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Peskin B, Norman J, Bagwell J, Lin A, Adhyapok P, Di Talia S, Bagnat M. Dynamic BMP signaling mediates notochord segmentation in zebrafish. Curr Biol 2023:S0960-9822(23)00671-1. [PMID: 37285843 DOI: 10.1016/j.cub.2023.05.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/12/2023] [Accepted: 05/16/2023] [Indexed: 06/09/2023]
Abstract
The vertebrate spine is a metameric structure composed of alternating vertebral bodies (centra) and intervertebral discs.1 Recent studies in zebrafish have shown that the epithelial sheath surrounding the notochord differentiates into alternating cartilage-like (col2a1/col9a2+) and mineralizing (entpd5a+) segments which serve as a blueprint for centra formation.2,3,4,5 This process also defines the trajectories of migrating sclerotomal cells that form the mature vertebral bodies.4 Previous work demonstrated that notochord segmentation is typically sequential and involves the segmented activation of Notch signaling.2 However, it is unclear how Notch is activated in an alternating and sequential fashion. Furthermore, the molecular components that define segment size, regulate segment growth, and produce sharp segment boundaries have not been identified. In this study, we uncover that a BMP signaling wave acts upstream of Notch during zebrafish notochord segmentation. Using genetically encoded reporters of BMP activity and signaling pathway components, we show that BMP signaling is dynamic as axial patterning progresses, leading to the sequential formation of mineralizing domains in the notochord sheath. Genetic manipulations reveal that type I BMP receptor activation is sufficient to ectopically trigger Notch signaling. Moreover, loss of Bmpr1ba and Bmpr1aa or Bmp3 function disrupts ordered segment formation and growth, which is recapitulated by notochord-specific overexpression of the BMP antagonist, Noggin3. Our data suggest that BMP signaling in the notochord sheath precedes Notch activation and instructs segment growth, facilitating proper spine morphogenesis.
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Affiliation(s)
- Brianna Peskin
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - James Norman
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer Bagwell
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Adam Lin
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Priyom Adhyapok
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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2
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Iftikhar N, Konig I, English C, Ivantsova E, Souders CL, Hashmi I, Martyniuk CJ. Sulfamethoxazole (SMX) Alters Immune and Apoptotic Endpoints in Developing Zebrafish (Danio rerio). TOXICS 2023; 11:178. [PMID: 36851053 PMCID: PMC9959310 DOI: 10.3390/toxics11020178] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Sulfamethoxazole (SMX) is a broad-range bacteriostatic antibiotic widely used in animal and fish farming and is also employed in human medicine. These antibiotics can ultimately end up in the aquatic ecosystem and affect non-target organisms such as fish. To discern the effect of SMX on developing zebrafish embryos and larvae, we investigated a broad range of sub-lethal toxicity endpoints. Higher concentrations of SMX affected survivability, caused hatch delay, and induced malformations including edema of the yolk sac, pericardial effusion, bent tail, and curved spine in developing embryos. Lower levels of SMX provoked an inflammatory response in larvae at seven days post fertilization (dpf), as noted by up-regulation of interferon (ifn-γ) and interleukin 1β (il-1β). SMX also increased the expression of genes related to apoptosis, including BCL2-Associated Agonist of Cell Death (bad) and BCL2 Associated X, Apoptosis Regulator (bax) at 50 µg/L and decreased caspase 3 (casp3) expression in a dose-dependent manner. SMX induced hyperactivity in larval fish at 500 and 2500 µg/L based upon the light/dark preference test. Collectively, this study revealed that exposure to SMX can disrupt the immune system by altering host defense mechanisms as well as transcripts related to apoptosis. These data improve understanding of antibiotic chemical toxicity in aquatic organisms and serves as a baseline for in-depth environmental risk assessment of SMX and antibiotics.
