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Yin Z, Kang J, Cheng X, Gao H, Huo S, Xu H. Investigating Müller glia reprogramming in mice: a retrospective of the last decade, and a look to the future. Neural Regen Res 2025; 20:946-959. [PMID: 38989930 DOI: 10.4103/nrr.nrr-d-23-01612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/05/2024] [Indexed: 07/12/2024] Open
Abstract
Müller glia, as prominent glial cells within the retina, plays a significant role in maintaining retinal homeostasis in both healthy and diseased states. In lower vertebrates like zebrafish, these cells assume responsibility for spontaneous retinal regeneration, wherein endogenous Müller glia undergo proliferation, transform into Müller glia-derived progenitor cells, and subsequently regenerate the entire retina with restored functionality. Conversely, Müller glia in the mouse and human retina exhibit limited neural reprogramming. Müller glia reprogramming is thus a promising strategy for treating neurodegenerative ocular disorders. Müller glia reprogramming in mice has been accomplished with remarkable success, through various technologies. Advancements in molecular, genetic, epigenetic, morphological, and physiological evaluations have made it easier to document and investigate the Müller glia programming process in mice. Nevertheless, there remain issues that hinder improving reprogramming efficiency and maturity. Thus, understanding the reprogramming mechanism is crucial toward exploring factors that will improve Müller glia reprogramming efficiency, and for developing novel Müller glia reprogramming strategies. This review describes recent progress in relatively successful Müller glia reprogramming strategies. It also provides a basis for developing new Müller glia reprogramming strategies in mice, including epigenetic remodeling, metabolic modulation, immune regulation, chemical small-molecules regulation, extracellular matrix remodeling, and cell-cell fusion, to achieve Müller glia reprogramming in mice.
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Affiliation(s)
- Zhiyuan Yin
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Yuan F, Zhang R, Li J, Lei Q, Wang S, Jiang F, Guo Y, Xiang M. CCR5-overexpressing mesenchymal stem cells protect against experimental autoimmune uveitis: insights from single-cell transcriptome analysis. J Neuroinflammation 2024; 21:136. [PMID: 38802924 PMCID: PMC11131209 DOI: 10.1186/s12974-024-03134-3] [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: 01/09/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
Autoimmune uveitis is a leading cause of severe vision loss, and animal models provide unique opportunities for studying its pathogenesis and therapeutic strategies. Here we employ scRNA-seq, RNA-seq and various molecular and cellular approaches to characterize mouse models of classical experimental autoimmune uveitis (EAU), revealing that EAU causes broad retinal neuron degeneration and marker downregulation, and that Müller glia may act as antigen-presenting cells. Moreover, EAU immune response is primarily driven by Th1 cells, and results in dramatic upregulation of CC chemokines, especially CCL5, in the EAU retina. Accordingly, overexpression of CCR5, a CCL5 receptor, in mesenchymal stem cells (MSCs) enhances their homing capacity and improves their immunomodulatory outcomes in preventing EAU, by reducing infiltrating T cells and activated microglia and suppressing Nlrp3 inflammasome activation. Taken together, our data not only provide valuable insights into the molecular characteristics of EAU but also open an avenue for innovative MSC-based therapy.
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Affiliation(s)
- Fa Yuan
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Rong Zhang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jiani Li
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qiannan Lei
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Shuyi Wang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Fanying Jiang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yanan Guo
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
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Chen X, Tong P, Jiang Y, Cheng Z, Zang L, Yang Z, Lan W, Xia K, Hu Z, Tian Q. CCDC66 mutations are associated with high myopia through affected cell mitosis. J Med Genet 2024; 61:262-269. [PMID: 37852749 DOI: 10.1136/jmg-2023-109434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND High myopia (HM) refers to an eye refractive error exceeding -5.00 D, significantly elevating blindness risk. The underlying mechanism of HM remains elusive. Given the extensive genetic heterogeneity and vast genetic base opacity, it is imperative to identify more causative genes and explore their pathogenic roles in HM. METHODS We employed exome sequencing to pinpoint the causal gene in an HM family. Sanger sequencing was used to confirm and analyse the gene mutations in this family and 200 sporadic HM cases. Single-cell RNA sequencing was conducted to evaluate the gene's expression patterns in developing human and mouse retinas. The CRISPR/Cas9 system facilitated the gene knockout cells, aiding in the exploration of the gene's function and its mutations. Immunofluorescent staining and immunoblot techniques were applied to monitor the functional shifts of the gene mutations at the cellular level. RESULTS A suspected nonsense mutation (c.C172T, p.Q58X) in CCDC66 was found to be co-segregated with the HM phenotype in the family. Additionally, six other rare variants were identified among the 200 sporadic patients. CCDC66 was consistently expressed in the embryonic retinas of both humans and mice. Notably, in CCDC66-deficient HEK293 cells, there was a decline in cell proliferation, microtube polymerisation rate and ace-tubulin level. Furthermore, the mutated CCDC66 failed to synchronise with the tubulin system during Hela cell mitosis, unlike its wild type counterpart. CONCLUSIONS Our research indicates that the CCDC66 variant c.C172T is associated with HM. A deficiency in CCDC66 might disrupt cell proliferation by influencing the mitotic process during retinal growth, leading to HM.
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Affiliation(s)
- Xiaozhen Chen
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Key Laboratory of Animal Models for Human Disease, Central South University, Changsha, Hunan, People's Republic of China
- Furong Laboratory, Central South University, Changsha, Hunan, People's Republic of China
| | - Ping Tong
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Ying Jiang
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Key Laboratory of Animal Models for Human Disease, Central South University, Changsha, Hunan, People's Republic of China
- Furong Laboratory, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhe Cheng
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Key Laboratory of Animal Models for Human Disease, Central South University, Changsha, Hunan, People's Republic of China
- Furong Laboratory, Central South University, Changsha, Hunan, People's Republic of China
| | - Liyu Zang
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Key Laboratory of Animal Models for Human Disease, Central South University, Changsha, Hunan, People's Republic of China
- Furong Laboratory, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhikuan Yang
- Aier Eye Hospital (Hunan), Aier Eye Hospital Group, Changsha, Hunan, People's Republic of China
- Aier School of Ophthalmology, Central South University, Changsha, Hunan, People's Republic of China
| | - Weizhong Lan
- Aier Eye Hospital (Hunan), Aier Eye Hospital Group, Changsha, Hunan, People's Republic of China
- Aier School of Ophthalmology, Central South University, Changsha, Hunan, People's Republic of China
| | - Kun Xia
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Key Laboratory of Animal Models for Human Disease, Central South University, Changsha, Hunan, People's Republic of China
- Furong Laboratory, Central South University, Changsha, Hunan, People's Republic of China
- MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Zhengmao Hu
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Key Laboratory of Animal Models for Human Disease, Central South University, Changsha, Hunan, People's Republic of China
- Furong Laboratory, Central South University, Changsha, Hunan, People's Republic of China
| | - Qi Tian
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Key Laboratory of Animal Models for Human Disease, Central South University, Changsha, Hunan, People's Republic of China
- Furong Laboratory, Central South University, Changsha, Hunan, People's Republic of China
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Xu Z, Guo Y, Xiang K, Xiao D, Xiang M. Rapid and efficient generation of a transplantable population of functional retinal ganglion cells from fibroblasts. Cell Prolif 2024; 57:e13550. [PMID: 37740641 PMCID: PMC10849786 DOI: 10.1111/cpr.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/24/2023] Open
Abstract
Glaucoma and other optic neuropathies lead to progressive and irreversible vision loss by damaging retinal ganglion cells (RGCs) and their axons. Cell replacement therapy is a potential promising treatment. However, current methods to obtain RGCs have inherent limitations, including time-consuming procedures, inefficient yields and complex protocols, which hinder their practical application. Here, we have developed a straightforward, rapid and efficient approach for directly inducing RGCs from mouse embryonic fibroblasts (MEFs) using a combination of triple transcription factors (TFs): ASCL1, BRN3B and PAX6 (ABP). We showed that on the 6th day following ABP induction, neurons with molecular characteristics of RGCs were observed, and more than 60% of induced neurons became iRGCs (induced retinal ganglion cells) in the end. Transplanted iRGCs had the ability to survive and appropriately integrate into the RGC layer of mouse retinal explants and N-methyl-D-aspartic acid (NMDA)-damaged retinas. Moreover, they exhibited electrophysiological properties typical of RGCs, and were able to regrow dendrites and axons and form synaptic connections with host retinal cells. Together, we have established a rapid and efficient approach to acquire functional RGCs for potential cell replacement therapy to treat glaucoma and other optic neuropathies.
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Affiliation(s)
- Zihui Xu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat‐sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Yanan Guo
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat‐sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Kangjian Xiang
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat‐sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Dongchang Xiao
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat‐sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
| | - Mengqing Xiang
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic Center, Sun Yat‐sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhouChina
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
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Qu Z, Batz Z, Singh N, Marchal C, Swaroop A. Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids. Cell Rep 2023; 42:113543. [PMID: 38048222 PMCID: PMC10790351 DOI: 10.1016/j.celrep.2023.113543] [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: 05/12/2023] [Revised: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
We have generated a high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive stage-specific alterations in DNA topology and correlate these changes with transcription of cell-type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift toward A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression, respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages (i.e., TAD cliques) localize in active chromatin regions with binding sites for eye-field transcription factors. These genes gain chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.
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Affiliation(s)
- Zepeng Qu
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Zachary Batz
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Nivedita Singh
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Claire Marchal
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA; In silichrom Ltd, 15 Digby Road, Newbury RG14 1TS, UK
| | - Anand Swaroop
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
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Peng YR. Cell-type specification in the retina: Recent discoveries from transcriptomic approaches. Curr Opin Neurobiol 2023; 81:102752. [PMID: 37499619 DOI: 10.1016/j.conb.2023.102752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
Understanding the formation of the complex nervous system hinges on decoding the mechanism that specifies a vast array of neuronal types, each endowed with a unique morphology, physiology, and connectivity. As a pivotal step towards addressing this problem, seminal work has been devoted to characterizing distinct neuronal types. In recent years, high-throughput, single-cell transcriptomic methods have enabled a rapid inventory of cell types in various regions of the nervous system, with the retina exhibiting complete molecular characterization across many vertebrate species. This invaluable resource has furnished a fresh perspective for investigating the molecular principles of cell-type specification, thereby advancing our understanding of retinal development. Accordingly, this review focuses on the most recent transcriptomic characterizations of retinal cells, with a particular focus on amacrine cells and retinal ganglion cells. These investigations have unearthed new insights into their cell-type specification.
