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Tang S, Janpoom S, Prasertlux S, Rongmung P, Ittarat W, Ratdee O, Khamnamtong B, Klinbunga S. Identification of pigmentation genes in skin, muscle and tail of a Thai-flag variety of Siamese fighting fish Betta splendens. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101243. [PMID: 38749208 DOI: 10.1016/j.cbd.2024.101243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/27/2024]
Abstract
Pigmentation genes expressed in skin, body muscle and tail of Thai-flag compared with Blue, White and Red varieties of Siamese fighting fish Betta splendens were identified. In total, 22,919 new unigenes were found. Pearson correlation and PCA analysis revealed that expression profiles of genes in muscle, skin and tail across solid color variety were similar. In contrast, those in skin and red tail part of Thai-flag were closely related but they showed different expression profiles with the white tail part. Moreover, 21,347-64,965 SNPs were identified in exonic regions of identified genes. In total, 28,899 genes were differentially expressed between paired comparisons of libraries where 13,907 genes (48.12 %) were upregulated and 14,992 genes (51.88 %) were downregulated. DEGs between paired libraries were 106-5775 genes relative to the compared libraries (56-2982 and 50-2782 for upregulated and downregulated DEGs). Interestingly, 432 pigmentation genes of B. splendens were found. Of these, 297 DEGs showed differential expression between varieties. Many DEGs in melanogenesis (Bsmcr1r, Bsmcr5r, and Bsslc2a15b), tyrosine metabolism (Bstyr, Bstyrp1b and Bsdct), stripe repressor (BsAsip1 and BsAsip2b), pteridine (Bsgch2) and carotenoid (BsBco2) biosynthesis were downregulated in the Thai-flag compared with solid color varieties. Expression of Bsbco1l, Bsfrem2b, Bskcnj13, Bszic2a and Bspah in skin, muscle and tail of Thai-flag, Blue, Red and White varieties was analyzed by qRT-PCR and revealed differential expression between fish varieties and showed anatomical tissue-preferred expression patterns in the same fish variety. The information could be applied to assist genetic-based development of new B. splendens varieties in the future.
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Affiliation(s)
- Sureerat Tang
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sirithorn Janpoom
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sirikan Prasertlux
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Puttawan Rongmung
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wanwipa Ittarat
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Onchuda Ratdee
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Bavornlak Khamnamtong
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sirawut Klinbunga
- Aquatic Molecular Genetics and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
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2
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Kairišs K, Sokolova N, Zilova L, Schlagheck C, Reinhardt R, Baumbach T, Faragó T, van de Kamp T, Wittbrodt J, Weinhardt V. Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach. Sci Rep 2024; 14:8543. [PMID: 38609416 PMCID: PMC11015006 DOI: 10.1038/s41598-024-58766-5] [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: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.
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Affiliation(s)
- Kristaps Kairišs
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Lucie Zilova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Robert Reinhardt
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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3
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Li X, Owen LA, Taylor KD, Ostmo S, Chen YDI, Coyner AS, Sonmez K, Hartnett ME, Guo X, Ipp E, Roll K, Genter P, Chan RVP, DeAngelis MM, Chiang MF, Campbell JP, Rotter JI. Genome-wide association identifies novel ROP risk loci in a multiethnic cohort. Commun Biol 2024; 7:107. [PMID: 38233474 PMCID: PMC10794688 DOI: 10.1038/s42003-023-05743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 12/26/2023] [Indexed: 01/19/2024] Open
Abstract
We conducted a genome-wide association study (GWAS) in a multiethnic cohort of 920 at-risk infants for retinopathy of prematurity (ROP), a major cause of childhood blindness, identifying 1 locus at genome-wide significance level (p < 5×10-8) and 9 with significance of p < 5×10-6 for ROP ≥ stage 3. The most significant locus, rs2058019, reached genome-wide significance within the full multiethnic cohort (p = 4.96×10-9); Hispanic and European Ancestry infants driving the association. The lead single nucleotide polymorphism (SNP) falls in an intronic region within the Glioma-associated oncogene family zinc finger 3 (GLI3) gene. Relevance for GLI3 and other top-associated genes to human ocular disease was substantiated through in-silico extension analyses, genetic risk score analysis and expression profiling in human donor eye tissues. Thus, we identify a novel locus at GLI3 with relevance to retinal biology, supporting genetic susceptibilities for ROP risk with possible variability by race and ethnicity.
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Affiliation(s)
- Xiaohui Li
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Leah A Owen
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT, USA.
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA.
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT, USA.
- Department of Ophthalmology, University at Buffalo the State University of New York, Buffalo, NY, USA.
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Susan Ostmo
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Aaron S Coyner
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Kemal Sonmez
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Eli Ipp
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kathryn Roll
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Pauline Genter
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - R V Paul Chan
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL, USA
| | - Margaret M DeAngelis
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
- Department of Ophthalmology, University at Buffalo the State University of New York, Buffalo, NY, USA
- Department of Biochemistry; Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York (SUNY), Buffalo, NY, USA
- Department of Neuroscience; Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York (SUNY), Buffalo, NY, USA
- Department of Genetics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York (SUNY), Buffalo, NY, USA
| | - Michael F Chiang
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - J Peter Campbell
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA.
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Herrera ML, Silva S, Berrosteguieta I, Casanova G, Rosillo JC, Fernández AS. Rod precursors in the adult retina of the Austrolebias charrua annual fish. Tissue Cell 2023; 83:102150. [PMID: 37423033 DOI: 10.1016/j.tice.2023.102150] [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: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/11/2023]
Abstract
Rod photoreceptors in the adult teleost retina are produced by rod precursors located in the outer nuclear layer (ONL). Annual fishes of the genus Austrolebias exhibit extensive adult retinal cell proliferation and neurogenesis, as well as surprising adaptive strategies to their extreme and changing environment, including adult retinal plasticity. Thus, here we identify and characterize rod precursors in the ONL of the Austrolebias charrua retina. For this aim we used classical histological techniques, transmission electron microscopy, detection of cell proliferation, and immunohistochemistry. Through these complementary approaches, we describe a cell population clearly distinguishable from photoreceptors in the ONL of the adult retina of A. charrua, which we propose corresponds to the rod precursor population. These cells exhibited particular morphological and ultrastructural characteristics, uptake of cell proliferation markers (BrdU+) and expression of stem cell markers (Sox2+). Determining the existence of the population of rod precursors is crucial to understand the sequence of events related to retinal plasticity and regeneration.
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Affiliation(s)
- M L Herrera
- Departamento Neurociencias Integrativas y Computacionales, Lab. Neurobiología Comparada, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Avenida. Italia 3318, 11600 Montevideo, Uruguay; Sección Fisiología y Nutrición, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - S Silva
- Departamento Neurociencias Integrativas y Computacionales, Lab. Neurobiología Comparada, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Avenida. Italia 3318, 11600 Montevideo, Uruguay
| | - I Berrosteguieta
- Departamento Neurociencias Integrativas y Computacionales, Lab. Neurobiología Comparada, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Avenida. Italia 3318, 11600 Montevideo, Uruguay
| | - G Casanova
- Unidad de Microscopía Electrónica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - J C Rosillo
- Departamento Neurociencias Integrativas y Computacionales, Lab. Neurobiología Comparada, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Avenida. Italia 3318, 11600 Montevideo, Uruguay; Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay.
| | - A S Fernández
- Departamento Neurociencias Integrativas y Computacionales, Lab. Neurobiología Comparada, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Avenida. Italia 3318, 11600 Montevideo, Uruguay; Laboratorio de Neurociencias, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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5
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Sokolova N, Zilova L, Wittbrodt J. Unravelling the link between embryogenesis and adult stem cell potential in the ciliary marginal zone: A comparative study between mammals and teleost fish. Cells Dev 2023; 174:203848. [PMID: 37172718 DOI: 10.1016/j.cdev.2023.203848] [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: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
The discovery and study of adult stem cells have revolutionized regenerative medicine by offering new opportunities for treating various medical conditions. Anamniote stem cells, which retain their full proliferative capacity and full differentiation range throughout their lifetime, harbour a greater potential compared to mammalian adult stem cells, which only exhibit limited stem cell potential. Therefore, understanding the mechanisms underlying these differences is of significant interest. In this review, we examine the similarities and differences of adult retinal stem cells in anamniotes and mammals, from their embryonic stages in the optic vesicle to their residence in the postembryonic retinal stem cell niche, the ciliary marginal zone located in the retinal periphery. In anamniotes, developing precursors of retinal stem cells are exposed to various environmental cues during their migration in the complex morphogenetic remodelling of the optic vesicle to the optic cup. In contrast, their mammalian counterparts in the retinal periphery are primarily instructed by neighbouring tissues once they are in place. We explore the distinct modes of optic cup morphogenesis in mammals and teleost fish and highlight molecular mechanisms governing morphogenesis and stem cells instruction. The review concludes with the molecular mechanisms of ciliary marginal zone formation and offers a perspective on the impact of comparative single cell transcriptomic studies to reveal the evolutionary similarities and differences.
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Affiliation(s)
- Natalia Sokolova
- Centre for Organismal Studies Heidelberg, Germany; Heidelberg Biosciences International Graduate School, Germany
| | - Lucie Zilova
- Centre for Organismal Studies Heidelberg, Germany.
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6
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Chen K, Zhou Y, Sheng M, Li M. Culture and identification of multipotent stem cells in guinea pig sclera. Int Ophthalmol 2023; 43:113-120. [PMID: 35794406 DOI: 10.1007/s10792-022-02393-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/14/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND To investigate whether the sclera of guinea pig contains stem cells with multiple differentiation potentials. METHODS Scleral tissue from guinea pig was separated from the retina and choroid and digested to release single cells. The cells cultured was identified as stem cells by flow cytometric analysis, semiquantitative RT-PCR. Abilities for multipotent differentiation were analyzed by histochemical staining technique (oil-red-O staining, alcian blue staining and alizarin red staining). Scleral fibroblast cell was treated as control group. RESULTS The cultured scleral stem cells were positive for CD44 and CD105 (mesenchymal stem cell surface markers) by flow cytometry. The cells cultured expressed stem cell markers ABCG2, Notch1, Six2, and Pax6, and the most important component of sclera type I collagen. The positive staining informed that the cells cultured were able to differentiate to adipogenic, chondrogenic, and osteogenic lineages. Scleral fibroblast cell was stained negative by oil-red-O staining and alizarin red staining. Expression of Sox9 in the cells cultured after chondrogenic differentiation significantly increased compared with scleral fibroblast cell. CONCLUSION The guinea pig sclera contained stem cells with multiple differentiation potentials. The cells were also related to scleral collagen and cartilage related proteins. The finding may provide a new tool to help clarify mechanisms of sclera related disease in further studies.