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Affiliation(s)
- Nazish Iftikhar
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Sector H-12, Islamabad 44000, Pakistan
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Isaac Konig
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
- Department of Chemistry, Federal University of Lavras (UFLA), Lavras 37203-202, Minas Gerais, Brazil
| | - Cole English
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Emma Ivantsova
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Christopher L. Souders
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Imran Hashmi
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Sector H-12, Islamabad 44000, Pakistan
| | - Christopher J. Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
- UF Genetics Institute and Interdisciplinary Program in Biomedical Sciences Neuroscience, University of Florida, Gainesville, FL 32611, USA
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3
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Clark BS, Miesfeld JB, Flinn MA, Collery RF, Link BA. Dynamic Polarization of Rab11a Modulates Crb2a Localization and Impacts Signaling to Regulate Retinal Neurogenesis. Front Cell Dev Biol 2021; 8:608112. [PMID: 33634099 PMCID: PMC7900515 DOI: 10.3389/fcell.2020.608112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/28/2020] [Indexed: 01/31/2023] Open
Abstract
Interkinetic nuclear migration (IKNM) is the process in which pseudostratified epithelial nuclei oscillate from the apical to basal surface and in phase with the mitotic cycle. In the zebrafish retina, neuroepithelial retinal progenitor cells (RPCs) increase Notch activity with apical movement of the nuclei, and the depth of nuclear migration correlates with the probability that the next cell division will be neurogenic. This study focuses on the mechanisms underlying the relationships between IKNM, cell signaling, and neurogenesis. In particular, we have explored the role IKNM has on endosome biology within RPCs. Through genetic manipulation and live imaging in zebrafish, we find that early (Rab5-positive) and recycling (Rab11a-positive) endosomes polarize in a dynamic fashion within RPCs and with reference to nuclear position. Functional analyses suggest that dynamic polarization of recycling endosomes and their activity within the neuroepithelia modulates the subcellular localization of Crb2a, consequently affecting multiple signaling pathways that impact neurogenesis including Notch, Hippo, and Wnt activities. As nuclear migration is heterogenous and asynchronous among RPCs, Rab11a-affected signaling within the neuroepithelia is modulated in a differential manner, providing mechanistic insight to the correlation of IKNM and selection of RPCs to undergo neurogenesis.
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Affiliation(s)
- Brian S Clark
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Joel B Miesfeld
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael A Flinn
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ross F Collery
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin Eye Institute, Milwaukee, WI, United States
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
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4
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Redox Signaling via Lipid Peroxidation Regulates Retinal Progenitor Cell Differentiation. Dev Cell 2019; 50:73-89.e6. [DOI: 10.1016/j.devcel.2019.05.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 02/07/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022]
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5
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Wopat S, Bagwell J, Sumigray KD, Dickson AL, Huitema LFA, Poss KD, Schulte-Merker S, Bagnat M. Spine Patterning Is Guided by Segmentation of the Notochord Sheath. Cell Rep 2019; 22:2026-2038. [PMID: 29466731 PMCID: PMC5860813 DOI: 10.1016/j.celrep.2018.01.084] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/10/2018] [Accepted: 01/26/2018] [Indexed: 01/05/2023] Open
Abstract
The spine is a segmented axial structure made of alternating vertebral bodies (centra) and intervertebral discs (IVDs) assembled around the notochord. Here, we show that, prior to centra formation, the outer epithelial cell layer of the zebrafish notochord, the sheath, segments into alternating domains corresponding to the prospective centra and IVD areas. This process occurs sequentially in an anteroposterior direction via the activation of Notch signaling in alternating segments of the sheath, which transition from cartilaginous to mineralizing domains. Subsequently, osteoblasts are recruited to the mineralized domains of the notochord sheath to form mature centra. Tissue-specific manipulation of Notch signaling in sheath cells produces notochord segmentation defects that are mirrored in the spine. Together, our findings demonstrate that notochord sheath segmentation provides a template for vertebral patterning in the zebrafish spine.
