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Shi X, Xue Z, Ye K, Yuan J, Zhang Y, Qu J, Su J. Roles of non-coding RNAs in eye development and diseases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1785. [PMID: 36849659 DOI: 10.1002/wrna.1785] [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: 09/29/2022] [Revised: 12/17/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
The prevalence of ocular disorders is dramatically increasing worldwide, especially those that cause visual impairment and permanent loss of vision, including cataract, glaucoma, age-related macular degeneration, and diabetic retinopathy. Extensive evidence has shown that ncRNAs are key regulators in various biogenesis and biological functions, controlling gene expression related to histogenesis and cell differentiation in ocular tissues. Aberrant expression and function of ncRNA can lead to dysfunction of visual system and mediate progression of eye disorders. Here, we mainly offer an overview of the role of precise modulation of ncRNAs in eye development and function in patients with eye diseases. We also highlight the challenges and future perspectives in conducting ncRNA studies, focusing specifically on the role of ncRNAs that may hold expanded promise for their diagnostic and therapeutic applications in various eye diseases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Xinrui Shi
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhengbo Xue
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kaicheng Ye
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jian Yuan
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Yan Zhang
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jia Qu
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
- Institute of PSI Genomics, Zhejiang, China
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2
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Identification of PAX6 and NFAT4 as the Transcriptional Regulators of the Long Noncoding RNA Mrhl in Neuronal Progenitors. Mol Cell Biol 2022; 42:e0003622. [PMID: 36317923 PMCID: PMC9670966 DOI: 10.1128/mcb.00036-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The long noncoding RNA (lncRNA) Mrhl has been shown to be involved in coordinating meiotic commitment of mouse spermatogonial progenitors and differentiation events in mouse embryonic stem cells. Here, we characterized the interplay of Mrhl with lineage-specific transcription factors during mouse neuronal lineage development. Our results demonstrate that Mrhl is expressed in the neuronal progenitor populations in mouse embryonic brains and in retinoic acid-derived radial-glia-like neuronal progenitor cells. Depletion of Mrhl leads to early differentiation of neuronal progenitors to a more committed state. A master transcription factor, PAX6, directly binds to the Mrhl promoter at a major site in the distal promoter, located at 2.9 kb upstream of the transcription start site (TSS) of Mrhl. Furthermore, NFAT4 occupies the Mrhl-proximal promoter at two sites, at 437 base pairs (bp) and 143 bp upstream of the TSS. Independent knockdown studies for PAX6 and NFAT4 confirm that they regulate Mrhl expression in neuronal progenitors. We also show that PAX6 and NFAT4 associate with each other in the same chromatin complex. NFAT4 occupies the Mrhl promoter in PAX6-bound chromatin, implying possible coregulation of Mrhl. Our studies are crucial for understanding how lncRNAs are regulated by major lineage-specific transcription factors, in order to define specific development and differentiation events.
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3
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Campla CK, Bocchero U, Strickland R, Nellissery J, Advani J, Ignatova I, Srivastava D, Aponte AM, Wang Y, Gumerson J, Martemyanov K, Artemyev NO, Pahlberg J, Swaroop A. Frmpd1 Facilitates Trafficking of G-Protein Transducin and Modulates Synaptic Function in Rod Photoreceptors of Mammalian Retina. eNeuro 2022; 9:ENEURO.0348-22.2022. [PMID: 36180221 PMCID: PMC9581579 DOI: 10.1523/eneuro.0348-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/23/2022] [Indexed: 12/15/2022] Open
Abstract
Trafficking of transducin (Gαt) in rod photoreceptors is critical for adaptive and modulatory responses of the retina to varying light intensities. In addition to fine-tuning phototransduction gain in rod outer segments (OSs), light-induced translocation of Gαt to the rod synapse enhances rod to rod bipolar synaptic transmission. Here, we show that the rod-specific loss of Frmpd1 (FERM and PDZ domain containing 1), in the retina of both female and male mice, results in delayed return of Gαt from the synapse back to outer segments in the dark, compromising the capacity of rods to recover from light adaptation. Frmpd1 directly interacts with Gpsm2 (G-protein signaling modulator 2), and the two proteins are required for appropriate sensitization of rod-rod bipolar signaling under saturating light conditions. These studies provide insight into how the trafficking and function of Gαt is modulated to optimize the photoresponse and synaptic transmission of rod photoreceptors in a light-dependent manner.