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Affiliation(s)
- Kaichuan Chen
- Department of Ophthalmology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanping Zhou
- Department of Ophthalmology, Zhongshan Hospital Affiliated with Fudan University, Shanghai, China
| | - Minjie Sheng
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Min Li
- Department of Ophthalmology, Zhongshan Hospital Affiliated with Fudan University, Shanghai, China.
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7
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Krueger LA, Morris AC. Eyes on CHARGE syndrome: Roles of CHD7 in ocular development. Front Cell Dev Biol 2022; 10:994412. [PMID: 36172288 PMCID: PMC9512043 DOI: 10.3389/fcell.2022.994412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
The development of the vertebrate visual system involves complex morphogenetic interactions of cells derived from multiple embryonic lineages. Disruptions in this process are associated with structural birth defects such as microphthalmia, anophthalmia, and coloboma (collectively referred to as MAC), and inherited retinal degenerative diseases such as retinitis pigmentosa and allied dystrophies. MAC and retinal degeneration are also observed in systemic congenital malformation syndromes. One important example is CHARGE syndrome, a genetic disorder characterized by coloboma, heart defects, choanal atresia, growth retardation, genital abnormalities, and ear abnormalities. Mutations in the gene encoding Chromodomain helicase DNA binding protein 7 (CHD7) cause the majority of CHARGE syndrome cases. However, the pathogenetic mechanisms that connect loss of CHD7 to the ocular complications observed in CHARGE syndrome have not been identified. In this review, we provide a general overview of ocular development and congenital disorders affecting the eye. This is followed by a comprehensive description of CHARGE syndrome, including discussion of the spectrum of ocular defects that have been described in this disorder. In addition, we discuss the current knowledge of CHD7 function and focus on its contributions to the development of ocular structures. Finally, we discuss outstanding gaps in our knowledge of the role of CHD7 in eye formation, and propose avenues of investigation to further our understanding of how CHD7 activity regulates ocular and retinal development.
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Affiliation(s)
| | - Ann C. Morris
- Department of Biology, University of Kentucky, Lexington, KY, United States
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8
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Lekchaoum T, Buddawong A, Ahi S, Chandee N, Weerachatyanukul W, Asuvapongpatana S. Effect of caffeine on genes expressions of developing retinas in the chick model. Anat Cell Biol 2022; 55:311-319. [PMID: 35918321 PMCID: PMC9519763 DOI: 10.5115/acb.22.034] [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: 02/14/2022] [Revised: 04/04/2022] [Accepted: 04/17/2022] [Indexed: 11/27/2022] Open
Abstract
It has been reported that overconsumption of caffeine during pregnancy leads to a deleterious effect within the nervous tissues during embryonic development. In this study, we further extrapolated the effect of caffeine in the developing retinas, which is known to be one of the most sensitive tissues in chick embryos. Morphological changes of retinal thickness and organization of neuroretinal epithelium were monitored using three gene markers, Atoh7, FoxN4, and Lim1. Upon treating with a single dose of caffeine (15 µmol at embryonic day 1 [E1]), relative thicknesses of developing retinas (particularly of E7 and E9) were significantly altered. Among the three genes studied, the expression pattern of Atoh7 was notably altered while those of FoxN4, and Lim1 mRNA showed only a slight change in these developing retinas. Quantitative polymerase chain reaction results supported the most notable changes of Atoh7 but not FoxN4, and Lim1 gene in the developing retinas, particularly at E7. The effect of caffeine towards other organs during development should be extrapolated and the awareness of its intensive consumption should be raised.
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Affiliation(s)
- Thanyarat Lekchaoum
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Aticha Buddawong
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, Thailand
| | - Sunalin Ahi
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nichapha Chandee
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Physical Therapy, Walailak University, Nakhon Si Thammarat, Thailand
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9
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Sharma P, Ramachandran R. Retina regeneration: lessons from vertebrates. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac012. [PMID: 38596712 PMCID: PMC10913848 DOI: 10.1093/oons/kvac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/24/2022] [Accepted: 06/25/2022] [Indexed: 04/11/2024]
Abstract
Unlike mammals, vertebrates such as fishes and frogs exhibit remarkable tissue regeneration including the central nervous system. Retina being part of the central nervous system has attracted the interest of several research groups to explore its regenerative ability in different vertebrate models including mice. Fishes and frogs completely restore the size, shape and tissue structure of an injured retina. Several studies have unraveled molecular mechanisms underlying retina regeneration. In teleosts, soon after injury, the Müller glial cells of the retina reprogram to form a proliferating population of Müller glia-derived progenitor cells capable of differentiating into various neural cell types and Müller glia. In amphibians, the transdifferentiation of retinal pigment epithelium and differentiation of ciliary marginal zone cells contribute to retina regeneration. In chicks and mice, supplementation with external growth factors or genetic modifications cause a partial regenerative response in the damaged retina. The initiation of retina regeneration is achieved through sequential orchestration of gene expression through controlled modulations in the genetic and epigenetic landscape of the progenitor cells. Several developmental biology pathways are turned on during the Müller glia reprogramming, retinal pigment epithelium transdifferentiation and ciliary marginal zone differentiation. Further, several tumorigenic pathways and gene expression events also contribute to the complete regeneration cascade of events. In this review, we address the various retinal injury paradigms and subsequent gene expression events governed in different vertebrate species. Further, we compared how vertebrates such as teleost fishes and amphibians can achieve excellent regenerative responses in the retina compared with their mammalian counterparts.
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Affiliation(s)
- Poonam Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO, 140306 Mohali, Punjab, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO, 140306 Mohali, Punjab, India
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10
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Leach LL, Fisher GB, Gross JM. Nitroreductase/Metronidazole-Mediated Ablation and a MATLAB Platform (RpEGEN) for Studying Regeneration of the Zebrafish Retinal Pigment Epithelium. J Vis Exp 2022:10.3791/63658. [PMID: 35311832 PMCID: PMC9036407 DOI: 10.3791/63658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The retinal pigment epithelium (RPE) resides at the back of the eye and performs functions essential for maintaining the health and integrity of adjacent retinal and vascular tissues. At present, the limited reparative capacity of mammalian RPE, which is restricted to small injuries, has hindered progress to understanding in vivo RPE regenerative processes. Here, a detailed methodology is provided to facilitate the study of in vivo RPE repair utilizing the zebrafish, a vertebrate model capable of robust tissue regeneration. This protocol describes a transgenic nitroreductase/metronidazole (NTR/MTZ)-mediated injury paradigm (rpe65a:nfsB-eGFP), which results in ablation of the central two-thirds of the RPE after 24 h treatment with MTZ, with subsequent tissue recovery. Focus is placed on RPE ablations in larval zebrafish and methods for testing the effects of pharmacological compounds on RPE regeneration are also outlined. Generation and validation of RpEGEN, a MATLAB script created to automate quantification of RPE regeneration based on pigmentation, is also discussed. Beyond active RPE repair mechanisms, this protocol can be expanded to studies of RPE degeneration and injury responses as well as the effects of RPE damage on adjacent retinal and vascular tissues, among other cellular and molecular processes. This zebrafish system holds significant promise in identifying genes, networks, and processes that drive RPE regeneration and RPE disease-related mechanisms, with the long-term goal of applying this knowledge to mammalian systems and, ultimately, toward therapeutic development.
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Affiliation(s)
- Lyndsay L. Leach
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine
| | - G. Burch Fisher
- Earth Research Institute, University of California, Santa Barbara
| | - Jeffrey M. Gross
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine,Department of Developmental Biology, University of Pittsburgh School of Medicine
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Chowdhury K, Lin S, Lai SL. Comparative Study in Zebrafish and Medaka Unravels the Mechanisms of Tissue Regeneration. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.783818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over evolution. Organisms with variable regenerative capacity are usually distinct in phylogeny, anatomy, and physiology. This phenomenon hinders the feasibility of studying tissue regeneration by directly comparing regenerative with non-regenerative animals, such as zebrafish (Danio rerio) and mice (Mus musculus). Medaka (Oryzias latipes) is a fish model with a complete reference genome and shares a common ancestor with zebrafish approximately 110–200 million years ago (compared to 650 million years with mice). Medaka shares similar features with zebrafish, including size, diet, organ system, gross anatomy, and living environment. However, while zebrafish regenerate almost every organ upon experimental injury, medaka shows uneven regenerative capacity. Their common and distinct biological features make them a unique platform for reciprocal analyses to understand the mechanisms of tissue regeneration. Here we summarize current knowledge about tissue regeneration in these fish models in terms of injured tissues, repairing mechanisms, available materials, and established technologies. We further highlight the concept of inter-species and inter-organ comparisons, which may reveal mechanistic insights and hint at therapeutic strategies for human diseases.
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12
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Zilova L, Weinhardt V, Tavhelidse T, Schlagheck C, Thumberger T, Wittbrodt J. Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development. eLife 2021; 10:e66998. [PMID: 34252023 PMCID: PMC8275126 DOI: 10.7554/elife.66998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Organoids derived from pluripotent stem cells promise the solution to current challenges in basic and biomedical research. Mammalian organoids are however limited by long developmental time, variable success, and lack of direct comparison to an in vivo reference. To overcome these limitations and address species-specific cellular organization, we derived organoids from rapidly developing teleosts. We demonstrate how primary embryonic pluripotent cells from medaka and zebrafish efficiently assemble into anterior neural structures, particularly retina. Within 4 days, blastula-stage cell aggregates reproducibly execute key steps of eye development: retinal specification, morphogenesis, and differentiation. The number of aggregated cells and genetic factors crucially impacted upon the concomitant morphological changes that were intriguingly reflecting the in vivo situation. High efficiency and rapid development of fish-derived organoids in combination with advanced genome editing techniques immediately allow addressing aspects of development and disease, and systematic probing of impact of the physical environment on morphogenesis and differentiation.