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Affiliation(s)
- Yi-Rong Peng
- Department of Ophthalmology and Stein Eye Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA.
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7
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Móvio MI, de Lima-Vasconcellos TH, Dos Santos GB, Echeverry MB, Colombo E, Mattos LS, Resende RR, Kihara AH. Retinal organoids from human-induced pluripotent stem cells: From studying retinal dystrophies to early diagnosis of Alzheimer's and Parkinson's disease. Semin Cell Dev Biol 2023; 144:77-86. [PMID: 36210260 DOI: 10.1016/j.semcdb.2022.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022]
Abstract
Human-induced pluripotent stem cells (hiPSCs) have provided new methods to study neurodegenerative diseases. In addition to their wide application in neuronal disorders, hiPSCs technology can also encompass specific conditions, such as inherited retinal dystrophies. The possibility of evaluating alterations related to retinal disorders in 3D organoids increases the truthfulness of in vitro models. Moreover, both Alzheimer's (AD) and Parkinson's disease (PD) have been described as causing early retinal alterations, generating beta-amyloid protein accumulation, or affecting dopaminergic amacrine cells. This review addresses recent advances and future perspectives obtained from in vitro modeling of retinal diseases, focusing on retinitis pigmentosa (RP). Additionally, we depicted the possibility of evaluating changes related to AD and PD in retinal organoids obtained from potential patients long before the onset of the disease, constituting a valuable tool in early diagnosis. With this, we pointed out prospects in the study of retinal dystrophies and early diagnosis of AD and PD.
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Affiliation(s)
- Marília Inês Móvio
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | | | | | - Marcela Bermudez Echeverry
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Elisabetta Colombo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Leonardo S Mattos
- Biomedical Robotics Laboratory, Department of Advanced Robotics, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Rodrigo Ribeiro Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexandre Hiroaki Kihara
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil; Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil.
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Li R, Liu J, Yi P, Yang X, Chen J, Zhao C, Liao X, Wang X, Xu Z, Lu H, Li H, Zhang Z, Liu X, Xiang J, Hu K, Qi H, Yu J, Yang P, Hou S. Integrative Single-Cell Transcriptomics and Epigenomics Mapping of the Fetal Retina Developmental Dynamics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206623. [PMID: 37017569 DOI: 10.1002/advs.202206623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/24/2023] [Indexed: 06/04/2023]
Abstract
The underlying mechanisms that determine gene expression and chromatin accessibility in retinogenesis are poorly understood. Herein, single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin sequencing are performed on human embryonic eye samples obtained 9-26 weeks after conception to explore the heterogeneity of retinal progenitor cells (RPCs) and neurogenic RPCs. The differentiation trajectory from RPCs to 7 major types of retinal cells are verified. Subsequently, diverse lineage-determining transcription factors are identified and their gene regulatory networks are refined at the transcriptomic and epigenomic levels. Treatment of retinospheres, with the inhibitor of RE1 silencing transcription factor, X5050, induces more neurogenesis with the regular arrangement, and a decrease in Müller glial cells. The signatures of major retinal cells and their correlation with pathogenic genes associated with multiple ocular diseases, including uveitis and age-related macular degeneration are also described. A framework for the integrated exploration of single-cell developmental dynamics of the human primary retina is provided.
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Affiliation(s)
- Ruonan Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Jiangyi Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, P. R. China
| | - Xianli Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, P. R. China
| | - Jun Chen
- Department of Obstetrics, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401147, P. R. China
| | - Chenyang Zhao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Xingyun Liao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, P. R. China
| | - Xiaotang Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Zongren Xu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
| | - Huiping Lu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Hongshun Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Zhi Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Xianyang Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Junjie Xiang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Ke Hu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Hongbo Qi
- Department of Obstetrics, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401147, P. R. China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, P. R. China
- The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100005, P. R. China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, 100730, P. R. China
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9
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Yu D, Wu Y, Zhu L, Wang Y, Sheng D, Zhao X, Liang G, Gan L. The landscape of the long non-coding RNAs in developing mouse retinas. BMC Genomics 2023; 24:252. [PMID: 37165305 PMCID: PMC10173636 DOI: 10.1186/s12864-023-09354-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND The long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for neurogenesis study, still needs to be made available. RESULTS Herein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways. CONCLUSIONS In summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.
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Affiliation(s)
- Dongliang Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China.
| | - Yuqing Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Leilei Zhu
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Yuying Wang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Donglai Sheng
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Xiaofeng Zhao
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Guoqing Liang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China.
| | - Lin Gan
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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10
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Urbán P, Pöstyéni E, Czuni L, Herczeg R, Fekete C, Gábriel R, Kovács-Valasek A. miRNA Profiling of Developing Rat Retina in the First Three Postnatal Weeks. Cell Mol Neurobiol 2023:10.1007/s10571-023-01347-3. [PMID: 37084144 DOI: 10.1007/s10571-023-01347-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
The morphogenesis of the mammalian retina depends on the precise control of gene expression during development. Small non-coding RNAs, including microRNAs play profound roles in various physiological and pathological processes via gene expression regulation. A systematic analysis of the expression profile of small non-coding RNAs in developing Wistar rat retinas (postnatally day 5 (P5), P7, P10, P15 and P21) was executed using IonTorrent PGM next-generation sequencing technique to reveal the crucial players in the early postnatal retinogenesis. Our analysis reveals extensive regulatory potential of microRNAs during retinal development. We found a group of microRNAs that show constant high abundance (miR-19, miR-101; miR-181, miR-183, miR-124 and let-7) during the development process. Others are present only in the early stages (miR-20a, miR-206, miR-133, miR-466, miR-1247, miR-3582), or at later stages (miR-29, miR-96, miR-125, miR-344 or miR-664). Further miRNAs were detected which are differentially expressed in time. Finally, pathway enrichment analysis has revealed 850 predicted target genes that mainly participate in lipid-, amino acid- and glycan metabolisms in the examined time-period (P5-P21). P5-P7 transition revealed the importance of miRNAs in glutamatergic synapse and gap junction pathways. Significantly downregulated miRNAs rno-miR-30c1 and 2, rno-miR-205 and rno-miR-503 were detected to target Prkx (ENSRNOG00000003696), Adcy6 (ENSRNOG00000011587), Gnai3 (ENSRNOG00000019465) and Gja1 (ENSRNOG00000000805) genes. The dataset described here will be a valuable resource for clarifying new regulatory mechanisms for retinal development and will greatly contribute to our understanding of the divergence and function of microRNAs.
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Affiliation(s)
- Péter Urbán
- János Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Department of General and Environmental Microbiology, University of Pécs, Pecs, Hungary
| | - Etelka Pöstyéni
- Experimental Zoology and Neurobiology, University of Pécs, Pecs, Hungary
| | - Lilla Czuni
- János Szentágothai Research Centre, University of Pécs, Pecs, Hungary
| | - Róbert Herczeg
- János Szentágothai Research Centre, University of Pécs, Pecs, Hungary
| | - Csaba Fekete
- Department of General and Environmental Microbiology, University of Pécs, Pecs, Hungary
| | - Róbert Gábriel
- János Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Experimental Zoology and Neurobiology, University of Pécs, Pecs, Hungary
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11
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Ge Y, Chen X, Nan N, Bard J, Wu F, Yergeau D, Liu T, Wang J, Mu X. Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res 2023; 51:2151-2176. [PMID: 36715342 PMCID: PMC10018358 DOI: 10.1093/nar/gkad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
How the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. In this study, we dissect the changes in the epigenetic landscape during early retinal cell differentiation by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages. Using CUT&Tag, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2 and Isl1, including those dependent on Atoh7, and uncover the sequential and combinatorial interactions of these factors with the epigenetic landscape to control gene expression along individual retinal cell lineages such as retinal ganglion cells (RGCs). Our results reveal a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from multipotent retinal progenitor cells (RPCs).
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xushen Chen
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Nan Nan
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jie Wang
- Correspondence may also be addressed to Jie Wang.
| | - Xiuqian Mu
- To whom correspondence should be addressed. Tel: +1 716 881 7463; Fax: +1 716 887 2991;
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12
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Zheng X, Guo Y, Zhang R, Chen H, Liu S, Qiu S, Xiang M. The mitochondrial micropeptide Stmp1 promotes retinal cell differentiation. Biochem Biophys Res Commun 2022; 636:79-86. [DOI: 10.1016/j.bbrc.2022.10.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
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13
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Insm1 promotes differentiation of retinal progenitor cells toward photoreceptor cells in the developing retina through up-regulation of SHH. J Mol Histol 2022; 53:947-954. [PMID: 36260151 DOI: 10.1007/s10735-022-10103-8] [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: 04/24/2022] [Accepted: 09/10/2022] [Indexed: 10/24/2022]
Abstract
This article investigated the effect of Insm1 on RPC differentiation in mice and the underlying mechanism. The retinal tissues of mouse embryo at 12.5 days (E12.5) and postnatal 14 days (P14) were collected, following by the detection of Insm1 and corresponding markers by immunofluorescent staining. RPCs isolated from retinal tissues at P1 were cultured in culture medium for 7 days. The differentiation of photoreceptor and glial cells was assessed after RPCs transferred to the differentiation medium for 20 days. Next, the effect of Insm1 overexpression on the differentiation of RPCs toward rod photoreceptor and glial cells were assessed. Insm1 was highly expressed in RPCs of retinal tissues and decline in photoreceptor cells, while hardly expressed in glial cells. Based on the results of Pax-6 positive immunofluorescent staining and flow cytometry detection, RPCs were successfully isolated from retinal tissues. After the culture in differentiation medium, RPCs showed positive staining of Rhodopsin and glial fibrillary acidic protein (GFAP). Further results showed that overexpression of Insm1 significantly increased the percentage of Rhodopsin positive cells, and up-regulated Sonic Hedgehog (SHH), hairy and enhancer of split homolog-1(Hes1), S-opsin and Rhodopsin levels, while decreased the percentage of Glutamine synthetase positive cells, and reduced Glutamine synthetase and GFAP levels. Whereas, the effect of Insm1 overexpression on these protein levels were partly abolished by the knockdown of SHH or Hes1. We conclude that Insm1 promotes the differentiation of RPCs into photoreceptor cells in the developing retina through up-regulation of SHH.
