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Emmerich K, Hageter J, Hoang T, Lyu P, Sharrock AV, Ceisel A, Thierer J, Chunawala Z, Nimmagadda S, Palazzo I, Matthews F, Zhang L, White DT, Rodriguez C, Graziano G, Marcos P, May A, Mulligan T, Reibman B, Saxena MT, Ackerley DF, Qian J, Blackshaw S, Horstick E, Mumm JS. A large-scale CRISPR screen reveals context-specific genetic regulation of retinal ganglion cell regeneration. Development 2024; 151:dev202754. [PMID: 39007397 DOI: 10.1242/dev.202754] [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: 02/01/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Many genes are known to regulate retinal regeneration after widespread tissue damage. Conversely, genes controlling regeneration after limited cell loss, as per degenerative diseases, are undefined. As stem/progenitor cell responses scale to injury levels, understanding how the extent and specificity of cell loss impact regenerative processes is important. Here, transgenic zebrafish enabling selective retinal ganglion cell (RGC) ablation were used to identify genes that regulate RGC regeneration. A single cell multiomics-informed screen of 100 genes identified seven knockouts that inhibited and 11 that promoted RGC regeneration. Surprisingly, 35 out of 36 genes known and/or implicated as being required for regeneration after widespread retinal damage were not required for RGC regeneration. The loss of seven even enhanced regeneration kinetics, including the proneural factors neurog1, olig2 and ascl1a. Mechanistic analyses revealed that ascl1a disruption increased the propensity of progenitor cells to produce RGCs, i.e. increased 'fate bias'. These data demonstrate plasticity in the mechanism through which Müller glia convert to a stem-like state and context specificity in how genes function during regeneration. Increased understanding of how the regeneration of disease-relevant cell types is specifically controlled will support the development of disease-tailored regenerative therapeutics.
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Affiliation(s)
- Kevin Emmerich
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- McKusick-Nathans Institute and the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John Hageter
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
| | - Thanh Hoang
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
| | - Pin Lyu
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Anneliese Ceisel
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - James Thierer
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zeeshaan Chunawala
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Saumya Nimmagadda
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Isabella Palazzo
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frazer Matthews
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Liyun Zhang
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David T White
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Catalina Rodriguez
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Gianna Graziano
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Patrick Marcos
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Adam May
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tim Mulligan
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Barak Reibman
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Meera T Saxena
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jiang Qian
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Seth Blackshaw
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- McKusick-Nathans Institute and the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eric Horstick
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
- Department of Neuroscience, West Virginia University, Morgantown, WV 26506, USA
| | - Jeff S Mumm
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- McKusick-Nathans Institute and the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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2
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Damuth DL, Cunningham DD, Silva EM. Sox21 homeologs autoregulate expression levels to control progression through neurogenesis. Genesis 2024; 62:e23612. [PMID: 39054872 DOI: 10.1002/dvg.23612] [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: 06/14/2023] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 07/27/2024]
Abstract
The SRY HMG box transcription factor Sox21 plays multiple critical roles in neurogenesis, with its function dependent on concentration and developmental stage. In the allotetraploid Xenopus laevis, there are two homeologs of sox21, namely sox21.S and sox21.L. Previous studies focused on Sox21.S, but its amino acid sequence is divergent, lacking conserved poly-A stretches and bearing more similarity with ancestral homologs. In contrast, Sox21.L shares higher sequence similarity with mouse and chick Sox21. To determine if Sox21.S and Sox21.L have distinct functions, we conducted gain and loss-of-function studies in Xenopus embryos. Our studies revealed that Sox21.S and Sox21.L are functionally redundant, but Sox21.L is more effective at driving changes than Sox21.S. These results also support our earlier findings in ectodermal explants, demonstrating that Sox21 function is dose-dependent. While Sox21 is necessary for primary neuron formation, high levels prevent their formation. Strikingly, these proteins autoregulate, with high levels of Sox21.L reducing sox21.S and sox21.L mRNA levels, and decreased Sox21.S promoting increased expression of sox21.L. Our findings shed light on the intricate concentration-dependent roles of Sox21 homeologs in Xenopus neurogenesis.
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Affiliation(s)
- Dillon L Damuth
- Department of Biology, Georgetown University, Washington, DC, USA
| | | | - Elena M Silva
- Department of Biology, Georgetown University, Washington, DC, USA
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3
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Li D, Cheng K, Zhu X. Construction and Identification of a Novel Mice Model of Microphthalmia. Transl Vis Sci Technol 2024; 13:11. [PMID: 39007834 PMCID: PMC467107 DOI: 10.1167/tvst.13.7.11] [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: 11/09/2023] [Accepted: 05/30/2024] [Indexed: 07/16/2024] Open
Abstract
Purpose Microphthalmia is a rare developmental eye disease that affects 1 in 7000 births. Currently, there is no cure for this condition. This study aimed to construct a stable mouse model of microphthalmia, thus providing a new tool for the study of the etiology of microphthalmia. Methods The Hedgehog signaling pathway plays a crucial role in eye development. One of the key mechanisms of the Sonic Hedgehog signaling is the strong transcriptional activation ability of GLI3, a major mediator of this pathway. This study used CRISPR/Cas9 system to construct a novel TgGli3Ki/Ki lens-specific over-expression mouse line. To identify the ocular characteristics of this line, quantitative PCR, Western blot, hematoxylin and eosin staining, immunofluorescent staining, and RNA-seq were performed on the ocular tissues of this line and normal mice. Results The TgGli3Ki/Ki lens-specific over-expression mouse model exhibits the ocular phenotype of microphthalmia. In the TgGli3Ki/Ki mouse, Gli3 is over-expressed in the lens, and the size of the eyeball and lens is significantly smaller than the normal one. RNA-seq analysis using the lens and the retina samples from TgGli3Ki/Ki and normal mice indicates that the phototransduction pathway is ectopically activated in the lens. Immunofluorescent staining of the lens samples confirmed this activation. Conclusions The TgGli3Ki/Ki mouse model consistently manifests the stereotypical microphthalmia phenotype across generations, making it an excellent tool for studying this severe eye disease. Translational Relevance This study developed a novel animal model to facilitate clinical research on microphthalmia.
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Affiliation(s)
- Dan Li
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Kaiwen Cheng
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xiangjia Zhu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
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Albano GA, Hackam AS. Repurposing development genes for axonal regeneration following injury: Examining the roles of Wnt signaling. Front Cell Dev Biol 2024; 12:1417928. [PMID: 38882059 PMCID: PMC11176474 DOI: 10.3389/fcell.2024.1417928] [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: 04/16/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
In this review, we explore the connections between developmental embryology and axonal regeneration. Genes that regulate embryogenesis and central nervous system (CNS) development are discussed for their therapeutic potential to induce axonal and cellular regeneration in adult tissues after neuronal injury. Despite substantial differences in the tissue environment in the developing CNS compared with the injured CNS, recent studies have identified multiple molecular pathways that promote axonal growth in both scenarios. We describe various molecular cues and signaling pathways involved in neural development, with an emphasis on the versatile Wnt signaling pathway. We discuss the capacity of developmental factors to initiate axonal regrowth in adult neural tissue within the challenging environment of the injured CNS. Our discussion explores the roles of Wnt signaling and also examines the potential of other embryonic genes including Pax, BMP, Ephrin, SOX, CNTF, PTEN, mTOR and STAT3 to contribute to axonal regeneration in various CNS injury model systems, including spinal cord and optic crush injuries in mice, Xenopus and zebrafish. Additionally, we describe potential contributions of Müller glia redifferentiation to neuronal regeneration after injury. Therefore, this review provides a comprehensive summary of the state of the field, and highlights promising research directions for the potential therapeutic applications of specific embryologic molecular pathways in axonal regeneration in adults.
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Affiliation(s)
- Gabrielle A Albano
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Abigail S Hackam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States
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5
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Shinsato RN, Correa CG, Herai RH. Genetic network analysis indicate that individuals affected by neurodevelopmental conditions have genetic variations associated with ophthalmologic alterations: A critical review of literature. Gene 2024; 908:148246. [PMID: 38325665 DOI: 10.1016/j.gene.2024.148246] [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: 07/21/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Changes in the nervous system are related to a wide range of mental disorders, which include neurodevelopmental disorders (NDD) that are characterized by early onset mental conditions, such as schizophrenia and autism spectrum disorders and correlated conditions (ASD). Previous studies have shown distinct genetic components associated with diverse schizophrenia and ASD phenotypes, with mostly focused on rescuing neural phenotypes and brain activity, but alterations related to vision are overlooked. Thus, as the vision is composed by the eyes that itself represents a part of the brain, with the retina being formed by neurons and cells originating from the glia, genetic variations affecting the brain can also affect the vision. Here, we performed a critical systematic literature review to screen for all genetic variations in individuals presenting NDD with reported alterations in vision. Using these restricting criteria, we found 20 genes with distinct types of genetic variations, inherited or de novo, that includes SNP, SNV, deletion, insertion, duplication or indel. The variations occurring within protein coding regions have different impact on protein formation, such as missense, nonsense or frameshift. Moreover, a molecular analysis of the 20 genes found revealed that 17 shared a common protein-protein or genetic interaction network. Moreover, gene expression analysis in samples from the brain and other tissues indicates that 18 of the genes found are highly expressed in the brain and retina, indicating their potential role in adult vision phenotype. Finally, we only found 3 genes from our study described in standard public databanks of ophthalmogenetics, suggesting that the other 17 genes could be novel target for vision diseases.
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Affiliation(s)
- Rogério N Shinsato
- Unisalesiano, Araçatuba, São Paulo, Brazil; Laboratory of Bioinformatics and Neurogenetics (LaBiN/LEM), Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, 80215-901, Brazil.
| | - Camila Graczyk Correa
- Laboratory of Bioinformatics and Neurogenetics (LaBiN/LEM), Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, 80215-901, Brazil
| | - Roberto H Herai
- Laboratory of Bioinformatics and Neurogenetics (LaBiN/LEM), Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, 80215-901, Brazil; Research Division, Buko Kaesemodel Institute (IBK), Curitiba, Paraná 80240-000, Brazil; Research Division, 9p Brazil Association (A9pB), Santa Maria, Rio Grande do Sul 97060-580, Brazil.