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Affiliation(s)
- Lucie Zilova
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Venera Weinhardt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Christina Schlagheck
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
- Heidelberg International Biosciences Graduate School HBIGS and HeiKa Graduate School on “Functional Materials”HeidelbergGermany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
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13
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Buono L, Corbacho J, Naranjo S, Almuedo-Castillo M, Moreno-Marmol T, de la Cerda B, Sanabria-Reinoso E, Polvillo R, Díaz-Corrales FJ, Bogdanovic O, Bovolenta P, Martínez-Morales JR. Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish. Nat Commun 2021; 12:3866. [PMID: 34162866 PMCID: PMC8222258 DOI: 10.1038/s41467-021-24169-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 06/03/2021] [Indexed: 01/04/2023] Open
Abstract
Sight depends on the tight cooperation between photoreceptors and pigmented cells, which derive from common progenitors through the bifurcation of a single gene regulatory network into the neural retina (NR) and retinal-pigmented epithelium (RPE) programs. Although genetic studies have identified upstream nodes controlling these networks, their regulatory logic remains poorly investigated. Here, we characterize transcriptome dynamics and chromatin accessibility in segregating NR/RPE populations in zebrafish. We analyze cis-regulatory modules and enriched transcription factor motives to show extensive network redundancy and context-dependent activity. We identify downstream targets, highlighting an early recruitment of desmosomal genes in the flattening RPE and revealing Tead factors as upstream regulators. We investigate the RPE specification network dynamics to uncover an unexpected sequence of transcription factors recruitment, which is conserved in humans. This systematic interrogation of the NR/RPE bifurcation should improve both genetic counseling for eye disorders and hiPSCs-to-RPE differentiation protocols for cell-replacement therapies in degenerative diseases.
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Affiliation(s)
- Lorena Buono
- Centro Andaluz de Biología del Desarrollo-CABD (CSIC/UPO/JA), Seville, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Seville, Spain
| | - Jorge Corbacho
- Centro Andaluz de Biología del Desarrollo-CABD (CSIC/UPO/JA), Seville, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo-CABD (CSIC/UPO/JA), Seville, Spain
| | | | | | - Berta de la Cerda
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER (CSIC/US/UPO/JA), Seville, Spain
| | | | - Rocío Polvillo
- Centro Andaluz de Biología del Desarrollo-CABD (CSIC/UPO/JA), Seville, Spain
| | | | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Seville, Spain.
- CIBERER, ISCIII, Madrid, Spain.
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14
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Retinal Stem Cell 'Retirement Plans': Growth, Regulation and Species Adaptations in the Retinal Ciliary Marginal Zone. Int J Mol Sci 2021; 22:ijms22126528. [PMID: 34207050 PMCID: PMC8234741 DOI: 10.3390/ijms22126528] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
The vertebrate retina develops from a specified group of precursor cells that adopt distinct identities and generate lineages of either the neural retina, retinal pigmented epithelium, or ciliary body. In some species, including teleost fish and amphibians, proliferative cells with stem-cell-like properties capable of continuously supplying new retinal cells post-embryonically have been characterized and extensively studied. This region, termed the ciliary or circumferential marginal zone (CMZ), possibly represents a conserved retinal stem cell niche. In this review, we highlight the research characterizing similar CMZ-like regions, or stem-like cells located at the peripheral margin, across multiple different species. We discuss the proliferative parameters, multipotency and growth mechanisms of these cells to understand how they behave in vivo and how different molecular factors and signalling networks converge at the CMZ niche to regulate their activity. The evidence suggests that the mature retina may have a conserved propensity for homeostatic growth and plasticity and that dysfunction in the regulation of CMZ activity may partially account for dystrophic eye growth diseases such as myopia and hyperopia. A better understanding of the properties of CMZ cells will enable important insight into how an endogenous generative tissue compartment can adapt to altered retinal physiology and potentially even restore vision loss caused by retinal degenerative conditions.
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15
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Gücüm S, Sakson R, Hoffmann M, Grote V, Becker C, Pakari K, Beedgen L, Thiel C, Rapp E, Ruppert T, Thumberger T, Wittbrodt J. A patient-based medaka alg2 mutant as a model for hypo-N-glycosylation. Development 2021; 148:269015. [PMID: 34106226 PMCID: PMC8217707 DOI: 10.1242/dev.199385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022]
Abstract
Defects in the evolutionarily conserved protein-glycosylation machinery during embryonic development are often fatal. Consequently, congenital disorders of glycosylation (CDG) in human are rare. We modelled a putative hypomorphic mutation described in an alpha-1,3/1,6-mannosyltransferase (ALG2) index patient (ALG2-CDG) to address the developmental consequences in the teleost medaka (Oryzias latipes). We observed specific, multisystemic, late-onset phenotypes, closely resembling the patient's syndrome, prominently in the facial skeleton and in neuronal tissue. Molecularly, we detected reduced levels of N-glycans in medaka and in the patient's fibroblasts. This hypo-N-glycosylation prominently affected protein abundance. Proteins of the basic glycosylation and glycoprotein-processing machinery were over-represented in a compensatory response, highlighting the regulatory topology of the network. Proteins of the retinal phototransduction machinery, conversely, were massively under-represented in the alg2 model. These deficiencies relate to a specific failure to maintain rod photoreceptors, resulting in retinitis pigmentosa characterized by the progressive loss of these photoreceptors. Our work has explored only the tip of the iceberg of N-glycosylation-sensitive proteins, the function of which specifically impacts on cells, tissues and organs. Taking advantage of the well-described human mutation has allowed the complex interplay of N-glycosylated proteins and their contribution to development and disease to be addressed.
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Affiliation(s)
- Sevinç Gücüm
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.,HBIGS, Heidelberg Biosciences International Graduate School, Heidelberg University, 69120 Heidelberg, Germany
| | - Roman Sakson
- HBIGS, Heidelberg Biosciences International Graduate School, Heidelberg University, 69120 Heidelberg, Germany.,Core facility for Mass Spectrometry and Proteomics, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Valerian Grote
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Clara Becker
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Kaisa Pakari
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Lars Beedgen
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany.,glyXera GmbH, 39120 Magdeburg, Germany
| | - Thomas Ruppert
- Core facility for Mass Spectrometry and Proteomics, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
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16
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The immune response is a critical regulator of zebrafish retinal pigment epithelium regeneration. Proc Natl Acad Sci U S A 2021; 118:2017198118. [PMID: 34006636 DOI: 10.1073/pnas.2017198118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Loss of the retinal pigment epithelium (RPE) because of dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self-repair is an attractive therapeutic strategy; however, mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues, including the RPE, but little is known about the mechanisms driving RPE regeneration. Here, utilizing transgenic and mutant zebrafish lines, pharmacological manipulations, transcriptomics, and imaging analyses, we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. After genetic ablation, the RPE express immune-related genes, including leukocyte recruitment factors such as interleukin 34 We demonstrate that macrophage/microglia cells are responsive to RPE damage and that their function is required for the timely progression of the regenerative response. These data identify the molecular and cellular underpinnings of RPE regeneration and hold significant potential for translational approaches aimed toward promoting a pro-regenerative environment in mammalian RPE.
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17
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George SM, Lu F, Rao M, Leach LL, Gross JM. The retinal pigment epithelium: Development, injury responses, and regenerative potential in mammalian and non-mammalian systems. Prog Retin Eye Res 2021; 85:100969. [PMID: 33901682 DOI: 10.1016/j.preteyeres.2021.100969] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/23/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022]
Abstract
Diseases that result in retinal pigment epithelium (RPE) degeneration, such as age-related macular degeneration (AMD), are among the leading causes of blindness worldwide. Atrophic (dry) AMD is the most prevalent form of AMD and there are currently no effective therapies to prevent RPE cell death or restore RPE cells lost from AMD. An intriguing approach to treat AMD and other RPE degenerative diseases is to develop therapies focused on stimulating endogenous RPE regeneration. For this to become feasible, a deeper understanding of the mechanisms underlying RPE development, injury responses and regenerative potential is needed. In mammals, RPE regeneration is extremely limited; small lesions can be repaired by the expansion of adjacent RPE cells, but large lesions cannot be repaired as remaining RPE cells are unable to functionally replace lost RPE tissue. In some injury paradigms, RPE cells proliferate but do not regenerate a morphologically normal monolayer, while in others, proliferation is pathogenic and results in further disruption to the retina. This is in contrast to non-mammalian vertebrates, which possess tremendous RPE regenerative potential. Here, we discuss what is known about RPE formation during development in mammalian and non-mammalian vertebrates, we detail the processes by which RPE cells respond to injury, and we describe examples of RPE-to-retina and RPE-to-RPE regeneration in non-mammalian vertebrates. Finally, we outline barriers to RPE-dependent regeneration in mammals that could potentially be overcome to stimulate a regenerative response from the RPE.
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Affiliation(s)
- Stephanie M George
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Fangfang Lu
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA; Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Mishal Rao
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Lyndsay L Leach
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Jeffrey M Gross
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA; Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
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18
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Becker C, Lust K, Wittbrodt J. Igf signaling couples retina growth with body growth by modulating progenitor cell division. Development 2021; 148:dev.199133. [PMID: 33722901 PMCID: PMC8077508 DOI: 10.1242/dev.199133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/04/2021] [Indexed: 12/19/2022]
Abstract
How the body and organs balance their relative growth is of key importance for coordinating size and function. This is of particular relevance in organisms, which continue to grow over their entire life span. We addressed this issue in the neuroretina of medaka fish (Oryzias latipes), a well-studied system with which to address vertebrate organ growth. We reveal that a central growth regulator, Igf1 receptor (Igf1r), is necessary and sufficient for proliferation control in the postembryonic retinal stem cell niche: the ciliary marginal zone (CMZ). Targeted activation of Igf1r signaling in the CMZ uncouples neuroretina growth from body size control, and we demonstrate that Igf1r operates on progenitor cells, stimulating their proliferation. Activation of Igf1r signaling increases retinal size while preserving its structural integrity, revealing a modular organization in which progenitor differentiation and neurogenesis are self-organized and highly regulated. Our findings position Igf signaling as a key module for controlling retinal size and composition, with important evolutionary implications. Highlighted Article: Targeted activation of Igf1r signaling in the retinal stem cell niche increases retina size through expanding the progenitor but not stem cell population.
