1
|
Farre AA, Sun C, Starostik MR, Hunter SS, English MA, Duncan A, Santhanam A, Shihabeddin E, O’Brien J, Swaroop A, Stenkamp DL. Long wavelength-sensing cones of zebrafish retina exhibit multiple layers of transcriptional heterogeneity. Front Cell Neurosci 2023; 17:1214084. [PMID: 37519633 PMCID: PMC10382231 DOI: 10.3389/fncel.2023.1214084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Understanding how photoreceptor genes are regulated is important for investigating retinal development and disease. While much is known about gene regulation in cones, the mechanism by which tandemly-replicated opsins, such as human long wavelength-sensitive and middle wavelength-sensitive opsins, are differentially regulated remains elusive. In this study, we aimed to further our understanding of transcriptional heterogeneity in cones that express tandemly-replicated opsins and the regulation of such differential expression using zebrafish, which express the tandemly-replicated opsins lws1 and lws2. Methods We performed bulk and single cell RNA-Seq of LWS1 and LWS2 cones, evaluated expression patterns of selected genes of interest using multiplex fluorescence in situ hybridization, and used exogenous thyroid hormone (TH) treatments to test selected genes for potential control by thyroid hormone: a potent, endogenous regulator of lws1 and lws2 expression. Results Our studies indicate that additional transcriptional differences beyond opsin expression exist between LWS1 and LWS2 cones. Bulk RNA-Seq results showed 95 transcripts enriched in LWS1 cones and 186 transcripts enriched in LWS2 cones (FC > 2, FDR < 0.05). In situ hybridization results also reveal underlying heterogeneity within the lws1- and lws2-expressing populations. This heterogeneity is evident in cones of mature zebrafish, and further heterogeneity is revealed in transcriptional responses to TH treatments. Discussion We found some evidence of coordinate regulation of lws opsins and other genes by exogenous TH in LWS1 vs. LWS2 cones, as well as evidence of gene regulation not mediated by TH. The transcriptional differences between LWS1 and LWS2 cones are likely controlled by multiple signals, including TH.
Collapse
Affiliation(s)
- Ashley A. Farre
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Chi Sun
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Margaret R. Starostik
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Samuel S. Hunter
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Milton A. English
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Audrey Duncan
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Abirami Santhanam
- Department of Vision Science, University of Houston College of Optometry, Houston, TX, United States
| | - Eyad Shihabeddin
- MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, United States
| | - John O’Brien
- Department of Vision Science, University of Houston College of Optometry, Houston, TX, United States
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Deborah L. Stenkamp
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| |
Collapse
|
2
|
Sharma P, Ramachandran R. Retina regeneration: lessons from vertebrates. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac012. [PMID: 38596712 PMCID: PMC10913848 DOI: 10.1093/oons/kvac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/24/2022] [Accepted: 06/25/2022] [Indexed: 04/11/2024]
Abstract
Unlike mammals, vertebrates such as fishes and frogs exhibit remarkable tissue regeneration including the central nervous system. Retina being part of the central nervous system has attracted the interest of several research groups to explore its regenerative ability in different vertebrate models including mice. Fishes and frogs completely restore the size, shape and tissue structure of an injured retina. Several studies have unraveled molecular mechanisms underlying retina regeneration. In teleosts, soon after injury, the Müller glial cells of the retina reprogram to form a proliferating population of Müller glia-derived progenitor cells capable of differentiating into various neural cell types and Müller glia. In amphibians, the transdifferentiation of retinal pigment epithelium and differentiation of ciliary marginal zone cells contribute to retina regeneration. In chicks and mice, supplementation with external growth factors or genetic modifications cause a partial regenerative response in the damaged retina. The initiation of retina regeneration is achieved through sequential orchestration of gene expression through controlled modulations in the genetic and epigenetic landscape of the progenitor cells. Several developmental biology pathways are turned on during the Müller glia reprogramming, retinal pigment epithelium transdifferentiation and ciliary marginal zone differentiation. Further, several tumorigenic pathways and gene expression events also contribute to the complete regeneration cascade of events. In this review, we address the various retinal injury paradigms and subsequent gene expression events governed in different vertebrate species. Further, we compared how vertebrates such as teleost fishes and amphibians can achieve excellent regenerative responses in the retina compared with their mammalian counterparts.