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14
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Chew SH, Martinez C, Chirco KR, Kandoi S, Lamba DA. Timed Notch Inhibition Drives Photoreceptor Fate Specification in Human Retinal Organoids. Invest Ophthalmol Vis Sci 2022; 63:12. [PMID: 36129723 PMCID: PMC9513742 DOI: 10.1167/iovs.63.10.12] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Transplanting photoreceptors from human pluripotent stem cell–derived retinal organoids have the potential to reverse vision loss in affected individuals. However, transplantable photoreceptors are only a subset of all cells in the organoids. Hence, the goal of our current study was to accelerate and synchronize photoreceptor differentiation in retinal organoids by inhibiting the Notch signaling pathway at different developmental time-points using a small molecule, PF-03084014 (PF). Methods Human induced pluripotent stem cell– and human embryonic stem cells–derived retinal organoids were treated with 10 µM PF for 3 days starting at day 45 (D45), D60, D90, and D120 of differentiation. Organoids were collected at post-treatment days 14, 28, and 42 and analyzed for progenitor and photoreceptor markers and Notch pathway inhibition by immunohistochemistry (IHC), quantitative PCR, and bulk RNA sequencing (n = 3–5 organoids from three independent experiments). Results Retinal organoids collected after treatment showed a decrease in progenitor markers (KI67, VSX2, PAX6, and LHX2) and an increase in differentiated pan-photoreceptor markers (OTX2, CRX, and RCVRN) at all organoid stages except D120. PF-treated organoids at D45 and D60 exhibited an increase in cone photoreceptor markers (RXRG and ARR3). PF treatment at D90 revealed an increase in cone and rod photoreceptors markers (ARR3, NRL, and NR2E3). Bulk RNA sequencing analysis mirrored the immunohistochemistry data and quantitative PCR confirmed Notch effector inhibition. Conclusions Timing the Notch pathway inhibition in human retinal organoids to align with progenitor competency stages can yield an enriched population of early cone or rod photoreceptors.
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Affiliation(s)
- Shereen H Chew
- Department of Ophthalmology, University of California San Francisco, California, United States.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, California, United States
| | - Cassandra Martinez
- Department of Ophthalmology, University of California San Francisco, California, United States.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, California, United States
| | - Kathleen R Chirco
- Department of Ophthalmology, University of California San Francisco, California, United States.,Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States
| | - Sangeetha Kandoi
- Department of Ophthalmology, University of California San Francisco, California, United States.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, California, United States
| | - Deepak A Lamba
- Department of Ophthalmology, University of California San Francisco, California, United States.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, California, United States
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15
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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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16
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Bachu VS, Kandoi S, Park KU, Kaufman ML, Schwanke M, Lamba DA, Brzezinski JA. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas. Dev Biol 2022; 488:131-150. [PMID: 35644251 PMCID: PMC10676565 DOI: 10.1016/j.ydbio.2022.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023]
Abstract
How cone photoreceptors are formed during retinal development is only partially known. This is in part because we do not fully understand the gene regulatory network responsible for cone genesis. We reasoned that cis-regulatory elements (enhancers) active in nascent cones would be regulated by the same upstream network that controls cone formation. To dissect this network, we searched for enhancers active in developing cones. By electroporating enhancer-driven fluorescent reporter plasmids, we observed that a sequence within an intron of the cone-specific Pde6c gene acted as an enhancer in developing mouse cones. Similar fluorescent reporter plasmids were used to generate stable transgenic human induced pluripotent stem cells that were then grown into three-dimensional human retinal organoids. These organoids contained fluorescently labeled cones, demonstrating that the Pde6c enhancer was also active in human cones. We observed that enhancer activity was transient and labeled a minor population of developing rod photoreceptors in both mouse and human systems. This cone-enriched pattern argues that the Pde6c enhancer is activated in cells poised between rod and cone fates. Additionally, it suggests that the Pde6c enhancer is activated by the same regulatory network that selects or stabilizes cone fate choice. To further understand this regulatory network, we identified essential enhancer sequence regions through a series of mutagenesis experiments. This suggested that the Pde6c enhancer was regulated by transcription factor binding at five or more locations. Binding site predictions implicated transcription factor families known to control photoreceptor formation and families not previously associated with cone development. These results provide a framework for deciphering the gene regulatory network that controls cone genesis in both human and mouse systems. Our new transgenic human stem cell lines provide a tool for determining which cone developmental mechanisms are shared and distinct between mice and humans.
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Affiliation(s)
- Vismaya S Bachu
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sangeetha Kandoi
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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17
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Self-Organization of the Retina during Eye Development, Retinal Regeneration In Vivo, and in Retinal 3D Organoids In Vitro. Biomedicines 2022; 10:biomedicines10061458. [PMID: 35740479 PMCID: PMC9221005 DOI: 10.3390/biomedicines10061458] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/23/2022] Open
Abstract
Self-organization is a process that ensures histogenesis of the eye retina. This highly intricate phenomenon is not sufficiently studied due to its biological complexity and genetic heterogeneity. The review aims to summarize the existing central theories and ideas for a better understanding of retinal self-organization, as well as to address various practical problems of retinal biomedicine. The phenomenon of self-organization is discussed in the spatiotemporal context and illustrated by key findings during vertebrate retina development in vivo and retinal regeneration in amphibians in situ. Described also are histotypic 3D structures obtained from the disaggregated retinal progenitor cells of birds and retinal 3D organoids derived from the mouse and human pluripotent stem cells. The review highlights integral parts of retinal development in these conditions. On the cellular level, these include competence, differentiation, proliferation, apoptosis, cooperative movements, and migration. On the physical level, the focus is on the mechanical properties of cell- and cell layer-derived forces and on the molecular level on factors responsible for gene regulation, such as transcription factors, signaling molecules, and epigenetic changes. Finally, the self-organization phenomenon is discussed as a basis for the production of retinal organoids, a promising model for a wide range of basic scientific and medical applications.
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18
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Ning R, Zheng D, Xie B, Gao G, Xu J, Xu P, Wang Y, Peng F, Jiang B, Ge J, Zhong X. Spatial and Temporal Development of Müller Glial Cells in hiPSC-Derived Retinal Organoids Facilitates the Cell Enrichment and Transcriptome Analysis. Front Cell Neurosci 2022; 16:820396. [PMID: 35663427 PMCID: PMC9160306 DOI: 10.3389/fncel.2022.820396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Müller glial cells (MGCs) play important roles in human retina during physiological and pathological conditions. However, the development process of human MGCs in vivo remains unclear, and how to obtain large numbers of human MGCs with high quality faces technical challenges, which hinder the further study and application of MGCs. Human induced pluripotent stem cell (hiPSC)-derived retinal organoids (ROs) with all retinal cell subtypes provide an unlimited cell resource and a platform for the studies of retinal development and disorders. This study explored the development of human MGCs in hiPSC-derived ROs and developed an approach to select and expand the induced MGCs (iMGCs). In ROs, retinal progenitor cells progressively differentiated into SOX9+ Ki67– MGC precursors during differentiation day (D) 60 to D90, while mature MGCs expressing markers CRALBP and GS gradually appeared since D120, which spanned the entire thickness of the neural retina layer. Cells isolated from ROs aged older than 120 days was an optimal source for the enrichment of iMGCs with high purity and expansion ability. They had typical features of human MGCs in morphological, structural, molecular and functional aspects, and could be passaged serially at least 10 times, yielding large numbers of cells in a short period. The transcriptome pattern of the expanded iMGCs was also revealed. This study firstly clarified the timecourse of human MGC development in the RO model, where the iMGCs could be enriched and expanded, paving the way for downstream investigation and application in MGC-related retinal disorders.
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Affiliation(s)
- Rong Ning
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dandan Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Bingbing Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Guanjie Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jinhai Xu
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ping Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yuan Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Fuhua Peng
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Bin Jiang
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jian Ge
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiufeng Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- *Correspondence: Xiufeng Zhong
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19
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Álvarez-Hernán G, de Mera-Rodríguez JA, Hernández-Núñez I, Acedo A, Marzal A, Gañán Y, Martín-Partido G, Rodríguez-León J, Francisco-Morcillo J. Timing and Distribution of Mitotic Activity in the Retina During Precocial and Altricial Modes of Avian Development. Front Neurosci 2022; 16:853544. [PMID: 35615284 PMCID: PMC9125163 DOI: 10.3389/fnins.2022.853544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
During development of the vertebrate retina, mitotic activity is defined as apical when is located at the external surface of the neuroepithelium or as non-apical when is found in more internal regions. Apical mitoses give rise to all retinal cell types. Non-apical mitoses are linked to committed horizontal cell precursors that subsequently migrate vitreo-sclerally, reaching their final position in the outer surface of the inner nuclear layer, where they differentiate. Previous studies have suggested differences in the timing of retinal maturation between altricial and precocial bird species. In the present study we analyze qualitatively and quantitatively the mitotic activity in the developing retina of an altricial (zebra finch, Taeniopygia guttata) and a precocial (Japanese quail, Coturnix coturnix) bird species. We found that pHisH3-immunoreactive apical and non-apical mitoses were abundant in the T. guttata retina at the hatching stage. In contrast, pHisH3 immunoreactivity almost disappeared from the quail retina at the embryonic day 10 (E10). Furthermore, we also found that the onset of the appearance of non-apical mitoses occurred at later stages in the altricial bird species than in the precocial one. The disappearance of apical mitoses and the spatiotemporal distribution of non-apical mitoses followed central to peripheral and dorsal to ventral gradients, similar to gradients of cell differentiation described in the retina of birds. Therefore, these results suggest that retinal neurogenesis is active at the hatching stage in T. guttata, and that horizontal cell differentiation is delayed in the altricial bird species compared to the precocial one. Together, this study reveals important insights into the timing differences that regulate bird retinal maturation and provides a better understanding of the evolution of avian altriciality and precociality.