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Affiliation(s)
- Clara Becker
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg 69120, Germany
| | - Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
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19
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Fuhrmann JF, Buono L, Adelmann L, Martinez-Morales JR, Centanin L. Genetic developmental timing revealed by inter-species transplantations in fish. Development 2020; 147:dev.192500. [PMID: 33033120 DOI: 10.1242/dev.192500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/02/2020] [Indexed: 12/22/2022]
Abstract
The path from a fertilised egg to an embryo involves the coordinated formation of cell types, tissues and organs. Developmental modules comprise discrete units specified by self-sufficient genetic programs that can interact with each other during embryogenesis. Here, we have taken advantage of the different span of embryonic development between two distantly related teleosts, zebrafish (Danio rerio) and medaka (Oryzias latipes) (3 and 9 days, respectively), to explore modularity principles. We report that inter-species blastula transplantations result in the ectopic formation of a retina formed by donor cells - a module. We show that the time taken for the retina to develop follows a genetic program: an ectopic zebrafish retina in medaka develops with zebrafish dynamics. Heterologous transplantation results in a temporal decoupling between the donor retina and host organism, illustrated by two paradigms that require retina-host interactions: lens recruitment and retino-tectal projections. Our results uncover a new experimental system for addressing temporal decoupling along embryonic development, and highlight the presence of largely autonomous but interconnected developmental modules that orchestrate organogenesis.
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Affiliation(s)
- Jana Franziska Fuhrmann
- Laboratory of Clonal Analysis, Center for Organismal Studies, Universität Heidelberg, INF230, 69120 Heidelberg, Germany
| | - Lorena Buono
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Carretera de Utrera km 1, 41013 Seville, Spain
| | - Leonie Adelmann
- Laboratory of Clonal Analysis, Center for Organismal Studies, Universität Heidelberg, INF230, 69120 Heidelberg, Germany
| | - Juan Ramón Martinez-Morales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Carretera de Utrera km 1, 41013 Seville, Spain
| | - Lazaro Centanin
- Laboratory of Clonal Analysis, Center for Organismal Studies, Universität Heidelberg, INF230, 69120 Heidelberg, Germany
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20
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Grigoryan EN. Potential Endogenous Cell Sources for Retinal Regeneration in Vertebrates and Humans: Progenitor Traits and Specialization. Biomedicines 2020; 8:E208. [PMID: 32664635 PMCID: PMC7400588 DOI: 10.3390/biomedicines8070208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/04/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
Retinal diseases often cause the loss of photoreceptor cells and, consequently, impairment of vision. To date, several cell populations are known as potential endogenous retinal regeneration cell sources (RRCSs): the eye ciliary zone, the retinal pigment epithelium, the iris, and Müller glia. Factors that can activate the regenerative responses of RRCSs are currently under investigation. The present review considers accumulated data on the relationship between the progenitor properties of RRCSs and the features determining their differentiation. Specialized RRCSs (all except the ciliary zone in low vertebrates), despite their differences, appear to be partially "prepared" to exhibit their plasticity and be reprogrammed into retinal neurons due to the specific gene expression and epigenetic landscape. The "developmental" characteristics of RRCS gene expression are predefined by the pathway by which these cell populations form during eye morphogenesis; the epigenetic features responsible for chromatin organization in RRCSs are under intracellular regulation. Such genetic and epigenetic readiness is manifested in vivo in lower vertebrates and in vitro in higher ones under conditions permissive for cell phenotype transformation. Current studies on gene expression in RRCSs and changes in their epigenetic landscape help find experimental approaches to replacing dead cells through recruiting cells from endogenous resources in vertebrates and humans.
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Affiliation(s)
- Eleonora N Grigoryan
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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21
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dnmt1 function is required to maintain retinal stem cells within the ciliary marginal zone of the zebrafish eye. Sci Rep 2020; 10:11293. [PMID: 32647199 PMCID: PMC7347529 DOI: 10.1038/s41598-020-68016-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/15/2020] [Indexed: 12/22/2022] Open
Abstract
The ciliary marginal zone (CMZ) of the zebrafish retina contains a population of actively proliferating resident stem cells, which generate retinal neurons throughout life. The maintenance methyltransferase, dnmt1, is expressed within the CMZ. Loss of dnmt1 function results in gene misregulation and cell death in a variety of developmental contexts, however, its role in retinal stem cell (RSC) maintenance is currently unknown. Here, we demonstrate that zebrafish dnmt1s872 mutants possess severe defects in RSC maintenance within the CMZ. Using a combination of immunohistochemistry, in situ hybridization, and a transgenic reporter assay, our results demonstrate a requirement for dnmt1 activity in the regulation of RSC proliferation, gene expression and in the repression of endogenous retroelements (REs). Ultimately, cell death is elevated in the dnmt1−/− CMZ, but in a p53-independent manner. Using a transgenic reporter for RE transposition activity, we demonstrate increased transposition in the dnmt1−/− CMZ. Taken together our data identify a critical role for dnmt1 function in RSC maintenance in the vertebrate eye.
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22
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Her9/Hes4 is required for retinal photoreceptor development, maintenance, and survival. Sci Rep 2020; 10:11316. [PMID: 32647335 PMCID: PMC7347560 DOI: 10.1038/s41598-020-68172-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/11/2020] [Indexed: 11/13/2022] Open
Abstract
The intrinsic and extrinsic factors that regulate vertebrate photoreceptor specification and differentiation are complex, and our understanding of all the players is far from complete. Her9, the zebrafish ortholog of human HES4, is a basic helix-loop-helix-orange transcriptional repressor that regulates neurogenesis in several developmental contexts. We have previously shown that her9 is upregulated during chronic rod photoreceptor degeneration and regeneration in adult zebrafish, but little is known about the role of her9 during retinal development. To better understand the function of Her9 in the retina, we generated zebrafish her9 CRISPR mutants. Her9 homozygous mutants displayed striking retinal phenotypes, including decreased numbers of rods and red/green cones, whereas blue and UV cones were relatively unaffected. The reduction in rods and red/green cones correlated with defects in photoreceptor subtype lineage specification. The remaining rods and double cones displayed abnormal outer segments, and elevated levels of apoptosis. In addition to the photoreceptor defects, her9 mutants also possessed a reduced proliferative ciliary marginal zone, and decreased and disorganized Müller glia. Mutation of her9 was larval lethal, with no mutants surviving past 13 days post fertilization. Our results reveal a previously undescribed role for Her9/Hes4 in photoreceptor differentiation, maintenance, and survival.
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23
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Covello G, Rossello FJ, Filosi M, Gajardo F, Duchemin A, Tremonti BF, Eichenlaub M, Polo JM, Powell D, Ngai J, Allende ML, Domenici E, Ramialison M, Poggi L. Transcriptome analysis of the zebrafish atoh7-/- Mutant, lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases. FASEB Bioadv 2020; 2:434-448. [PMID: 32676583 PMCID: PMC7354691 DOI: 10.1096/fba.2020-00030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/02/2020] [Accepted: 04/28/2020] [Indexed: 12/21/2022] Open
Abstract
Expression of the bHLH transcription protein Atoh7 is a crucial factor conferring competence to retinal progenitor cells for the development of retinal ganglion cells. Several studies have emerged establishing ATOH7 as a retinal disease gene. Remarkably, such studies uncovered ATOH7 variants associated with global eye defects including optic nerve hypoplasia, microphthalmia, retinal vascular disorders, and glaucoma. The complex genetic networks and cellular decisions arising downstream of atoh7 expression, and how their dysregulation cause development of such disease traits remains unknown. To begin to understand such Atoh7-dependent events in vivo, we performed transcriptome analysis of wild-type and atoh7 mutant (lakritz) zebrafish embryos at the onset of retinal ganglion cell differentiation. We investigated in silico interplays of atoh7 and other disease-related genes and pathways. By network reconstruction analysis of differentially expressed genes, we identified gene clusters enriched in retinal development, cell cycle, chromatin remodeling, stress response, and Wnt pathways. By weighted gene coexpression network, we identified coexpression modules affected by the mutation and enriched in retina development genes tightly connected to atoh7. We established the groundwork whereby Atoh7-linked cellular and molecular processes can be investigated in the dynamic multi-tissue environment of the developing normal and diseased vertebrate eye.
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Affiliation(s)
- Giuseppina Covello
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
- Present address:
Department of BiologyUniversity of PadovaPadovaItaly
| | - Fernando J. Rossello
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
- Present address:
University of Melbourne Centre for Cancer ResearchUniversity of MelbourneMelbourneVictoriaAustralia
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Felipe Gajardo
- Center for Genome RegulationFacultad de Ciencias, SantiagoUniversidad de ChileSantiagoChile
| | | | - Beatrice F. Tremonti
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Michael Eichenlaub
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
| | - Jose M. Polo
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
- BDIMonash University Clayton VICClaytonAustralia
| | - David Powell
- Monash Bioinformatics PlatformMonash University Clayton VICClaytonAustralia
| | - John Ngai
- Department of Molecular and Cell Biology & Helen Wills Neuroscience InstituteUniversity of CaliforniaBerkeleyCAUSA
| | - Miguel L. Allende
- Center for Genome RegulationFacultad de Ciencias, SantiagoUniversidad de ChileSantiagoChile
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
- Fondazione The Microsoft Research ‐ University of Trento Centre for Computational and Systems BiologyTrentoItaly
| | - Mirana Ramialison
- Australian Regenerative Medicine InstituteMonash University Clayton VICClaytonAustralia
| | - Lucia Poggi
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
- Centre for Organismal StudyHeidelberg UniversityHeidelbergGermany
- Department of PhysiologyDevelopment and NeuroscienceUniversity of CambridgeCambridgeUnited Kingdom
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24
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Xu B, Tang X, Jin M, Zhang H, Du L, Yu S, He J. Unifying developmental programs for embryonic and postembryonic neurogenesis in the zebrafish retina. Development 2020; 147:dev.185660. [PMID: 32467236 DOI: 10.1242/dev.185660] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 05/13/2020] [Indexed: 01/14/2023]
Abstract
The zebrafish retina grows for a lifetime. Whether embryonic and postembryonic retinogenesis conform to the same developmental program is an outstanding question that remains under debate. Using single-cell RNA sequencing of ∼20,000 cells of the developing zebrafish retina at four different stages, we identified seven distinct developmental states. Each state explicitly expresses a gene set. Disruption of individual state-specific marker genes results in various defects ranging from small eyes to the loss of distinct retinal cell types. Using a similar approach, we further characterized the developmental states of postembryonic retinal stem cells (RSCs) and their progeny in the ciliary marginal zone. Expression pattern analysis of state-specific marker genes showed that the developmental states of postembryonic RSCs largely recapitulated those of their embryonic counterparts, except for some differences in rod photoreceptor genesis. Thus, our findings reveal the unifying developmental program used by the embryonic and postembryonic retinogenesis in zebrafish.