Collapse
Affiliation(s)
- Poonam Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO, 140306 Mohali, Punjab, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO, 140306 Mohali, Punjab, India
| |
Collapse
|
3
|
Berrosteguieta I, Rosillo JC, Herrera ML, Olivera-Bravo S, Casanova G, Herranz-Pérez V, García-Verdugo JM, Fernández AS. Plasticity of cell proliferation in the retina of Austrolebias charrua fish under light and darkness conditions. CURRENT RESEARCH IN NEUROBIOLOGY 2022; 3:100042. [DOI: 10.1016/j.crneur.2022.100042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
|
4
|
Fitzgerald JA, Könemann S, Krümpelmann L, Županič A, Vom Berg C. Approaches to Test the Neurotoxicity of Environmental Contaminants in the Zebrafish Model: From Behavior to Molecular Mechanisms. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2021; 40:989-1006. [PMID: 33270929 DOI: 10.1002/etc.4951] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/15/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
The occurrence of neuroactive chemicals in the aquatic environment is on the rise and poses a potential threat to aquatic biota of currently unpredictable outcome. In particular, subtle changes caused by these chemicals to an organism's sensation or behavior are difficult to tackle with current test systems that focus on rodents or with in vitro test systems that omit whole-animal responses. In recent years, the zebrafish (Danio rerio) has become a popular model organism for toxicological studies and testing strategies, such as the standardized use of zebrafish early life stages in the Organisation for Economic Co-operation and Development's guideline 236. In terms of neurotoxicity, the zebrafish provides a powerful model to investigate changes to the nervous system from several different angles, offering the ability to tackle the mechanisms of action of chemicals in detail. The mechanistic understanding gained through the analysis of this model species provides a good basic knowledge of how neuroactive chemicals might interact with a teleost nervous system. Such information can help infer potential effects occurring to other species exposed to neuroactive chemicals in their aquatic environment and predicting potential risks of a chemical for the aquatic ecosystem. In the present article, we highlight approaches ranging from behavioral to structural, functional, and molecular analysis of the larval zebrafish nervous system, providing a holistic view of potential neurotoxic outcomes. Environ Toxicol Chem 2021;40:989-1006. © 2020 SETAC.
Collapse
Affiliation(s)
- Jennifer A Fitzgerald
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Könemann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- EPF Lausanne, School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland
| | - Laura Krümpelmann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Anže Županič
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- National Institute of Biology, Ljubljana, Slovenia
| | - Colette Vom Berg
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| |
Collapse
|
5
|
Nadolski NJ, Wong CXL, Hocking JC. Electroretinogram analysis of zebrafish retinal function across development. Doc Ophthalmol 2020; 142:99-109. [PMID: 32691203 DOI: 10.1007/s10633-020-09783-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/01/2020] [Indexed: 11/25/2022]
Abstract
PURPOSE The electroretinogram (ERG) is a powerful approach for investigating visual function in zebrafish ocular disease models. However, complexity, cost, and a literature gap present as significant barriers for the introduction of this technology to new zebrafish laboratories. Here, we introduce a simplified and effective method to obtain zebrafish ERGs. METHODS In-house assembled recording electrodes and a custom 3D-printed platform were used to gather high-quality and consistent ERG data from zebrafish at 3 developmental timepoints-larval, juvenile, and adult. Fish were tested under both scotopic (dark-adapted) and photopic (light-adapted) conditions to differentiate between the rod and cone systems, respectively. RESULTS Robust ERG waveforms across all developmental timepoints were obtained using the methodology presented here. We observed an overall increase in signal amplitude as development progressed, reflecting maturation of the zebrafish retina. Oscillatory potentials could also be isolated from the generated waveforms. CONCLUSIONS This simplified approach to the zebrafish ERG can generate waveforms comparable to the existing approaches and helps reduce barriers for zebrafish laboratories studying ocular development and disease.
Collapse
Affiliation(s)
- Nathan J Nadolski
- Department of Medical Genetics, University of Alberta, Edmonton, Canada
| | - Casey X L Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Women & Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Jennifer C Hocking
- Department of Medical Genetics, University of Alberta, Edmonton, Canada.
- Women & Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada.
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada.
