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Shrestha SK, Lachke SA. Lens Regeneration: The Application of iSyTE and In Silico Approaches to Evaluate Gene Expression in Lens Organoids. Methods Mol Biol 2025; 2848:37-58. [PMID: 39240515 DOI: 10.1007/978-1-0716-4087-6_3] [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] [Indexed: 09/07/2024]
Abstract
Several protocols have been established for the generation of lens organoids from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and other cells with regenerative potential in humans or various animal models. It is important to examine how well the regenerated lens organoids reflect lens biology, in terms of its development, homeostasis, and aging. Toward this goal, the iSyTE database (integrated Systems Tool for Eye gene discovery; https://research.bioinformatics.udel.edu/iSyTE/ ), a bioinformatics resource tool that contains meta-analyzed gene expression data in wild-type lens across different embryonic, postnatal, and adult stages, can serve as a resource for comparative analysis. This article outlines the approaches toward effective use of iSyTE to gain insights into normal gene expression in the mouse lens, enriched expression in the lens, and differential gene expression in select mouse gene-perturbation cataract/lens defects models, which in turn can be used to evaluate expression of key lens-relevant genes in lens organoids by transcriptomics (e.g., RNA-sequencing (RNA-seq), microarrays, etc.) or other downstream methods (e.g., RT-qPCR, etc.).
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Affiliation(s)
- Sanjaya K Shrestha
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, USA.
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2
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Zhang L, Luo K, Gao J, You J, Guo J, Li M, Wei Y, Lin Y, Zhang L. Abnormal eyes and spine development in zebrafish (Danio rerio) embryos and larvae induced by triphenyltin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173246. [PMID: 38768728 DOI: 10.1016/j.scitotenv.2024.173246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/22/2024]
Abstract
Triphenyltin (TPT) is widely used in crop pest control and ship antifouling coatings, which leads to its entry into aquatic environment and poses a threat to aquatic organisms. However, the effects of TPT on the early life stages of wild fish in natural water environments remains unclear. The aim of this study was to assess the toxic effects of TPT on the early life stages of fish under two different environments: field investigation and laboratory experiment. The occurrence of deformities in wild fish embryos and larvae in the Three Gorges Reservoir (TGR) and the developmental toxicity of TPT at different concentrations (0, 0.15, 1.5 and 15 μg Sn/L) to zebrafish embryos and larvae were observed. The results showed that TPT content was higher in wild larvae, reaching 27.21 ng Sn/g w, and the malformation of wild fish larvae mainly occurred in the eyes and spine under natural water environment. Controlled experiment exposure of zebrafish larvae to TPT also resulted in eye and spinal deformities. Gene expression analysis showed that compared with the control group, the expression levels of genes related to eye development (sox2, otx2, stra6 and rx1) and spine development (sox9a and bmp2b) were significantly up-regulated in the 15 μg Sn/L exposure group, which may be the main cause of eye and spine deformity in the early development stage of fish. In addition, the molecular docking results further elucidate that the strong hydrophobic and electrostatic interactions between TPT and protein residues are the main mechanism of TPT induced abnormal gene expression. Based on these results, it can be inferred that TPT is one of the teratogenic factors of abnormal eye and spine development in the early life stage of fish in the TGR. These findings have important implications for understanding the toxicity of TPT on fish.
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Affiliation(s)
- Lixia Zhang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Kongyan Luo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Junmin Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Jia You
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jinsong Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Maoqiu Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yunmei Wei
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Ying Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Ling Zhang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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Eintracht J, Owen N, Harding P, Moosajee M. Disruption of common ocular developmental pathways in patient-derived optic vesicle models of microphthalmia. Stem Cell Reports 2024; 19:839-858. [PMID: 38821055 PMCID: PMC11390689 DOI: 10.1016/j.stemcr.2024.05.001] [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: 09/13/2023] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Genetic perturbations influencing early eye development can result in microphthalmia, anophthalmia, and coloboma (MAC). Over 100 genes are associated with MAC, but little is known about common disease mechanisms. In this study, we generated induced pluripotent stem cell (iPSC)-derived optic vesicles (OVs) from two unrelated microphthalmia patients and healthy controls. At day 20, 35, and 50, microphthalmia patient OV diameters were significantly smaller, recapitulating the "small eye" phenotype. RNA sequencing (RNA-seq) analysis revealed upregulation of apoptosis-initiating and extracellular matrix (ECM) genes at day 20 and 35. Western blot and immunohistochemistry revealed increased expression of lumican, nidogen, and collagen type IV, suggesting ECM overproduction. Increased apoptosis was observed in microphthalmia OVs with reduced phospho-histone 3 (pH3+) cells confirming decreased cell proliferation at day 35. Pharmacological inhibition of caspase-8 activity with Z-IETD-FMK decreased apoptosis in one patient model, highlighting a potential therapeutic approach. These data reveal shared pathophysiological mechanisms contributing to a microphthalmia phenotype.
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Affiliation(s)
| | | | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; Moorfields Eye Hospital NHS Foundation Trust, London EC1V 9EL, UK; Francis Crick Institute, London NW1 1AT, UK.
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4
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Yang N, Zhang N, Lu G, Zeng S, Xing Y, Du L. RNA-binding proteins potentially regulate the alternative splicing of cell cycle-associated genes in proliferative diabetic retinopathy. Sci Rep 2024; 14:6731. [PMID: 38509306 PMCID: PMC10954754 DOI: 10.1038/s41598-024-57516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 03/22/2024] Open
Abstract
RNA-binding proteins (RBPs) contribute to the pathogenesis of proliferative diabetic retinopathy (PDR) by regulating gene expression through alternative splicing events (ASEs). However, the RBPs differentially expressed in PDR and the underlying mechanisms remain unclear. Thus, this study aimed to identify the differentially expressed genes in the neovascular membranes (NVM) and retinas of patients with PDR. The public transcriptome dataset GSE102485 was downloaded from the Gene Expression Omnibus database, and samples of PDR and normal retinas were analyzed. A mouse model of oxygen-induced retinopathy was used to confirm the results. The top 20 RBPs were screened for co-expression with alternative splicing genes (ASGs). A total of 403 RBPs were abnormally expressed in the NVM and retina samples. Functional analysis demonstrated that the ASGs were enriched in cell cycle pathways. Cell cycle-associated ASEs and an RBP-AS regulatory network, including 15 RBPs and their regulated ASGs, were extracted. Splicing factor proline/glutamine rich (SFPQ), microtubule-associated protein 1 B (MAP1B), heat-shock protein 90-alpha (HSP90AA1), microtubule-actin crosslinking factor 1 (MACF1), and CyclinH (CCNH) expression remarkably differed in the mouse model. This study provides novel insights into the RBP-AS interaction network in PDR and for developing screening and treatment options to prevent diabetic retinopathy-related blindness.