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Affiliation(s)
- Baijie Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Xia Tang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China .,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Mengmeng Jin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Hui Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Lei Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Shuguang Yu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Jie He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China .,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
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25
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Shen H, Ding C, Yuan S, Pan T, Li D, Li H, Huang B, Liu Q. Vitamin C- and Valproic Acid-Induced Fetal RPE Stem-like Cells Recover Retinal Degeneration via Regulating SOX2. Mol Ther 2020; 28:1645-1657. [PMID: 32353323 DOI: 10.1016/j.ymthe.2020.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 02/06/2023] Open
Abstract
Retinal pigment epithelial (RPE) cell replacement therapy has provided promising outcomes in the treatment of retinal degenerative diseases (RDDs), but the resulting limited visual improvement has raised questions about graft survival and differentiation. Through combined treatment with vitamin C and valproic acid (together, VV), we activated human fetal RPE (fRPE) cells to become highly proliferative fetal RPE stem-like cells (fRPESCs). In this study, we report that SOX2 (SRY-box 2) activation contributed to mesenchymal-epithelial transition and elevated the retinal progenitor and mesenchymal stromal markers expressions of fRPESCs. These fRPESCs could differentiate into RPE cells, rod photoreceptors, and mesenchymal lineage progenies under defined conditions. Finally, fRPESCs were transplanted into the subretinal space of an RDD mouse model, and a photoreceptor rescue benefit was demonstrated. The RPE and rod photoreceptor differentiation of transplanted fRPESCs may account for the neural retinal recovery. This study establishes fRPESCs as a highly proliferative, multi-lineage differentiation potential (including RPE, rod photoreceptor, and mesenchymal lineage differentiation), mesenchymal-to-epithelial-transitioned retinal stem-like cell source for cell-based therapy of RDDs.
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Affiliation(s)
- Han Shen
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Chenyue Ding
- Center of Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215002, China
| | - Songtao Yuan
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ting Pan
- The Affiliated Changzhou No. 2 People's Hospital with Nanjing Medical University, Changzhou 213000, China
| | - Duo Li
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Hong Li
- Center of Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215002, China
| | - Boxian Huang
- Center of Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215002, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China.
| | - Qinghuai Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
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26
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Eckert P, Knickmeyer MD, Heermann S. In Vivo Analysis of Optic Fissure Fusion in Zebrafish: Pioneer Cells, Basal Lamina, Hyaloid Vessels, and How Fissure Fusion is Affected by BMP. Int J Mol Sci 2020; 21:ijms21082760. [PMID: 32316164 PMCID: PMC7215994 DOI: 10.3390/ijms21082760] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
Colobomata, persistent optic fissures, frequently cause congenital blindness. Here, we focused on optic fissure fusion using in vivo time-lapse imaging in zebrafish. We identified the fusion initiating cells, which we termed “pioneer cells.” Based on morphology, localization, and downregulation of the neuroretinal (NR) precursor marker rx2, these cells could be considered as retinal pigment epithelial (RPE) progenitors. Notably, pioneer cells regain rx2 expression and integrate into the NR after fusion, indicating that they do not belong to the pool of RPE progenitors, supported by the lack of RPE marker expression in pioneer cells. They establish the first cellular contact between the margins in the proximal fissure region and separate the hyaloid artery and vein. After initiation, the fusion site is progressing distally, increasing the distance between the hyaloid artery and vein. A timed BMP (Bone Morphogenetic Protein) induction, resulting in coloboma, did not alter the morphology of the fissure margins, but it did affect the expression of NR and RPE markers within the margins. In addition, it resulted in a persisting basal lamina and persisting remnants of periocular mesenchyme and hyaloid vasculature within the fissure, supporting the necessity of BMP antagonism within the fissure margins. The hampered fissure fusion had severe effects on the vasculature of the eye.
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Affiliation(s)
- Priska Eckert
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University Freiburg, 79104 Freiburg, Germany; (P.E.); (M.D.K.)
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Max D. Knickmeyer
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University Freiburg, 79104 Freiburg, Germany; (P.E.); (M.D.K.)
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Stephan Heermann
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University Freiburg, 79104 Freiburg, Germany; (P.E.); (M.D.K.)
- Correspondence:
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27
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Zhao Q, Zhang R, Xiao Y, Niu Y, Shao F, Li Y, Peng Z. Comparative Transcriptome Profiling of the Loaches Triplophysa bleekeri and Triplophysa rosa Reveals Potential Mechanisms of Eye Degeneration. Front Genet 2020; 10:1334. [PMID: 32010191 PMCID: PMC6977438 DOI: 10.3389/fgene.2019.01334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri. Compared with the normal eyes of the surface loach, those of the cave loach were found to possess a small abnormal lens and a defective retina containing photoreceptor cells that lack outer segments. Sequencing of the transcriptomes of both species to identify differentially expressed genes (DEGs) and genes under positive selection revealed 4,802 DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we identified one Gene Ontology category related to vision that was significantly enriched in downregulated genes. Specifically, we found that many of the downregulated genes, including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and β|γ-crystallin are associated with lens/retinal development and maintenance. However, compared with those in the surface loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa indicate that changes in amino acid sequences might be involved in the adaptation and visual degeneration of cave loaches. We also found that genes associated with light perception and light-stimulated vision have evolved at higher rates (some genes dN/dS > 1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of cavefish vision is probably associated with both gene expression and amino acid changes and provide new insights into the mechanisms underlying the degeneration of cavefish eyes.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yingqi Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yabing Niu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
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28
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DeOliveira-Mello L, Lara JM, Arevalo R, Velasco A, Mack AF. Sox2 expression in the visual system of two teleost species. Brain Res 2019; 1722:146350. [DOI: 10.1016/j.brainres.2019.146350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/20/2019] [Accepted: 07/23/2019] [Indexed: 12/13/2022]
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29
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Redox Signaling via Lipid Peroxidation Regulates Retinal Progenitor Cell Differentiation. Dev Cell 2019; 50:73-89.e6. [DOI: 10.1016/j.devcel.2019.05.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 02/07/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022]
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30
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Stolper J, Ambrosio EM, Danciu DP, Buono L, Elliott DA, Naruse K, Martínez-Morales JR, Marciniak-Czochra A, Centanin L. Stem cell topography splits growth and homeostatic functions in the fish gill. eLife 2019; 8:43747. [PMID: 31090541 PMCID: PMC6534379 DOI: 10.7554/elife.43747] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
While lower vertebrates contain adult stem cells (aSCs) that maintain homeostasis and drive un-exhaustive organismal growth, mammalian aSCs display mainly the homeostatic function. Here, we use lineage analysis in the medaka fish gill to address aSCs and report separate stem cell populations for homeostasis and growth. These aSCs are fate-restricted during the entire post-embryonic life and even during re-generation paradigms. We use chimeric animals to demonstrate that p53 mediates growth coordination among fate-restricted aSCs, suggesting a hierarchical organisation among lineages in composite organs like the fish gill. Homeostatic and growth aSCs are clonal but differ in their topology; modifications in tissue architecture can convert the homeostatic zone into a growth zone, indicating a leading role for the physical niche defining stem cell output. We hypothesise that physical niches are main players to restrict aSCs to a homeostatic function in animals with fixed adult size.
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Affiliation(s)
- Julian Stolper
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | | | | | - Lorena Buono
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Seville, Spain
| | - David A Elliott
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | | | - Anna Marciniak-Czochra
- Institute of Applied Mathematics, Heidelberg University, Heidelberg, Germany.,Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Lazaro Centanin
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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31
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Tsingos E, Höckendorf B, Sütterlin T, Kirchmaier S, Grabe N, Centanin L, Wittbrodt J. Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish. eLife 2019; 8:42646. [PMID: 30910010 PMCID: PMC6486154 DOI: 10.7554/elife.42646] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/13/2019] [Indexed: 12/22/2022] Open
Abstract
Combining clonal analysis with a computational agent based model, we investigate how tissue-specific stem cells for neural retina (NR) and retinal pigmented epithelium (RPE) of the teleost medaka (Oryzias latipes) coordinate their growth rates. NR cell division timing is less variable, consistent with an upstream role as growth inducer. RPE cells divide with greater variability, consistent with a downstream role responding to inductive signals. Strikingly, the arrangement of the retinal ciliary marginal zone niche results in a spatially biased random lineage loss, where stem- and progenitor cell domains emerge spontaneously. Further, our data indicate that NR cells orient division axes to regulate organ shape and retinal topology. We highlight an unappreciated mechanism for growth coordination, where one tissue integrates cues to synchronize growth of nearby tissues. This strategy may enable evolution to modulate cell proliferation parameters in one tissue to adapt whole-organ morphogenesis in a complex vertebrate organ. By the time babies reach adulthood, they have grown many times larger than they were at birth. This development is driven by an increase in the number and size of cells in the body. In particular, special types of cells, called stem cells, act as a reservoir for tissues: they divide to create new cells that will mature into various specialized structures. The retina is the light-sensitive part of the eye. It consists of the neural retina, a tissue that contains light-detecting cells, which is supported by the retinal pigment epithelium or RPE. In fish, the RPE and neural retina are replenished by distinct groups of stem cells that do not mix, despite the tissues being close together. Unlike humans, fish grow throughout adulthood, and their eyes must then keep pace with the body. This means that the different tissues in the retina must somehow coordinate to expand at the same rate: otherwise, the retina would get wrinkled and not work properly. Tsingos et al. therefore wanted to determine how stem cells in the neural retina and RPE co-operated to produce the right number of new cells at the right time. First, stem cells in the eyes of newly hatched fish were labelled with a visible marker so that their divisions could be tracked over time to build cell family trees. This showed that stem cells behaved differently in the neural retina and the RPE. Computer simulations of the growing retina explained this behavior: stem cells in the neural retina were telling the RPE stem cells when it was time to divide. Combining results from the simulations with data from the experiments revealed that a stem cell decided to keep up dividing partly because of its position in the tissue, and partly because of random chance. To be healthy, the body needs to fine-tune the number of cells it produces: creating too few cells may make it difficult to heal after injury, but making too many could lead to diseases such as cancer. Understanding how tissues normally agree to grow together could therefore open new avenues of treatment for these conditions.