- Division of Anatomy, Department of Surgery, University of Alberta, 5-01 Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada.
| |
Collapse
|
6
|
Allan K, DiCicco R, Ramos M, Asosingh K, Yuan A. Preparing a Single Cell Suspension from Zebrafish Retinal Tissue for Flow Cytometric Cell Sorting of Müller Glia. Cytometry A 2020; 97:638-646. [PMID: 31769194 PMCID: PMC7246168 DOI: 10.1002/cyto.a.23936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022]
Abstract
Preparation of a single cell suspension from solid tissue is vital for a successful flow cytometry experiment. We report a detailed and reproducible method to produce a quality cell suspension from the zebrafish retina. Zebrafish retinas, especially their Müller glia cells, are of particular interest for their inherent regenerative capacity, making them a useful model for regenerative medicine and cell therapy research. Here, we detail a papain-based dissociation that is gentle enough to keep cells intact, but strong enough to disrupt cell-cell and cell-matrix interactions to yield a cell suspension that produces clean and reliable flow cytometric cell sorting results. This procedure consistently results in over 90% viability and three populations of cells based on GFP expression. The dissociation procedure described herein has been optimized for the collection of Müller glia from Tg(apoe:gfp) zebrafish retinas; however, the overall process may be applicable to other cell types in the fish retina, additional flow cytometric techniques, or preparing cell suspensions from similar tissues. © 2019 International Society for Advancement of Cytometry.
Collapse
Affiliation(s)
- Kristin Allan
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
- Department of Ophthalmic Research, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
- Cole Eye Institute, The Cleveland Clinic, Cleveland, Ohio
| | - Rose DiCicco
- Department of Ophthalmic Research, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
- Cole Eye Institute, The Cleveland Clinic, Cleveland, Ohio
| | - Michael Ramos
- Department of Ophthalmic Research, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
- Cole Eye Institute, The Cleveland Clinic, Cleveland, Ohio
| | - Kewal Asosingh
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
- Flow Cytometry Core, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
| | - Alex Yuan
- Department of Ophthalmic Research, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
- Cole Eye Institute, The Cleveland Clinic, Cleveland, Ohio
| |
Collapse
|
7
|
McGinn TE, Galicia CA, Leoni DC, Partington N, Mitchell DM, Stenkamp DL. Rewiring the Regenerated Zebrafish Retina: Reemergence of Bipolar Neurons and Cone-Bipolar Circuitry Following an Inner Retinal Lesion. Front Cell Dev Biol 2019; 7:95. [PMID: 31245369 PMCID: PMC6562337 DOI: 10.3389/fcell.2019.00095] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
We previously reported strikingly normal morphologies and functional connectivities of regenerated retinal bipolar neurons (BPs) in zebrafish retinas sampled 60 days after a ouabain-mediated lesion of inner retinal neurons (60 DPI) (McGinn et al., 2018). Here we report early steps in the birth of BPs and formation of their dendritic trees and axonal arbors during regeneration. Adult zebrafish were subjected to ouabain-mediated lesion that destroys inner retinal neurons but spares photoreceptors and Müller glia, and were sampled at 13, 17, and 21 DPI, a timeframe over which plexiform layers reemerge. We show that this timeframe corresponds to reemergence of two populations of BPs (PKCα+ and nyx::mYFP+). Sequential BrdU, EdU incorporation reveals that similar fractions of PKCα+ BPs and HuC/D+ amacrine/ganglion cells are regenerated concurrently, suggesting that the sequence of neuronal production during retinal regeneration does not strictly match that observed during embryonic development. Further, accumulation of regenerated BPs appears protracted, at least through 21 DPI. The existence of isolated, nyx::mYFP+ BPs allowed examination of cytological detail through confocal microscopy, image tracing, morphometric analyses, identification of cone synaptic contacts, and rendering/visualization. Apically-projecting neurites (=dendrites) of regenerated BPs sampled at 13, 17, and 21 DPI are either truncated, or display smaller dendritic trees when compared to controls. In cases where BP dendrites reach the outer plexiform layer (OPL), numbers of dendritic tips are similar to those of controls at all sampling times. Further, by 13-17 DPI, BPs with dendritic tips reaching the outer nuclear layer (ONL) show patterns of photoreceptor connections that are statistically indistinguishable from controls, while those sampled at 21 DPI slightly favor contacts with double cone synaptic terminals over those of blue-sensitive cones. These findings suggest that once regenerated BP dendrites reach the OPL, normal photoreceptor connectomes are established, albeit with some plasticity. Through 17 DPI, some basally-projecting neurites (=axons) of regenerated nyx::mYFP+ BPs traverse long distances, branch into inappropriate layers, or appear to abruptly terminate. These findings suggest that, after a tissue-disrupting lesion, regeneration of inner retinal neurons is a dynamic process that includes ongoing genesis of new neurons and changes in BP morphology.