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Affiliation(s)
- Guadalupe Álvarez-Hernán
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | | | - Ismael Hernández-Núñez
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Abel Acedo
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Alfonso Marzal
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Yolanda Gañán
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, Badajoz, Spain
| | - Gervasio Martín-Partido
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Joaquín Rodríguez-León
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, Badajoz, Spain
- *Correspondence: Joaquín Rodríguez-León,
| | - Javier Francisco-Morcillo
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
- Javier Francisco-Morcillo,
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20
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One-step induction of photoreceptor-like cells from human iPSCs by delivering transcription factors. iScience 2022; 25:103987. [PMID: 35330684 PMCID: PMC8938283 DOI: 10.1016/j.isci.2022.103987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/10/2022] [Accepted: 02/24/2022] [Indexed: 11/22/2022] Open
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21
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Wang X, Sarver AL, Han Q, Seiler CL, Xie C, Lu H, Forster CL, Tretyakova NY, Hallstrom TC. UHRF2 regulates cell cycle, epigenetics and gene expression to control the timing of retinal progenitor and ganglion cell differentiation. Development 2022; 149:274710. [PMID: 35285483 PMCID: PMC8984156 DOI: 10.1242/dev.195644] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 01/28/2022] [Indexed: 11/20/2022]
Abstract
Ubiquitin-like, containing PHD and RING finger domains 2 (UHRF2) regulates cell cycle and binds 5-hydroxymethylcytosine (5hmC) to promote completion of DNA demethylation. Uhrf2-/- mice are without gross phenotypic defects; however, the cell cycle and epigenetic regulatory functions of Uhrf2 during retinal tissue development are unclear. Retinal progenitor cells (RPCs) produce all retinal neurons and Müller glia in a predictable sequence controlled by the complex interplay between extrinsic signaling, cell cycle, epigenetic changes and cell-specific transcription factor activation. In this study, we find that UHRF2 accumulates in RPCs, and its conditional deletion from mouse RPCs reduced 5hmC, altered gene expressions and disrupted retinal cell proliferation and differentiation. Retinal ganglion cells were overproduced in Uhrf2-deficient retinae at the expense of VSX2+ RPCs. Most other cell types were transiently delayed in differentiation. Expression of each member of the Tet3/Uhrf2/Tdg active demethylation pathway was reduced in Uhrf2-deficient retinae, consistent with locally reduced 5hmC in their gene bodies. This study highlights a novel role of UHRF2 in controlling the transition from RPCs to differentiated cell by regulating cell cycle, epigenetic and gene expression decisions.
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Affiliation(s)
- Xiaohong Wang
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron L Sarver
- Institute for Health Informatics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Qiyuan Han
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher L Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chencheng Xie
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Huarui Lu
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Colleen L Forster
- BioNet, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy C Hallstrom
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
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22
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Tan S, Yao Y, Yang Q, Yuan XL, Cen LP, Ng TK. Diversified Treatment Options of Adult Stem Cells for Optic Neuropathies. Cell Transplant 2022; 31. [PMID: 36165292 PMCID: PMC9523835 DOI: 10.1177/09636897221123512] [Citation(s) in RCA: 2] [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: 04/21/2022] [Revised: 07/28/2022] [Accepted: 08/16/2022] [Indexed: 02/05/2023] Open
Abstract
Optic neuropathies refer to a group of ocular disorders with abnormalities or dysfunction of the optic nerve, sharing a common pathophysiology of retinal ganglion cell (RGC) death and axonal loss. RGCs, as the retinal neurons in the central nervous system, show limited capacity in regeneration or recovery upon diseases or after injuries. Critically, there is still no effective clinical treatment to cure most types of optic neuropathies. Recently, stem cell therapy was proposed as a potential treatment strategy for optic neuropathies. Adult stem cells, including mesenchymal stem cells and hematopoietic stem cells, have been applied in clinical trials based on their neuroprotective properties. In this article, the applications of adult stem cells on different types of optic neuropathies and the related mechanisms will be reviewed. Research updates on the strategies to enhance the neuroprotective effects of human adult stem cells will be summarized. This review article aims to enlighten the research scientists on the diversified functions of adult stem cells and consideration of adult stem cells as a potential treatment for optic neuropathies in future clinical practices.
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Affiliation(s)
- Shaoying Tan
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong
- Research Centre for SHARP Vision, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Yao Yao
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Qichen Yang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong
| | - Xiang-Ling Yuan
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Ling-Ping Cen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
- Shantou University Medical College, Shantou, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong
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23
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Xiao D, Jin K, Qiu S, Lei Q, Huang W, Chen H, Su J, Xu Q, Xu Z, Gou B, Tie X, Liu F, Liu S, Liu Y, Xiang M. In vivo Regeneration of Ganglion Cells for Vision Restoration in Mammalian Retinas. Front Cell Dev Biol 2021; 9:755544. [PMID: 34671605 PMCID: PMC8520940 DOI: 10.3389/fcell.2021.755544] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022] Open
Abstract
Glaucoma and other optic neuropathies affect millions of people worldwide, ultimately causing progressive and irreversible degeneration of retinal ganglion cells (RGCs) and blindness. Previous research into cell replacement therapy of these neurodegenerative diseases has been stalled due to the incapability for grafted RGCs to integrate into the retina and project properly along the long visual pathway. In vivo RGC regeneration would be a promising alternative approach but mammalian retinas lack regenerative capacity. It therefore has long been a great challenge to regenerate functional and properly projecting RGCs for vision restoration in mammals. Here we show that the transcription factors (TFs) Math5 and Brn3b together are able to reprogram mature mouse Müller glia (MG) into RGCs. The reprogrammed RGCs extend long axons that make appropriate intra-retinal and extra-retinal projections through the entire visual pathway to innervate both image-forming and non-image-forming brain targets. They exhibit typical neuronal electrophysiological properties and improve visual responses in RGC loss mouse models. Together, our data provide evidence that mammalian MG can be reprogrammed by defined TFs to achieve in vivo regeneration of functional RGCs as well as a promising new therapeutic approach to restore vision to patients with glaucoma and other optic neuropathies.
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Affiliation(s)
- Dongchang Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Kangxin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Suo Qiu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiannan Lei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wanjing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Haiqiao Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jing Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiang Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zihui Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bin Gou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoxiu Tie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Feng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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24
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Chen K, Chen C, Li H, Yang J, Xiang M, Wang H, Xie Z. Widespread translational control regulates retinal development in mouse. Nucleic Acids Res 2021; 49:9648-9664. [PMID: 34469513 PMCID: PMC8464051 DOI: 10.1093/nar/gkab749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022] Open
Abstract
Retinal development is tightly regulated to ensure the generation of appropriate cell types and the assembly of functional neuronal circuitry. Despite remarkable advances have been made in understanding regulation of gene expression during retinal development, how translational regulation guides retinogenesis is less understood. Here, we conduct a comprehensive translatome and transcriptome survey to the mouse retinogenesis from the embryonic to the adult stages. We discover thousands of genes that have dynamic changes at the translational level and pervasive translational regulation in a developmental stage-specific manner with specific biological functions. We further identify genes whose translational efficiencies are frequently controlled by changing usage in upstream open reading frame during retinal development. These genes are enriched for biological functions highly important to neurons, such as neuron projection organization and microtubule-based protein transport. Surprisingly, we discover hundreds of previously uncharacterized micropeptides, translated from putative long non-coding RNAs and circular RNAs. We validate their protein products in vitro and in vivo and demonstrate their potentials in regulating retinal development. Together, our study presents a rich and complex landscape of translational regulation and provides novel insights into their roles during retinogenesis.
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Affiliation(s)
- Kaining Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Congying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Huihui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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25
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Features of Retinal Neurogenesis as a Key Factor of Age-Related Neurodegeneration: Myth or Reality? Int J Mol Sci 2021; 22:ijms22147373. [PMID: 34298993 PMCID: PMC8303671 DOI: 10.3390/ijms22147373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex multifactorial neurodegenerative disease that constitutes the most common cause of irreversible blindness in the elderly in the developed countries. Incomplete knowledge about its pathogenesis prevents the search for effective methods of prevention and treatment of AMD, primarily of its "dry" type which is by far the most common (90% of all AMD cases). In the recent years, AMD has become "younger": late stages of the disease are now detected in relatively young people. It is known that AMD pathogenesis-according to the age-related structural and functional changes in the retina-is linked with inflammation, hypoxia, oxidative stress, mitochondrial dysfunction, and an impairment of neurotrophic support, but the mechanisms that trigger the conversion of normal age-related changes to the pathological process as well as the reason for early AMD development remain unclear. In the adult mammalian retina, de novo neurogenesis is very limited. Therefore, the structural and functional features that arise during its maturation and formation can exert long-term effects on further ontogenesis of this tissue. The aim of this review was to discuss possible contributions of the changes/disturbances in retinal neurogenesis to the early development of AMD.
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26
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Wu M, Deng Q, Lei X, Du Y, Shen Y. Elavl2 Regulates Retinal Function Via Modulating the Differentiation of Amacrine Cells Subtype. Invest Ophthalmol Vis Sci 2021; 62:1. [PMID: 34061953 PMCID: PMC8185395 DOI: 10.1167/iovs.62.7.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose The neuronal ELAV-like proteins (nElavls; Elavl2, Elavl3, Elavl4) have been known to regulate neuronal differentiation, maintenance, and axonogenesis in the brain. However, the specific role of nElavls in retina remains unclear. Here, we attempted to identify the expression pattern of Elavl2 during retinogenesis and aimed to decipher the function of Elavl2 in the retina. Methods We have used the Cre-loxP system to conditionally inactivate Elavl2 in order to examine its role in developing retina. Eyes were collected for histology, immunohistochemistry, and TUNEL analysis to identify the structure of retina, and examined by RNA sequencing to analyze the function and pathway enrichment of differentially expressed genes in transgenic mice. Moreover, the mechanism by which Elavl2 regulates the differentiation of amacrine cells (ACs) was explored by RNA immunoprecipitation assays. Finally, eyes were functionally assessed by whole-cell patch-clamp, electroretinography (ERG) and optomotor response. Results Elavl2 was expressed in retinal progenitor cells and retinal ganglion cells (RGCs), ACs, and horizontal cells. Retina-specific ablation of Elavl2 led to the loss of ACs and the transcription factors involved in ACs differentiation were also downregulated. In addition, the spontaneous activities of RGCs were obviously increased in Elavl2-deficient mice. Meanwhile, the loss of ACs that induced by Elavl2 deficiency lead to a decrease in ERG responses and visual acuity. Conclusions Elavl2 is an intrinsic factor that involved in the differentiation of ACs subtype during retinogenesis, and essential for maintaining the normal retinal function.