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6
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Hung SS, Tsai PS, Po CW, Hou PS. Pax6 isoforms shape eye development: Insights from developmental stages and organoid models. Differentiation 2024; 137:100781. [PMID: 38631141 DOI: 10.1016/j.diff.2024.100781] [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: 10/10/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Pax6 is a critical transcription factor involved in the development of the central nervous system. However, in humans, mutations in Pax6 predominantly result in iris deficiency rather than neurological phenotypes. This may be attributed to the distinct functions of Pax6 isoforms, Pax6a and Pax6b. In this study, we investigated the spatial and temporal expression patterns of Pax6 isoforms during different stages of mouse eye development. We observed a strong correlation between Pax6a expression and the neuroretina gene Sox2, while Pax6b showed a high correlation with iris-component genes, including the mesenchymal gene Foxc1. During early patterning from E10.5, Pax6b was expressed in the hinge of the optic cup and neighboring mesenchymal cells, whereas Pax6a was absent in these regions. At E14.5, both Pax6a and Pax6b were expressed in the future iris and ciliary body, coinciding with the integration of mesenchymal cells and Mitf-positive cells in the outer region. From E18.5, Pax6 isoforms exhibited distinct expression patterns as lineage genes became more restricted. To further validate these findings, we utilized ESC-derived eye organoids, which recapitulated the temporal and spatial expression patterns of lineage genes and Pax6 isoforms. Additionally, we found that the spatial expression patterns of Foxc1 and Mitf were impaired in Pax6b-mutant ESC-derived eye organoids. This in vitro eye organoids model suggested the involvement of Pax6b-positive local mesodermal cells in iris development. These results provide valuable insights into the regulatory roles of Pax6 isoforms during iris and neuroretina development and highlight the potential of ESC-derived eye organoids as a tool for studying normal and pathological eye development.
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Affiliation(s)
- Shih-Shun Hung
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Beitou Dist, Taipei, 11221, Taiwan.
| | - Po-Sung Tsai
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Beitou Dist, Taipei, 11221, Taiwan.
| | - Ching-Wen Po
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Beitou Dist, Taipei, 11221, Taiwan; Institute of Brain Science, School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Pei-Shan Hou
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., Beitou Dist, Taipei, 11221, Taiwan; Institute of Brain Science, School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
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7
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Dorgau B, Collin J, Rozanska A, Zerti D, Unsworth A, Crosier M, Hussain R, Coxhead J, Dhanaseelan T, Patel A, Sowden JC, FitzPatrick DR, Queen R, Lako M. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina. Nat Commun 2024; 15:3567. [PMID: 38670973 PMCID: PMC11053058 DOI: 10.1038/s41467-024-47933-x] [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: 07/11/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids.
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Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Darin Zerti
- Biosciences Institute, Newcastle University, Newcastle, UK
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Moira Crosier
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Aara Patel
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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8
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Varner LR, Chaya T, Maeda Y, Tsutsumi R, Zhou S, Tsujii T, Okuzaki D, Furukawa T. The deubiquitinase Otud7b suppresses cone photoreceptor degeneration in mouse models of retinal degenerative diseases. iScience 2024; 27:109380. [PMID: 38510130 PMCID: PMC10951987 DOI: 10.1016/j.isci.2024.109380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Primary and secondary cone photoreceptor death in retinal degenerative diseases, including age-related macular degeneration (AMD) and retinitis pigmentosa (RP), leads to severe visual impairment and blindness. Although the cone photoreceptor protection in retinal degenerative diseases is crucial for maintaining vision, the underlying molecular mechanisms are unclear. Here, we found that the deubiquitinase Otud7b/Cezanne is predominantly expressed in photoreceptor cells in the retina. We analyzed Otud7b-/- mice, which were subjected to light-induced damage, a dry AMD model, or were mated with an RP mouse model, and observed increased cone photoreceptor degeneration. Using RNA-sequencing and bioinformatics analysis followed by a luciferase reporter assay, we found that Otud7b downregulates NF-κB activity. Furthermore, inhibition of NF-κB attenuated cone photoreceptor degeneration in the light-exposed Otud7b-/- retina and stress-induced neuronal cell death resulting from Otud7b deficiency. Together, our findings suggest that Otud7b protects cone photoreceptors in retinal degenerative diseases by modulating NF-κB activity.
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Affiliation(s)
- Leah Rie Varner
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Taro Chaya
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Yamato Maeda
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Ryotaro Tsutsumi
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shanshan Zhou
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Toshinori Tsujii
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
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9
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Birch S, McGee L, Provencher C, DeMio C, Plachetzki D. Phototactic preference and its genetic basis in the planulae of the colonial Hydrozoan Hydractinia symbiolongicarpus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.585045. [PMID: 38617216 PMCID: PMC11014542 DOI: 10.1101/2024.03.28.585045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Background Marine organisms with sessile adults commonly possess motile larval stages that make settlement decisions based on integrating environmental sensory cues. Phototaxis, the movement toward or away from light, is a common behavioral characteristic of aquatic and marine metazoan larvae, and of algae, protists, and fungi. In cnidarians, behavioral genomic investigations of motile planulae larvae have been conducted in anthozoans (corals and sea anemones) and scyphozoans (true jellyfish), but such studies are presently lacking in hydrozoans. Here, we examined the behavioral genomics of phototaxis in planulae of the hydrozoan Hydractinia symbiolongicarpus. Results A behavioral phototaxis study of day 3 planulae indicated preferential phototaxis to green (523 nm) and blue (470 nm) wavelengths of light, but not red (625 nm) wavelengths. A developmental transcriptome study where planula larvae were collected from four developmental time points for RNA-seq revealed that many genes critical to the physiology and development of ciliary photosensory systems are dynamically expressed in planula development and correspond to the expression of phototactic behavior. Microscopical investigations using immunohistochemistry and in situ hybridization demonstrated that several transcripts with predicted function in photoreceptors, including cnidops class opsin, CNG ion channel, and CRX-like transcription factor, localize to ciliated bipolar sensory neurons of the aboral sensory neural plexus, which is associated with the direction of phototaxis and the site of settlement. Conclusions The phototactic preference displayed by planulae is consistent with the shallow sandy marine habitats they experience in nature. Our genomic investigations add further evidence of similarities between cnidops-mediated photoreceptors of hydrozoans and other cnidarians and ciliary photoreceptors as found in the eyes of humans and other bilaterians, suggesting aspects of their shared evolutionary history.
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Affiliation(s)
- Sydney Birch
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
- Department of Biological Sciences; University of North Carolina Charlotte; Charlotte, NC, 28223; USA
| | - Lindy McGee
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
| | - Curtis Provencher
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
| | - Christine DeMio
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
| | - David Plachetzki
- Department of Molecular, Cellular, and Biomedical Sciences; University of New Hampshire; Durham, NH, 03824; USA
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10
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Fisher J, Verhagen M, Long Z, Moissidis M, Yan Y, He C, Wang J, Micoli E, Alastruey CM, Moors R, Marín O, Mi D, Lim L. Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories. Neuron 2024; 112:558-573.e8. [PMID: 38086373 DOI: 10.1016/j.neuron.2023.11.013] [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: 11/07/2022] [Revised: 08/22/2023] [Accepted: 11/10/2023] [Indexed: 02/24/2024]
Abstract
The mammalian cerebral cortex contains an extraordinary diversity of cell types that emerge by implementing different developmental programs. Delineating when and how cellular diversification occurs is particularly challenging for cortical inhibitory neurons because they represent a small proportion of all cortical cells and have a protracted development. Here, we combine single-cell RNA sequencing and spatial transcriptomics to characterize the emergence of neuronal diversity among somatostatin-expressing (SST+) cells in mice. We found that SST+ inhibitory neurons segregate during embryonic stages into long-range projection (LRP) neurons and two types of interneurons, Martinotti cells and non-Martinotti cells, following distinct developmental trajectories. Two main subtypes of LRP neurons and several subtypes of interneurons are readily distinguishable in the embryo, although interneuron diversity is likely refined during early postnatal life. Our results suggest that the timing for cellular diversification is unique for different subtypes of SST+ neurons and particularly divergent for LRP neurons and interneurons.
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Affiliation(s)
- Josephine Fisher
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Marieke Verhagen
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Zhen Long
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Monika Moissidis
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Yiming Yan
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chenyi He
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyu Wang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Elia Micoli
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Clara Milían Alastruey
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Rani Moors
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK.
| | - Da Mi
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Lynette Lim
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium.
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11
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Singleton KS, Silva-Rodriguez P, Cunningham DD, Silva EM. Xenopus Sox11 Partner Proteins and Functional Domains in Neurogenesis. Genes (Basel) 2024; 15:243. [PMID: 38397232 PMCID: PMC10887758 DOI: 10.3390/genes15020243] [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: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Sox11, a member of the SoxC family of transcription factors, has distinct functions at different times in neural development. Studies in mouse, frog, chick, and zebrafish show that Sox11 promotes neural fate, neural differentiation, and neuron maturation in the central nervous system. These diverse roles are controlled in part by spatial and temporal-specific protein interactions. However, the partner proteins and Sox11-interaction domains underlying these diverse functions are not well defined. Here, we identify partner proteins and the domains of Xenopus laevis Sox11 required for protein interaction and function during neurogenesis. Our data show that Sox11 co-localizes and interacts with Pou3f2 and Neurog2 in the anterior neural plate and in early neurons, respectively. We also demonstrate that Sox11 does not interact with Neurog1, a high-affinity partner of Sox11 in the mouse cortex, suggesting that Sox11 has species-specific partner proteins. Additionally, we determined that the N-terminus including the HMG domain of Sox11 is necessary for interaction with Pou3f2 and Neurog2, and we established a novel role for the N-terminal 46 amino acids in the specification of placodal progenitors. This is the first identification of partner proteins for Sox11 and of domains required for partner-protein interactions and distinct roles in neurogenesis.