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Affiliation(s)
- Erika Tsingos
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Burkhard Höckendorf
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas Sütterlin
- National Center for Tumor Diseases, Hamamatsu TIGA Center, Bioquant, Heidelberg University, Heidelberg, Germany
| | - Stephan Kirchmaier
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Niels Grabe
- National Center for Tumor Diseases, Hamamatsu TIGA Center, Bioquant, Heidelberg University, Heidelberg, Germany
| | - Lazaro Centanin
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
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32
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Hanovice NJ, Leach LL, Slater K, Gabriel AE, Romanovicz D, Shao E, Collery R, Burton EA, Lathrop KL, Link BA, Gross JM. Regeneration of the zebrafish retinal pigment epithelium after widespread genetic ablation. PLoS Genet 2019; 15:e1007939. [PMID: 30695061 PMCID: PMC6368336 DOI: 10.1371/journal.pgen.1007939] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/08/2019] [Accepted: 01/07/2019] [Indexed: 01/17/2023] Open
Abstract
The retinal pigment epithelium (RPE) is a specialized monolayer of pigmented cells within the eye that is critical for maintaining visual system function. Diseases affecting the RPE have dire consequences for vision, and the most prevalent of these is atrophic (dry) age-related macular degeneration (AMD), which is thought to result from RPE dysfunction and degeneration. An intriguing possibility for treating RPE degenerative diseases like atrophic AMD is the stimulation of endogenous RPE regeneration; however, very little is known about the mechanisms driving successful RPE regeneration in vivo. Here, we developed a zebrafish transgenic model (rpe65a:nfsB-eGFP) that enabled ablation of large swathes of mature RPE. RPE ablation resulted in rapid RPE degeneration, as well as degeneration of Bruch’s membrane and underlying photoreceptors. Using this model, we demonstrate for the first time that zebrafish are capable of regenerating a functional RPE monolayer after RPE ablation. Regenerated RPE cells first appear at the periphery of the RPE, and regeneration proceeds in a peripheral-to-central fashion. RPE ablation elicits a robust proliferative response in the remaining RPE. Subsequently, proliferative cells move into the injury site and differentiate into RPE. BrdU incorporation assays demonstrate that the regenerated RPE is likely derived from remaining peripheral RPE cells. Pharmacological disruption using IWR-1, a Wnt signaling antagonist, significantly reduces cell proliferation in the RPE and impairs overall RPE recovery. These data demonstrate that the zebrafish RPE possesses a robust capacity for regeneration and highlight a potential mechanism through which endogenous RPE regenerate in vivo. Diseases resulting in retinal pigment epithelium (RPE) degeneration are among the leading causes of blindness worldwide, and no therapy exists that can replace RPE or restore lost vision. One intriguing possibility is the development of therapies focused on stimulating endogenous RPE regeneration. For this to be possible, we must first gain a deeper understanding of the mechanisms underlying RPE regeneration. Here, we develop a transgenic zebrafish system through which we ablate large swathes of mature RPE and demonstrate that zebrafish regenerate RPE after widespread injury. Injury-adjacent RPE proliferate and regenerate RPE, suggesting that they are the source of regenerated tissue. Finally, we demonstrate that Wnt signaling may be involved in RPE regeneration. These findings establish a versatile in vivo model through which the molecular and cellular underpinnings of RPE regeneration can be further characterized.
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Affiliation(s)
- Nicholas J. Hanovice
- Department of Ophthalmology, Louis J Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Lyndsay L. Leach
- Department of Ophthalmology, Louis J Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kayleigh Slater
- Department of Ophthalmology, Louis J Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Ana E. Gabriel
- Department of Ophthalmology, Louis J Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Dwight Romanovicz
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, Texas, United States of America
| | - Enhua Shao
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Tsinghua University Medical School, Beijing, China
| | - Ross Collery
- Department of Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Edward A. Burton
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Geriatric Research, Education and Clinical Center, Pittsburgh VA Healthcare System, Pittsburgh, Pennsylvania, United States of America
| | - Kira L. Lathrop
- Department of Ophthalmology, Louis J Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Bioengineering, University of Pittsburgh Swanson School of Engineering, Pittsburgh, Pennsylvania, United States of America
| | - Brian A. Link
- Department of Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Jeffrey M. Gross
- Department of Ophthalmology, Louis J Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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33
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Pérez Saturnino A, Lust K, Wittbrodt J. Notch signalling patterns retinal composition by regulating atoh7 during post-embryonic growth. Development 2018; 145:dev.169698. [PMID: 30337377 PMCID: PMC6240314 DOI: 10.1242/dev.169698] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023]
Abstract
Patterning of a continuously growing naive field in the context of a life-long growing organ such as the teleost eye is of high functional relevance. Intrinsic and extrinsic signals have been proposed to regulate lineage specification in progenitors that exit the stem cell niche in the ciliary marginal zone (CMZ). The proper cell-type composition arising from those progenitors is a prerequisite for retinal function. Our findings in the teleost medaka (Oryzias latipes) uncover that the Notch-Atoh7 axis continuously patterns the CMZ. The complement of cell types originating from the two juxtaposed progenitors marked by Notch or Atoh7 activity contains all constituents of a retinal column. Modulation of Notch signalling specifically in Atoh7-expressing cells demonstrates the crucial role of this axis in generating the correct cell-type proportions. After transiently blocking Notch signalling, retinal patterning and differentiation is re-initiated de novo. Taken together, our data show that Notch activity in the CMZ continuously structures the growing retina by juxtaposing Notch and Atoh7 progenitors that give rise to distinct complementary lineages, revealing coupling of de novo patterning and cell-type specification in the respective lineages. Summary: Mutually exclusive activity of Notch and Atoh7 in the ciliary marginal zone gives rise to two distinct lineages resulting in specification of the full complement of cell types in medaka retina.
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Affiliation(s)
- Alicia Pérez Saturnino
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg 69120, Germany
| | - Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
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34
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Gutierrez-Triana JA, Tavhelidse T, Thumberger T, Thomas I, Wittbrodt B, Kellner T, Anlas K, Tsingos E, Wittbrodt J. Efficient single-copy HDR by 5' modified long dsDNA donors. eLife 2018; 7:39468. [PMID: 30156184 PMCID: PMC6125127 DOI: 10.7554/elife.39468] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/14/2018] [Indexed: 12/03/2022] Open
Abstract
CRISPR/Cas9 efficiently induces targeted mutations via non-homologous-end-joining but for genome editing, precise, homology-directed repair (HDR) of endogenous DNA stretches is a prerequisite. To favor HDR, many approaches interfere with the repair machinery or manipulate Cas9 itself. Using Medaka we show that the modification of 5’ ends of long dsDNA donors strongly enhances HDR, favors efficient single-copy integration by retaining a monomeric donor conformation thus facilitating successful gene replacement or tagging. CRISPR/Cas9 technology has revolutionized the ability of researchers to edit the DNA of any organism whose genome has already been sequenced. In the editing process, a section of RNA acts as a guide to match up to the location of the target DNA. The enzyme Cas9 then makes a cut in both strands of the DNA at this specific location. New segments of DNA can be introduced to the cell, incorporated into DNA ‘templates’. The cell uses the template to help it to heal the double-strand break, and in doing so adds the new DNA segment into the organism’s genome. A drawback of CRISPR/Cas9 is that it often introduces multiple copies of the new DNA segment into the genome because the templates can bind to each other before being pasted into place. In addition, some parts of the new DNA segment can be missed off during the editing process. However, most applications of CRISPR/Cas9 – for example, to replace a defective gene with a working version – require exactly one whole copy of the desired DNA to be inserted into the genome. In order to achieve more accurate CRISPR/Cas9 genome editing, Gutierrez-Triana, Tavhelidse, Thumberger et al. attached additional molecules to the end of the DNA template to shield the DNA from mistakes during editing. The modified template was used to couple a stem cell gene to a reporter that produces a green fluorescent protein into the genome of fish embryos. The fluorescent proteins made it easy to identify when the coupling was successful. Gutierrez-Triana et al. found that the additional molecules prevented multiple templates from joining together end to end, and ensured the full DNA segment was inserted into the genome. Furthermore, the results of the experiments showed that only one copy of the template was inserted into the DNA of the fish. In the future, the new template will allow DNA to be edited in a more controlled way both in basic research and in therapeutic applications.
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Affiliation(s)
| | | | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Isabelle Thomas
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Beate Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Kerim Anlas
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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35
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Ma Y, Li G, Hu J, Liu X, Shi B. MicroRNA-494 regulates Gli3 expression and inhibits pancreatic cancer cells growth and migration. J Cell Biochem 2018; 119:5324-5331. [PMID: 29315756 DOI: 10.1002/jcb.26658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/04/2018] [Indexed: 02/04/2023]
Abstract
MicroRNA (miR)-494 has been identified as a predictor and inhibitor in pancreatic cancer. This study aimed to explore the role of miR-494 in pancreatic cancer cells, and the regulation of glioma-associated oncogene 3 (Gli3) by miR-494. The mRNA level of Gli3 in 99 pairs of pancreatic cancer and correspondingly adjacent tissues was monitored by qRT-PCR. Correlation of Gli3 expression with miR-494 level was assessed by Pearson χ2 test. Dual-luciferase reporter assay was used to detect whether Gli3 was a target of miR-494. Following miR-494 mimics and miR-494 inhibitor transfection, the changes in cell viability and migration were detected by using CCK-8 and Transwell chamber. Furthermore, Gli3 siRNA was co-transfected with miR-494 inhibitor, and then cell viability and migration were redetected. Result showed that, the mRNA level of Gli3 in tumor tissues was higher than in the adjacent tissues (P < 0.01). There were 45 in 99 patients with pancreatic cancer expressed Gli3, and significant correlations were observed between the Gli3 level and vascular invasion (P = 0.04), distant metastasis (P = 0.001), and histologic grade (P = 0.03). Gli3 was a direct target of miR-494 (P < 0.01) and it was negatively related by miR-494 (P < 0.01). Overexpression of miR-494 suppressed PANC-1 cells viability (P < 0.05, P < 0.01, or P < 0.001) and migration (P < 0.01). Additionally, Gli3 silence suppresses miR-494 suppression-induced cell viability and migration (P < 0.01). In conclusion, these data demonstrate miR-494 exhibits tumor-suppressive effects on pancreatic cancer, possibly via targeting Gli3.