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Affiliation(s)
- Mengjuan Wu
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Qinqin Deng
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Xinlan Lei
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Yuxin Du
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Yin Shen
- Eye Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, Hubei, China
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27
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Zhang X, Mandric I, Nguyen KH, Nguyen TTT, Pellegrini M, Grove JCR, Barnes S, Yang XJ. Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development. Front Cell Dev Biol 2021; 9:653305. [PMID: 34055784 PMCID: PMC8155690 DOI: 10.3389/fcell.2021.653305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog2 in human ES cell-derived retinal organoids. Single cell transcriptome analyses identify three states of proliferating retinal progenitors: pre-neurogenic, neurogenic, and cell cycle-exiting progenitors. Each shows different expression profile of bHLH factors. The cell cycle-exiting progenitors feed into a postmitotic heterozygous neuroblast pool that gives rise to early born neuronal lineages. Elevating ATOH7 or Neurog2 expression accelerates the transition from the pre-neurogenic to the neurogenic state, and expands the exiting progenitor and neuroblast populations. In addition, ATOH7 and Neurog2 significantly, yet differentially, enhance retinal ganglion cell and cone photoreceptor production. Moreover, single cell transcriptome analyses reveal that ATOH7 and Neurog2 each assert positive autoregulation, and both suppress key bHLH factors associated with the pre-neurogenic and states and elevate bHLH factors expressed by exiting progenitors and differentiating neuroblasts. This study thus provides novel insight regarding how ATOH7 and Neurog2 impact human retinal progenitor behaviors and neuroblast fate choices.
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Affiliation(s)
- Xiangmei Zhang
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Igor Mandric
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin H Nguyen
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thao T T Nguyen
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - James C R Grove
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Steven Barnes
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Doheny Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xian-Jie Yang
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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28
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Shams Najafabadi H, Sadeghi M, Zibaii MI, Soheili ZS, Samiee S, Ghasemi P, Hosseini M, Gholami Pourbadie H, Ahmadieh H, Taghizadeh S, Ranaei Pirmardan E. Optogenetic control of neural differentiation in Opto-mGluR6 engineered retinal pigment epithelial cell line and mesenchymal stem cells. J Cell Biochem 2021; 122:851-869. [PMID: 33847009 DOI: 10.1002/jcb.29918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 11/11/2022]
Abstract
In retinal degenerative disorders, when neural retinal cells are damaged, cell transplantation is one of the most promising therapeutic approaches. Optogenetic technology plays an essential role in the neural differentiation of stem cells via membrane depolarization. This study explored the efficacy of blue light stimulation in neuroretinal differentiation of Opto-mGluR6-engineered mouse retinal pigment epithelium (mRPE) and bone marrow mesenchymal stem cells (BMSCs). mRPE and BMSCs were selected for optogenetic study due to their capability to differentiate into retinal-specific neurons. BMSCs were isolated and phenotypically characterized by the expression of mesenchymal stem cell-specific markers, CD44 (99%) and CD105 (98.8%). mRPE culture identity was confirmed by expression of RPE-specific marker, RPE65, and epithelial cell marker, ZO-1. mRPE cells and BMSCs were transduced with AAV-MCS-IRES-EGFP-Opto-mGluR6 viral vector and stimulated for 5 days with blue light (470 nm). RNA and protein expression of Opto-mGluR6 were verified. Optogenetic stimulation-induced elevated intracellular Ca2+ levels in mRPE- and BMS-treated cells. Significant increase in cell growth rate and G1/S phase transition were detected in mRPE- and BMSCs-treated cultures. Pou4f1, Dlx2, Eomes, Barlh2, Neurod2, Neurod6, Rorb, Rxrg, Nr2f2, Ascl1, Hes5, and Sox8 were overexpressed in treated BMSCs and Barlh2, Rorb, and Sox8 were overexpressed in treated mRPE cells. Expression of Rho, Thy1, OPN1MW, Recoverin, and CRABP, as retinal-specific neuron markers, in mRPE and BMS cell cultures were demonstrated. Differentiation of ganglion, amacrine, photoreceptor cells, and bipolar and Muller precursors were determined in BMSCs-treated culture and were compared with mRPE. mRPE cells represented more abundant terminal Muller glial differentiation compared with BMSCs. Our results also demonstrated that optical stimulation increased the intracellular Ca2+ level and proliferation and differentiation of Opto-mGluR6-engineered BMSCs. It seems that optogenetic stimulation of mRPE- and BMSCs-engineered cells would be a potential therapeutic approach for retinal degenerative disorders.
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Affiliation(s)
- Hoda Shams Najafabadi
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mehdi Sadeghi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad I Zibaii
- Laser & Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Zahra-Soheila Soheili
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Shahram Samiee
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Pouria Ghasemi
- Laser & Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Hosseini
- Laser & Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
| | | | - Hamid Ahmadieh
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepideh Taghizadeh
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Ehsan Ranaei Pirmardan
- Molecular Biomarkers Nano-imaging Laboratory, Brigham & Women's Hospital, Department of Radiology, Harvard Medical School, Boston, MA, USA
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29
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Wu F, Bard JE, Kann J, Yergeau D, Sapkota D, Ge Y, Hu Z, Wang J, Liu T, Mu X. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nat Commun 2021; 12:1465. [PMID: 33674582 PMCID: PMC7935890 DOI: 10.1038/s41467-021-21704-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Atoh7 has been believed to be essential for establishing the retinal ganglion cell (RGC) lineage, and Pou4f2 and Isl1 are known to regulate RGC specification and differentiation. Here we report our further study of the roles of these transcription factors. Using bulk RNA-seq, we identify genes regulated by the three transcription factors, which expand our understanding of the scope of downstream events. Using scRNA-seq on wild-type and mutant retinal cells, we reveal a transitional cell state of retinal progenitor cells (RPCs) co-marked by Atoh7 and other genes for different lineages and shared by all early retinal lineages. We further discover the unexpected emergence of the RGC lineage in the absence of Atoh7. We conclude that competence of RPCs for different retinal fates is defined by lineage-specific genes co-expressed in the transitional state and that Atoh7 defines the RGC competence and collaborates with other factors to shepherd transitional RPCs to the RGC lineage.
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Affiliation(s)
- Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jonathan E Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Julien Kann
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Zihua Hu
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA.
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA.
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30
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Pöstyéni E, Kovács-Valasek A, Urbán P, Czuni L, Sétáló G, Fekete C, Gabriel R. Analysis of mir-9 Expression Pattern in Rat Retina during Postnatal Development. Int J Mol Sci 2021; 22:ijms22052577. [PMID: 33806574 PMCID: PMC7961372 DOI: 10.3390/ijms22052577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 12/31/2022] Open
Abstract
It is well established that miR-9 contributes to retinal neurogenesis. However, little is known about its presence and effects in the postnatal period. To expand our knowledge, miRNA-small RNA sequencing and in situ hybridization supported by RT-qPCR measurement were carried out. Mir-9 expression showed two peaks in the first three postnatal weeks in Wistar rats. The first peak was detected at postnatal Day 3 (P3) and the second at P10, then the expression gradually decreased until P21. Furthermore, we performed in silico prediction and established that miR-9 targets OneCut2 or synaptotagmin-17. Another two microRNAs (mir-135, mir-218) were found from databases which also target these proteins. They showed a similar tendency to mir-9; their lowest expression was at P7 and afterwards, they showed increase. We revealed that miR-9 is localized mainly in the inner retina. Labeling was observed in ganglion and amacrine cells. Additionally, horizontal cells were also marked. By dual miRNA-in situ hybridization/immunocytochemistry and qPCR, we revealed alterations in their temporal and spatial expression. Our results shed light on the significance of mir-9 regulation during the first three postnatal weeks in rat retina and suggest that miRNA could act on their targets in a stage-specific manner.
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Affiliation(s)
- Etelka Pöstyéni
- Department of Experimental Zoology and Neurobiology, University of Pécs, 7624 Pécs, Hungary;
| | - Andrea Kovács-Valasek
- Department of Experimental Zoology and Neurobiology, University of Pécs, 7624 Pécs, Hungary;
- Correspondence: (A.K.-V.); (R.G.)
| | - Péter Urbán
- János Szentágothai Research Centre, 7624 Pécs, Hungary; (P.U.); (L.C.); (C.F.)
| | - Lilla Czuni
- János Szentágothai Research Centre, 7624 Pécs, Hungary; (P.U.); (L.C.); (C.F.)
| | - György Sétáló
- Department of Medical Biology, Medical School, University of Pécs, 7624 Pécs, Hungary;
| | - Csaba Fekete
- János Szentágothai Research Centre, 7624 Pécs, Hungary; (P.U.); (L.C.); (C.F.)
| | - Robert Gabriel
- Department of Experimental Zoology and Neurobiology, University of Pécs, 7624 Pécs, Hungary;
- Department of Medical Biology, Medical School, University of Pécs, 7624 Pécs, Hungary;
- Correspondence: (A.K.-V.); (R.G.)
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de Mera-Rodríguez JA, Álvarez-Hernán G, Gañán Y, Martín-Partido G, Rodríguez-León J, Francisco-Morcillo J. Is Senescence-Associated β-Galactosidase a Reliable in vivo Marker of Cellular Senescence During Embryonic Development? Front Cell Dev Biol 2021; 9:623175. [PMID: 33585480 PMCID: PMC7876289 DOI: 10.3389/fcell.2021.623175] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 01/10/2023] Open
Abstract
During vertebrate embryonic development, cellular senescence occurs at multiple locations. To date, it has been accepted that when there has been induction of senescence in an embryonic tissue, β-galactosidase activity is detectable at a pH as high as 6.0, and this has been extensively used as a marker of cellular senescence in vivo in both whole-mount and cryosections. Such senescence-associated β-galactosidase (SA-β-GAL) labeling appears enhanced in degenerating regions of the vertebrate embryo that are also affected by programmed cell death. In this sense, there is a strong SA-β-GAL signal which overlaps with the pattern of cell death in the interdigital tissue of the developing limbs, and indeed, many of the labeled cells detected go on to subsequently undergo apoptosis. However, it has been reported that β-GAL activity at pH 6.0 is also enhanced in healthy neurons, and some retinal neurons are strongly labeled with this histochemical technique when they begin to differentiate during early embryonic development. These labeled early post-mitotic neurons also express other senescence markers such as p21. Therefore, the reliability of this histochemical technique in studying senescence in cells such as neurons that undergo prolonged and irreversible cell-cycle arrest is questionable because it is also expressed in healthy post-mitotic cells. The identification of new biomarkers of cellular senescence would, in combination with established markers, increase the specificity and efficiency of detecting cellular senescence in embryonic and healthy mature tissues.