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Affiliation(s)
- Susan Wopat
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jennifer Bagwell
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kaelyn D Sumigray
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Dermatology, Duke University Medical Center, Durham, NC 27710, USA
| | - Amy L Dickson
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Leonie F A Huitema
- Hubrecht Institute - KNAW & UMC Utrecht, 3584 CT, Utrecht, the Netherlands
| | - Kenneth D Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Stefan Schulte-Merker
- Hubrecht Institute - KNAW & UMC Utrecht, 3584 CT, Utrecht, the Netherlands; Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU Münster, 48149 Münster, Germany; CiM Cluster of Excellence (EXC1003-CiM), 48149 Münster, Germany
| | - Michel Bagnat
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA.
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Owen N, Moosajee M. RNA-sequencing in ophthalmology research: considerations for experimental design and analysis. Ther Adv Ophthalmol 2019; 11:2515841419835460. [PMID: 30911735 PMCID: PMC6421592 DOI: 10.1177/2515841419835460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/08/2019] [Indexed: 12/13/2022] Open
Abstract
High-throughput, massively parallel sequence analysis has revolutionized the way that researchers design and execute scientific investigations. Vast amounts of sequence data can be generated in short periods of time. Regarding ophthalmology and vision research, extensive interrogation of patient samples for underlying causative DNA mutations has resulted in the discovery of many new genes relevant to eye disease. However, such analysis remains functionally limited. RNA-sequencing accurately snapshots thousands of genes, capturing many subtypes of RNA molecules, and has become the gold standard for transcriptome gene expression quantification. RNA-sequencing has the potential to advance our understanding of eye development and disease; it can reveal new candidates to improve our molecular diagnosis rates and highlight therapeutic targets for intervention. But with a wide range of applications, the design of such experiments can be problematic, no single optimal pipeline exists, and therefore, several considerations must be undertaken for optimal study design. We review the key steps involved in RNA-sequencing experimental design and the downstream bioinformatic pipelines used for differential gene expression. We provide guidance on the application of RNA-sequencing to ophthalmology and sources of open-access eye-related data sets.
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Affiliation(s)
- Nicholas Owen
- Development, Ageing and Disease Theme, UCL Institute of Ophthalmology, University College London, London, UK
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Zhou X, Cao CY, Wan ATY, Yue GGL, Kwok FHF, Fung KP, Sun H, Lau CBS, Puno PT, Tsui SKW. Functional roles of eriocalyxin B in zebrafish revealed by transcriptome analysis. Mol Omics 2018; 14:156-169. [PMID: 29676772 DOI: 10.1039/c7mo00125h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eriocalyxin B (EriB) is a naturalent-kaurane diterpenoid obtained fromIsodon eriocalyxvar.laxiflora(family Lamiaceae), which exerted multiple biological activities (e.g.anti-tumor and anti-inflammatory)viathe alteration of gene expression and signaling transduction.
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Affiliation(s)
- Xunian Zhou
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
| | - Cyanne Ye Cao
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
| | - Grace Gar-Lee Yue
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
- China
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- The Chinese University of Hong Kong
| | - Frankie Hin-Fai Kwok
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
- China
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- The Chinese University of Hong Kong
| | - Kwok-Pui Fung
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
| | - Handong Sun
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- Kunming Institute of Botany
- Chinese Academy of Sciences
- Kunming 650201
- China
| | - Clara Bik-San Lau
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
- China
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- The Chinese University of Hong Kong
| | - Pema-Tenzin Puno
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- Kunming Institute of Botany
- Chinese Academy of Sciences
- Kunming 650201
- China
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8
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Huang Y, Ng TK, Chen CB, Huang B, Liang J, Pang CP, Zhang M. Notch Signaling Activation Enhances Human Adipose-Derived Stem Cell Retinal Differentiation. Stem Cells Int 2018; 2018:9201374. [PMID: 30410544 PMCID: PMC6206515 DOI: 10.1155/2018/9201374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/01/2018] [Accepted: 08/14/2018] [Indexed: 02/05/2023] Open
Abstract
Retinal disease treatment by stem cell-based replacement relies on stem cell differentiation into retinal cells. We previously demonstrated that human periodontal ligament-derived stem cells can be directed into retinal lineage upon induction. Here, we report the transdifferentiation potential of human adipose-derived stem cells (ASCs) into retinal lineage and its enhancement by Notch signaling modulation. Human ASCs, isolated from abdominal fat, expressed mesenchymal but not hematopoietic stem cell markers, and they can differentiate into adipocytes, chondrocytes, and osteoblasts in vitro. Upon noggin/Dkk-1/IGF-1 induction, the treated ASCs showed elevated expression of retinal progenitor, retinal ganglion, and photoreceptor cell markers as well as the glutamate-evoked calcium response, which was not observed in the noninduced cells. Compared to the regular induction treatment, Notch signaling activation by JAG1 enhanced the expression of retinal progenitor and precursor markers without affecting the glutamate-evoked calcium response. In contrast, Notch signaling inhibition by DAPT showed more retinal ganglion cells, but delayed the response to glutamate stimulation. In summary, our results revealed that human ASCs possess a retinal transdifferentiation potential upon noggin/Dkk-1/IGF-1 induction, which can further be enhanced by Notch signaling activation.