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Affiliation(s)
- Kaela S. Singleton
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
| | - Pablo Silva-Rodriguez
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Doreen D. Cunningham
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Elena M. Silva
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
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12
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Sun H, Zhang H. Lysine Methylation-Dependent Proteolysis by the Malignant Brain Tumor (MBT) Domain Proteins. Int J Mol Sci 2024; 25:2248. [PMID: 38396925 PMCID: PMC10889763 DOI: 10.3390/ijms25042248] [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: 12/14/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Lysine methylation is a major post-translational protein modification that occurs in both histones and non-histone proteins. Emerging studies show that the methylated lysine residues in non-histone proteins provide a proteolytic signal for ubiquitin-dependent proteolysis. The SET7 (SETD7) methyltransferase specifically transfers a methyl group from S-Adenosyl methionine to a specific lysine residue located in a methylation degron motif of a protein substrate to mark the methylated protein for ubiquitin-dependent proteolysis. LSD1 (Kdm1a) serves as a demethylase to dynamically remove the methyl group from the modified protein. The methylated lysine residue is specifically recognized by L3MBTL3, a methyl-lysine reader that contains the malignant brain tumor domain, to target the methylated proteins for proteolysis by the CRL4DCAF5 ubiquitin ligase complex. The methylated lysine residues are also recognized by PHF20L1 to protect the methylated proteins from proteolysis. The lysine methylation-mediated proteolysis regulates embryonic development, maintains pluripotency and self-renewal of embryonic stem cells and other stem cells such as neural stem cells and hematopoietic stem cells, and controls other biological processes. Dysregulation of the lysine methylation-dependent proteolysis is associated with various diseases, including cancers. Characterization of lysine methylation should reveal novel insights into how development and related diseases are regulated.
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Affiliation(s)
| | - Hui Zhang
- Department of Chemistry and Biochemistry, Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 South Maryland Parkway, P.O. Box 454003, Las Vegas, NV 89154-4003, USA;
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13
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Yoo W, Song YW, Kim J, Ahn J, Kim J, Shin Y, Ryu JK, Kim KK. Molecular basis for SOX2-dependent regulation of super-enhancer activity. Nucleic Acids Res 2023; 51:11999-12019. [PMID: 37930832 PMCID: PMC10711550 DOI: 10.1093/nar/gkad908] [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: 08/16/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 11/08/2023] Open
Abstract
Pioneer transcription factors (TFs) like SOX2 are vital for stemness and cancer through enhancing gene expression within transcriptional condensates formed with coactivators, RNAs and mediators on super-enhancers (SEs). Despite their importance, how these factors work together for transcriptional condensation and activation remains unclear. SOX2, a pioneer TF found in SEs of pluripotent and cancer stem cells, initiates SE-mediated transcription by binding to nucleosomes, though the mechanism isn't fully understood. To address SOX2's role in SEs, we identified mSE078 as a model SOX2-enriched SE and p300 as a coactivator through bioinformatic analysis. In vitro and cell assays showed SOX2 forms condensates with p300 and SOX2-binding motifs in mSE078. We further proved that SOX2 condensation is highly correlated with mSE078's enhancer activity in cells. Moreover, we successfully demonstrated that p300 not only elevated transcriptional activity but also triggered chromatin acetylation via its direct interaction with SOX2 within these transcriptional condensates. Finally, our validation of SOX2-enriched SEs showcased their contribution to target gene expression in both stem cells and cancer cells. In its entirety, this study imparts valuable mechanistic insights into the collaborative interplay of SOX2 and its coactivator p300, shedding light on the regulation of transcriptional condensation and activation within SOX2-enriched SEs.
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Affiliation(s)
- Wanki Yoo
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Yi Wei Song
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jihye Ahn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Je-Kyung Ryu
- Department of Physics & Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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14
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Dubaic M, Peskova L, Hampl M, Weissova K, Celiker C, Shylo NA, Hruba E, Kavkova M, Zikmund T, Weatherbee SD, Kaiser J, Barta T, Buchtova M. Role of ciliopathy protein TMEM107 in eye development: insights from a mouse model and retinal organoid. Life Sci Alliance 2023; 6:e202302073. [PMID: 37863656 PMCID: PMC10589122 DOI: 10.26508/lsa.202302073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023] Open
Abstract
Primary cilia are cellular surface projections enriched in receptors and signaling molecules, acting as signaling hubs that respond to stimuli. Malfunctions in primary cilia have been linked to human diseases, including retinopathies and ocular defects. Here, we focus on TMEM107, a protein localized to the transition zone of primary cilia. TMEM107 mutations were found in patients with Joubert and Meckel-Gruber syndromes. A mouse model lacking Tmem107 exhibited eye defects such as anophthalmia and microphthalmia, affecting retina differentiation. Tmem107 expression during prenatal mouse development correlated with phenotype occurrence, with enhanced expression in differentiating retina and optic stalk. TMEM107 deficiency in retinal organoids resulted in the loss of primary cilia, down-regulation of retina-specific genes, and cyst formation. Knocking out TMEM107 in human ARPE-19 cells prevented primary cilia formation and impaired response to Smoothened agonist treatment because of ectopic activation of the SHH pathway. Our data suggest TMEM107 plays a crucial role in early vertebrate eye development and ciliogenesis in the differentiating retina.
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Affiliation(s)
- Marija Dubaic
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucie Peskova
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Hampl
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kamila Weissova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Canan Celiker
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Natalia A Shylo
- Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Eva Hruba
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Michaela Kavkova
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomas Zikmund
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Scott D Weatherbee
- Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
- Biology Department, Fairfield University, Fairfield, CT, USA
| | - Jozef Kaiser
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomas Barta
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marcela Buchtova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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15
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Bonasoni MP, Comitini G, Pati M, Bizzarri V, Barbieri V, Marinelli M, Caraffi SG, Zuntini R, Pollazzon M, Palicelli A, Garavelli L. Prenatal Array-CGH Detection of 3q26.32q26.33 Interstitial Deletion Encompassing the SOX2 Gene: Ultrasound, Pathological, and Cytogenetic Findings. Fetal Pediatr Pathol 2023; 42:979-989. [PMID: 37747279 DOI: 10.1080/15513815.2023.2261043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/14/2023] [Indexed: 09/26/2023]
Abstract
Background: SOX2 disorders are associated with anophthalmia-esophageal-genital syndrome or microphthalmia, syndromic 3 (MCOPS3- # 206900). Case Report: We describe a third fetal case with a de novo 3q26.32q26.33 deletion extending for 4.31 Mb, detected in a 15-week fetus. After legal interruption of pregnancy, at autopsy, the fetus presented bilateral microphthalmia, right cleft lip and palate, bilateral cerebral ventriculomegaly and dilated third ventricle, microcystic left lung, and intestinal malrotation. Histologically, the left lung showed congenital pulmonary airway malformation (CPAM) type 2. Retinal dysplasia was found in both eyes. Discussion/Conclusion: The human SOX2 gene (OMIM #184429) is located on chromosome 3 at position q26.3-27 and encodes a transcription factor involved in the development of the central and peripheral nervous systems, retina, and lung. In our case, the combination of cerebral, retinal, and pulmonary anomalies, not previously described, are consistent with SOX2 haploinsufficiency due to chromosomal deletion.
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Affiliation(s)
| | - Giuseppina Comitini
- Department of Obstetrics & Gynaecology, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Mariangela Pati
- Department of Obstetrics & Gynaecology, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Veronica Bizzarri
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Veronica Barbieri
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Maria Marinelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Marzia Pollazzon
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Andrea Palicelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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16
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Abatti LE, Lado-Fernández P, Huynh L, Collado M, Hoffman M, Mitchell J. Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. Nucleic Acids Res 2023; 51:10109-10131. [PMID: 37738673 PMCID: PMC10602899 DOI: 10.1093/nar/gkad734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023] Open
Abstract
Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung adenocarcinoma. Deletion of the SRR124-134 cluster disrupts expression of the SOX2 oncogene, dysregulates genome-wide transcription and chromatin accessibility and reduces the ability of cancer cells to form colonies in vitro. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124-134 activity and SOX2 transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.
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Affiliation(s)
- Luis E Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Lado-Fernández
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
- Department of Physiology and Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Linh Huynh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Manuel Collado
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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17
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Wong NK, Yip SP, Huang CL. Establishing Functional Retina in a Dish: Progress and Promises of Induced Pluripotent Stem Cell-Based Retinal Neuron Differentiation. Int J Mol Sci 2023; 24:13652. [PMID: 37686457 PMCID: PMC10487913 DOI: 10.3390/ijms241713652] [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: 08/03/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
The human eye plays a critical role in vision perception, but various retinal degenerative diseases such as retinitis pigmentosa (RP), glaucoma, and age-related macular degeneration (AMD) can lead to vision loss or blindness. Although progress has been made in understanding retinal development and in clinical research, current treatments remain inadequate for curing or reversing these degenerative conditions. Animal models have limited relevance to humans, and obtaining human eye tissue samples is challenging due to ethical and legal considerations. Consequently, researchers have turned to stem cell-based approaches, specifically induced pluripotent stem cells (iPSCs), to generate distinct retinal cell populations and develop cell replacement therapies. iPSCs offer a novel platform for studying the key stages of human retinogenesis and disease-specific mechanisms. Stem cell technology has facilitated the production of diverse retinal cell types, including retinal ganglion cells (RGCs) and photoreceptors, and the development of retinal organoids has emerged as a valuable in vitro tool for investigating retinal neuron differentiation and modeling retinal diseases. This review focuses on the protocols, culture conditions, and techniques employed in differentiating retinal neurons from iPSCs. Furthermore, it emphasizes the significance of molecular and functional validation of the differentiated cells.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
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18
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Kuang L, Zhang M, Wang T, Huang T, Li J, Gan R, Yu M, Cao W, Yan X. The molecular genetics of anterior segment dysgenesis. Exp Eye Res 2023; 234:109603. [PMID: 37495069 DOI: 10.1016/j.exer.2023.109603] [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: 01/19/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 07/28/2023]
Abstract
Anterior segment dysgenesis is a severe developmental eye disorder that leads to blindness in children. The exact mechanisms underlying this condition remain elusive. Recently, an increasing amount of studies have focused on genes and signal transduction pathways that affect anterior segment dysgenesis;these factors include transcription factors, developmental regulators, extracellular matrix genes, membrane-related proteins, cytoskeleton proteins and other associated genes. To date, dozens of gene variants have been found to cause anterior segment dysgenesis. However, there is still a lack of effective treatments. With a broader and deeper understanding of the molecular mechanisms underlying anterior segment development in the future, gene editing technology and stem cell technology may be new treatments for anterior segment dysgenesis. Further studies on the mechanisms of how different genes influence the onset and progression of anterior segment dysgenesis are still needed.