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Affiliation(s)
- José Antonio de Mera-Rodríguez
- Área de Biología Celular, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Guadalupe Álvarez-Hernán
- Área de Biología Celular, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Yolanda Gañán
- Área de Anatomía y Embriología Humana, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Gervasio Martín-Partido
- Área de Biología Celular, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Joaquín Rodríguez-León
- Área de Anatomía y Embriología Humana, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Javier Francisco-Morcillo
- Área de Biología Celular, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
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Kadkhodaeian HA. Mesenchymal Stem Cells: Signaling Pathways in Transdifferentiation Into Retinal Progenitor Cells. Basic Clin Neurosci 2021; 12:29-42. [PMID: 33995925 PMCID: PMC8114861 DOI: 10.32598/bcn.9.10.510] [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: 07/16/2018] [Revised: 08/25/2018] [Accepted: 02/02/2020] [Indexed: 11/29/2022] Open
Abstract
Several signaling pathways and transcription factors control the cell fate in its in vitro development and differentiation. The orchestrated use of these factors results in cell specification. In coculture methods, many of these factors secrete from host cells but control the process. Today, transcription factors required for retinal progenitor cells are well known, but the generation of these cells from mesenchymal stem cells is an ideal goal. The purpose of the paper is to review novel methods for retinal progenitor cell production and selecting a set of signaling molecules in the presence of adult retinal pigment epithelium and extraocular mesenchyme acting as inducers of retinal cell differentiation.
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Álvarez-Hernán G, de Mera-Rodríguez JA, Gañán Y, Solana-Fajardo J, Martín-Partido G, Rodríguez-León J, Francisco-Morcillo J. Development and postnatal neurogenesis in the retina: a comparison between altricial and precocial bird species. Neural Regen Res 2021; 16:16-20. [PMID: 32788442 PMCID: PMC7818864 DOI: 10.4103/1673-5374.286947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/14/2020] [Accepted: 04/07/2020] [Indexed: 01/09/2023] Open
Abstract
The visual system is affected by neurodegenerative diseases caused by the degeneration of specific retinal neurons, the leading cause of irreversible blindness in humans. Throughout vertebrate phylogeny, the retina has two kinds of specialized niches of constitutive neurogenesis: the retinal progenitors located in the circumferential marginal zone and Müller glia. The proliferative activity in the retinal progenitors located in the circumferential marginal zone in precocial birds such as the chicken, the commonest bird model used in developmental and regenerative studies, is very low. This region adds only a few retinal cells to the peripheral edge of the retina during several months after hatching, but does not seem to be involved in retinal regeneration. Müller cells in the chicken retina are not proliferative under physiological conditions, but after acute damage some of them undergo a reprogramming event, dedifferentiating into retinal stem cells and generating new retinal neurons. Therefore, regenerative response after injury occurs with low efficiency in the precocial avian retina. In contrast, it has recently been shown that neurogenesis is intense in the retina of altricial birds at hatching. In particular, abundant proliferative activity is detected both in the circumferential marginal zone and in the outer half of the inner nuclear layer. Therefore, stem cell niches are very active in the retina of altricial birds. Although more extensive research is needed to assess the potential of proliferating cells in the adult retina of altricial birds, it emerges as an attractive model for studying different aspects of neurogenesis and neural regeneration in vertebrates.
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Affiliation(s)
- Guadalupe Álvarez-Hernán
- Área de Biología Celular, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - José Antonio de Mera-Rodríguez
- Área de Anatomía Humana, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Yolanda Gañán
- Área de Anatomía Humana, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Jorge Solana-Fajardo
- Servicio de Oftalmología, Complejo Hospitalario Universitario de Badajoz, Badajoz, Spain
| | - Gervasio Martín-Partido
- Área de Biología Celular, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | - Joaquín Rodríguez-León
- Área de Anatomía Humana, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Medicina, Universidad de Extremadura, Badajoz, Spain
| | - Javier Francisco-Morcillo
- Área de Biología Celular, Departamento de Anatomía, Biología Celular y Zoología, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
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Ge Y, Wu F, Cheng M, Bard J, Mu X. Two new genetically modified mouse alleles labeling distinct phases of retinal ganglion cell development by fluorescent proteins. Dev Dyn 2020; 249:1514-1528. [PMID: 32741043 PMCID: PMC7855626 DOI: 10.1002/dvdy.233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND During development, all retinal cell types arise from retinal progenitor cells (RPCs) in a step-wise fashion. Atoh7 and Pou4f2 mark, and function in, two phases of retinal ganglion cell (RGC) genesis; Atoh7 functions in a subpopulation of RPCs to render them competent for the RGC fate, whereas Pou4f2 participates in RGC fate specification and RGC differentiation. Despite extensive research on their roles, the properties of the two phases represented by these two factors have not been well studied, likely due to the retinal cellular heterogeneity. RESULTS In this report, we describe two novel knock-in mouse alleles, Atoh7zsGreenCreERT2 and Pou4f2FlagtdTomato , which labeled retinal cells in the two phases of RGC development by fluorescent proteins. Also, the Atoh7zsGreenCreERT2 allele allowed for indirect labeling of RGCs and other cell types upon tamoxifen induction in a dose-dependent manner. Further, these alleles could be used to purify retinal cells in the different phases by fluorescence assisted cell sorting (FACS). Single cell RNA-seq analysis of purified cells from Atoh7zsGreenCreERT2 retinas further validated that this allele labeled both transitional/competent RPCs and their progenies including RGCs. CONCLUSIONS Thus, these two alleles are very useful tools for studying the molecular and genetic mechanisms underlying RGC formation.
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
| | - Mobin Cheng
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY
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Iwagawa T, Honda H, Watanabe S. Jmjd3 Plays Pivotal Roles in the Proper Development of Early-Born Retinal Lineages: Amacrine, Horizontal, and Retinal Ganglion Cells. Invest Ophthalmol Vis Sci 2020; 61:43. [PMID: 32986815 PMCID: PMC7533738 DOI: 10.1167/iovs.61.11.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Purpose Trimethylation of histone H3 at lysine 27 (H3K27me3) is a critical mediator of transcriptional gene repression, and Jmjd3 and Utx are the demethylases specific to H3K27me3. Using an in vitro retinal explant culture system, we previously revealed the role of Jmjd3 in the development of rod bipolar cells; however, the roles of Jmjd3 in the development of early-born retinal cells are unknown due to limitations concerning the use of retinal explant culture systems. In this study, we investigated the roles of Jmjd3 in the development of early-born retinal cells. Methods We examined retina-specific conditional Jmjd3 knockout (Jmjd3-cKO) mice using immunohistochemistry and quantitative reverse transcription PCR and JMJD3 binding to a target locus by chromatin immunoprecipitation analysis. Results We observed reductions in amacrine cells (ACs) and horizontal cells (HCs), as well as lowered expression levels of several transcription factors involved in the development of ACs and HCs in the Jmjd3-cKO mouse retina. JMJD3 bound the promoter regions of these transcription factors. Notably, an elevated number of retinal ganglion cells (RGCs) was observed at embryonic stages, whereas RGCs were moderately reduced at later postnatal stages in the Jmjd3-cKO retina. We also observed reduced expression of Eomes, which is required for the maintenance of RGCs, as well as lower H3K27me3 level and lower JMJD3 binding in the promoter region of Eomes in RGC-enriched cells. Conclusions The results indicated that Jmjd3 has critical roles in the development of early-born retinal subtypes, and suggested biphasic roles of Jmjd3 in RGC production and maintenance.
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Affiliation(s)
- Toshiro Iwagawa
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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Dose-dependent regulation of horizontal cell fate by Onecut family of transcription factors. PLoS One 2020; 15:e0237403. [PMID: 32790713 PMCID: PMC7425962 DOI: 10.1371/journal.pone.0237403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/24/2020] [Indexed: 11/19/2022] Open
Abstract
Genome duplication leads to an emergence of gene paralogs that are essentially free to undergo the process of neofunctionalization, subfunctionalization or degeneration (gene loss). Onecut1 (Oc1) and Onecut2 (Oc2) transcription factors, encoded by paralogous genes in mammals, are expressed in precursors of horizontal cells (HCs), retinal ganglion cells and cone photoreceptors. Previous studies have shown that ablation of either Oc1 or Oc2 gene in the mouse retina results in a decreased number of HCs, while simultaneous deletion of Oc1 and Oc2 leads to a complete loss of HCs. Here we study the genetic redundancy between Oc1 and Oc2 paralogs and focus on how the dose of Onecut transcription factors influences abundance of individual retinal cell types and overall retina physiology. Our data show that reducing the number of functional Oc alleles in the developing retina leads to a gradual decrease in the number of HCs, progressive thinning of the outer plexiform layer and diminished electrophysiology responses. Taken together, these observations indicate that in the context of HC population, the alleles of Oc1/Oc2 paralogous genes are mutually interchangeable, function additively to support proper retinal function and their molecular evolution does not follow one of the typical routes after gene duplication.
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Goodson NB, Kaufman MA, Park KU, Brzezinski JA. Simultaneous deletion of Prdm1 and Vsx2 enhancers in the retina alters photoreceptor and bipolar cell fate specification, yet differs from deleting both genes. Development 2020; 147:dev190272. [PMID: 32541005 PMCID: PMC10666920 DOI: 10.1242/dev.190272] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022]
Abstract
The transcription factor OTX2 is required for photoreceptor and bipolar cell formation in the retina. It directly activates the transcription factors Prdm1 and Vsx2 through cell type-specific enhancers. PRDM1 and VSX2 work in opposition, such that PRDM1 promotes photoreceptor fate and VSX2 bipolar cell fate. To determine how OTX2+ cell fates are regulated in mice, we deleted Prdm1 and Vsx2 or their cell type-specific enhancers simultaneously using a CRISPR/Cas9 in vivo retina electroporation strategy. Double gene or enhancer targeting effectively removed PRDM1 and VSX2 protein expression. However, double enhancer targeting favored bipolar fate outcomes, whereas double gene targeting favored photoreceptor fate. Both conditions generated excess amacrine cells. Combined, these fate changes suggest that photoreceptors are a default fate outcome in OTX2+ cells and that VSX2 must be present in a narrow temporal window to drive bipolar cell formation. Prdm1 and Vsx2 also appear to redundantly restrict the competence of OTX2+ cells, preventing amacrine cell formation. By taking a combinatorial deletion approach of both coding sequences and enhancers, our work provides new insights into the complex regulatory mechanisms that control cell fate choice.