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Affiliation(s)
- Ning Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ningzhi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Guojing Lu
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Siyu Zeng
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lei Du
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China.
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Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Del Rio-Tsonis K. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. Development 2024; 151:dev202249. [PMID: 38180241 PMCID: PMC10906490 DOI: 10.1242/dev.202249] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataracts. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq and CUT&RUN-seq to discover previously unreported mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Furthermore, we identify an epigenetic paradigm of cellular differentiation, defined by progressive loss of the H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
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Affiliation(s)
- Jared A. Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Sofia M. Rebull
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jacob M. Weaver
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Stacy Bendezu-Sayas
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Michael L. Robinson
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA
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6
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Benítez-Burraco A, Uriagereka J, Nataf S. The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development. Dev Genes Evol 2023; 233:123-135. [PMID: 37552321 PMCID: PMC10746608 DOI: 10.1007/s00427-023-00709-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain.
- Área de Lingüística General, Departamento de Lengua Española, Lingüística y Teoría de la Literatura, Facultad de Filología, Universidad de Sevilla, C/ Palos de la Frontera s/n., 41007-, Sevilla, España.
| | - Juan Uriagereka
- Department of Linguistics and School of Languages, Literatures & Cultures, University of Maryland, College Park, MD, USA
| | - Serge Nataf
- Stem-cell and Brain Research Institute, 18 avenue de Doyen Lépine, F-69500, Bron, France
- University of Lyon 1, 43 Bd du 11 Novembre 1918, F-69100, Villeurbanne, France
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d'Arsonval, F-69003, Lyon, France
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7
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Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Rio-Tsonis KD. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548451. [PMID: 37502967 PMCID: PMC10369908 DOI: 10.1101/2023.07.10.548451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Further, we divulge a conserved epigenetic paradigm of cellular differentiation, defined by progressive loss of H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
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Affiliation(s)
- Jared A Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Sofia M Rebull
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
| | - Jacob M Weaver
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Stacy Bendezu-Sayas
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Michael L Robinson
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056 USA
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 USA
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8
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet 2023; 142:927-947. [PMID: 37191732 PMCID: PMC10680127 DOI: 10.1007/s00439-023-02570-0] [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: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA.
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9
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Siddam AD, Duot M, Coomson SY, Anand D, Aryal S, Weatherbee BAT, Audic Y, Paillard L, Lachke SA. High-Throughput Transcriptomics of Celf1 Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology. Cells 2023; 12:1070. [PMID: 37048143 PMCID: PMC10093462 DOI: 10.3390/cells12071070] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Defects in the development of the ocular lens can cause congenital cataracts. To understand the various etiologies of congenital cataracts, it is important to characterize the genes linked to this developmental defect and to define their downstream pathways that are relevant to lens biology and pathology. Deficiency or alteration of several RNA-binding proteins, including the conserved RBP Celf1 (CUGBP Elav-like family member 1), has been described to cause lens defects and early onset cataracts in animal models and/or humans. Celf1 is involved in various aspects of post-transcriptional gene expression control, including regulation of mRNA stability/decay, alternative splicing and translation. Celf1 germline knockout mice and lens conditional knockout (Celf1cKO) mice develop fully penetrant cataracts in early postnatal stages. To define the genome-level changes in RNA transcripts that result from Celf1 deficiency, we performed high-throughput RNA-sequencing of Celf1cKO mouse lenses at postnatal day (P) 0. Celf1cKO lenses exhibit 987 differentially expressed genes (DEGs) at cut-offs of >1.0 log2 counts per million (CPM), ≥±0.58 log2 fold-change and <0.05 false discovery rate (FDR). Of these, 327 RNAs were reduced while 660 were elevated in Celf1cKO lenses. The DEGs were subjected to various downstream analyses including iSyTE lens enriched-expression, presence in Cat-map, and gene ontology (GO) and representation of regulatory pathways. Further, a comparative analysis was done with previously generated microarray datasets on Celf1cKO lenses P0 and P6. Together, these analyses validated and prioritized several key genes mis-expressed in Celf1cKO lenses that are relevant to lens biology, including known cataract-linked genes (e.g., Cryab, Cryba2, Cryba4, Crybb1, Crybb2, Cryga, Crygb, Crygc, Crygd, Cryge, Crygf, Dnase2b, Bfsp1, Gja3, Pxdn, Sparc, Tdrd7, etc.) as well as novel candidates (e.g., Ell2 and Prdm16). Together, these data have defined the alterations in lens transcriptome caused by Celf1 deficiency, in turn uncovering downstream genes and pathways (e.g., structural constituents of eye lenses, lens fiber cell differentiation, etc.) associated with lens development and early-onset cataracts.
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Affiliation(s)
- Archana D. Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Matthieu Duot
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- CNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, France
| | - Sarah Y. Coomson
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | | | - Yann Audic
- CNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, France
| | - Luc Paillard
- CNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, France
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
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10
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Wang Y, Zhang C, Peng W, Du H, Xi Y, Xu Z. RBM24 is required for mouse hair cell development through regulating pre-mRNA alternative splicing and mRNA stability. J Cell Physiol 2023; 238:1095-1110. [PMID: 36947695 DOI: 10.1002/jcp.31003] [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: 12/30/2022] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
As the sensory receptor cells in vertebrate inner ear and lateral lines, hair cells are characterized by the hair bundle that consists of one tubulin-based kinocilium and dozens of actin-based stereocilia on the apical surface of each hair cell. Hair cell development is tightly regulated, and deficits in this process usually lead to hearing loss and/or balance dysfunctions. RNA-binding motif protein 24 (RBM24) is an RNA-binding protein that is specifically expressed in the hair cells in the inner ear. Previously, we showed that RBM24 affects hair cell development in zebrafish by regulating messenger RNA (mRNA) stability. In the present work, we further investigate the role of RBM24 in hearing and balance using conditional knockout mice. Our results show that Rbm24 knockout results in severe hearing and balance deficits. Hair cell development is significantly affected in Rbm24 knockout cochlea, as the hair bundles are poorly developed and eventually degenerated. Hair bundle disorganization is also observed in Rbm24 knockout vestibular hair cells, although to a lesser extent. Consistently, significant hair cell loss is observed in the cochlea but not vestibule. RNAseq analysis identified several genes whose mRNA stability or pre-mRNA alternative splicing is affected by Rbm24 knockout. Among them are Cdh23, Pcdh15, and Myo7a, which have been shown to play important roles in stereocilia development as well as mechano-electrical transduction. Taken together, our present work suggests that RBM24 is required for mouse hair cell development through regulating pre-mRNA alternative splicing as well as mRNA stability.