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Affiliation(s)
- Longhao Kuang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Min Zhang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232000, China
| | - Ting Wang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Tao Huang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Jin Li
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Run Gan
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Mingyu Yu
- Department of the Second Clinical Medical College, Jinan University (Shenzhen Eye Hospital), Shenzhen, 518020, China
| | - Wenchao Cao
- Department of the Second Clinical Medical College, Jinan University (Shenzhen Eye Hospital), Shenzhen, 518020, China
| | - Xiaohe Yan
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China.
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19
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Yasuda T, Nakazawa T, Hirakawa K, Matsumoto I, Nagata K, Mori S, Igarashi K, Sagara H, Oda S, Mitani H. Retinal regeneration after injury induced by gamma-ray irradiation during early embryogenesis in medaka, Oryzias latipes. Int J Radiat Biol 2023; 100:131-138. [PMID: 37555698 DOI: 10.1080/09553002.2023.2242932] [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: 09/11/2022] [Revised: 07/06/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
PURPOSE Zebrafish, a small fish model, exhibits a multipotent ability for retinal regeneration after damage throughout its lifetime. Compared with zebrafish, birds and mammals exhibit such a regenerative capacity only during the embryonic period, and this capacity decreases with age. In medaka, another small fish model that has also been used extensively in biological research, the retina's inner nuclear layer (INL) failed to regenerate after injury in the hatchling at eight days postfertilization (dpf). We characterized the regenerative process of the embryonic retina when the retinal injury occurred during the early embryonic period in medaka. METHODS We employed a 10 Gy dose of gamma-ray irradiation to initiate retinal injury in medaka embryos at 3 dpf and performed histopathological analyses up to 21 dpf. RESULTS One day after irradiation, numerous apoptotic neurons were observed in the INL; however, these neurons were rarely observed in the ciliary marginal zone and the photoreceptor layer. Numerous pyknotic cells were clustered in the irradiated retina until two days after irradiation. These disappeared four days after irradiation, but the abnormal bridging structures between the INL and ganglion cell layer (GCL) were present until 11 days after irradiation, and the neural layers were completely regenerated 18 days after irradiation. After gamma-ray irradiation, the spindle-like Müller glial cells in the INL became rounder but did not lose their ability to express SOX2. CONCLUSIONS Irradiated retina at 3 dpf of medaka embryos could be completely regenerated at 18 days after irradiation (21 dpf), although the abnormal layer structures bridging the INL and GCL were transiently formed in the retinas of all the irradiated embryos. Four days after irradiation, embryonic medaka Müller glia were reduced in number but maintained SOX2 expression as in nonirradiated embryos. This finding contrasts with previous reports that 8 dpf medaka larvae could not fully regenerate damaged retinas because of loss of SOX2 expression.
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Affiliation(s)
- Takako Yasuda
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan
| | - Takuya Nakazawa
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Kei Hirakawa
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Ikumi Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Kento Nagata
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
- Department of Radiation Effects Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Shunta Mori
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Kento Igarashi
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
- Department of Applied Pharmacology, Kagoshima University, Kagoshima, Japan
| | - Hiroshi Sagara
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shoji Oda
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
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20
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Okoye O, Capasso J, Kopinsky SM, Amlie-Wolf L, Levin AV, Schneider A. SOX2 pathogenic variants with normal eyes: Expanding the phenotypic spectrum. Am J Med Genet A 2023; 191:2198-2203. [PMID: 37163579 DOI: 10.1002/ajmg.a.63239] [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: 02/01/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023]
Abstract
SOX2 pathogenic variants, though rare, constitute the most commonly known genetic cause of clinical anophthalmia and microphthalmia. However, patients without major ocular malformation, but with multi-system developmental disorders, have been reported, suggesting that the range of clinical phenotypes is broader than previously appreciated. We detail two patients with bilateral structurally normal eyes along with 11 other previously published patients. Our findings suggest that there is no obvious phenotypic or genotypic pattern that may help set apart patients with normal eyes. Our patients provide further evidence for broadening the phenotypic spectrum of SOX2 mutations and re-appraising the designation of SOX2 disorder as an anophthalmia/microphthalmia syndrome. We emphasize the importance of considering SOX2 pathogenic variants in the differential diagnoses of individuals with normal eyes, who may have varying combinations of features such as developmental delay, urogenital abnormalities, gastro-intestinal anomalies, pituitary dysfunction, midline structural anomalies, and complex movement disorders, seizures or other neurological issues.
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Affiliation(s)
- Onochie Okoye
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, University of Rochester, New York, New York, USA
- Department of Ophthalmology, University of Nigeria Teaching Hospital, Enugu, Nigeria
| | - Jenina Capasso
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, University of Rochester, New York, New York, USA
- Pediatric Genetics, Golisano Children's Hospital, University of Rochester, Rochester, New York, USA
| | | | | | - Alex V Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, University of Rochester, New York, New York, USA
- Pediatric Genetics, Golisano Children's Hospital, University of Rochester, Rochester, New York, USA
| | - Adele Schneider
- Department of Pediatrics, Wills Eye Hospital, Philadelphia, Pennsylvania, USA
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21
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Wei J, Dai S, Yan Y, Li S, Yang P, Zhu R, Huang T, Li X, Duan Y, Wang Z, Ji W, Si W. Spatiotemporal proteomic atlas of multiple brain regions across early fetal to neonatal stages in cynomolgus monkey. Nat Commun 2023; 14:3917. [PMID: 37400444 PMCID: PMC10317979 DOI: 10.1038/s41467-023-39411-7] [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: 10/14/2022] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
Fetal stages are critical periods for brain development. However, the protein molecular signature and dynamics of the human brain remain unclear due to sampling difficulty and ethical limitations. Non-human primates present similar developmental and neuropathological features to humans. This study constructed a spatiotemporal proteomic atlas of cynomolgus macaque brain development from early fetal to neonatal stages. Here we showed that (1) the variability across stages was greater than that among brain regions, and comparisons of cerebellum vs. cerebrum and cortical vs. subcortical regions revealed region-specific dynamics across early fetal to neonatal stages; (2) fluctuations in abundance of proteins associated with neural disease suggest the risk of nervous disorder at early fetal stages; (3) cross-species analysis (human, monkey, and mouse) and comparison between proteomic and transcriptomic data reveal the proteomic specificity and genes with mRNA/protein discrepancy. This study provides insight into fetal brain development in primates.
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Affiliation(s)
- Jingkuan Wei
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Shaoxing Dai
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Yaping Yan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Shulin Li
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
| | - Pengpeng Yang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
| | - Ran Zhu
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
| | - Tianzhuang Huang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Xi Li
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Yanchao Duan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Zhengbo Wang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China.
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China.
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China.
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China.
- Chinese Primate Biomedical Research Alliance (CPBRA), 650500, Kunming, Yunnan, China.
| | - Wei Si
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China.
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China.
- Chinese Primate Biomedical Research Alliance (CPBRA), 650500, Kunming, Yunnan, China.
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22
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Shim S, Goyal R, Panoutsopoulos AA, Balashova OA, Lee D, Borodinsky LN. Calcium dynamics at the neural cell primary cilium regulate Hedgehog signaling-dependent neurogenesis in the embryonic neural tube. Proc Natl Acad Sci U S A 2023; 120:e2220037120. [PMID: 37252980 PMCID: PMC10266006 DOI: 10.1073/pnas.2220037120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/18/2023] [Indexed: 06/01/2023] Open
Abstract
The balance between neural stem cell proliferation and neuronal differentiation is paramount for the appropriate development of the nervous system. Sonic hedgehog (Shh) is known to sequentially promote cell proliferation and specification of neuronal phenotypes, but the signaling mechanisms responsible for the developmental switch from mitogenic to neurogenic have remained unclear. Here, we show that Shh enhances Ca2+ activity at the neural cell primary cilium of developing Xenopus laevis embryos through Ca2+ influx via transient receptor potential cation channel subfamily C member 3 (TRPC3) and release from intracellular stores in a developmental stage-dependent manner. This ciliary Ca2+ activity in turn antagonizes canonical, proliferative Shh signaling in neural stem cells by down-regulating Sox2 expression and up-regulating expression of neurogenic genes, enabling neuronal differentiation. These discoveries indicate that the Shh-Ca2+-dependent switch in neural cell ciliary signaling triggers the switch in Shh action from canonical-mitogenic to neurogenic. The molecular mechanisms identified in this neurogenic signaling axis are potential targets for the treatment of brain tumors and neurodevelopmental disorders.
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Affiliation(s)
- Sangwoo Shim
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Raman Goyal
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Alexios A. Panoutsopoulos
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Olga A. Balashova
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - David Lee
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
| | - Laura N. Borodinsky
- Department of Physiology and Membrane Biology, University of California Davis, Sacramento, CA95817
- Shriners Hospital for Children, University of California Davis, Sacramento, CA95817
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23
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Ferrena A, Zhang X, Shrestha R, Zheng D, Liu W. Six3 and Six6 jointly regulate the identities and developmental trajectories of multipotent retinal progenitor cells in the mouse retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539288. [PMID: 37205402 PMCID: PMC10187238 DOI: 10.1101/2023.05.03.539288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Formation, maintenance, and differentiation of tissue-specific progenitor cells are fundamental tasks during organogenesis. Retinal development is an excellent model for dissecting these processes; mechanisms of retinal differentiation can be harnessed for retinal regeneration toward curing blindness. Using single-cell RNA sequencing of embryonic mouse eye cups in which transcription factor Six3 was conditionally inactivated in peripheral retinas on top of germline deletion of its close paralog Six6 ("DKO"), we identified cell clusters and then inferred developmental trajectories in the integrated dataset. In control retinas, naïve retinal progenitor cells had two major trajectories leading to ciliary margin cells and retinal neurons, respectively. The ciliary margin trajectory was directly from naïve retinal progenitor cells at G1 phase, and the retinal neuron trajectory was through a neurogenic state marked by Atoh7 expression. Upon Six3 and Six6 dual deficiency, both naïve and neurogenic retinal progenitor cells were defective. Ciliary margin differentiation was enhanced, and multi-lineage retinal differentiation was disrupted. An ectopic neuronal trajectory lacking the Atoh7+ state led to ectopic neurons. Differential expression analysis not only confirmed previous phenotype studies but also identified novel candidate genes regulated by Six3/Six6 . Six3 and Six6 were jointly required for balancing the opposing gradients of the Fgf and Wnt signaling in the central-peripheral patterning of the eye cups. Taken together, we identify transcriptomes and developmental trajectories jointly regulated by Six3 and Six6, providing deeper insight into molecular mechanisms underlying early retinal differentiation.