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Affiliation(s)
- Noah B Goodson
- Sue Anschutz Rodgers Eye Center, Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael A Kaufman
- Sue Anschutz Rodgers Eye Center, Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Cell Biology, Stem Cells, and Development Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ko U Park
- Sue Anschutz Rodgers Eye Center, Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joseph A Brzezinski
- Sue Anschutz Rodgers Eye Center, Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Zerti D, Collin J, Queen R, Cockell SJ, Lako M. Understanding the complexity of retina and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospective. Curr Eye Res 2020; 45:385-396. [PMID: 31794277 PMCID: PMC7034531 DOI: 10.1080/02713683.2019.1697453] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 12/21/2022]
Abstract
Single-cell sequencing technologies have emerged as a revolutionary tool with transformative new methods to profile genetic, epigenetic, spatial, and lineage information in individual cells. Single-cell RNA sequencing (scRNA-Seq) allows researchers to collect large datasets detailing the transcriptomes of individual cells in space and time and is increasingly being applied to reveal cellular heterogeneity in retinal development, normal physiology, and disease, and provide new insights into cell-type specific markers and signaling pathways. In recent years, scRNA-Seq datasets have been generated from retinal tissue and pluripotent stem cell-derived retinal organoids. Their cross-comparison enables staging of retinal organoids, identification of specific cells in developing and adult human neural retina and provides deeper insights into cell-type sub-specification and geographical differences. In this article, we review the recent rapid progress in scRNA-Seq analyses of retina and retinal organoids, the questions that remain unanswered and the technical challenges that need to be overcome to achieve consistent results that reflect the complexity, functionality, and interactions of all retinal cell types.
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Affiliation(s)
- Darin Zerti
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Joseph Collin
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Rachel Queen
- Bioinformatics Core Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Simon J. Cockell
- Bioinformatics Core Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
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Markitantova Y, Simirskii V. Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes. Int J Mol Sci 2020; 21:E1602. [PMID: 32111086 PMCID: PMC7084737 DOI: 10.3390/ijms21051602] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Retinal development is under the coordinated control of overlapping networks of signaling pathways and transcription factors. The paper was conceived as a review of the data and ideas that have been formed to date on homeobox genes mutations that lead to the disruption of eye organogenesis and result in inherited eye/retinal diseases. Many of these diseases are part of the same clinical spectrum and have high genetic heterogeneity with already identified associated genes. We summarize the known key regulators of eye development, with a focus on the homeobox genes associated with monogenic eye diseases showing retinal manifestations. Recent advances in the field of genetics and high-throughput next-generation sequencing technologies, including single-cell transcriptome analysis have allowed for deepening of knowledge of the genetic basis of inherited retinal diseases (IRDs), as well as improve their diagnostics. We highlight some promising avenues of research involving molecular-genetic and cell-technology approaches that can be effective for IRDs therapy. The most promising neuroprotective strategies are aimed at mobilizing the endogenous cellular reserve of the retina.
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Foxn4 is a temporal identity factor conferring mid/late-early retinal competence and involved in retinal synaptogenesis. Proc Natl Acad Sci U S A 2020; 117:5016-5027. [PMID: 32071204 DOI: 10.1073/pnas.1918628117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During development, neural progenitors change their competence states over time to sequentially generate different types of neurons and glia. Several cascades of temporal transcription factors (tTFs) have been discovered in Drosophila to control the temporal identity of neuroblasts, but the temporal regulation mechanism is poorly understood in vertebrates. Mammalian retinal progenitor cells (RPCs) give rise to several types of neuronal and glial cells following a sequential yet overlapping temporal order. Here, by temporal cluster analysis, RNA-sequencing analysis, and loss-of-function and gain-of-function studies, we show that the Fox domain TF Foxn4 functions as a tTF during retinogenesis to confer RPCs with the competence to generate the mid/late-early cell types: amacrine, horizontal, cone, and rod cells, while suppressing the competence of generating the immediate-early cell type: retinal ganglion cells (RGCs). In early embryonic retinas, Foxn4 inactivation causes down-regulation of photoreceptor marker genes and decreased photoreceptor generation but increased RGC production, whereas its overexpression has the opposite effect. Just as in Drosophila, Foxn4 appears to positively regulate its downstream tTF Casz1 while negatively regulating its upstream tTF Ikzf1. Moreover, retina-specific ablation of Foxn4 reveals that it may be indirectly involved in the synaptogenesis, establishment of laminar structure, visual signal transmission, and long-term maintenance of the retina. Together, our data provide evidence that Foxn4 acts as a tTF to bias RPCs toward the mid/late-early cell fates and identify a missing member of the tTF cascade that controls RPC temporal identities to ensure the generation of proper neuronal diversity in the retina.
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Quinn PM, Wijnholds J. Retinogenesis of the Human Fetal Retina: An Apical Polarity Perspective. Genes (Basel) 2019; 10:E987. [PMID: 31795518 PMCID: PMC6947654 DOI: 10.3390/genes10120987] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
The Crumbs complex has prominent roles in the control of apical cell polarity, in the coupling of cell density sensing to downstream cell signaling pathways, and in regulating junctional structures and cell adhesion. The Crumbs complex acts as a conductor orchestrating multiple downstream signaling pathways in epithelial and neuronal tissue development. These pathways lead to the regulation of cell size, cell fate, cell self-renewal, proliferation, differentiation, migration, mitosis, and apoptosis. In retinogenesis, these are all pivotal processes with important roles for the Crumbs complex to maintain proper spatiotemporal cell processes. Loss of Crumbs function in the retina results in loss of the stratified appearance resulting in retinal degeneration and loss of visual function. In this review, we begin by discussing the physiology of vision. We continue by outlining the processes of retinogenesis and how well this is recapitulated between the human fetal retina and human embryonic stem cell (ESC) or induced pluripotent stem cell (iPSC)-derived retinal organoids. Additionally, we discuss the functionality of in utero and preterm human fetal retina and the current level of functionality as detected in human stem cell-derived organoids. We discuss the roles of apical-basal cell polarity in retinogenesis with a focus on Leber congenital amaurosis which leads to blindness shortly after birth. Finally, we discuss Crumbs homolog (CRB)-based gene augmentation.
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Affiliation(s)
- Peter M.J. Quinn
- Department of Ophthalmology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
- The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
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Lin S, Guo J, Chen S. Transcriptome and DNA Methylome Signatures Associated With Retinal Müller Glia Development, Injury Response, and Aging. ACTA ACUST UNITED AC 2019; 60:4436-4450. [DOI: 10.1167/iovs.19-27361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Siyuan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jingyi Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuyi Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Dvoriantchikova G, Seemungal RJ, Ivanov D. DNA Methylation Dynamics During the Differentiation of Retinal Progenitor Cells Into Retinal Neurons Reveal a Role for the DNA Demethylation Pathway. Front Mol Neurosci 2019; 12:182. [PMID: 31396051 PMCID: PMC6667802 DOI: 10.3389/fnmol.2019.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/10/2019] [Indexed: 12/18/2022] Open
Abstract
To evaluate the contribution of the DNA methylation and DNA demethylation pathways in retinal development, we studied DNA methylation in retinal progenitor cells (RPCs) and retinal neurons using a combination of whole genome bisulfite sequencing (WGBS) data obtained in our study and WGBS data collected from previous studies. The data was analyzed using Hidden Markov Model- and change point-based methods to identify methylome states in different segments of the studied genomes following genome annotation. We found that promoters of rod and cone phototransduction genes and rod photoreceptor genes, but not genes required for the development and function of other retinal phenotypes, were highly methylated in DNA isolated from human and murine fetal retinas (which mostly contain RPCs) and postnatal murine RPCs. While these highly methylated genomic regions were inherited by non-photoreceptor phenotypes during RPC differentiation, the methylation of these promoters was significantly reduced during RPC differentiation into photoreceptors and accompanied by increased expression of these genes. Our analysis of DNA methylation during embryogenesis revealed low methylation levels in genomic regions containing photoreceptor genes at the inner cell mass stage, but a sharp increase in methylation at the epiblast stage, which remained the same later on (except for DNA demethylation in photoreceptors). Thus, our data suggest that the DNA demethylation pathway is required for photoreceptor phenotypes in the developing retina. Meanwhile, the role of the DNA methylation and DNA demethylation pathways during RPC differentiation into non-photoreceptor retinal phenotypes might be less important.
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Affiliation(s)
- Galina Dvoriantchikova
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Rajeev J Seemungal
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Dmitry Ivanov
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
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44
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Wan Y, Liu X, Zheng D, Wang Y, Chen H, Zhao X, Liang G, Yu D, Gan L. Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing. BMC Genomics 2019; 20:559. [PMID: 31286854 PMCID: PMC6615288 DOI: 10.1186/s12864-019-5903-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Background A great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, the biological roles of lncRNAs in the mouse retina remains largely unknown due to the lack of a comprehensive annotation of lncRNAs expressed in the retina. Results In this study, we applied the long-reads sequencing strategy to unravel the transcriptomes of developing mouse retinas and identified a total of 940 intergenic lncRNAs (lincRNAs) in embryonic and neonatal retinas, including about 13% of them were transcribed from unannotated gene loci. Subsequent analysis revealed that function of lincRNAs expressed in mouse retinas were closely related to the physiological roles of this tissue, including 90 lincRNAs that were differentially expressed after the functional loss of key regulators of retinal ganglion cell (RGC) differentiation. In situ hybridization results demonstrated the enrichment of three class IV POU-homeobox genes adjacent lincRNAs (linc-3a, linc-3b and linc-3c) in ganglion cell layer and indicated they were potentially RGC-specific. Conclusions In summary, this study systematically annotated the lincRNAs expressed in embryonic and neonatal mouse retinas and implied their crucial regulatory roles in retinal development such as RGC differentiation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5903-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ying Wan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | - Xiaoyang Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | | | - Yuying Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | - Huan Chen
- Key Laboratory of microbiological technology and Bioinformatics in Zhejiang Province, Hangzhou, China
| | - Xiaofeng Zhao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | - Guoqing Liang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China. .,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China.
| | - Lin Gan
- Department of Ophthalmology and Flaum Eye Institute, University of Rochester, Rochester, NY, 14642, USA.