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Affiliation(s)
- Yanfei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Cuiqiao Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Wu Peng
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Haibo Du
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Yuehui Xi
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
- Shandong Provincial Collaborative Innovation Center of Cell Biology, Shandong Normal University, Jinan, Shandong, China
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11
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. RESEARCH SQUARE 2023:rs.3.rs-2652395. [PMID: 36993571 PMCID: PMC10055508 DOI: 10.21203/rs.3.rs-2652395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ³2.5 average spectral counts, ³2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Hongzhan Huang
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry L. David
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
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12
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Wang X, Fan W, Xu Z, Zhang Q, Li N, Li R, Wang G, He S, Li W, Liao D, Zhang Z, Shu N, Huang J, Zhao C, Hou S. SOX2-positive retinal stem cells are identified in adult human pars plicata by single-cell transcriptomic analyses. MedComm (Beijing) 2023; 4:e198. [PMID: 36582303 PMCID: PMC9790047 DOI: 10.1002/mco2.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/26/2022] Open
Abstract
Stem cell therapy is a promising strategy to rescue visual impairment caused by retinal degeneration. Previous studies have proposed controversial theories about whether in situ retinal stem cells (RSCs) are present in adult human eye tissue. Single-cell RNA sequencing (scRNA-seq) has emerged as one of the most powerful tools to reveal the heterogeneity of tissue cells. By using scRNA-seq, we explored the cell heterogeneity of different subregions of adult human eyes, including pars plicata, pars plana, retinal pigment epithelium (RPE), iris, and neural retina (NR). We identified one subpopulation expressing SRY-box transcription factor 2 (SOX2) as RSCs, which were present in the pars plicata of the adult human eye. Further analysis showed the identified subpopulation of RSCs expressed specific markers aquaporin 1 (AQP1) and tetraspanin 12 (TSPAN12). We, therefore, isolated this subpopulation using these two markers by flow sorting and found that the isolated RSCs could proliferate and differentiate into some retinal cell types, including photoreceptors, neurons, RPE cells, microglia, astrocytes, horizontal cells, bipolar cells, and ganglion cells; whereas, AQP1- TSPAN12- cells did not have this differentiation potential. In conclusion, our results showed that SOX2-positive RSCs are present in the pars plicata and may be valuable for treating human retinal diseases due to their proliferation and differentiation potential.
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13
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Li J, Yang W, Wang YJ, Ma C, Curry CJ, McGoldrick D, Nickerson DA, Chong JX, Blue EE, Mullikin JC, Reefhuis J, Nembhard WN, Romitti PA, Werler MM, Browne ML, Olshan AF, Finnell RH, Feldkamp ML, Pangilinan F, Almli LM, Bamshad MJ, Brody LC, Jenkins MM, Shaw GM. Exome sequencing identifies genetic variants in anophthalmia and microphthalmia. Am J Med Genet A 2022; 188:2376-2388. [PMID: 35716026 PMCID: PMC9283271 DOI: 10.1002/ajmg.a.62874] [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: 11/09/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/10/2022]
Abstract
Anophthalmia and microphthalmia (A/M) are rare birth defects affecting up to 2 per 10,000 live births. These conditions are manifested by the absence of an eye or reduced eye volumes within the orbit leading to vision loss. Although clinical case series suggest a strong genetic component in A/M, few systematic investigations have been conducted on potential genetic contributions owing to low population prevalence. To overcome this challenge, we utilized DNA samples and data collected as part of the National Birth Defects Prevention Study (NBDPS). The NBDPS employed multi-center ascertainment of infants affected by A/M. We performed exome sequencing on 67 family trios and identified numerous genes affected by rare deleterious nonsense and missense variants in this cohort, including de novo variants. We identified 9 nonsense changes and 86 missense variants that are absent from the reference human population (Genome Aggregation Database), and we suggest that these are high priority candidate genes for A/M. We also performed literature curation, single cell transcriptome comparisons, and molecular pathway analysis on the candidate genes and performed protein structure modeling to determine the potential pathogenic variant consequences on PAX6 in this disease.
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Affiliation(s)
- Jingjing Li
- Department of Neurology School of Medicine, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, The Bakar Computational Health Sciences Institute, The Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, California, USA
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Yuejun Jessie Wang
- Department of Neurology School of Medicine, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, The Bakar Computational Health Sciences Institute, The Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, California, USA
| | - Chen Ma
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Daniel McGoldrick
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Elizabeth E Blue
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James C Mullikin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennita Reefhuis
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wendy N Nembhard
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Paul A Romitti
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, Iowa, USA
| | - Martha M Werler
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Marilyn L Browne
- Birth Defects Registry, New York State Department of Health, Albany, New York, USA.,Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, New York, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Richard H Finnell
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA.,Department of Molecular and Human Genetics, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA.,Department of Medicine, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Marcia L Feldkamp
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Faith Pangilinan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lynn M Almli
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mike J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Lawrence C Brody
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
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- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland, USA
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- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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14
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Young TL, Whisenhunt KN, LaMartina SM, Hewitt AW, Mackey DA, Tompson SW. Sonic Hedgehog Intron Variant Associated With an Unusual Pediatric Cortical Cataract. Invest Ophthalmol Vis Sci 2022; 63:25. [PMID: 35749127 PMCID: PMC9234370 DOI: 10.1167/iovs.63.6.25] [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] [Indexed: 11/24/2022] Open
Abstract
Purpose To identify the genetic basis of an unusual pediatric cortical cataract demonstrating autosomal dominant inheritance in a large European–Australian pedigree. Methods DNA from four affected individuals were exome sequenced utilizing a NimbleGen SeqCap EZ Exome V3 kit and HiSeq 2500. DNA from 12 affected and four unaffected individuals were genotyped using Human OmniExpress-24 BeadChips. Multipoint linkage and haplotyping were performed (Superlink-Online SNP). DNA from one affected individual and his unaffected father were whole-genome sequenced on a HiSeq X Ten system. Rare small insertions/deletions and single-nucleotide variants (SNVs) were identified in the disease-linked region (Golden Helix SVS). Combined Annotation Dependent Depletion (CADD) analysis predicted variant deleteriousness. Putative enhancer function and variant effects were determined using the Dual-Glo Luciferase Assay system. Results Linkage mapping identified a 6.23-centimorgan support interval at chromosome 7q36. A co-segregating haplotype refined the critical region to 6.03 Mbp containing 21 protein-coding genes. Whole-genome sequencing uncovered 114 noncoding variants from which CADD predicted one was highly deleterious, a novel substitution within intron-1 of the sonic hedgehog signaling molecule (SHH) gene. ENCODE data suggested this site was a putative enhancer, subsequently confirmed by luciferase reporter assays with variant-associated gene overexpression. Conclusions In a large pedigree, we have identified a SHH intron variant that co-segregates with an unusual pediatric cortical cataract phenotype. SHH is important for lens formation, and mutations in its receptor (PTCH1) cause syndromic cataract. Our data implicate increased function of an enhancer important for SHH expression primarily within developing eye tissues.