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24
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Mercurio S. SOX2-Sensing: Insights into the Role of SOX2 in the Generation of Sensory Cell Types in Vertebrates. Int J Mol Sci 2023; 24:ijms24087637. [PMID: 37108798 PMCID: PMC10141063 DOI: 10.3390/ijms24087637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The SOX2 transcription factor is a key regulator of nervous system development, and its mutation in humans leads to a rare disease characterized by severe eye defects, cognitive defects, hearing defects, abnormalities of the CNS and motor control problems. SOX2 has an essential role in neural stem cell maintenance in specific regions of the brain, and it is one of the master genes required for the generation of induced pluripotent stem cells. Sox2 is expressed in sensory organs, and this review will illustrate how it regulates the differentiation of sensory cell types required for hearing, touching, tasting and smelling in vertebrates and, in particular, in mice.
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Affiliation(s)
- Sara Mercurio
- Department of Biotechnologies and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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25
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Xu Y, Li L, Shan J, Du L, Jin X, Zhou P. Extreme myopia is more susceptible to SOX2 gene than high myopia. Exp Eye Res 2023; 230:109435. [PMID: 36921835 DOI: 10.1016/j.exer.2023.109435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/10/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023]
Abstract
PURPOSE To explore the association between two single-nucleotide polymorphisms (SNPs) in the SOX2 gene and high and extreme myopia in the Han Chinese population. MATERIALS AND METHODS A genetic association study using a case-control method was performed with 139 high myopia, 318 extreme myopia, and 918 healthy participants from the Chinese Han population. Two SNPs (rs4459940 and rs4575941) near SOX2 gene were selected for genotyping. We compared the allelic frequencies and haplotypes of the SNPs to assess their association with high and extreme myopia. This study was adjusted for sex and age of participants in the groups. RESULT The mean ages of the extreme myopia and control subjects were 47.44 ± 15.59 and 44.15 ± 14.08 years, respectively. The rs4575941 SNP of the SOX2 gene and the GG and AG genotypes showed no significant association with the risk of high myopia as opposed to the AA genotype (GG, OR = 0.94, 95% CI = 0.55-1.60, P = 0.820, Pc = NS; AG, OR = 0.91, 95% CI = 0.54-1.52, P = 0.708, Pc = NS). However, the frequency of the risk G allele of rs4575941 was significantly higher in the extreme myopia group than in the control group (OR = 1.31, 95% CI = 1.08-1.59; P = 0.007; Pc = 0.014). Furthermore, there were significant differences in the GG genotype frequency between the extreme myopia and control groups (OR = 1.77, 95% CI = 1.45-2.74, P = 0.009, Pc = 0.036). The A-G haplotype frequency was higher in the extreme group (OR = 1.27, 95% CI = 1.05-1.55, P = 0.014), while there were no significant differences found in high myopia group (OR = 1.18, 95% CI = 0.77-1.31, P = 0.979). CONCLUSION The SOX2 rs4575941 polymorphism, in Chinese Han population, contributes to the susceptibility of extreme myopia. SOX2 may thus be implicated in extreme myopia rather than in high myopia.
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Affiliation(s)
- Youmei Xu
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Lin Li
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Jiankang Shan
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Liping Du
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Xuemin Jin
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China.
| | - Pengyi Zhou
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China.
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26
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Fujii Y, Arima M, Murakami Y, Sonoda KH. Rhodopsin-positive cell production by intravitreal injection of small molecule compounds in mouse models of retinal degeneration. PLoS One 2023; 18:e0282174. [PMID: 36821627 PMCID: PMC9949636 DOI: 10.1371/journal.pone.0282174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
We aimed to verify whether the intravitreal injection of small molecule compounds alone can create photoreceptor cells in mouse models of retinal degeneration. Primary cultured mouse Müller cells were stimulated in vitro with combinations of candidate compounds and the rhodopsin expression was measured on day 7 using polymerase chain reaction and immunostaining. We used 6-week-old N-methyl-N-nitrosourea-treated and 4-week-old rd10 mice as representative in vivo models of retinal degeneration. The optimal combination of compounds selected via in vitro screening was injected into the vitreous and the changes in rhodopsin expression were investigated on day 7 using polymerase chain reaction and immunostaining. The origin of rhodopsin-positive cells was also analyzed via lineage tracing and the recovery of retinal function was assessed using electroretinography. The in vitro mRNA expression of rhodopsin in Müller cells increased 30-fold, and 25% of the Müller cells expressed rhodopsin protein 7 days after stimulation with a combination of 4 compounds: transforming growth factor-β inhibitor, bone morphogenetic protein inhibitor, glycogen synthase kinase 3 inhibitor, and γ-secretase inhibitor. The in vivo rhodopsin mRNA expression and the number of rhodopsin-positive cells in the outer retina were significantly increased on day 7 after the intravitreal injection of these 4 compounds in both N-methyl-N-nitrosourea-treated and rd10 mice. Lineage tracing in td-Tomato mice treated with N-methyl-N-nitrosourea suggested that the rhodopsin-positive cells originated from endogenous Müller cells, accompanied with the recovery of the rhodopsin-derived scotopic function. It was suggested that rhodopsin-positive cells generated by compound stimulation contributes to the recovery of retinal function impaired by degeneration.
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Affiliation(s)
- Yuya Fujii
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsuru Arima
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan,Center for Clinical and Translational Research, Kyushu University Hospital, Fukuoka, Japan,* E-mail:
| | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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27
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Javed A, Santos-França PL, Mattar P, Cui A, Kassem F, Cayouette M. Ikaros family proteins redundantly regulate temporal patterning in the developing mouse retina. Development 2023; 150:286611. [PMID: 36537580 DOI: 10.1242/dev.200436] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Temporal identity factors regulate competence of neural progenitors to generate specific cell types in a time-dependent manner, but how they operate remains poorly defined. In the developing mouse retina, the Ikaros zinc-finger transcription factor Ikzf1 regulates production of early-born cell types, except cone photoreceptors. In this study we show that, during early stages of retinal development, another Ikaros family protein, Ikzf4, functions redundantly with Ikzf1 to regulate cone photoreceptor production. Using CUT&RUN and functional assays, we show that Ikzf4 binds and represses genes involved in late-born rod photoreceptor specification, hence favoring cone production. At late stages, when Ikzf1 is no longer expressed in progenitors, we show that Ikzf4 re-localizes to target genes involved in gliogenesis and is required for Müller glia production. We report that Ikzf4 regulates Notch signaling genes and is sufficient to activate the Hes1 promoter through two Ikzf GGAA-binding motifs, suggesting a mechanism by which Ikzf4 may influence gliogenesis. These results uncover a combinatorial role for Ikaros family members during nervous system development and provide mechanistic insights on how they temporally regulate cell fate output.
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Affiliation(s)
- Awais Javed
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
| | - Pedro L Santos-França
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
| | - Allie Cui
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
| | - Fatima Kassem
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 0G4, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 0G4, Canada
- Department of Medicine, Université de Montréal, Montreal H3T 1J4, Canada
- Department of Anatomy and Cell Biology, Division of Experimental Medicine, McGill University, Montreal H3A 0G4, Canada
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28
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Domingo-Muelas A, Morante-Redolat JM, Moncho-Amor V, Jordán-Pla A, Pérez-Villalba A, Carrillo-Barberà P, Belenguer G, Porlan E, Kirstein M, Bachs O, Ferrón SR, Lovell-Badge R, Fariñas I. The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2. Cell Mol Life Sci 2023; 80:36. [PMID: 36627412 PMCID: PMC9832098 DOI: 10.1007/s00018-022-04676-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 01/12/2023]
Abstract
Cell differentiation involves profound changes in global gene expression that often has to occur in coordination with cell cycle exit. Because cyclin-dependent kinase inhibitor p27 reportedly regulates proliferation of neural progenitor cells in the subependymal neurogenic niche of the adult mouse brain, but can also have effects on gene expression, we decided to molecularly analyze its role in adult neurogenesis and oligodendrogenesis. At the cell level, we show that p27 restricts residual cyclin-dependent kinase activity after mitogen withdrawal to antagonize cycling, but it is not essential for cell cycle exit. By integrating genome-wide gene expression and chromatin accessibility data, we find that p27 is coincidentally necessary to repress many genes involved in the transit from multipotentiality to differentiation, including those coding for neural progenitor transcription factors SOX2, OLIG2 and ASCL1. Our data reveal both a direct association of p27 with regulatory sequences in the three genes and an additional hierarchical relationship where p27 repression of Sox2 leads to reduced levels of its downstream targets Olig2 and Ascl1. In vivo, p27 is also required for the regulation of the proper level of SOX2 necessary for neuroblasts and oligodendroglial progenitor cells to timely exit cell cycle in a lineage-dependent manner.
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Affiliation(s)
- Ana Domingo-Muelas
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
- Department of Cell and Developmental Biology, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jose Manuel Morante-Redolat
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Verónica Moncho-Amor
- The Francis Crick Institute, London, NW1 1AT, UK
- IIS Biodonostia, 48013, Bilbao, Spain
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Ana Pérez-Villalba
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Pau Carrillo-Barberà
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
- Institute for Research in Biomedicine, 6500, Bellinzona, Switzerland
| | - Germán Belenguer
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Eva Porlan
- Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Instituto de Salud Carlos III, Madrid, Spain
| | - Martina Kirstein
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Oriol Bachs
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, Barcelona, Spain
| | - Sacri R Ferrón
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | | | - Isabel Fariñas
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain.
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain.
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29
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The Role of SOX Transcription Factors in Ageing and Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24010851. [PMID: 36614288 PMCID: PMC9821406 DOI: 10.3390/ijms24010851] [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: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
The quest for eternal youth and immortality is as old as humankind. Ageing is an inevitable physiological process accompanied by many functional declines that are driving factors for age-related diseases. Stem cell exhaustion is one of the major hallmarks of ageing. The SOX transcription factors play well-known roles in self-renewal and differentiation of both embryonic and adult stem cells. As a consequence of ageing, the repertoire of adult stem cells present in various organs steadily declines, and their dysfunction/death could lead to reduced regenerative potential and development of age-related diseases. Thus, restoring the function of aged stem cells, inducing their regenerative potential, and slowing down the ageing process are critical for improving the health span and, consequently, the lifespan of humans. Reprograming factors, including SOX family members, emerge as crucial players in rejuvenation. This review focuses on the roles of SOX transcription factors in stem cell exhaustion and age-related diseases, including neurodegenerative diseases, visual deterioration, chronic obstructive pulmonary disease, osteoporosis, and age-related cancers. A better understanding of the molecular mechanisms of ageing and the roles of SOX transcription factors in this process could open new avenues for developing novel strategies that will delay ageing and prevent age-related diseases.