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45
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Dvoriantchikova G, Seemungal RJ, Ivanov D. Development and epigenetic plasticity of murine Müller glia. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1584-1594. [PMID: 31276697 DOI: 10.1016/j.bbamcr.2019.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/24/2019] [Accepted: 06/30/2019] [Indexed: 12/14/2022]
Abstract
The ability to regenerate the entire retina and restore lost sight after injury is found in some species and relies mostly on the epigenetic plasticity of Müller glia. To understand the role of mammalian Müller glia as a source of progenitors for retinal regeneration, we investigated changes in gene expression during differentiation of retinal progenitor cells (RPCs) into Müller glia and analyzed the global epigenetic profile of adult Müller glia. We observed significant changes in gene expression during differentiation of RPCs into Müller glia in only a small group of genes and found a high similarity between RPCs and Müller glia on the transcriptomic and epigenomic levels. Our findings also indicate that Müller glia are epigenetically very close to late-born retinal neurons, but not early-born retinal neurons. Importantly, we found that key genes required for phototransduction were highly methylated. Thus, our data suggest that Müller glia are epigenetically very similar to late RPCs; however, obstacles for regeneration of the entire mammalian retina from Müller glia may consist of repressive chromatin and highly methylated DNA in the promoter regions of many genes required for the development of early-born retinal neurons. In addition, DNA demethylation may be required for proper reprogramming and differentiation of Müller glia into rod photoreceptors.
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Affiliation(s)
- Galina Dvoriantchikova
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Rajeev J Seemungal
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Dmitry Ivanov
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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46
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Hu Y, Wang X, Hu B, Mao Y, Chen Y, Yan L, Yong J, Dong J, Wei Y, Wang W, Wen L, Qiao J, Tang F. Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis. PLoS Biol 2019; 17:e3000365. [PMID: 31269016 PMCID: PMC6634428 DOI: 10.1371/journal.pbio.3000365] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/16/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022] Open
Abstract
The developmental pathway of the neural retina (NR) and retinal pigment epithelium (RPE) has been revealed by extensive research in mice. However, the molecular mechanisms underlying the development of the human NR and RPE, as well as the interactions between these two tissues, have not been well defined. Here, we analyzed 2,421 individual cells from human fetal NR and RPE using single-cell RNA sequencing (RNA-seq) technique and revealed the tightly regulated spatiotemporal gene expression network of human retinal cells. We identified major cell classes of human fetal retina and potential crucial transcription factors for each cell class. We dissected the dynamic expression patterns of visual cycle- and ligand-receptor interaction-related genes in the RPE and NR. Moreover, we provided a map of disease-related genes for human fetal retinal cells and highlighted the importance of retinal progenitor cells as potential targets of inherited retinal diseases. Our findings captured the key in vivo features of the development of the human NR and RPE and offered insightful clues for further functional studies.
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Affiliation(s)
- Yuqiong Hu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Xiaoye Wang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
| | - Boqiang Hu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Yunuo Mao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Yidong Chen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Liying Yan
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
| | - Jun Yong
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
| | - Ji Dong
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Yuan Wei
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
| | - Wei Wang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
| | - Lu Wen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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47
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Chang KC, Sun C, Cameron EG, Madaan A, Wu S, Xia X, Zhang X, Tenerelli K, Nahmou M, Knasel CM, Russano KR, Hertz J, Goldberg JL. Opposing Effects of Growth and Differentiation Factors in Cell-Fate Specification. Curr Biol 2019; 29:1963-1975.e5. [PMID: 31155355 PMCID: PMC6581615 DOI: 10.1016/j.cub.2019.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/15/2019] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
Abstract
Following ocular trauma or in diseases such as glaucoma, irreversible vision loss is due to the death of retinal ganglion cell (RGC) neurons. Although strategies to replace these lost cells include stem cell replacement therapy, few differentiated stem cells turn into RGC-like neurons. Understanding the regulatory mechanisms of RGC differentiation in vivo may improve outcomes of cell transplantation by directing the fate of undifferentiated cells toward mature RGCs. Here, we report a new mechanism by which growth and differentiation factor-15 (GDF-15), a ligand in the transforming growth factor-beta (TGF-β) superfamily, strongly promotes RGC differentiation in the developing retina in vivo in rodent retinal progenitor cells (RPCs) and in human embryonic stem cells (hESCs). This effect is in direct contrast to the closely related ligand GDF-11, which suppresses RGC-fate specification. We find these opposing effects are due in part to GDF-15's ability to specifically suppress Smad-2, but not Smad-1, signaling induced by GDF-11, which can be recapitulated by pharmacologic or genetic blockade of Smad-2 in vivo to increase RGC specification. No other retinal cell types were affected by GDF-11 knockout, but a slight reduction in photoreceptor cells was observed by GDF-15 knockout in the developing retina in vivo. These data define a novel regulatory mechanism of GDFs' opposing effects and their relevance in RGC differentiation and suggest a potential approach for advancing ESC-to-RGC cell-based replacement therapies.
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Affiliation(s)
- Kun-Che Chang
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Catalina Sun
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Evan G Cameron
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Ankush Madaan
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Suqian Wu
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Eye, Ear, Nose, & Throat Hospital, Department of Ophthalmology & Visual Science, Fudan University, 200031 Shanghai, China
| | - Xin Xia
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Xiong Zhang
- Shiley Eye Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin Tenerelli
- Shiley Eye Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael Nahmou
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Cara M Knasel
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Kristina R Russano
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Shiley Eye Center, University of California San Diego, La Jolla, CA 92093, USA; Bascom Palmer Eye Institute, University of Miami, Miami, FL 33136, USA
| | - Jonathan Hertz
- Bascom Palmer Eye Institute, University of Miami, Miami, FL 33136, USA
| | - Jeffrey L Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Shiley Eye Center, University of California San Diego, La Jolla, CA 92093, USA; Bascom Palmer Eye Institute, University of Miami, Miami, FL 33136, USA
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48
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Dvoriantchikova G, Seemungal RJ, Ivanov D. The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue. Sci Rep 2019; 9:3860. [PMID: 30846751 PMCID: PMC6405859 DOI: 10.1038/s41598-019-40262-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/12/2019] [Indexed: 11/12/2022] Open
Abstract
The epigenetic plasticity of amphibian retinal pigment epithelium (RPE) allows them to regenerate the entire retina, a trait known to be absent in mammals. In this study, we investigated the epigenetic plasticity of adult murine RPE to identify possible mechanisms that prevent mammalian RPE from regenerating retinal tissue. RPE were analyzed using microarray, ChIP-seq, and whole-genome bisulfite sequencing approaches. We found that the majority of key genes required for progenitor phenotypes were in a permissive chromatin state and unmethylated in RPE. We observed that the majority of non-photoreceptor genes had promoters in a repressive chromatin state, but these promoters were in unmethylated or low-methylated regions. Meanwhile, the majority of promoters for photoreceptor genes were found in a permissive chromatin state, but were highly-methylated. Methylome states of photoreceptor-related genes in adult RPE and embryonic retina (which mostly contain progenitors) were very similar. However, promoters of these genes were demethylated and activated during retinal development. Our data suggest that, epigenetically, adult murine RPE cells are a progenitor-like cell type. Most likely two mechanisms prevent adult RPE from reprogramming and differentiating into retinal neurons: 1) repressive chromatin in the promoter regions of non-photoreceptor retinal neuron genes; 2) highly-methylated promoters of photoreceptor-related genes.
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Affiliation(s)
- Galina Dvoriantchikova
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Rajeev J Seemungal
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Dmitry Ivanov
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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49
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Iwagawa T, Watanabe S. Molecular mechanisms of H3K27me3 and H3K4me3 in retinal development. Neurosci Res 2018; 138:43-48. [PMID: 30227167 DOI: 10.1016/j.neures.2018.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 10/28/2022]
Abstract
The retina consists of six types of neuron and Müller glia, and they are individually derived from common retinal progenitors in a chronologically defined order. Therefore, the signaling environment and competency of retinal progenitors change during retinal development, and the retina serves as an excellent model system to analyze molecular events during development. Much attention has been given to the identification of transcription factors and epigenetic mechanisms. The dynamic changing of the histone modification levels of retina-specific genes has been observed, and the modification patterns of H3K4me3 and H3K27me3 are regulated in a retinal cell type-specific manner. Therefore, it appears that the dynamism of histone modification in the developing retina is regulated both chronologically and in a cell type-specific manner in a particular gene category. Loss- and gain-of-function analyses of enzymes involved in the methylation and demethylation of H3K4 and K27 in the retina have indicated their critical roles in proliferation, differentiation, and determinations of the timing for differentiation. We summarize recent findings related to the roles of H3K4me3 and H3K27me3 in retinal development to discuss how the retinal system provides intriguing data on and contributes to concepts regarding the roles of histone modification in the chronological regulation of tissue development.
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Affiliation(s)
- Toshiro Iwagawa
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
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50
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Xiao D, Jin K, Xiang M. Necessity and Sufficiency of Ldb1 in the Generation, Differentiation and Maintenance of Non-photoreceptor Cell Types During Retinal Development. Front Mol Neurosci 2018; 11:271. [PMID: 30127719 PMCID: PMC6087769 DOI: 10.3389/fnmol.2018.00271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/17/2018] [Indexed: 12/28/2022] Open
Abstract
During mammalian retinal development, the multipotent progenitors differentiate into all classes of retinal cells under the delicate control of transcriptional factors. The deficiency of a transcription cofactor, the LIM-domain binding protein Ldb1, has been shown to cause proliferation and developmental defects in multiple tissues including cardiovascular, hematopoietic, and nervous systems; however, it remains unclear whether and how it regulates retinal development. By expression profiling, RNA in situ hybridization and immunostaining, here we show that Ldb1 is expressed in the progenitors during early retinal development, but later its expression gradually shifts to non-photoreceptor cell types including bipolar, amacrine, horizontal, ganglion, and Müller glial cells. Retina-specific ablation of Ldb1 in mice resulted in microphthalmia, optic nerve hypoplasia, retinal thinning and detachment, and profound vision impairment as determined by electroretinography. In the mutant retina, there was precocious differentiation of amacrine and horizontal cells, indicating a requirement of Ldb1 in maintaining the retinal progenitor pool. Additionally, all non-photoreceptor cell types were greatly reduced which appeared to be caused by a generation defect and/or retinal degeneration via excessive cell apoptosis. Furthermore, we showed that misexpressed Ldb1 was sufficient to promote the generation of bipolar, amacrine, horizontal, ganglion, and Müller glial cells at the expense of photoreceptors. Together, these results demonstrate that Ldb1 is not only necessary but also sufficient for the development and/or maintenance of non-photoreceptor cell types, and implicate that the pleiotropic functions of Ldb1 during retinal development are context-dependent and determined by its interaction with diverse LIM-HD (LIM-homeodomain) and LMO (LIM domain-only) binding protein partners.
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Affiliation(s)
- Dongchang Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Kangxin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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