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Affiliation(s)
- Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Kristina N Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Sarah M LaMartina
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia, Australia.,Eye Department, Royal Hobart Hospital, University of Tasmania, Hobart, Tasmania, Australia
| | - David A Mackey
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia, Australia.,Eye Department, Royal Hobart Hospital, University of Tasmania, Hobart, Tasmania, Australia
| | - Stuart W Tompson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
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15
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Wang Y, Li W, Zhang C, Peng W, Xu Z. RBM24 is localized to stress granules in cells under various stress conditions. Biochem Biophys Res Commun 2022; 608:96-101. [PMID: 35395551 DOI: 10.1016/j.bbrc.2022.03.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/31/2022] [Indexed: 11/02/2022]
Abstract
Stress granules (SGs) are formed when untranslated messenger ribonucleoproteins (mRNPs) accumulate in cells under stress, and are thought to minimize stress-induced damage and promote cell survival. RBM24 (RNA-binding motif protein 24) is an RNA-binding protein that plays pivotal roles in regulating the stability or translation initiation of target mRNAs as well as alternative splicing of target pre-mRNAs. Its important physiological functions are highlighted by the fact that Rbm24 knockout mice or zebrafish suffer from dysfunction of heart, eye, and inner ear. Here we show that RBM24 is recruited into SGs under various stress conditions, suggesting that it might protect its target RNAs in cells under stress. However, SG formation is unaffected when Rbm24 expression is down-regulated. Nevertheless, RBM24 overexpression in cultured cells is sufficient to induce SG formation, suggesting that RBM24 might play an important role in SG formation. In conclusion, our present work reveals that RBM24 is a SG component, which implies that RBM24 could protect its target mRNAs in stressed cells.
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Affiliation(s)
- Yanfei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Wei Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Cuiqiao Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Wu Peng
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China; Shandong Provincial Collaborative Innovation Center of Cell Biology, Shandong Normal University, Jinan, Shandong, 250014, China.
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16
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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17
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Rojo Arias JE, Jászai J. Gene expression profile of the murine ischemic retina and its response to Aflibercept (VEGF-Trap). Sci Rep 2021; 11:15313. [PMID: 34321516 PMCID: PMC8319207 DOI: 10.1038/s41598-021-94500-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Ischemic retinal dystrophies are leading causes of acquired vision loss. Although the dysregulated expression of the hypoxia-responsive VEGF-A is a major driver of ischemic retinopathies, implication of additional VEGF-family members in their pathogenesis has led to the development of multivalent anti-angiogenic tools. Designed as a decoy receptor for all ligands of VEGFR1 and VEGFR2, Aflibercept is a potent anti-angiogenic agent. Notwithstanding, the molecular mechanisms mediating Aflibercept's efficacy remain only partially understood. Here, we used the oxygen-induced retinopathy (OIR) mouse as a model system of pathological retinal vascularization to investigate the transcriptional response of the murine retina to hypoxia and of the OIR retina to Aflibercept. While OIR severely impaired transcriptional changes normally ensuing during retinal development, analysis of gene expression patterns hinted at alterations in leukocyte recruitment during the recovery phase of the OIR protocol. Moreover, the levels of Angiopoietin-2, a major player in the progression of diabetic retinopathy, were elevated in OIR tissues and consistently downregulated by Aflibercept. Notably, GO term, KEGG pathway enrichment, and expression dynamics analyses revealed that, beyond regulating angiogenic processes, Aflibercept also modulated inflammation and supported synaptic transmission. Altogether, our findings delineate novel mechanisms potentially underlying Aflibercept's efficacy against ischemic retinopathies.
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Affiliation(s)
- Jesús Eduardo Rojo Arias
- grid.4488.00000 0001 2111 7257Department of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Saxony, Germany ,grid.5335.00000000121885934Present Address: Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - József Jászai
- grid.4488.00000 0001 2111 7257Department of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Saxony, Germany
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18
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Choquet H, Melles RB, Anand D, Yin J, Cuellar-Partida G, Wang W, Hoffmann TJ, Nair KS, Hysi PG, Lachke SA, Jorgenson E. A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects. Nat Commun 2021; 12:3595. [PMID: 34127677 PMCID: PMC8203611 DOI: 10.1038/s41467-021-23873-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/17/2021] [Indexed: 01/16/2023] Open
Abstract
Cataract is the leading cause of blindness among the elderly worldwide and cataract surgery is one of the most common operations performed in the United States. As the genetic etiology of cataract formation remains unclear, we conducted a multiethnic genome-wide association meta-analysis, combining results from the GERA and UK Biobank cohorts, and tested for replication in the 23andMe research cohort. We report 54 genome-wide significant loci, 37 of which were novel. Sex-stratified analyses identified CASP7 as an additional novel locus specific to women. We show that genes within or near 80% of the cataract-associated loci are significantly expressed and/or enriched-expressed in the mouse lens across various spatiotemporal stages as per iSyTE analysis. Furthermore, iSyTE shows 32 candidate genes in the associated loci have altered gene expression in 9 different gene perturbation mouse models of lens defects/cataract, suggesting their relevance to lens biology. Our work provides further insight into the complex genetic architecture of cataract susceptibility.