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Affiliation(s)
- Yongbiao Ma
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Hepatobiliary Surgery, Weifang People's Hospital, Weifang, China
| | - Gaoxue Li
- Department of Gastroenterology, Shouguang People's Hospital, Shouguang, China
| | - Jingxia Hu
- Department of General Surgery, Shouguang People's Hospital, Shouguang, China
| | - Xin Liu
- Department of Medical Oncology, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Baomin Shi
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of General Surgery, Tongji Hospital of Tongji University, Shanghai, China
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Lust K, Wittbrodt J. Activating the regenerative potential of Müller glia cells in a regeneration-deficient retina. eLife 2018; 7:32319. [PMID: 29376827 PMCID: PMC5815849 DOI: 10.7554/elife.32319] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/26/2018] [Indexed: 12/22/2022] Open
Abstract
Regeneration responses in animals are widespread across phyla. To identify molecular players that confer regenerative capacities to non-regenerative species is of key relevance for basic research and translational approaches. Here, we report a differential response in retinal regeneration between medaka (Oryzias latipes) and zebrafish (Danio rerio). In contrast to zebrafish, medaka Müller glia (olMG) cells behave like progenitors and exhibit a restricted capacity to regenerate the retina. After injury, olMG cells proliferate but fail to self-renew and ultimately only restore photoreceptors. In our injury paradigm, we observed that in contrast to zebrafish, proliferating olMG cells do not maintain sox2 expression. Sustained sox2 expression in olMG cells confers regenerative responses similar to those of zebrafish MG (drMG) cells. We show that a single, cell-autonomous factor reprograms olMG cells and establishes a regeneration-like mode. Our results position medaka as an attractive model to delineate key regeneration factors with translational potential. All animals have at least some ability to repair their bodies after injury. But certain species can regenerate entire body parts and even internal organs. Salamanders, for example, can regrow their tail and limbs, as well as their eyes and heart. Many species of fish can also regenerate organs and tissues. In comparison, mammals have only limited regenerative capacity. Why does regeneration vary between species, and is it possible to convert a non-regenerating system into a regenerating one? Laboratory studies of regeneration often use the model organism, zebrafish. Zebrafish can restore their sight after an eye injury by regenerating the retina, the light-sensitive tissue at the back of the eye. They are able to do this thanks to cells in the retina called Müller glial cells. These behave like stem cells. They divide to produce identical copies of themselves, which then transform into all of the different cell types necessary to produce a new retina. Lust and Wittbrodt now show that a distant relative of the zebrafish, the Japanese ricefish ‘medaka’, lacks these regenerative skills. Although Müller glial cells in medaka also divide after injury, they give rise to only a single type of retinal cell. This means that these fish cannot regenerate an entire retina. Lust and Wittbrodt demonstrate that in medaka, but not zebrafish, levels of a protein called Sox2 fall after eye injury. As Sox2 has been shown to be important for regeneration in zebrafish Müller glial cells, the loss of Sox2 may be preventing regeneration in medaka. Consistent with this, restoring Sox2 levels in medaka Müller glial cells enabled them to turn into several different types of retinal cell. Sox2 is also present in the Müller glial cells of other species with backbones, including chickens, mice, and humans. Future experiments should test whether loss of Sox2 after injury contributes to the lack of regeneration in these species. If it does, the next question will be whether restoring Sox2 can drive a regenerative response.
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Affiliation(s)
- Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Hartmut Hoffmann-Berling International Graduate School, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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Seleit A, Krämer I, Riebesehl BF, Ambrosio EM, Stolper JS, Lischik CQ, Dross N, Centanin L. Neural stem cells induce the formation of their physical niche during organogenesis. eLife 2017; 6. [PMID: 28950935 PMCID: PMC5617629 DOI: 10.7554/elife.29173] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/05/2017] [Indexed: 12/18/2022] Open
Abstract
Most organs rely on stem cells to maintain homeostasis during post-embryonic life. Typically, stem cells of independent lineages work coordinately within mature organs to ensure proper ratios of cell types. Little is known, however, on how these different stem cells locate to forming organs during development. Here we show that neuromasts of the posterior lateral line in medaka are composed of two independent life-long lineages with different embryonic origins. Clonal analysis and 4D imaging revealed a hierarchical organisation with instructing and responding roles: an inner, neural lineage induces the formation of an outer, border cell lineage (nBC) from the skin epithelium. Our results demonstrate that the neural lineage is necessary and sufficient to generate nBCs highlighting self-organisation principles at the level of the entire embryo. We hypothesise that induction of surrounding tissues plays a major role during the establishment of vertebrate stem cell niches.
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Affiliation(s)
- Ali Seleit
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg, Heidelberg, Germany
| | - Isabel Krämer
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg, Heidelberg, Germany
| | - Bea F Riebesehl
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany
| | - Elizabeth M Ambrosio
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany
| | - Julian S Stolper
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Australia
| | - Colin Q Lischik
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg, Heidelberg, Germany
| | - Nicolas Dross
- Nikon Imaging Center at the University of Heidelberg, Heidelberg, Germany
| | - Lazaro Centanin
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany
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38
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Tang X, Gao J, Jia X, Zhao W, Zhang Y, Pan W, He J. Bipotent progenitors as embryonic origin of retinal stem cells. J Cell Biol 2017; 216:1833-1847. [PMID: 28465291 PMCID: PMC5461025 DOI: 10.1083/jcb.201611057] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/01/2017] [Accepted: 04/03/2017] [Indexed: 01/24/2023] Open
Abstract
In lower vertebrates, retinal stem cells (RSCs) capable of producing all retinal cell types are a resource for retinal tissue growth throughout life. However, the embryonic origin of RSCs remains largely elusive. Using a Zebrabow-based clonal analysis, we characterized the RSC niche in the ciliary marginal zone of zebrafish retina and illustrate that blood vessels associated with RSCs are required for the maintenance of actively proliferating RSCs. Full lineage analysis of RSC progenitors reveals lineage patterns of RSC production. Moreover, in vivo lineage analysis demonstrates that these RSC progenitors are the direct descendants of a set of bipotent progenitors in the medial epithelial layer of developing optic vesicles, suggesting the involvement of the mixed-lineage states in the RSC lineage specification.
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Affiliation(s)
- Xia Tang
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianan Gao
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinling Jia
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wencao Zhao
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Yijie Zhang
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Weijun Pan
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Jie He
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
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39
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Shi D, Tavhelidse T, Thumberger T, Wittbrodt J, Greb T. Bifacial stem cell niches in fish and plants. Curr Opin Genet Dev 2017; 45:28-33. [PMID: 28242480 DOI: 10.1016/j.gde.2017.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/01/2017] [Accepted: 02/07/2017] [Indexed: 12/20/2022]
Abstract
Embryonic development is key for determining the architecture and shape of multicellular bodies. However, most cells are produced postembryonically in, at least partly, differentiated organs. In this regard, organismal growth faces common challenges in coordinating expansion and function of body structures. Here we compare two examples for postembryonic growth processes from two different kingdoms of life to reveal common regulatory principles: lateral growth of plants and the enlargement of the fish retina. In both cases, growth is based on stem cell systems mediating radial growth by a bifacial mode of tissue production. Surprisingly, although being evolutionary distinct, we find similar patterns in regulatory circuits suggesting the existence of preferable solutions to a common developmental problem.
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Affiliation(s)
- Dongbo Shi
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Greb
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.
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40
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Schäfer P, Karl MO. Prospective purification and characterization of Müller glia in the mouse retina regeneration assay. Glia 2017; 65:828-847. [PMID: 28220544 DOI: 10.1002/glia.23130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 01/06/2023]
Abstract
Reactive gliosis is an umbrella term for various glia functions in neurodegenerative diseases and upon injury. Specifically, Müller glia (MG) in some species readily regenerate retinal neurons to restore vision loss after insult, whereas mammalian MG respond by reactive gliosis-a heterogeneous response which frequently includes cell hypertrophy and proliferation. Limited regeneration has been stimulated in mammals, with a higher propensity in young MG, and in vitro compared to in vivo, but the underlying processes are unknown. To facilitate studies on the mechanisms regulating and limiting glia functions, we developed a strategy to purify glia and their progeny by fluorescence-activated cell sorting. Dual-transgenic nuclear reporter mice, which label neurons and glia with red and green fluorescent proteins, respectively, have enabled MG enrichment up to 93% purity. We applied this approach to MG in a mouse retina regeneration ex vivo assay. Combined cell size and cell cycle analysis indicates that most MG hypertrophy and a subpopulation proliferates which, over time, become even larger in cell size than the ones that do not proliferate. MG undergo timed differential genomic changes in genes controlling stemness and neurogenic competence; and glial markers are downregulated. Genes that are potentially required for, or associated with, regeneration and reactive gliosis are differentially regulated by retina explant culture time, epidermal growth factor stimulation, and animal age. Thus, MG enrichment facilitates cellular and molecular studies which, in combination with the mouse retina regeneration assay, provide an experimental approach for deciphering mechanisms that possibly regulate reactive gliosis and limit regeneration in mammals.
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Affiliation(s)
- Patrick Schäfer
- TU Dresden, Center for Regenerative Therapies Dresden (CRTD), Fetscherstr. 107, Dresden, 01307, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Arnoldstr. 13, Dresden, 01307, Germany
| | - Mike O Karl
- TU Dresden, Center for Regenerative Therapies Dresden (CRTD), Fetscherstr. 107, Dresden, 01307, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Arnoldstr. 13, Dresden, 01307, Germany
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41
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Cepero Malo M, Duchemin AL, Guglielmi L, Patzel E, Sel S, Auffarth GU, Carl M, Poggi L. The Zebrafish Anillin-eGFP Reporter Marks Late Dividing Retinal Precursors and Stem Cells Entering Neuronal Lineages. PLoS One 2017; 12:e0170356. [PMID: 28107513 PMCID: PMC5249142 DOI: 10.1371/journal.pone.0170356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/03/2017] [Indexed: 01/09/2023] Open
Abstract
Monitoring cycling behaviours of stem and somatic cells in the living animal is a powerful tool to better understand tissue development and homeostasis. The tg(anillin:anillin-eGFP) transgenic line carries the full-length zebrafish F-actin binding protein Anillin fused to eGFP from a bacterial artificial chromosome (BAC) containing Anillin cis-regulatory sequences. Here we report the suitability of the Anillin-eGFP reporter as a direct indicator of cycling cells in the late embryonic and post-embryonic retina. We show that combining the anillin:anillin-eGFP with other transgenes such as ptf1a:dsRed and atoh7:gap-RFP allows obtaining spatial and temporal resolution of the mitotic potentials of specific retinal cell populations. This is exemplified by the analysis of the origin of the previously reported apically and non-apically dividing late committed precursors of the photoreceptor and horizontal cell layers.