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Affiliation(s)
- Yuqiang Huang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guandong, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Chong-Bo Chen
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Bing Huang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Jiajian Liang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Chi Pui Pang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mingzhi Zhang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
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Seritrakul P, Gross JM. Tet-mediated DNA hydroxymethylation regulates retinal neurogenesis by modulating cell-extrinsic signaling pathways. PLoS Genet 2017; 13:e1006987. [PMID: 28926578 PMCID: PMC5621703 DOI: 10.1371/journal.pgen.1006987] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/29/2017] [Accepted: 08/18/2017] [Indexed: 12/28/2022] Open
Abstract
DNA hydroxymethylation has recently been shown to play critical roles in regulating gene expression and terminal differentiation events in a variety of developmental contexts. However, little is known about its function during eye development. Methylcytosine dioxygenases of the Tet family convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), an epigenetic mark thought to serve as a precursor for DNA demethylation and as a stable mark in neurons. Here, we report a requirement for Tet activity during zebrafish retinal neurogenesis. In tet2-/-;tet3-/- mutants, retinal neurons are specified but most fail to terminally differentiate. While differentiation of the first born retinal neurons, the retinal ganglion cells (RGCs), is less affected in tet2-/-;tet3-/- mutants than other retinal cell types, the majority of RGCs do not undergo terminal morphogenesis and form axons. Moreover, the few photoreceptors that differentiate in tet2-/-;tet3-/- mutants fail to form outer segments, suggesting that Tet function is also required for terminal morphogenesis of differentiated retinal neurons. Mosaic analyses revealed a surprising cell non-autonomous requirement for tet2 and tet3 activity in facilitating retinal neurogenesis. Through a combination of candidate gene analysis, transcriptomics and pharmacological manipulations, we identified the Notch and Wnt pathways as cell-extrinsic pathways regulated by tet2 and tet3 activity during RGC differentiation and morphogenesis. Transcriptome analyses also revealed the ectopic expression of non-retinal genes in tet2-/-;tet3-/- mutant retinae, and this correlated with locus-specific reduction in 5hmC. These data provide the first evidence that Tet-dependent regulation of 5hmC formation is critical for retinal neurogenesis, and highlight an additional layer of complexity in the progression from retinal progenitor cell to differentiated retinal neuron during development of the vertebrate retina.