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Wang Y, Zhang S, Lan Z, Doan V, Kim B, Liu S, Zhu M, Hull VL, Rihani S, Zhang CL, Gray JA, Guo F. SOX2 is essential for astrocyte maturation and its deletion leads to hyperactive behavior in mice. Cell Rep 2022; 41:111842. [PMID: 36543123 PMCID: PMC9875714 DOI: 10.1016/j.celrep.2022.111842] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 09/23/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
Children with SOX2 deficiency develop ocular disorders and extra-ocular CNS anomalies. Animal data show that SOX2 is essential for retinal and neural stem cell development. In the CNS parenchyma, SOX2 is primarily expressed in astroglial and oligodendroglial cells. Here, we report a crucial role of astroglial SOX2 in postnatal brain development. Astroglial Sox2-deficient mice develop hyperactivity in locomotion and increased neuronal excitability in the corticostriatal circuit. Sox2 deficiency inhibits postnatal astrocyte maturation molecularly, morphologically, and electrophysiologically without affecting astroglia proliferation. Mechanistically, SOX2 directly binds to a cohort of astrocytic signature and functional genes, the expression of which is significantly reduced in Sox2-deficient CNS and astrocytes. Consistently, Sox2 deficiency remarkably reduces glutamate transporter expression and compromised astrocyte function of glutamate uptake. Our study provides insights into the cellular mechanisms underlying brain defects in children with SOX2 mutations and suggests a link of astrocyte SOX2 with extra-ocular abnormalities in SOX2-mutant subjects.
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Affiliation(s)
- Yan Wang
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Sheng Zhang
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Zhaohui Lan
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Vui Doan
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA
| | - Bokyung Kim
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Sihan Liu
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Meina Zhu
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Vanessa L Hull
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Sami Rihani
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Chun-Li Zhang
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John A Gray
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - Fuzheng Guo
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA.
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Napoli FR, Daly CM, Neal S, McCulloch KJ, Zaloga AR, Liu A, Koenig KM. Cephalopod retinal development shows vertebrate-like mechanisms of neurogenesis. Curr Biol 2022; 32:5045-5056.e3. [PMID: 36356573 PMCID: PMC9729453 DOI: 10.1016/j.cub.2022.10.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022]
Abstract
Coleoid cephalopods, including squid, cuttlefish, and octopus, have large and complex nervous systems and high-acuity, camera-type eyes. These traits are comparable only to features that are independently evolved in the vertebrate lineage. The size of animal nervous systems and the diversity of their constituent cell types is a result of the tight regulation of cellular proliferation and differentiation in development. Changes in the process of development during evolution that result in a diversity of neural cell types and variable nervous system size are not well understood. Here, we have pioneered live-imaging techniques and performed functional interrogation to show that the squid Doryteuthis pealeii utilizes mechanisms during retinal neurogenesis that are hallmarks of vertebrate processes. We find that retinal progenitor cells in the squid undergo nuclear migration until they exit the cell cycle. We identify retinal organization corresponding to progenitor, post-mitotic, and differentiated cells. Finally, we find that Notch signaling may regulate both retinal cell cycle and cell fate. Given the convergent evolution of elaborate visual systems in cephalopods and vertebrates, these results reveal common mechanisms that underlie the growth of highly proliferative neurogenic primordia. This work highlights mechanisms that may alter ontogenetic allometry and contribute to the evolution of complexity and growth in animal nervous systems.
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Affiliation(s)
- Francesca R Napoli
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Christina M Daly
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Stephanie Neal
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Kyle J McCulloch
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Alexandra R Zaloga
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Alicia Liu
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Kristen M Koenig
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA.
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Kandoi S, Martinez C, Merriman DK, Lamba DA. Characterization of Retinal Development in 13-Lined Ground Squirrels. Transl Vis Sci Technol 2022; 11:17. [DOI: 10.1167/tvst.11.11.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Sangeetha Kandoi
- Department of Ophthalmology, UCSF Medical Center, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Martinez
- Department of Ophthalmology, UCSF Medical Center, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Dana K. Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Deepak A. Lamba
- Department of Ophthalmology, UCSF Medical Center, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
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Sox2 in the dermal papilla regulates hair follicle pigmentation. Cell Rep 2022; 40:111100. [PMID: 35858560 DOI: 10.1016/j.celrep.2022.111100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 04/15/2022] [Accepted: 06/23/2022] [Indexed: 12/18/2022] Open
Abstract
Within the hair follicle (HF) niche, dermal papilla (DP) cells are well known for the hair induction capacity; however, DP cell signaling also regulates HF pigmentation. Here we describe how Sox2 in the DP is a key regulator of melanocyte signaling. To study the largely unknown regulatory role the DP has on hair pigmentation, we characterize leptin receptor (Lepr) expression in the skin and as a genetic tool to target the DP. Sox2 ablation in the DP results in a phenotypic switch from eumelanin to pheomelanin. Mechanistically, we describe a temporal upregulation of Agouti and downregulation of Corin, directly by Sox2 in the DP. We also show that bone morphogenic protein (BMP) signaling regulation by Sox2 is responsible for downregulating MC1R, Dct, and Tyr in melanocytes of Sox2 cKO mice. Thus, we demonstrate that Sox2 in the DP regulates not only the choice of hair pigment but also the overall HF pigment production.
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Hagey DW, Bergsland M, Muhr J. SOX2 transcription factor binding and function. Development 2022; 149:276045. [DOI: 10.1242/dev.200547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The transcription factor SOX2 is a vital regulator of stem cell activity in various developing and adult tissues. Mounting evidence has demonstrated the importance of SOX2 in regulating the induction and maintenance of stemness as well as in controlling cell proliferation, lineage decisions and differentiation. Recent studies have revealed that the ability of SOX2 to regulate these stem cell features involves its function as a pioneer factor, with the capacity to target nucleosomal DNA, modulate chromatin accessibility and prepare silent genes for subsequent activation. Moreover, although SOX2 binds to similar DNA motifs in different stem cells, its multifaceted and cell type-specific functions are reliant on context-dependent features. These cell type-specific properties include variations in partner factor availability and SOX2 protein expression levels. In this Primer, we discuss recent findings that have increased our understanding of how SOX2 executes its versatile functions as a master regulator of stem cell activities.
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Affiliation(s)
- Daniel W. Hagey
- Karolinska Institutet 1 Department of Laboratory Medicine , , SE-171 77 Stockholm , Sweden
| | - Maria Bergsland
- Karolinska Institutet 2 Department of Cell and Molecular Biology , , Solnavägen 9, SE-171 65 Stockholm , Sweden
| | - Jonas Muhr
- Karolinska Institutet 2 Department of Cell and Molecular Biology , , Solnavägen 9, SE-171 65 Stockholm , Sweden
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Radial Glia and Neuronal-like Ependymal Cells Are Present within the Spinal Cord of the Trunk (Body) in the Leopard Gecko (Eublepharis macularius). J Dev Biol 2022; 10:jdb10020021. [PMID: 35735912 PMCID: PMC9224675 DOI: 10.3390/jdb10020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022] Open
Abstract
As is the case for many lizards, leopard geckos (Eublepharis macularius) can self-detach a portion of their tail to escape predation, and then regenerate a replacement complete with a spinal cord. Previous research has shown that endogenous populations of neural stem/progenitor cells (NSPCs) reside within the spinal cord of the original tail. In response to tail loss, these NSPCs are activated and contribute to regeneration. Here, we investigate whether similar populations of NSPCs are found within the spinal cord of the trunk (body). Using a long-duration 5-bromo-2′-deoxyuridine pulse-chase experiment, we determined that a population of cells within the ependymal layer are label-retaining following a 20-week chase. Tail loss does not significantly alter rates of ependymal cell proliferation within the trunk spinal cord. Ependymal cells of the trunk spinal cord express SOX2 and represent at least two distinct cell populations: radial glial-like (glial fibrillary acidic protein- and Vimentin-expressing) cells; and neuronal-like (HuCD-expressing) cells. Taken together, these data demonstrate that NSPCs of the trunk spinal cord closely resemble those of the tail and support the use of the tail spinal cord as a less invasive proxy for body spinal cord injury investigations.
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Mercurio S, Serra L, Pagin M, Nicolis SK. Deconstructing Sox2 Function in Brain Development and Disease. Cells 2022; 11:cells11101604. [PMID: 35626641 PMCID: PMC9139651 DOI: 10.3390/cells11101604] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
SOX2 is a transcription factor conserved throughout vertebrate evolution, whose expression marks the central nervous system from the earliest developmental stages. In humans, SOX2 mutation leads to a spectrum of CNS defects, including vision and hippocampus impairments, intellectual disability, and motor control problems. Here, we review how conditional Sox2 knockout (cKO) in mouse with different Cre recombinases leads to very diverse phenotypes in different regions of the developing and postnatal brain. Surprisingly, despite the widespread expression of Sox2 in neural stem/progenitor cells of the developing neural tube, some regions (hippocampus, ventral forebrain) appear much more vulnerable than others to Sox2 deletion. Furthermore, the stage of Sox2 deletion is also a critical determinant of the resulting defects, pointing to a stage-specificity of SOX2 function. Finally, cKOs illuminate the importance of SOX2 function in different cell types according to the different affected brain regions (neural precursors, GABAergic interneurons, glutamatergic projection neurons, Bergmann glia). We also review human genetics data regarding the brain defects identified in patients carrying mutations within human SOX2 and examine the parallels with mouse mutants. Functional genomics approaches have started to identify SOX2 molecular targets, and their relevance for SOX2 function in brain development and disease will be discussed.
