, NSW, Australia,Brain and Mind Research Institute, Sydney Medical School, University of Sydney, 94 Mallet Street, Camperdown, NSW 2050, Australia. E-mail: or or
| | - T S Becker
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia,Brain and Mind Research Institute, Sydney Medical School, University of Sydney, 94 Mallet Street, Camperdown, NSW 2050, Australia. E-mail: or or
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Abstract
The zebrafish model is the only available high-throughput vertebrate assessment system, and it is uniquely suited for studies of in vivo cell biology. A sequenced and annotated genome has revealed a large degree of evolutionary conservation in comparison to the human genome. Due to our shared evolutionary history, the anatomical and physiological features of fish are highly homologous to humans, which facilitates studies relevant to human health. In addition, zebrafish provide a very unique vertebrate data stream that allows researchers to anchor hypotheses at the biochemical, genetic, and cellular levels to observations at the structural, functional, and behavioral level in a high-throughput format. In this review, we will draw heavily from toxicological studies to highlight advances in zebrafish high-throughput systems. Breakthroughs in transgenic/reporter lines and methods for genetic manipulation, such as the CRISPR-Cas9 system, will be comprised of reports across diverse disciplines.
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Affiliation(s)
- Gloria R Garcia
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA
| | - Pamela D Noyes
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA
| | - Robert L Tanguay
- Oregon State University, Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Corvallis, OR 97331, USA.
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Laird AS, Mackovski N, Rinkwitz S, Becker TS, Giacomotto J. Tissue-specific models of spinal muscular atrophy confirm a critical role of SMN in motor neurons from embryonic to adult stages. Hum Mol Genet 2016; 25:1728-38. [PMID: 26908606 DOI: 10.1093/hmg/ddw044] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/15/2016] [Indexed: 11/14/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disease linked to survival motor neuron (SMN) protein deficiency. While SMN protein is expressed ubiquitously, its deficiency triggers tissue-specific hallmarks, including motor neuron death and muscle atrophy, leading to impaired motor functions and premature death. Here, using stable miR-mediated knockdown technology in zebrafish, we developed the first vertebrate system allowing transgenic spatio-temporal control of the smn1 gene. Using this new model it is now possible to investigate normal and pathogenic SMN function(s) in specific cell types, independently or in synergy with other cell populations. We took advantage of this new system to first test the effect of motor neuron or muscle-specific smn1 silencing. Anti-smn1 miRNA expression in motor neurons, but not in muscles, reproduced SMA hallmarks, including abnormal motor neuron development, poor motor function and premature death. Interestingly, smn1 knockdown in motor neurons also induced severe late-onset phenotypes including scoliosis-like body deformities, weight loss, muscle atrophy and, seen for the first time in zebrafish, reduction in the number of motor neurons, indicating motor neuron degeneration. Taken together, we have developed a new transgenic system allowing spatio-temporal control of smn1 expression in zebrafish, and using this model, we have demonstrated that smn1 silencing in motor neurons alone is sufficient to reproduce SMA hallmarks in zebrafish. It is noteworthy that this research is going beyond SMA as this versatile gene-silencing transgenic system can be used to knockdown any genes of interest, filling the gap in the zebrafish genetic toolbox and opening new avenues to study gene functions in this organism.
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Affiliation(s)
- Angela S Laird
- ANZAC Research Institute, Concord Repatriation Hospital, University of Sydney, Sydney, New South Wales, Australia, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, Australia
| | - Nikolce Mackovski
- ANZAC Research Institute, Concord Repatriation Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Silke Rinkwitz
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia and
| | - Thomas S Becker
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia and
| | - Jean Giacomotto
- Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia and Queensland Brain Institute, The University of Queensland, Building #79, St Lucia, Queensland 4072, Australia
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35
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Fowler DK, Williams C, Gerritsen AT, Washbourne P. Improved knockdown from artificial microRNAs in an enhanced miR-155 backbone: a designer's guide to potent multi-target RNAi. Nucleic Acids Res 2015; 44:e48. [PMID: 26582923 PMCID: PMC4797272 DOI: 10.1093/nar/gkv1246] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/31/2015] [Indexed: 01/24/2023] Open
Abstract
Artificial microRNA (amiRNA) sequences embedded in natural microRNA (miRNA) backbones have proven to be useful tools for RNA interference (RNAi). amiRNAs have reduced off-target and toxic effects compared to other RNAi-based methods such as short-hairpin RNAs (shRNA). amiRNAs are often less effective for knockdown, however, compared to their shRNA counterparts. We screened a large empirically-designed amiRNA set in the synthetic inhibitory BIC/miR-155 RNA (SIBR) scaffold and show common structural and sequence-specific features associated with effective amiRNAs. We then introduced exogenous motifs into the basal stem region which increase amiRNA biogenesis and knockdown potency. We call this modified backbone the enhanced SIBR (eSIBR) scaffold. Using chained amiRNAs for multi-gene knockdown, we show that concatenation of miRNAs targeting different genes is itself sufficient for increased knockdown efficacy. Further, we show that eSIBR outperforms wild-type SIBR (wtSIBR) when amiRNAs are chained. Finally, we use a lentiviral expression system in cultured neurons, where we again find that eSIBR amiRNAs are more potent for multi-target knockdown of endogenous genes. eSIBR will be a valuable tool for RNAi approaches, especially for studies where knockdown of multiple targets is desired.
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Affiliation(s)
- Daniel K Fowler
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Carly Williams
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Alida T Gerritsen
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Philip Washbourne
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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