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Affiliation(s)
- Pawat Seritrakul
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States of America
- Departments of Ophthalmology, and Developmental Biology, The Louis J. Fox Center for Vision Restoration, The McGowan Institute for Regenerative Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Jeffrey M. Gross
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States of America
- Departments of Ophthalmology, and Developmental Biology, The Louis J. Fox Center for Vision Restoration, The McGowan Institute for Regenerative Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
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10
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Taylor SM, Alvarez-Delfin K, Saade CJ, Thomas JL, Thummel R, Fadool JM, Hitchcock PF. The bHLH Transcription Factor NeuroD Governs Photoreceptor Genesis and Regeneration Through Delta-Notch Signaling. Invest Ophthalmol Vis Sci 2015; 56:7496-515. [PMID: 26580854 PMCID: PMC4654396 DOI: 10.1167/iovs.15-17616] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/06/2015] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Photoreceptor genesis in the retina requires precise regulation of progenitor cell competence, cell cycle exit, and differentiation, although information around the mechanisms that govern these events currently is lacking. In zebrafish, the basic helix-loop-helix (bHLH) transcription factor NeuroD governs photoreceptor genesis, but the signaling pathways through which NeuroD functions are unknown. The purpose of this study was to identify these pathways, and during photoreceptor genesis, Notch signaling was investigated as the putative mediator of NeuroD function. METHODS In embryos, genetic mosaic analysis was used to determine if NeuroD functions is cell- or non-cell-autonomous. Morpholino-induced NeuroD knockdown, CRISPR/Cas9 mutation, and pharmacologic and transgenic approaches were used, followed by in situ hybridization, immunocytochemistry, and quantitative RT-PCR (qRT-PCR), to identify mechanisms through which NeuroD functions. In adults, following photoreceptor ablation and NeuroD knockdown, similar methods as above were used to identify NeuroD function during photoreceptor regeneration. RESULTS In embryos, NeuroD function is non-cell-autonomous, NeuroD knockdown increases Notch pathway gene expression, Notch inhibition rescues the NeuroD knockdown-induced deficiency in cell cycle exit but not photoreceptor maturation, and Notch activation and CRISPR/Cas9 mutation of neurod recapitulate NeuroD knockdown. In adults, NeuroD knockdown prevents cell cycle exit and photoreceptor regeneration and increases Notch pathway gene expression, and Notch inhibition rescues this phenotype. CONCLUSIONS These data demonstrate that during embryonic development, NeuroD governs photoreceptor genesis via non-cell-autonomous mechanisms and that, during photoreceptor development and regeneration, Notch signaling is a mechanistic link between NeuroD and cell cycle exit. In contrast, during embryonic development, NeuroD governs photoreceptor maturation via mechanisms that are independent of Notch signaling.
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Affiliation(s)
- Scott M. Taylor
- Department of Ophthalmology and Visual Sciences University of Michigan, W. K. Kellogg Eye Center, Ann Arbor, Michigan, United States
| | - Karen Alvarez-Delfin
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States
| | - Carole J. Saade
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States
| | - Jennifer L. Thomas
- Departments of Anatomy/Cell Biology and Ophthalmology, Wayne State University, Detroit, Michigan, United States
| | - Ryan Thummel
- Departments of Anatomy/Cell Biology and Ophthalmology, Wayne State University, Detroit, Michigan, United States
| | - James M. Fadool
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States
| | - Peter F. Hitchcock
- Department of Ophthalmology and Visual Sciences University of Michigan, W. K. Kellogg Eye Center, Ann Arbor, Michigan, United States
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11
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Miesfeld JB, Gestri G, Clark BS, Flinn MA, Poole RJ, Bader JR, Besharse JC, Wilson SW, Link BA. Yap and Taz regulate retinal pigment epithelial cell fate. Development 2015; 142:3021-32. [PMID: 26209646 PMCID: PMC4582179 DOI: 10.1242/dev.119008] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 07/10/2015] [Indexed: 12/20/2022]
Abstract
The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz-Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Tead-responsive transgene is expressed within the domain of the optic cup from which RPE arises, and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz (wwtr1) mutant alleles such that, when Yap and Taz are both absent, optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap-dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co-factor. In contrast to loss of Yap and Taz, overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosage-dependent manner. Overall, this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson's chorioretinal atrophy and congenital retinal coloboma.