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Affiliation(s)
- Hélène Choquet
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA.
| | | | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | | | | | | | - Thomas J Hoffmann
- Institute for Human Genetics, UCSF, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - K Saidas Nair
- Departments of Ophthalmology and Anatomy, School of Medicine, UCSF, San Francisco, CA, USA
| | - Pirro G Hysi
- King's College London, Section of Ophthalmology, School of Life Course Sciences, London, UK.,King's College London, Department of Twin Research and Genetic Epidemiology, London, UK.,University College London, Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Eric Jorgenson
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
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19
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Farnsworth DR, Posner M, Miller AC. Single cell transcriptomics of the developing zebrafish lens and identification of putative controllers of lens development. Exp Eye Res 2021; 206:108535. [PMID: 33705730 PMCID: PMC8092445 DOI: 10.1016/j.exer.2021.108535] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/31/2021] [Accepted: 03/02/2021] [Indexed: 01/10/2023]
Abstract
The vertebrate lens is a valuable model system for investigating the gene expression changes that coordinate tissue differentiation due to its inclusion of two spatially separated cell types, the outer epithelial cells and the deeper denucleated fiber cells that they support. Zebrafish are a useful model system for studying lens development given the organ's rapid development in the first several days of life in an accessible, transparent embryo. While we have strong foundational knowledge of the diverse lens crystallin proteins and the basic gene regulatory networks controlling lens development, no study has detailed gene expression in a vertebrate lens at single cell resolution. Here we report an atlas of lens gene expression in zebrafish embryos and larvae at single cell resolution through five days of development, identifying a number of novel putative regulators of lens development. Our data address open questions about the temperospatial expression of α-crystallins during lens development that will support future studies of their function and provide the first detailed view of β- and γ-crystallin expression in and outside the lens. We describe divergent expression in transcription factor genes that occur as paralog pairs in the zebrafish. Finally, we examine the expression dynamics of cytoskeletal, membrane associated, RNA-binding, and transcription factor genes, identifying a number of novel patterns. Overall these data provide a foundation for identifying and characterizing lens developmental regulatory mechanisms and revealing targets for future functional studies with potential therapeutic impact.
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Affiliation(s)
| | - Mason Posner
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA.
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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20
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Cvekl A, Eliscovich C. Crystallin gene expression: Insights from studies of transcriptional bursting. Exp Eye Res 2021; 207:108564. [PMID: 33894228 DOI: 10.1016/j.exer.2021.108564] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/05/2021] [Accepted: 03/22/2021] [Indexed: 01/26/2023]
Abstract
Cellular differentiation is marked by temporally and spatially regulated gene expression. The ocular lens is one of the most powerful mammalian model system since it is composed from only two cell subtypes, called lens epithelial and fiber cells. Lens epithelial cells differentiate into fiber cells through a series of spatially and temporally orchestrated processes, including massive production of crystallins, cellular elongation and the coordinated degradation of nuclei and other organelles. Studies of transcriptional and posttranscriptional gene regulatory mechanisms in lens provide a wide range of opportunities to understand global molecular mechanisms of gene expression as steady-state levels of crystallin mRNAs reach very high levels comparable to globin genes in erythrocytes. Importantly, dysregulation of crystallin gene expression results in lens structural abnormalities and cataracts. The mRNA life cycle is comprised of multiple stages, including transcription, splicing, nuclear export into cytoplasm, stabilization, localization, translation and ultimate decay. In recent years, development of modern mRNA detection methods with single molecule and single cell resolution enabled transformative studies to visualize the mRNA life cycle to generate novel insights into the sequential regulatory mechanisms of gene expression during embryogenesis. This review is focused on recent major advancements in studies of transcriptional bursting in differentiating lens fiber cells, analysis of nascent mRNA expression from bi-directional promoters, transient nuclear accumulation of specific mRNAs, condensation of chromatin prior lens fiber cell denucleation, and outlines future studies to probe the interactions of individual mRNAs with specific RNA-binding proteins (RBPs) in the cytoplasm and regulation of translation and mRNA decay.
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Affiliation(s)
- Ales Cvekl
- Department of Ophthalmology and VIsual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Carolina Eliscovich
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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21
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Anand D, Al Saai S, Shrestha SK, Barnum CE, Chuma S, Lachke SA. Genome-Wide Analysis of Differentially Expressed miRNAs and Their Associated Regulatory Networks in Lenses Deficient for the Congenital Cataract-Linked Tudor Domain Containing Protein TDRD7. Front Cell Dev Biol 2021; 9:615761. [PMID: 33665188 PMCID: PMC7921330 DOI: 10.3389/fcell.2021.615761] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
Mutations/deficiency of TDRD7, encoding a tudor domain protein involved in post-transcriptional gene expression control, causes early onset cataract in humans. While Tdrd7 is implicated in the control of key lens mRNAs, the impact of Tdrd7 deficiency on microRNAs (miRNAs) and how this contributes to transcriptome misexpression and to cataracts, is undefined. We address this critical knowledge-gap by investigating Tdrd7-targeted knockout (Tdrd7-/-) mice that exhibit fully penetrant juvenile cataracts. We performed Affymetrix miRNA 3.0 microarray analysis on Tdrd7-/- mouse lenses at postnatal day (P) 4, a stage preceding cataract formation. This analysis identifies 22 miRNAs [14 over-expressed (miR-15a, miR-19a, miR-138, miR-328, miR-339, miR-345, miR-378b, miR-384, miR-467a, miR-1224, miR-1935, miR-1946a, miR-3102, miR-3107), 8 reduced (let-7b, miR-34c, miR-298, miR-382, miR-409, miR-1198, miR-1947, miR-3092)] to be significantly misexpressed (fold-change ≥ ± 1.2, p-value < 0.05) in Tdrd7-/- lenses. To understand how these misexpressed miRNAs impact Tdrd7-/- cataract, we predicted their mRNA targets and examined their misexpression upon Tdrd7-deficiency by performing comparative transcriptomics analysis on P4 and P30 Tdrd7-/- lens. To prioritize these target mRNAs, we used various stringency filters (e.g., fold-change in Tdrd7-/- lens, iSyTE-based lens-enriched expression) and identified 98 reduced and 89 elevated mRNA targets for overexpressed and reduced miRNAs, respectively, which were classified as “top-priority” “high-priority,” and “promising” candidates. For Tdrd7-/- lens overexpressed miRNAs, this approach identified 18 top-priority reduced target mRNAs: Alad, Ankrd46, Ceacam10, Dgat2, Ednrb, H2-Eb1, Klhl22, Lin7a, Loxl1, Lpin1, Npc1, Olfm1, Ppm1e, Ppp1r1a, Rgs8, Shisa4, Snx22 and Wnk2. Majority of these targets were also altered in other gene-specific perturbation mouse models (e.g., Brg1, E2f1/E2f2/E2f3, Foxe3, Hsf4, Klf4, Mafg/Mafk, Notch) of lens defects/cataract, suggesting their importance to lens biology. Gene ontology (GO) provided further insight into their relevance to lens pathology. For example, the Tdrd7-deficient lens capsule defect may be explained by reduced mRNA targets (e.g., Col4a3, Loxl1, Timp2, Timp3) associated with “basement membrane”. GO analysis also identified new genes (e.g., Casz1, Rasgrp1) recently linked to lens biology/pathology. Together, these analyses define a new Tdrd7-downstream miRNA-mRNA network, in turn, uncovering several new mRNA targets and their associated pathways relevant to lens biology and offering molecular insights into the pathology of congenital cataract.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Salma Al Saai
- Department of Biological Sciences, University of Delaware, Newark, DE, United States.,Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, United States
| | - Sanjaya K Shrestha
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Shinichiro Chuma
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, United States.,Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, United States
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22
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Brastrom LK, Scott CA, Wang K, Slusarski DC. Functional Role of the RNA-Binding Protein Rbm24a and Its Target sox2 in Microphthalmia. Biomedicines 2021; 9:100. [PMID: 33494192 PMCID: PMC7909789 DOI: 10.3390/biomedicines9020100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 01/21/2023] Open
Abstract
Congenital eye defects represent a large class of disorders affecting roughly 21 million children worldwide. Microphthalmia and anophthalmia are relatively common congenital defects, with approximately 20% of human cases caused by mutations in SOX2. Recently, we identified the RNA-binding motif protein 24a (Rbm24a) which binds to and regulates sox2 in zebrafish and mice. Here we show that morpholino knockdown of rbm24a leads to microphthalmia and visual impairment. By utilizing sequential injections, we demonstrate that addition of exogenous sox2 RNA to rbm24a-deplete embryos is sufficient to suppress morphological and visual defects. This research demonstrates a critical role for understanding the post-transcriptional regulation of genes needed for development.
