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Uribe-Salazar JM, Kaya G, Weyenberg K, Radke B, Hino K, Soto DC, Shiu JL, Zhang W, Ingamells C, Haghani NK, Xu E, Rosas J, Simó S, Miesfeld J, Glaser T, Baraban SC, Jao LE, Dennis MY. Zebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612570. [PMID: 39314374 PMCID: PMC11418993 DOI: 10.1101/2024.09.11.612570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The expansion of the human SRGAP2 family, resulting in a human-specific paralog SRGAP2C, likely contributed to altered evolutionary brain features. The introduction of SRGAP2C in mouse models is associated with changes in cortical neuronal migration, axon guidance, synaptogenesis, and sensory-task performance. Truncated SRGAP2C heterodimerizes with the full-length ancestral gene product SRGAP2A and antagonizes its functions. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring and that these larvae phenocopy "humanized" SRGAP2C larvae, including altered morphometric features (i.e., reduced body length and inter-eye distance) and differential expression of synapse-, axonogenesis-, and vision-related genes. Through single-cell transcriptome analysis, we demonstrate a skewed balance of excitatory and inhibitory neurons that likely contribute to increased susceptibility to seizures displayed by Srgap2 mutant larvae, a phenotype resembling SRGAP2 loss-of-function in a child with early infantile epileptic encephalopathy. Single-cell data also shows strong endogenous expression of srgap2 in microglia with mutants exhibiting altered membrane dynamics and likely delayed maturation of microglial cells. Microglia cells expressing srgap2 were also detected in the developing eye together with altered expression of genes related to axonogenesis in mutant retinal cells. Consistent with the perturbed gene expression in the retina, we found that SRGAP2 mutant larvae exhibited increased sensitivity to broad and fine visual cues. Finally, comparing the transcriptomes of relevant cell types between human (+SRGAP2C) and non-human primates (-SRGAP2C) revealed significant overlaps of gene alterations with mutant cells in our zebrafish models; this suggests that SRGAP2C plays a similar role altering microglia and the visual system in modern humans. Together, our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features.
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Affiliation(s)
- José M. Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - Gulhan Kaya
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - KaeChandra Weyenberg
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - Brittany Radke
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - Keiko Hino
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Daniela C. Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - Jia-Lin Shiu
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Wenzhu Zhang
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Cole Ingamells
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - Nicholas K. Haghani
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - Emily Xu
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
| | - Joseph Rosas
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Sergi Simó
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Joel Miesfeld
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, WI, USA
| | - Tom Glaser
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Scott C. Baraban
- Department of Neurological Surgery and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Li-En Jao
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
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Cacialli P, Ricci S, Servetto GP, Franceschini V, Ruiz-Zepeda F, Vigliaturo R. Altered Morpho-Functional Features of Neurogenesis in Zebrafish Embryos Exposed to Non-Combustion-Derived Magnetite. Int J Mol Sci 2024; 25:6459. [PMID: 38928164 PMCID: PMC11203806 DOI: 10.3390/ijms25126459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Neurogenesis is the process by which new brain cells are formed. This crucial event emerges during embryonic life and proceeds in adulthood, and it could be influenced by environmental pollution. Non-combustion-derived magnetite represents a portion of the coarse particulate matter (PM) contributing to air and water pollution in urban settings. Studies on humans have reported that magnetite and other iron oxides have significant damaging effects at a central level, where these particles accumulate and promote oxidative stress. Similarly, magnetite nanoparticles can cross the placenta and damage the embryo brain during development, but the impact on neurogenesis is still unknown. Furthermore, an abnormal Fe cation concentration in cells and tissues might promote reactive oxygen species (ROS) generation and has been associated with multiple neurodegenerative conditions. In the present study, we used zebrafish as an in vivo system to analyze the specific effects of magnetite on embryonic neurogenesis. First, we characterized magnetite using mineralogical and spectroscopic analyses. Embryos treated with magnetite at sub-lethal concentrations showed a dose-response increase in ROS in the brain, which was accompanied by a massive decrease in antioxidant genes (sod2, cat, gsr, and nrf2). In addition, a higher number of apoptotic cells was observed in embryos treated with magnetite. Next, interestingly, embryos exposed to magnetite displayed a decrease in neural staminal progenitors (nestin, sox2, and pcna markers) and a neuronal marker (elavl3). Finally, we observed significative increases in apoeb (specific microglia marker) and interleukin-1b (il1b), confirming a status of inflammation in the brain embryos treated with magnetite. Our study represents the very first in vivo evidence concerning the effects of magnetite on brain development.