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Aygun H, Akin AT, Kızılaslan N, Sumbul O, Karabulut D. Probiotic supplementation alleviates absence seizures and anxiety- and depression-like behavior in WAG/Rij rat by increasing neurotrophic factors and decreasing proinflammatory cytokines. Epilepsy Behav 2022; 128:108588. [PMID: 35152169 DOI: 10.1016/j.yebeh.2022.108588] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 01/15/2023]
Abstract
AIM Epilepsy is one of the most common chronic brain disorders that affect millions of people worldwide. In the present study, we investigated the effects of probiotic supplementation on absence epilepsy and anxiety-and depression-like behavior in WAG/Rij rats. MATERIAL AND METHOD Fourteen male WAG/Rij rats (absence-epileptic) and seven male Wistar rats (nonepileptic) were used. The effects of probiotic VSL#3 (12.86 bn living bacteria/kg/day for 30 day/gavage) on absence seizures, and related psychiatric comorbidities were evaluated in WAG/Rij rats. Anxiety-like behavior was evaluated by the open-field test and depression-like behavior by the forced swimming test. In addition, the brain tissues of rats were evaluated histopathologically for nerve growth factor [NGF], brain-derived neurotrophic factor [BDNF], SRY sex-determining region Y-box 2 [SOX2] and biochemically for nitric oxide [NO], tumor necrosis factor-alpha [TNF-α] ,and Interleukin-6 [IL-6]. RESULTS Compared to Wistar rats, WAG/Rij rats exhibited anxiety- and depression-like behavior, and had lower BDNF, NGF and SOX2 immunoreactivity, and higher TNF-α, IL-6 levels in brain tissue. VSL#3 supplementation reduced the duration and number of spike-wave discharges (SWDs) and exhibited anxiolytic or anti-depressive effect. VSL#3 supplement also increased the NGF immunoreactivity while decreasing IL-6, TNF-α and NO levels in WAG/Rij rat brain. CONCLUSION The findings of the present study showed that neurotrophins, SOX2 deficiency, and pro-inflammatory cytokines may play a role in the pathogenesis of absence epilepsy. Our data support the hypothesis that the probiotics have anti-inflammatory effect. The present study is the first to show the positive effects of probiotic bacteria on absence seizures and anxiety- and depression-like behavior.
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Affiliation(s)
- Hatice Aygun
- Department of Physiology, Faculty of Medicine, University of Tokat Gaziosmanpasa, Tokat, Turkey.
| | - Ali Tugrul Akin
- Department of Biology, Faculty of Science and Literature, University of Erciyes, Kayseri, Turkey
| | - Nildem Kızılaslan
- Department of Nutrition and Dietetics, Faculty of Health Sciences, University of Tokat Gaziosmanpasa Tokat, Turkey
| | - Orhan Sumbul
- Department of Neurology Faculty of Medicine University of Tokat Gaziosmanpasa, Tokat, Turkey
| | - Derya Karabulut
- Department of Histology-Embryology, Faculty of Medicine, University of Erciyes, Kayseri, Turkey
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38
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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39
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Aghanoori MR, Burns KM, Subha M, Williams L, Hua M, Nobakht F, Krawec T, Yang G. Immunohistochemical analysis of the developing mouse cortex. Methods Cell Biol 2022; 170:31-46. [DOI: 10.1016/bs.mcb.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Co-activation of Sonic hedgehog and Wnt signaling in murine retinal precursor cells drives ocular lesions with features of intraocular medulloepithelioma. Oncogenesis 2021; 10:78. [PMID: 34785636 PMCID: PMC8595639 DOI: 10.1038/s41389-021-00369-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
Intraocular medulloepithelioma (IO-MEPL) is a rare embryonal ocular neoplasm, prevalently occurring in children. IO-MEPLs share histomorphological features with CNS embryonal tumors with multilayered rosettes (ETMRs), referred to as intracranial medulloepitheliomas. While Sonic hedgehog (SHH) and WNT signaling pathways are crucial for ETMR pathogenesis, the impact of these pathways on human IO-MEPL development is unclear. Gene expression analyses of human embryonal tumor samples revealed similar gene expression patterns and significant overrepresentation of SHH and WNT target genes in both IO-MEPL and ETMR. In order to unravel the function of Shh and Wnt signaling for IO-MEPL pathogenesis in vivo, both pathways were activated in retinal precursor cells in a time point specific manner. Shh and Wnt co-activation in early Sox2- or Rax-expressing precursor cells resulted in infiltrative ocular lesions that displayed extraretinal expansion. Histomorphological, immunohistochemical, and molecular features showed a strong concordance with human IO-MEPL. We demonstrate a relevant role of WNT and SHH signaling in IO-MEPL and report the first mouse model to generate tumor-like lesions with features of IO-MEPL. The presented data may be fundamental for comprehending IO-MEPL initiation and developing targeted therapeutic approaches.
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Lyu P, Hoang T, Santiago CP, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza DF, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, Blackshaw S. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina. Cell Rep 2021; 37:109994. [PMID: 34788628 PMCID: PMC8642835 DOI: 10.1016/j.celrep.2021.109994] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. These GRNs control temporal patterning in primary progenitors, regulate transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. This study inventories cis- and trans-acting factors that control retinal development and can guide cell-based therapies aimed at replacing retinal neurons lost to disease.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric D Thomas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Haley Appel
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Megan Gimmen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nguyet Le
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dong Won Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Siqi Chen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David F Espinoza
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ariel E Telger
- Department of Ophthalmology and Visual Sciences, Brotman Baty Institute, Seattle, WA 98195, USA
| | - Kurt Weir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Brian S Clark
- Department of Ophthalmology and Visual Sciences, Brotman Baty Institute, Seattle, WA 98195, USA; Brotman Baty Institute, Seattle, WA 98195, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy J Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute, Seattle, WA 98195, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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42
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Daghsni M, Aldiri I. Building a Mammalian Retina: An Eye on Chromatin Structure. Front Genet 2021; 12:775205. [PMID: 34764989 PMCID: PMC8576187 DOI: 10.3389/fgene.2021.775205] [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: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression by chromatin structure has been under intensive investigation, establishing nuclear organization and genome architecture as a potent and effective means of regulating developmental processes. The substantial growth in our knowledge of the molecular mechanisms underlying retinogenesis has been powered by several genome-wide based tools that mapped chromatin organization at multiple cellular and biochemical levels. Studies profiling the retinal epigenome and transcriptome have allowed the systematic annotation of putative cis-regulatory elements associated with transcriptional programs that drive retinal neural differentiation, laying the groundwork to understand spatiotemporal retinal gene regulation at a mechanistic level. In this review, we outline recent advances in our understanding of the chromatin architecture in the mammalian retina during development and disease. We focus on the emerging roles of non-coding regulatory elements in controlling retinal cell-type specific transcriptional programs, and discuss potential implications in untangling the etiology of eye-related disorders.
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Affiliation(s)
- Marwa Daghsni
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Issam Aldiri
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, United States
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43
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Lourenço R, Brandão AS, Borbinha J, Gorgulho R, Jacinto A. Yap Regulates Müller Glia Reprogramming in Damaged Zebrafish Retinas. Front Cell Dev Biol 2021; 9:667796. [PMID: 34616723 PMCID: PMC8488126 DOI: 10.3389/fcell.2021.667796] [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: 02/14/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
Vertebrates such as zebrafish have the outstanding ability to fully regenerate their retina upon injury, while mammals, including humans, do not. In zebrafish, upon light-induced injury, photoreceptor regeneration is achieved through reprogramming of Müller glia cells, which proliferate and give rise to a self-renewing population of progenitors that migrate to the lesion site to differentiate into the new photoreceptors. The Hippo pathway effector YAP was recently implicated in the response to damage in the retina, but how this transcription coactivator is integrated into the signaling network regulating Müller glia reprogramming has not yet been explored. Here, we show that Yap is required in Müller glia to engage their response to a lesion by regulating their cell cycle reentry and progenitor cell formation, contributing to the differentiation of new photoreceptors. We propose that this regulation is accomplished through a lin28a–ascl1a-dependent mechanism, bona fide Müller glia-reprogramming factors. Overall, this study presents Yap as a key regulator of zebrafish Müller glia reprogramming and consequently retina regeneration upon injury.
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Affiliation(s)
- Raquel Lourenço
- Chronic Diseases Research Centre (CEDOC), NOVA Medical School, NOVA University of Lisbon, Lisboa, Portugal
| | - Ana S Brandão
- Chronic Diseases Research Centre (CEDOC), NOVA Medical School, NOVA University of Lisbon, Lisboa, Portugal
| | - Jorge Borbinha
- Chronic Diseases Research Centre (CEDOC), NOVA Medical School, NOVA University of Lisbon, Lisboa, Portugal
| | - Rita Gorgulho
- Chronic Diseases Research Centre (CEDOC), NOVA Medical School, NOVA University of Lisbon, Lisboa, Portugal
| | - António Jacinto
- Chronic Diseases Research Centre (CEDOC), NOVA Medical School, NOVA University of Lisbon, Lisboa, Portugal
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Features of Retinal Neurogenesis as a Key Factor of Age-Related Neurodegeneration: Myth or Reality? Int J Mol Sci 2021; 22:ijms22147373. [PMID: 34298993 PMCID: PMC8303671 DOI: 10.3390/ijms22147373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex multifactorial neurodegenerative disease that constitutes the most common cause of irreversible blindness in the elderly in the developed countries. Incomplete knowledge about its pathogenesis prevents the search for effective methods of prevention and treatment of AMD, primarily of its "dry" type which is by far the most common (90% of all AMD cases). In the recent years, AMD has become "younger": late stages of the disease are now detected in relatively young people. It is known that AMD pathogenesis-according to the age-related structural and functional changes in the retina-is linked with inflammation, hypoxia, oxidative stress, mitochondrial dysfunction, and an impairment of neurotrophic support, but the mechanisms that trigger the conversion of normal age-related changes to the pathological process as well as the reason for early AMD development remain unclear. In the adult mammalian retina, de novo neurogenesis is very limited. Therefore, the structural and functional features that arise during its maturation and formation can exert long-term effects on further ontogenesis of this tissue. The aim of this review was to discuss possible contributions of the changes/disturbances in retinal neurogenesis to the early development of AMD.