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Affiliation(s)
- Lindy K. Brastrom
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA;
| | | | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, IA 52245, USA;
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23
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Harding P, Cunha DL, Moosajee M. Animal and cellular models of microphthalmia. THERAPEUTIC ADVANCES IN RARE DISEASE 2021; 2:2633004021997447. [PMID: 37181112 PMCID: PMC10032472 DOI: 10.1177/2633004021997447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
Microphthalmia is a rare developmental eye disorder affecting 1 in 7000 births. It is defined as a small (axial length ⩾2 standard deviations below the age-adjusted mean) underdeveloped eye, caused by disruption of ocular development through genetic or environmental factors in the first trimester of pregnancy. Clinical phenotypic heterogeneity exists amongst patients with varying levels of severity, and associated ocular and systemic features. Up to 11% of blind children are reported to have microphthalmia, yet currently no treatments are available. By identifying the aetiology of microphthalmia and understanding how the mechanisms of eye development are disrupted, we can gain a better understanding of the pathogenesis. Animal models, mainly mouse, zebrafish and Xenopus, have provided extensive information on the genetic regulation of oculogenesis, and how perturbation of these pathways leads to microphthalmia. However, differences exist between species, hence cellular models, such as patient-derived induced pluripotent stem cell (iPSC) optic vesicles, are now being used to provide greater insights into the human disease process. Progress in 3D cellular modelling techniques has enhanced the ability of researchers to study interactions of different cell types during eye development. Through improved molecular knowledge of microphthalmia, preventative or postnatal therapies may be developed, together with establishing genotype-phenotype correlations in order to provide patients with the appropriate prognosis, multidisciplinary care and informed genetic counselling. This review summarises some key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future. Plain language summary Animal and Cellular Models of the Eye Disorder, Microphthalmia (Small Eye) Microphthalmia, meaning a small, underdeveloped eye, is a rare disorder that children are born with. Genetic changes or variations in the environment during the first 3 months of pregnancy can disrupt early development of the eye, resulting in microphthalmia. Up to 11% of blind children have microphthalmia, yet currently no treatments are available. By understanding the genes necessary for eye development, we can determine how disruption by genetic changes or environmental factors can cause this condition. This helps us understand why microphthalmia occurs, and ensure patients are provided with the appropriate clinical care and genetic counselling advice. Additionally, by understanding the causes of microphthalmia, researchers can develop treatments to prevent or reduce the severity of this condition. Animal models, particularly mice, zebrafish and frogs, which can also develop small eyes due to the same genetic/environmental changes, have helped us understand the genes which are important for eye development and can cause birth eye defects when disrupted. Studying a patient's own cells grown in the laboratory can further help researchers understand how changes in genes affect their function. Both animal and cellular models can be used to develop and test new drugs, which could provide treatment options for patients living with microphthalmia. This review summarises the key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future.
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Affiliation(s)
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, 11-43 Bath
Street, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Foundation Trust, London, UK
- The Francis Crick Institute, London, UK
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24
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Zhang Y, Wang Y, Yao X, Wang C, Chen F, Liu D, Shao M, Xu Z. Rbm24a Is Necessary for Hair Cell Development Through Regulating mRNA Stability in Zebrafish. Front Cell Dev Biol 2020; 8:604026. [PMID: 33392193 PMCID: PMC7773828 DOI: 10.3389/fcell.2020.604026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/01/2020] [Indexed: 11/30/2022] Open
Abstract
Hair cells in the inner ear and lateral lines are mechanosensitive receptor cells whose development and function are tightly regulated. Several transcription factors as well as splicing factors have been identified to play important roles in hair cell development, whereas the role of RNA stability in this process is poorly understood. In the present work, we report that RNA-binding motif protein 24a (Rbm24a) is indispensable for hair cell development in zebrafish. Rbm24a expression is detected in the inner ear as well as lateral line neuromasts. Albeit rbm24a deficient zebrafish do not survive beyond 9 days post fertilization (dpf) due to effects outside of the inner ear, rbm24a deficiency does not affect the early development of inner ear except for delayed otolith formation and semicircular canal fusion. However, hair cell development is severely affected and hair bundle is disorganized in rbm24a mutants. As a result, the auditory and vestibular function of rbm24a mutants are compromised. RNAseq analyses identified several Rbm24a-target mRNAs that are directly bound by Rbm24a and are dysregulated in rbm24a mutants. Among the identified Rbm24a-target genes, lrrc23, dfna5b, and smpx are particularly interesting as their dysregulation might contribute to the inner ear phenotypes in rbm24a mutants. In conclusion, our data suggest that Rbm24a affects hair cell development in zebrafish through regulating mRNA stability.
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Affiliation(s)
- Yan Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Yanfei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xuebo Yao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Changquan Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Fangyi Chen
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dong Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, School of Life Sciences, Nantong University, Nantong, China
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China.,Shandong Provincial Collaborative Innovation Center of Cell Biology, Shandong Normal University, Jinan, China
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25
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Cheng X, Zhang JJ, Shi DL. Loss of Rbm24a causes defective hair cell development in the zebrafish inner ear and neuromasts. J Genet Genomics 2020; 47:403-406. [PMID: 33036919 DOI: 10.1016/j.jgg.2020.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Xiaoning Cheng
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China
| | - Jing-Jing Zhang
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China.
| | - De-Li Shi
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Develompental Biology Laboratory, CNRS UMR7622, Institut de Biologie Paris-Seine, Sorbonne University, 75005, Paris, France.