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Affiliation(s)
- Pietro Cacialli
- Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, 40126 Bologna, Italy
| | - Serena Ricci
- Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, 40126 Bologna, Italy
| | | | - Valeria Franceschini
- Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, 40126 Bologna, Italy
| | - Francisco Ruiz-Zepeda
- Department of Physics and Chemistry of Materials, Institute of Metals and Technology, Lepi pot 11, 1000 Ljubljana, Slovenia
- Department of Materials Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ruggero Vigliaturo
- Department of Earth Sciences, University of Turin, 10124 Turin, Italy
- Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10124 Turin, Italy
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Baeza-Loya S, Raible DW. Vestibular physiology and function in zebrafish. Front Cell Dev Biol 2023; 11:1172933. [PMID: 37143895 PMCID: PMC10151581 DOI: 10.3389/fcell.2023.1172933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/06/2023] [Indexed: 05/06/2023] Open
Abstract
The vestibular system of the inner ear provides information about head motion and spatial orientation relative to gravity to ensure gaze stability, balance, and postural control. Zebrafish, like humans, have five sensory patches per ear that serve as peripheral vestibular organs, with the addition of the lagena and macula neglecta. The zebrafish inner ear can be easily studied due to its accessible location, the transparent tissue of larval fish, and the early development of vestibular behaviors. Thus, zebrafish are an excellent model for studying the development, physiology, and function of the vestibular system. Recent work has made great strides to elucidate vestibular neural circuitry in fish, tracing sensory transmission from receptors in the periphery to central computational circuits driving vestibular reflexes. Here we highlight recent work that illuminates the functional organization of vestibular sensory epithelia, innervating first-order afferent neurons, and second-order neuronal targets in the hindbrain. Using a combination of genetic, anatomical, electrophysiological, and optical techniques, these studies have probed the roles of vestibular sensory signals in fish gaze, postural, and swimming behaviors. We discuss remaining questions in vestibular development and organization that are tractable in the zebrafish model.
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Affiliation(s)
| | - David W. Raible
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology-HNS and Biological Structure, University of Washington, Seattle, WA, United States
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New Insights into the Identity of the DFNA58 Gene. Genes (Basel) 2022; 13:genes13122274. [PMID: 36553541 PMCID: PMC9777997 DOI: 10.3390/genes13122274] [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: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Hearing loss is the most common sensory deficit, affecting 466 million people worldwide. The vast and diverse genes involved reflect the complexity of auditory physiology, which requires the use of animal models in order to gain a fuller understanding. Among the loci with a yet-to-be validated gene is the DFNA58, in which ~200 Kb genomic duplication, including three protein-coding genes (PLEK, CNRIP1, and PPP3R1's exon1), was found to segregate with autosomal dominant hearing loss. Through whole genome sequencing, the duplication was found to be in tandem and inserted in an intergenic region, without the disruption of the topological domains. Reanalysis of transcriptomes data studies (zebrafish and mouse), and RT-qPCR analysis of adult zebrafish target organs, in order to access their orthologues expression, highlighted promising results with Cnrip1a, corroborated by zebrafish in situ hybridization and immunofluorescence. Mouse data also suggested Cnrip1 as the best candidate for a relevant role in auditory physiology, and its importance in hearing seems to have remained conserved but the cell type exerting its function might have changed, from hair cells to spiral ganglion neurons.
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Palumbo F, Serneels B, Yaksi E. Optimized protocol for conditioned place avoidance learning in juvenile zebrafish. STAR Protoc 2021; 2:100465. [PMID: 33912851 PMCID: PMC8065339 DOI: 10.1016/j.xpro.2021.100465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Conditioned place avoidance assays are broadly used in mammals to study different cognitive aspects of operant learning. Here, we introduce a series of experimental designs for training juvenile zebrafish in short-term and long-term conditioned place avoidance assays. Our goal is to promote standardization of animal handling procedures and setup conditions to improve animal welfare and reproducibility while studying operant learning behaviors in juvenile zebrafish. For complete details on the use and execution of this protocol, please refer to Palumbo et al. (2020). We describe juvenile zebrafish handling procedures for operant learning behavior We detail experimental designs for short- and long-term learning We introduce potential pitfalls for chemogenetic ablation of neurons We highlight the importance of animal welfare for successful learning performance
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Affiliation(s)
- Fabrizio Palumbo
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7030 Trondheim, Norway
| | - Bram Serneels
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7030 Trondheim, Norway
| | - Emre Yaksi
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7030 Trondheim, Norway
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