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Affiliation(s)
- Joel B Miesfeld
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Gaia Gestri
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
| | - Brian S Clark
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael A Flinn
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Richard J Poole
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
| | - Jason R Bader
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Joseph C Besharse
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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12
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Diotel N, Beil T, Strähle U, Rastegar S. Differential expression of id genes and their potential regulator znf238 in zebrafish adult neural progenitor cells and neurons suggests distinct functions in adult neurogenesis. Gene Expr Patterns 2015; 19:1-13. [PMID: 26107416 DOI: 10.1016/j.gep.2015.05.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
Abstract
Teleost fish display a remarkable ability to generate new neurons and to repair brain lesions during adulthood. They are, therefore, a very popular model to investigate the molecular mechanisms of constitutive and induced neurogenesis in adult vertebrates. In this study, we investigated the expression patterns of inhibitor of DNA binding (id) genes and of their potential transcriptional repressor, znf238, in the whole brain of adult zebrafish. We show that while id1 is exclusively expressed in ventricular cells in the whole brain, id2a, id3 and id4 genes are expressed in broader areas. Interestingly, znf238 was also detected in these regions, its expression overlapping with id2a, id3 and id4 expression. Further detailed characterization of the id-expressing cells demonstrated that (a) id1 is expressed in type 1 and type 2 neural progenitors as previously published, (b) id2a in type 1, 2 and 3 neural progenitors, (c) id3 in type 3 neural progenitors and (d) id4 in postmitotic neurons. Our data provide a detailed map of id and znf238 expression in the brain of adult zebrafish, supplying a framework for studies of id genes function during adult neurogenesis and brain regeneration in the zebrafish.
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Affiliation(s)
- Nicolas Diotel
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany; Inserm, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Plateforme CYROI, Sainte-Clotilde, F-97490, France; Université de La Réunion, UMR 1188, Sainte-Clotilde, F-97490, France.
| | - Tanja Beil
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Uwe Strähle
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Sepand Rastegar
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany.
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Gao H, Bu Y, Wu Q, Wang X, Chang N, Lei L, Chen S, Liu D, Zhu X, Hu K, Xiong JW. Mecp2 regulates neural cell differentiation by suppressing the Id1 to Her2 axis in zebrafish. J Cell Sci 2015; 128:2340-50. [DOI: 10.1242/jcs.167874] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/28/2015] [Indexed: 01/20/2023] Open
Abstract
ABSTRACT
Rett syndrome (RTT) is a progressive neurological disorder caused by mutations in the X-linked protein methyl-CpG-binding protein 2 (MeCP2). The endogenous function of MeCP2 during neural differentiation is still unclear. Here, we report that mecp2 is required for brain development in zebrafish. Mecp2 was broadly expressed initially in embryos and enriched later in the brain. Either morpholino knockdown or genetic depletion of mecp2 inhibited neuronal differentiation, whereas its overexpression promoted neuronal differentiation, suggesting an essential role of mecp2 in directing neural precursors into differentiated neurons. Mechanistically, her2 (the zebrafish ortholog of mammalian Hes5) was upregulated in mecp2 morphants in an Id1-dependent manner. Moreover, knockdown of either her2 or id1 fully rescued neuronal differentiation in mecp2 morphants. These results suggest that Mecp2 plays an important role in neural cell development by suppressing the Id1–Her2 axis, and provide new evidence that embryonic neural defects contribute to the later motor and cognitive dysfunctions in RTT.
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Affiliation(s)
- Hai Gao
- Research Center for Pharmacology and Toxicology, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ye Bu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Wu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xu Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Nannan Chang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Lei Lei
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Shilin Chen
- Research Center for Pharmacology and Toxicology, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Dong Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Peking University, Beijing, China
| | - Xiaojun Zhu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Keping Hu
- Research Center for Pharmacology and Toxicology, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Jing-Wei Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, Beijing, China
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14
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Id2a is required for hepatic outgrowth during liver development in zebrafish. Mech Dev 2015; 138 Pt 3:399-414. [PMID: 26022495 DOI: 10.1016/j.mod.2015.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/24/2015] [Accepted: 05/14/2015] [Indexed: 12/19/2022]
Abstract
During development, inhibitor of DNA binding (Id) proteins, a subclass of the helix-loop-helix family of proteins, regulate cellular proliferation, differentiation, and apoptosis in various organs. However, a functional role of Id2a in liver development has not yet been reported. Here, using zebrafish as a model organism, we provide in vivo evidence that Id2a regulates hepatoblast proliferation and cell death during liver development. Initially, in the liver, id2a is expressed in hepatoblasts and after their differentiation, id2a expression is restricted to biliary epithelial cells. id2a knockdown in zebrafish embryos had no effect on hepatoblast specification or hepatocyte differentiation. However, liver size was greatly reduced in id2a morpholino-injected embryos, indicative of a hepatic outgrowth defect attributable to the significant decrease in proliferating hepatoblasts concomitant with the significant increase in hepatoblast cell death. Altogether, these data support the role of Id2a as an important regulator of hepatic outgrowth via modulation of hepatoblast proliferation and survival during liver development in zebrafish.