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Affiliation(s)
- Meret Cepero Malo
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Luca Guglielmi
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Eva Patzel
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Saadettin Sel
- The David J Apple Center for Vision Research, Department of Ophthalmology, Heidelberg University Hospital, Heidelberg, Germany
| | - Gerd U. Auffarth
- The David J Apple Center for Vision Research, Department of Ophthalmology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias Carl
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lucia Poggi
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
- The David J Apple Center for Vision Research, Department of Ophthalmology, Heidelberg University Hospital, Heidelberg, Germany
- * E-mail:
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43
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Orquera DP, de Souza FSJ. Evolution of the Rax family of developmental transcription factors in vertebrates. Mech Dev 2016; 144:163-170. [PMID: 27838261 DOI: 10.1016/j.mod.2016.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 11/01/2016] [Accepted: 11/07/2016] [Indexed: 02/09/2023]
Abstract
Rax proteins comprise a small family of paired-type, homeodomain-containing transcription factors with essential functions in eye and forebrain development. While invertebrates possess only one Rax gene, vertebrates can have several Rax paralogue genes, but the evolutionary history of the members of the family has not been studied in detail. Here, we present a thorough analysis of the evolutionary relationships between vertebrate Rax genes and proteins available in diverse genomic databases. Phylogenetic and synteny analyses indicate that Rax genes went through a duplication in an ancestor of all jawed vertebrates (Gnathostomata), giving rise to the ancestral vertebrate Rax1 and Rax2 genes. This duplication event is likely related to the proposed polyploidisations that occurred during early vertebrate evolution. Subsequent genome-wide duplications in the lineage of ray-finned fish (Actinopterygii) originated new Rax2 paralogues in the genomes of teleosts. In the lobe-finned fish lineage (Sarcopterygii), the N-terminal octapeptide domain of Rax2 was lost in a common ancestor of tetrapods, giving rise to a shorter version of Rax2 in this lineage. Within placental mammals, the Rax2 gene was lost altogether in an ancestor of rodents and lagomorphs (Glires). Finally, we discuss the scientific literature in the light of Rax gene evolution and propose new avenues of research on the function of this important family of transcriptional regulators.
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Affiliation(s)
- Daniela P Orquera
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, 1428 Buenos Aires, Argentina
| | - Flávio S J de Souza
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, 1428 Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina.
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44
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Gutierrez-Triana JA, Mateo JL, Ibberson D, Ryu S, Wittbrodt J. iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins. Development 2016; 143:4272-4278. [PMID: 27707796 PMCID: PMC5117216 DOI: 10.1242/dev.139261] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/26/2016] [Indexed: 02/02/2023]
Abstract
DNA adenine methyltransferase identification (DamID) has emerged as an alternative method to profile protein-DNA interactions; however, critical issues limit its widespread applicability. Here, we present iDamIDseq, a protocol that improves specificity and sensitivity by inverting the steps DpnI-DpnII and adding steps that involve a phosphatase and exonuclease. To determine genome-wide protein-DNA interactions efficiently, we present the analysis tool iDEAR (iDamIDseq Enrichment Analysis with R). The combination of DamID and iDEAR permits the establishment of consistent profiles for transcription factors, even in transient assays, as we exemplify using the small teleost medaka (Oryzias latipes). We report that the bacterial Dam-coding sequence induces aberrant splicing when it is used with different promoters to drive tissue-specific expression. Here, we present an optimization of the sequence to avoid this problem. This and our other improvements will allow researchers to use DamID effectively in any organism, in a general or targeted manner. Summary: Critical improvements to the DamID protocol improve specificity and sensitivity in determining genome-wide protein-DNA interactions in transient or stable transgenic animal lines.
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Affiliation(s)
- Jose Arturo Gutierrez-Triana
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg D-69120, Germany
| | - Juan L Mateo
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg D-69120, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, Cell Networks, University of Heidelberg, Im Neuenheimer 267, Heidelberg D-69120, Germany
| | - Soojin Ryu
- Developmental Genetics of the Nervous System, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg D-69120, Germany.,Focus Program Translational Neuroscience, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg D-69120, Germany
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45
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Hedgehog-dependent E3-ligase Midline1 regulates ubiquitin-mediated proteasomal degradation of Pax6 during visual system development. Proc Natl Acad Sci U S A 2016; 113:10103-8. [PMID: 27555585 DOI: 10.1073/pnas.1600770113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pax6 is a key transcription factor involved in eye, brain, and pancreas development. Although pax6 is expressed in the whole prospective retinal field, subsequently its expression becomes restricted to the optic cup by reciprocal transcriptional repression of pax6 and pax2 However, it remains unclear how Pax6 protein is removed from the eyestalk territory on time. Here, we report that Mid1, a member of the RBCC/TRIM E3 ligase family, which was first identified in patients with the X-chromosome-linked Opitz BBB/G (OS) syndrome, interacts with Pax6. We found that the forming eyestalk is a major domain of mid1 expression, controlled by the morphogen Sonic hedgehog (Shh). Here, Mid1 regulates the ubiquitination and proteasomal degradation of Pax6 protein. Accordantly, when Mid1 levels are knocked down, Pax6 expression is expanded and eyes are enlarged. Our findings indicate that remaining or misaddressed Pax6 protein is cleared from the eyestalk region to properly set the border between the eyestalk territory and the retina via Mid1. Thus, we identified a posttranslational mechanism, regulated by Sonic hedgehog, which is important to suppress Pax6 activity and thus breaks pax6 autoregulation at defined steps during the formation of the visual system.
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46
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Lust K, Sinn R, Pérez Saturnino A, Centanin L, Wittbrodt J. De novo neurogenesis by targeted expression of atoh7 to Müller glia cells. Development 2016; 143:1874-83. [PMID: 27068106 PMCID: PMC4920165 DOI: 10.1242/dev.135905] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/05/2016] [Indexed: 01/11/2023]
Abstract
Regenerative responses in the vertebrate CNS depend on quiescent radial glia stem cells, which re-enter the cell cycle and eventually differentiate into neurons. The entry into the cell cycle and the differentiation into neurons are events of opposite nature, and therefore efforts to force quiescent radial glia into neurons require different factors. Here, we use fish to show that a single neurogenic factor, Atoh7, directs retinal radial glia (Müller glia, MG) into proliferation. The resulting neurogenic clusters differentiate in vivo into various retinal neurons. We use signaling reporters to demonstrate that the Atoh7-induced regeneration-like response of MG cells is mimicked by Notch, resembling the behavior of early progenitors during retinogenesis. Activation of Notch signaling in MG cells is sufficient to trigger proliferation and differentiation. Our results uncover a new role for Atoh7 as a universal neurogenic factor, and illustrate how signaling modules are re-employed in diverse contexts to trigger different biological responses. Highlighted article: Induced activation of atoh7 in Müller glia cells in vivo is sufficient to drive cell cycle re-entry and proliferation, followed by the formation of neurogenic clusters and de novo neurogenesis.
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Affiliation(s)
- Katharina Lust
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg, Germany
| | - Rebecca Sinn
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg, Germany
| | - Alicia Pérez Saturnino
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg, Germany
| | - Lázaro Centanin
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
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47
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Abstract
This chapter introduces the principles and advantages of selective plane illumination microscopy (SPIM) and compares it to commonly used epifluorescence or confocal setups. Due to the low phototoxicity, speed of imaging, high penetration depth, and spatiotemporal resolution, SPIM is predestined for in vivo imaging but can as well be used for in toto analysis of large fixed samples. Key points of light-sheet microscopy are highlighted and discussed priming the investigator to choose the best suitable system from the large collection of possible SPIM setups. Mounting of samples is shown and the demands for data acquisition, processing, handling, and visualization are discussed.
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Affiliation(s)
- D Kromm
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - T Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - J Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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48
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Wan Y, Almeida AD, Rulands S, Chalour N, Muresan L, Wu Y, Simons BD, He J, Harris WA. The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue. Development 2016; 143:1099-107. [PMID: 26893352 PMCID: PMC4852496 DOI: 10.1242/dev.133314] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/09/2016] [Indexed: 01/07/2023]
Abstract
Clonal analysis is helping us understand the dynamics of cell replacement in homeostatic adult tissues (Simons and Clevers, 2011). Such an analysis, however, has not yet been achieved for continuously growing adult tissues, but is essential if we wish to understand the architecture of adult organs. The retinas of lower vertebrates grow throughout life from retinal stem cells (RSCs) and retinal progenitor cells (RPCs) at the rim of the retina, called the ciliary marginal zone (CMZ). Here, we show that RSCs reside in a niche at the extreme periphery of the CMZ and divide asymmetrically along a radial (peripheral to central) axis, leaving one daughter in the peripheral RSC niche and the other more central where it becomes an RPC. We also show that RPCs of the CMZ have clonal sizes and compositions that are statistically similar to progenitor cells of the embryonic retina and fit the same stochastic model of proliferation. These results link embryonic and postembryonic cell behaviour, and help to explain the constancy of tissue architecture that has been generated over a lifetime. Summary: A quantitative study of cell proliferation and fate choice in the zebrafish retina - a continuously growing neural tissue - reveals key features of late retinal neurogenesis.
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Affiliation(s)
- Yinan Wan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Alexandra D Almeida
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Steffen Rulands
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Cavendish Laboratory, Department of Physics, J.J. Thomson Avenue, University of Cambridge, Cambridge CB3 0HE, UK Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Naima Chalour
- Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Leila Muresan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Yunmin Wu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, J.J. Thomson Avenue, University of Cambridge, Cambridge CB3 0HE, UK Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jie He
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - William A Harris
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
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Alonso-Barba JI, Rahman RU, Wittbrodt J, Mateo JL. MEPD: medaka expression pattern database, genes and more. Nucleic Acids Res 2015; 44:D819-21. [PMID: 26450962 PMCID: PMC4702773 DOI: 10.1093/nar/gkv1029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The Medaka Expression Pattern Database (MEPD; http://mepd.cos.uni-heidelberg.de/) is designed as a repository of medaka expression data for the scientific community. In this update we present two main improvements. First, we have changed the previous clone-centric view for in situ data to a gene-centric view. This is possible because now we have linked all the data present in MEPD to the medaka gene annotation in ENSEMBL. In addition, we have also connected the medaka genes in MEPD to their corresponding orthologous gene in zebrafish, again using the ENSEMBL database. Based on this, we provide a link to the Zebrafish Model Organism Database (ZFIN) to allow researches to compare expression data between these two fish model organisms. As a second major improvement, we have modified the design of the database to enable it to host regulatory elements, promoters or enhancers, expression patterns in addition to gene expression. The combination of gene expression, by traditional in situ, and regulatory element expression, typically by fluorescence reporter gene, within the same platform assures consistency in terms of annotation. In our opinion, this will allow researchers to uncover new insights between the expression domain of genes and their regulatory landscape.
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Affiliation(s)
- Juan I Alonso-Barba
- Department of Computing Systems, University of Castilla-La Mancha, Albacete, 02071, Spain
| | - Raza-Ur Rahman
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Juan L Mateo
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
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