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26
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Grifone R, Shao M, Saquet A, Shi DL. RNA-Binding Protein Rbm24 as a Multifaceted Post-Transcriptional Regulator of Embryonic Lineage Differentiation and Cellular Homeostasis. Cells 2020; 9:E1891. [PMID: 32806768 PMCID: PMC7463526 DOI: 10.3390/cells9081891] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins control the metabolism of RNAs at all stages of their lifetime. They are critically required for the post-transcriptional regulation of gene expression in a wide variety of physiological and pathological processes. Rbm24 is a highly conserved RNA-binding protein that displays strongly regionalized expression patterns and exhibits dynamic changes in subcellular localization during early development. There is increasing evidence that it acts as a multifunctional regulator to switch cell fate determination and to maintain tissue homeostasis. Dysfunction of Rbm24 disrupts cell differentiation in nearly every tissue where it is expressed, such as skeletal and cardiac muscles, and different head sensory organs, but the molecular events that are affected may vary in a tissue-specific, or even a stage-specific manner. Recent works using different animal models have uncovered multiple post-transcriptional regulatory mechanisms by which Rbm24 functions in key developmental processes. In particular, it represents a major splicing factor in muscle cell development, and plays an essential role in cytoplasmic polyadenylation during lens fiber cell terminal differentiation. Here we review the advances in understanding the implication of Rbm24 during development and disease, by focusing on its regulatory roles in physiological and pathological conditions.
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Affiliation(s)
- Raphaëlle Grifone
- Developmental Biology Laboratory, CNRS-UMR7622, IBPS, Sorbonne University, 75005 Paris, France; (R.G.); (A.S.)
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China;
| | - Audrey Saquet
- Developmental Biology Laboratory, CNRS-UMR7622, IBPS, Sorbonne University, 75005 Paris, France; (R.G.); (A.S.)
| | - De-Li Shi
- Developmental Biology Laboratory, CNRS-UMR7622, IBPS, Sorbonne University, 75005 Paris, France; (R.G.); (A.S.)
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27
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Alternative Splicing of Cdh23 Exon 68 Is Regulated by RBM24, RBM38, and PTBP1. Neural Plast 2020; 2020:8898811. [PMID: 32774357 PMCID: PMC7397384 DOI: 10.1155/2020/8898811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/19/2020] [Accepted: 07/01/2020] [Indexed: 01/08/2023] Open
Abstract
Alternative splicing plays a pivotal role in modulating the function of eukaryotic proteins. In the inner ear, many genes undergo alternative splicing, and errors in this process lead to hearing loss. Cadherin 23 (CDH23) forms part of the so-called tip links, which are indispensable for mechanoelectrical transduction (MET) in the hair cells. Cdh23 gene contains 69 exons, and exon 68 is subjected to alternative splicing. Exon 68 of the Cdh23 gene is spliced into its mRNA only in a few cell types including hair cells. The mechanism responsible for the alternative splicing of Cdh23 exon 68 remains elusive. In the present work, we performed a cell-based screening to look for splicing factors that regulate the splicing of Cdh23 exon 68. RBM24 and RBM38 were identified to enhance the inclusion of Cdh23 exon 68. The splicing of Cdh23 exon 68 is affected in Rbm24 knockdown or knockout cells. Moreover, we also found that PTBP1 inhibits the inclusion of Cdh23 exon 68. Taken together, we show here that alternative splicing of Cdh23 exon 68 is regulated by RBM24, RBM38, and PTBP1.
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28
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Barnum CE, Al Saai S, Patel SD, Cheng C, Anand D, Xu X, Dash S, Siddam AD, Glazewski L, Paglione E, Polson SW, Chuma S, Mason RW, Wei S, Batish M, Fowler VM, Lachke SA. The Tudor-domain protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 (HSP27) and lens fiber cell morphology. Hum Mol Genet 2020; 29:2076-2097. [PMID: 32420594 PMCID: PMC7390939 DOI: 10.1093/hmg/ddaa096] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/10/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations of the RNA granule component TDRD7 (OMIM: 611258) cause pediatric cataract. We applied an integrated approach to uncover the molecular pathology of cataract in Tdrd7-/- mice. Early postnatal Tdrd7-/- animals precipitously develop cataract suggesting a global-level breakdown/misregulation of key cellular processes. High-throughput RNA sequencing integrated with iSyTE-bioinformatics analysis identified the molecular chaperone and cytoskeletal modulator, HSPB1, among high-priority downregulated candidates in Tdrd7-/- lens. A protein fluorescence two-dimensional difference in-gel electrophoresis (2D-DIGE)-coupled mass spectrometry screen also identified HSPB1 downregulation, offering independent support for its importance to Tdrd7-/- cataractogenesis. Lens fiber cells normally undergo nuclear degradation for transparency, posing a challenge: how is their cell morphology, also critical for transparency, controlled post-nuclear degradation? HSPB1 functions in cytoskeletal maintenance, and its reduction in Tdrd7-/- lens precedes cataract, suggesting cytoskeletal defects may contribute to Tdrd7-/- cataract. In agreement, scanning electron microscopy (SEM) revealed abnormal fiber cell morphology in Tdrd7-/- lenses. Further, abnormal phalloidin and wheat germ agglutinin (WGA) staining of Tdrd7-/- fiber cells, particularly those exhibiting nuclear degradation, reveals distinct regulatory mechanisms control F-actin cytoskeletal and/or membrane maintenance in post-organelle degradation maturation stage fiber cells. Indeed, RNA immunoprecipitation identified Hspb1 mRNA in wild-type lens lysate TDRD7-pulldowns, and single-molecule RNA imaging showed co-localization of TDRD7 protein with cytoplasmic Hspb1 mRNA in differentiating fiber cells, suggesting that TDRD7-ribonucleoprotein complexes may be involved in optimal buildup of key factors. Finally, Hspb1 knockdown in Xenopus causes eye/lens defects. Together, these data uncover TDRD7's novel upstream role in elevation of stress-responsive chaperones for cytoskeletal maintenance in post-nuclear degradation lens fiber cells, perturbation of which causes early-onset cataracts.