Collapse
Affiliation(s)
- Timothy E McGinn
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Carlos A Galicia
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Dylan C Leoni
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Natalie Partington
- Department of Biology, Brigham Young University-Idaho, Rexburg, ID, United States
| | - Diana M Mitchell
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Deborah L Stenkamp
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| |
Collapse
|
8
|
Endoglin is a conserved regulator of vasculogenesis in zebrafish - implications for hereditary haemorrhagic telangiectasia. Biosci Rep 2019; 39:BSR20182320. [PMID: 31064821 PMCID: PMC6527926 DOI: 10.1042/bsr20182320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 04/21/2019] [Accepted: 04/30/2019] [Indexed: 01/05/2023] Open
Abstract
Hereditary haemorrhagic telangiectasia (HHT) is a progressive vascular disease with high mortality and prevalence. There is no effective treatment of HHT due to the lack of comprehensive knowledge of its underlying pathological mechanisms. The majority of HHT1 patients carry endoglin (ENG) mutations. Here, we used Danio rerio (zebrafish) as an in vivo model to investigate the effects of endoglin knockdown on vascular development. According to phylogenetic analyses and amino acid sequence similarity analyses, we confirmed that endoglin is conserved in vertebrates and descended from a single common ancestor. Endoglin is highly expressed in the vasculature beginning at the segmentation period in zebrafish. Upon endoglin knockdown by morpholinos, we observed disruption in the intersegmental vessels (ISVs) and decreased expression of several vascular markers. RNA sequencing (RNA-Seq) results implied that the BMP-binding endothelial regulator (bmper) is a gene affected by endoglin knockdown. Rescue experiments demonstrated that overexpression of bmper significantly increased the number of endothelial cells (ECs) and reduced the defects at ISVs in zebrafish. Moreover, there was enhanced tube formation in ENG mutant ECs derived from a HHT patient after human recombinant BMPER (hrBMPER) stimulation. Taken together, our results suggest that bmper, a potential downstream gene of ENG, could be targeted to improve vascular integrity in HHT.
Collapse
|
9
|
Mitchell DM, Sun C, Hunter SS, New DD, Stenkamp DL. Regeneration associated transcriptional signature of retinal microglia and macrophages. Sci Rep 2019; 9:4768. [PMID: 30886241 PMCID: PMC6423051 DOI: 10.1038/s41598-019-41298-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/04/2019] [Indexed: 02/08/2023] Open
Abstract
Zebrafish have the remarkable capacity to regenerate retinal neurons following a variety of damage paradigms. Following initial tissue insult and a period of cell death, a proliferative phase ensues that generates neuronal progenitors, which ultimately regenerate damaged neurons. Recent work has revealed that Müller glia are the source of regenerated neurons in zebrafish. However, the roles of another important class of glia present in the retina, microglia, during this regenerative phase remain elusive. Here, we examine retinal tissue and perform QuantSeq. 3'mRNA sequencing/transcriptome analysis to reveal localization and putative functions, respectively, of mpeg1 expressing cells (microglia/macrophages) during Müller glia-mediated regeneration, corresponding to a time of progenitor proliferation and production of new neurons. Our results indicate that in this regenerative state, mpeg1-expressing cells are located in regions containing regenerative Müller glia and are likely engaged in active vesicle trafficking. Further, mpeg1+ cells congregate at and around the optic nerve head. Our transcriptome analysis reveals several novel genes not previously described in microglia. This dataset represents the first report, to our knowledge, to use RNA sequencing to probe the microglial transcriptome in such context, and therefore provides a resource towards understanding microglia/macrophage function during successful retinal (and central nervous tissue) regeneration.
Collapse
Affiliation(s)
- Diana M Mitchell
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA.
| | - Chi Sun
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
- Ophthalmology, Washington University in St. Louis, 4523 Clayton Ave St. Louis, Missouri, 63110, USA
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Daniel D New
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Deborah L Stenkamp
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| |
Collapse
|