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Dash S, Brastrom LK, Patel SD, Scott CA, Slusarski DC, Lachke SA. The master transcription factor SOX2, mutated in anophthalmia/microphthalmia, is post-transcriptionally regulated by the conserved RNA-binding protein RBM24 in vertebrate eye development. Hum Mol Genet 2021; 29:591-604. [PMID: 31814023 DOI: 10.1093/hmg/ddz278] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/24/2019] [Accepted: 11/10/2019] [Indexed: 11/14/2022] Open
Abstract
Mutations in the key transcription factor, SOX2, alone account for 20% of anophthalmia (no eye) and microphthalmia (small eye) birth defects in humans-yet its regulation is not well understood, especially on the post-transcription level. We report the unprecedented finding that the conserved RNA-binding motif protein, RBM24, positively controls Sox2 mRNA stability and is necessary for optimal SOX2 mRNA and protein levels in development, perturbation of which causes ocular defects, including microphthalmia and anophthalmia. RNA immunoprecipitation assay indicates that RBM24 protein interacts with Sox2 mRNA in mouse embryonic eye tissue. and electrophoretic mobility shift assay shows that RBM24 directly binds to the Sox2 mRNA 3'UTR, which is dependent on AU-rich elements (ARE) present in the Sox2 mRNA 3'UTR. Further, we demonstrate that Sox2 3'UTR AREs are necessary for RBM24-based elevation of Sox2 mRNA half-life. We find that this novel RBM24-Sox2 regulatory module is essential for early eye development in vertebrates. We show that Rbm24-targeted deletion using a constitutive CMV-driven Cre in mouse, and rbm24a-CRISPR/Cas9-targeted mutation or morpholino knockdown in zebrafish, results in Sox2 downregulation and causes the developmental defects anophthalmia or microphthalmia, similar to human SOX2-deficiency defects. We further show that Rbm24 deficiency leads to apoptotic defects in mouse ocular tissue and downregulation of eye development markers Lhx2, Pax6, Jag1, E-cadherin and gamma-crystallins. These data highlight the exquisite specificity that conserved RNA-binding proteins like RBM24 mediate in the post-transcriptional control of key transcription factors, namely, SOX2, associated with organogenesis and human developmental defects.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Lindy K Brastrom
- Department of Biology, University of Iowa, Iowa City, IA 52242 USA
| | - Shaili D Patel
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - C Anthony Scott
- Department of Biology, University of Iowa, Iowa City, IA 52242 USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716 USA
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Golden EJ, Larson ED, Shechtman LA, Trahan GD, Gaillard D, Fellin TJ, Scott JK, Jones KL, Barlow LA. Onset of taste bud cell renewal starts at birth and coincides with a shift in SHH function. eLife 2021; 10:64013. [PMID: 34009125 PMCID: PMC8172241 DOI: 10.7554/elife.64013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
Embryonic taste bud primordia are specified as taste placodes on the tongue surface and differentiate into the first taste receptor cells (TRCs) at birth. Throughout adult life, TRCs are continually regenerated from epithelial progenitors. Sonic hedgehog (SHH) signaling regulates TRC development and renewal, repressing taste fate embryonically, but promoting TRC differentiation in adults. Here, using mouse models, we show TRC renewal initiates at birth and coincides with onset of SHHs pro-taste function. Using transcriptional profiling to explore molecular regulators of renewal, we identified Foxa1 and Foxa2 as potential SHH target genes in lingual progenitors at birth and show that SHH overexpression in vivo alters FoxA1 and FoxA2 expression relevant to taste buds. We further bioinformatically identify genes relevant to cell adhesion and cell locomotion likely regulated by FOXA1;FOXA2 and show that expression of these candidates is also altered by forced SHH expression. We present a new model where SHH promotes TRC differentiation by regulating changes in epithelial cell adhesion and migration.
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Affiliation(s)
- Erin J Golden
- Department of Cell & Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,The Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Eric D Larson
- The Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States.,Department of Otolaryngology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Lauren A Shechtman
- Department of Cell & Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,The Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - G Devon Trahan
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Dany Gaillard
- Department of Cell & Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,The Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Timothy J Fellin
- Department of Cell & Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,The Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Jennifer K Scott
- Department of Cell & Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,The Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Linda A Barlow
- Department of Cell & Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,The Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States
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Ciccarelli A, Weijers D, Kwan W, Warner C, Bourne J, Gross CT. Sexually dimorphic perineuronal nets in the rodent and primate reproductive circuit. J Comp Neurol 2021; 529:3274-3291. [PMID: 33950531 DOI: 10.1002/cne.25167] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 12/21/2022]
Abstract
Perineuronal nets are extracellular glycoprotein structures that have been found on some neurons in the central nervous system and that have been shown to regulate their structural plasticity. Until now work on perineuronal nets has been focused on their role in cortical structures where they are selectively expressed on parvalbumin-positive neurons and are reported to restrict the experience-dependent plasticity of inhibitory afferents. Here, we examined the expression of perineuronal nets subcortically, showing that they are expressed in several discrete structures, including nuclei that comprise the brain network controlling reproductive behaviors (e.g., mounting, lordosis, aggression, and social defense). In particular, perineuronal nets were found in the posterior dorsal division of the medial amygdala, the medial preoptic nucleus, the posterior medial bed nucleus of the stria terminalis, the ventrolateral ventromedial hypothalamus and adjacent tuberal nucleus, and the ventral premammillary nucleus in both the mouse and primate brain. Comparison of perineuronal nets in male and female mice revealed a significant sexually dimorphic expression, with expression found prominently on estrogen receptor expressing neurons in the medial amygdala. These findings suggest that perineuronal nets may be involved in regulating neural plasticity in the mammalian reproductive system.
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Affiliation(s)
- Alessandro Ciccarelli
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Rome
| | - Dilys Weijers
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Rome
| | - William Kwan
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Claire Warner
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - James Bourne
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Cornelius T Gross
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Rome
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48
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Lyu J, Mu X. Genetic control of retinal ganglion cell genesis. Cell Mol Life Sci 2021; 78:4417-4433. [PMID: 33782712 DOI: 10.1007/s00018-021-03814-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/27/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
Retinal ganglion cells (RGCs) are the only projection neurons in the neural retina. They receive and integrate visual signals from upstream retinal neurons in the visual circuitry and transmit them to the brain. The function of RGCs is performed by the approximately 40 RGC types projecting to various central brain targets. RGCs are the first cell type to form during retinogenesis. The specification and differentiation of the RGC lineage is a stepwise process; a hierarchical gene regulatory network controlling the RGC lineage has been identified and continues to be elaborated. Recent studies with single-cell transcriptomics have led to unprecedented new insights into their types and developmental trajectory. In this review, we summarize our current understanding of the functions and relationships of the many regulators of the specification and differentiation of the RGC lineage. We emphasize the roles of these key transcription factors and pathways in different developmental steps, including the transition from retinal progenitor cells (RPCs) to RGCs, RGC differentiation, generation of diverse RGC types, and central projection of the RGC axons. We discuss critical issues that remain to be addressed for a comprehensive understanding of these different aspects of RGC genesis and emerging technologies, including single-cell techniques, novel genetic tools and resources, and high-throughput genome editing and screening assays, which can be leveraged in future studies.
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Affiliation(s)
- Jianyi Lyu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA.
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Wu F, Bard JE, Kann J, Yergeau D, Sapkota D, Ge Y, Hu Z, Wang J, Liu T, Mu X. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nat Commun 2021; 12:1465. [PMID: 33674582 PMCID: PMC7935890 DOI: 10.1038/s41467-021-21704-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Atoh7 has been believed to be essential for establishing the retinal ganglion cell (RGC) lineage, and Pou4f2 and Isl1 are known to regulate RGC specification and differentiation. Here we report our further study of the roles of these transcription factors. Using bulk RNA-seq, we identify genes regulated by the three transcription factors, which expand our understanding of the scope of downstream events. Using scRNA-seq on wild-type and mutant retinal cells, we reveal a transitional cell state of retinal progenitor cells (RPCs) co-marked by Atoh7 and other genes for different lineages and shared by all early retinal lineages. We further discover the unexpected emergence of the RGC lineage in the absence of Atoh7. We conclude that competence of RPCs for different retinal fates is defined by lineage-specific genes co-expressed in the transitional state and that Atoh7 defines the RGC competence and collaborates with other factors to shepherd transitional RPCs to the RGC lineage.
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Affiliation(s)
- Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jonathan E Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Julien Kann
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Zihua Hu
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA.
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA.
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50
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Bosch i Ara L, Katugampola H, Dattani MT. Congenital Hypopituitarism During the Neonatal Period: Epidemiology, Pathogenesis, Therapeutic Options, and Outcome. Front Pediatr 2021; 8:600962. [PMID: 33634051 PMCID: PMC7902025 DOI: 10.3389/fped.2020.600962] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction: Congenital hypopituitarism (CH) is characterized by a deficiency of one or more pituitary hormones. The pituitary gland is a central regulator of growth, metabolism, and reproduction. The anterior pituitary produces and secretes growth hormone (GH), adrenocorticotropic hormone, thyroid-stimulating hormone, follicle-stimulating hormone, luteinizing hormone, and prolactin. The posterior pituitary hormone secretes antidiuretic hormone and oxytocin. Epidemiology: The incidence is 1 in 4,000-1 in 10,000. The majority of CH cases are sporadic; however, a small number of familial cases have been identified. In the latter, a molecular basis has frequently been identified. Between 80-90% of CH cases remain unsolved in terms of molecular genetics. Pathogenesis: Several transcription factors and signaling molecules are involved in the development of the pituitary gland. Mutations in any of these genes may result in CH including HESX1, PROP1, POU1F1, LHX3, LHX4, SOX2, SOX3, OTX2, PAX6, FGFR1, GLI2, and FGF8. Over the last 5 years, several novel genes have been identified in association with CH, but it is likely that many genes remain to be identified, as the majority of patients with CH do not have an identified mutation. Clinical manifestations: Genotype-phenotype correlations are difficult to establish. There is a high phenotypic variability associated with different genetic mutations. The clinical spectrum includes severe midline developmental disorders, hypopituitarism (in isolation or combined with other congenital abnormalities), and isolated hormone deficiencies. Diagnosis and treatment: Key investigations include MRI and baseline and dynamic pituitary function tests. However, dynamic tests of GH secretion cannot be performed in the neonatal period, and a diagnosis of GH deficiency may be based on auxology, MRI findings, and low growth factor concentrations. Once a hormone deficit is confirmed, hormone replacement should be started. If onset is acute with hypoglycaemia, cortisol deficiency should be excluded, and if identified this should be rapidly treated, as should TSH deficiency. This review aims to give an overview of CH including management of this complex condition.
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Affiliation(s)
- Laura Bosch i Ara
- Department of Paediatric Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Harshini Katugampola
- Department of Paediatric Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Mehul T. Dattani
- Department of Paediatric Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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