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Affiliation(s)
- Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salma Al Saai
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shaili D Patel
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Catherine Cheng
- School of Optometry, Indiana University, Bloomington, IN 47405, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Lisa Glazewski
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Emily Paglione
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shawn W Polson
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Shinichiro Chuma
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Robert W Mason
- Nemours Biomedical Research Department, Alfred I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Velia M Fowler
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA
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29
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Aryal S, Viet J, Weatherbee BAT, Siddam AD, Hernandez FG, Gautier-Courteille C, Paillard L, Lachke SA. The cataract-linked RNA-binding protein Celf1 post-transcriptionally controls the spatiotemporal expression of the key homeodomain transcription factors Pax6 and Prox1 in lens development. Hum Genet 2020; 139:1541-1554. [PMID: 32594240 DOI: 10.1007/s00439-020-02195-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022]
Abstract
The homeodomain transcription factors (TFs) Pax6 (OMIM: 607108) and Prox1 (OMIM: 601546) critically regulate gene expression in lens development. While PAX6 mutations in humans can cause cataract, aniridia, microphthalmia, and anophthalmia, among other defects, Prox1 deletion in mice causes severe lens abnormalities, in addition to other organ defects. Furthermore, the optimal dosage/spatiotemporal expression of these key TFs is essential for development. In lens development, Pax6 expression is elevated in cells of the anterior epithelium compared to fiber cells, while Prox1 exhibits the opposite pattern. Whether post-transcriptional regulatory mechanisms control these precise TF expression patterns is unknown. Here, we report the unprecedented finding that the cataract-linked RNA-binding protein (RBP), Celf1 (OMIM: 601074), post-transcriptionally regulates Pax6 and Prox1 protein expression in lens development. Immunostaining shows that Celf1 lens-specific conditional knockout (Celf1cKO) mice exhibit abnormal elevation of Pax6 protein in fiber cells and abnormal Prox1 protein levels in epithelial cells-directly opposite to their normal expression patterns in development. Furthermore, RT-qPCR shows no change in Pax6 and Prox1 transcript levels in Celf1cKO lenses, suggesting that Celf1 regulates these TFs on the translational level. Indeed, RNA-immunoprecipitation assays using Celf1 antibody indicate that Celf1 protein binds to Pax6 and Prox1 transcripts. Furthermore, reporter assays in Celf1 knockdown and Celf1-overexpression cells demonstrate that Celf1 negatively controls Pax6 and Prox1 translation via their 3' UTRs. These data define a new mechanism of RBP-based post-transcriptional regulation that enables precise control over spatiotemporal expression of Pax6 and Prox1 in lens development, thereby uncovering a new etiological mechanism for Celf1 deficiency-based cataract.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Justine Viet
- Institut de Génétique et Développement de Rennes, Univ Rennes, CNRS, IGDR-UMR 6290, 35000, Rennes, France
| | | | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | | | - Carole Gautier-Courteille
- Institut de Génétique et Développement de Rennes, Univ Rennes, CNRS, IGDR-UMR 6290, 35000, Rennes, France
| | - Luc Paillard
- Institut de Génétique et Développement de Rennes, Univ Rennes, CNRS, IGDR-UMR 6290, 35000, Rennes, France.
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA. .,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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30
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Viet J, Reboutier D, Hardy S, Lachke SA, Paillard L, Gautier-Courteille C. Modeling ocular lens disease in Xenopus. Dev Dyn 2020; 249:610-621. [PMID: 31872467 PMCID: PMC7759097 DOI: 10.1002/dvdy.147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Ocular lens clouding is termed as cataract, which depending on the onset, is classified as congenital or age-related. Developing new cataract treatments requires new models. Thus far, Xenopus embryos have not been evaluated as a system for studying cataract. RESULTS We characterized the developmental process of lens formation in Xenopus laevis tailbuds and tadpoles, and we disrupted the orthologues of three mammalian cataract-linked genes in F0 by CRISPR/Cas9. We assessed the consequences of gene inactivation by combining external examination with histochemical analyses and functional vision assays. Inactivating the key metazoan eye development transcription factor gene pax6 produces a strong eye phenotype including an absence of eye tissue. Inactivating the genes for gap-junction protein and a nuclease, gja8 and dnase2b, produces lens defects that share several features of human cataracts, including impaired vision acuity, nuclei retention in lens fiber cells, and actin fibers disorganization. We tested the potential improvement of the visual acuity of gja8 crispant tadpoles upon treatment with the molecular chaperone 4-phenylbutyrate. CONCLUSION Xenopus is a valuable model organism to understand the molecular pathology of congenital eye defects, including cataracts, and to screen molecules with a potential to prevent or reverse cataracts.
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Affiliation(s)
- Justine Viet
- Univ Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France
| | | | - Serge Hardy
- Univ Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Luc Paillard
- Univ Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France
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31
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Rbm24 controls poly(A) tail length and translation efficiency of crystallin mRNAs in the lens via cytoplasmic polyadenylation. Proc Natl Acad Sci U S A 2020; 117:7245-7254. [PMID: 32170011 PMCID: PMC7132282 DOI: 10.1073/pnas.1917922117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lens transparency critically requires the abundant accumulation of crystallin proteins, and deregulation of this process causes congenital cataracts in humans. Rbm24 is an RNA-binding protein with highly conserved expression in differentiating lens fiber cells among all vertebrates. We use a zebrafish model to demonstrate that loss of Rbm24 function specifically impedes lens fiber cell differentiation, resulting in cataract formation and blindness. Molecular analyses reveal that Rbm24 interacts with cytoplasmic polyadenylation complex and binds to a large number of lens-expressed messenger RNAs to maintain their stability and protect their poly(A) tail length, thereby crucially contributing to their efficient translation into functional proteins. This work identifies an important mechanism by which Rbm24 posttranscriptionally controls lens gene expression to establish transparency and refraction power. Lens transparency is established by abundant accumulation of crystallin proteins and loss of organelles in the fiber cells. It requires an efficient translation of lens messenger RNAs (mRNAs) to overcome the progressively reduced transcriptional activity that results from denucleation. Inappropriate regulation of this process impairs lens differentiation and causes cataract formation. However, the regulatory mechanism promoting protein synthesis from lens-expressed mRNAs remains unclear. Here we show that in zebrafish, the RNA-binding protein Rbm24 is critically required for the accumulation of crystallin proteins and terminal differentiation of lens fiber cells. In the developing lens, Rbm24 binds to a wide spectrum of lens-specific mRNAs through the RNA recognition motif and interacts with cytoplasmic polyadenylation element-binding protein (Cpeb1b) and cytoplasmic poly(A)-binding protein (Pabpc1l) through the C-terminal region. Loss of Rbm24 reduces the stability of a subset of lens mRNAs encoding heat shock proteins and shortens the poly(A) tail length of crystallin mRNAs encoding lens structural components, thereby preventing their translation into functional proteins. This severely impairs lens transparency and results in blindness. Consistent with its highly conserved expression in differentiating lens fiber cells, the findings suggest that vertebrate Rbm24 represents a key regulator of cytoplasmic polyadenylation and plays an essential role in the posttranscriptional control of lens development.
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