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15
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Wong L, Power N, Miles A, Tropepe V. Mutual antagonism of the paired-type homeobox genes, vsx2 and dmbx1, regulates retinal progenitor cell cycle exit upstream of ccnd1 expression. Dev Biol 2015; 402:216-28. [PMID: 25872183 DOI: 10.1016/j.ydbio.2015.03.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/17/2015] [Accepted: 03/25/2015] [Indexed: 01/04/2023]
Abstract
Understanding the mechanisms that regulate the transition between the proliferative and a post-mitotic state of retinal progenitor cells (RPCs) is key to advancing our knowledge of retinal growth and maturation. In the present study we determined that during zebrafish embryonic retinal neurogenesis, two paired-type homeobox genes - vsx2 and dmbx1 - function in a mutually antagonistic manner. We demonstrate that vsx2 gene expression requires active Fgf signaling and that this in turn suppresses dmbx1 expression and maintains cells in an undifferentiated, proliferative RPC state. This vsx2-dependent RPC state can be prolonged cell-autonomously by knockdown of dmbx1, or it can be suppressed prematurely by the over-expression of dmbx1, which we show can inhibit vsx2 expression and lead to precocious neuronal differentiation. dmbx1 loss of function also results in altered expression of canonical cell cycle genes, and in particular up-regulation of ccnd1, which correlates with our previous finding of a prolonged RPC cell cycle. By knocking down ccnd1 and dmbx1 simultaneously, we show that RPCs can overcome this phenotype to exit the cell cycle on time and differentiate normally into retinal neurons. Collectively, our data provide novel insight into the mechanism that enables RPCs to exit the cell cycle through a previously unrecognized antagonistic interaction of two paired-type homeobox genes that are central regulators of an Fgf-vsx2-dmbx1-ccnd1 signaling axis.
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Affiliation(s)
- Loksum Wong
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Namita Power
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Amanda Miles
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada M5T 3A9; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada M5S 3B2.
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16
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Qian X, Ba Y, Zhuang Q, Zhong G. RNA-Seq technology and its application in fish transcriptomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 18:98-110. [PMID: 24380445 DOI: 10.1089/omi.2013.0110] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.
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Affiliation(s)
- Xi Qian
- 1 Department of Animal Science, University of Vermont , Burlington, Vermont
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D'Andrea D, Grassi L, Mazzapioda M, Tramontano A. FIDEA: a server for the functional interpretation of differential expression analysis. Nucleic Acids Res 2013; 41:W84-8. [PMID: 23754850 PMCID: PMC3692084 DOI: 10.1093/nar/gkt516] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathways or InterPro families they belong to, their GO Molecular Function, Biological Process or Cellular Component. A statistically significant overrepresentation of one or more category terms in the set of differentially expressed genes is an essential step for the interpretation of the biological significance of the results. Ideally, the analysis should be performed by scientists who are well acquainted with the biological problem, as they have a wealth of knowledge about the system and can, more easily than a bioinformatician, discover less obvious and, therefore, more interesting relationships. To allow experimentalists to explore their data in an easy and at the same time exhaustive fashion within a single tool and to test their hypothesis quickly and effortlessly, we developed FIDEA. The FIDEA server is located at http://www.biocomputing.it/fidea; it is free and open to all users, and there is no login requirement.
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Affiliation(s)
- Daniel D'Andrea
- Department of Physics, Sapienza University, Rome, 00185, Italy
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