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Affiliation(s)
- Christie K Campla
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ulisse Bocchero
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
- Photoreceptor Physiology Group, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ryan Strickland
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jacob Nellissery
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Irina Ignatova
- Photoreceptor Physiology Group, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Dhiraj Srivastava
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Angel M Aponte
- Proteomics Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yuchen Wang
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458
| | - Jessica Gumerson
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kirill Martemyanov
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Johan Pahlberg
- Photoreceptor Physiology Group, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
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4
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Guan Y, Wang Y, Zheng D, Xie B, Xu P, Gao G, Zhong X. Generation of an RCVRN-eGFP Reporter hiPSC Line by CRISPR/Cas9 to Monitor Photoreceptor Cell Development and Facilitate the Cell Enrichment for Transplantation. Front Cell Dev Biol 2022; 10:870441. [PMID: 35573687 PMCID: PMC9096726 DOI: 10.3389/fcell.2022.870441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Stem cell-based cell therapies are considered to be promising treatments for retinal disorders with dysfunction or death of photoreceptors. However, the enrichment of human photoreceptors suitable for transplantation has been highly challenging so far. This study aimed to generate a photoreceptor-specific reporter human induced pluripotent stem cell (hiPSC) line using CRISPR/Cas9 genome editing, which harbored an enhanced green fluorescent protein (eGFP) sequence at the endogenous locus of the pan photoreceptor marker recoverin (RCVRN). After confirmation of successful targeting and gene stability, three-dimensional retinal organoids were induced from this reporter line. The RCVRN-eGFP reporter faithfully replicated endogenous protein expression of recoverin and revealed the developmental characteristics of photoreceptors during retinal differentiation. The RCVRN-eGFP specifically and steadily labeled photoreceptor cells from photoreceptor precursors to mature rods and cones. Additionally, abundant eGFP-positive photoreceptors were enriched by fluorescence-activated cell sorting, and their transcriptome signatures were revealed by RNA sequencing and data analysis. Moreover, potential clusters of differentiation (CD) biomarkers were extracted for the enrichment of photoreceptors for clinical applications, such as CD133 for the positive selection of photoreceptors. Altogether, the RCVRN-eGFP reporter hiPSC line was successfully established and the first global expression database of recoverin-positive photoreceptors was constructed. These achievements will provide a powerful tool for dynamically monitoring photoreceptor cell development and purification of human photoreceptors, thus facilitating photoreceptor cell therapy for advanced retinal disorders.
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5
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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6
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Carrella S, Banfi S, Karali M. Sophisticated Gene Regulation for a Complex Physiological System: The Role of Non-coding RNAs in Photoreceptor Cells. Front Cell Dev Biol 2021; 8:629158. [PMID: 33537317 PMCID: PMC7848107 DOI: 10.3389/fcell.2020.629158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/18/2020] [Indexed: 12/26/2022] Open
Abstract
Photoreceptors (PRs) are specialized neuroepithelial cells of the retina responsible for sensory transduction of light stimuli. In the highly structured vertebrate retina, PRs have a highly polarized modular structure to accommodate the demanding processes of phototransduction and the visual cycle. Because of their function, PRs are exposed to continuous cellular stress. PRs are therefore under pressure to maintain their function in defiance of constant environmental perturbation, besides being part of a highly sophisticated developmental process. All this translates into the need for tightly regulated and responsive molecular mechanisms that can reinforce transcriptional programs. It is commonly accepted that regulatory non-coding RNAs (ncRNAs), and in particular microRNAs (miRNAs), are not only involved but indeed central in conferring robustness and accuracy to developmental and physiological processes. Here we integrate recent findings on the role of regulatory ncRNAs (e.g., miRNAs, lncRNAs, circular RNAs, and antisense RNAs), and of their contribution to PR pathophysiology. We also outline the therapeutic implications of translational studies that harness ncRNAs to prevent PR degeneration and promote their survival and function.
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Affiliation(s)
- Sabrina Carrella
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marianthi Karali
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
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7
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Targeting of the NRL Pathway as a Therapeutic Strategy to Treat Retinitis Pigmentosa. J Clin Med 2020; 9:jcm9072224. [PMID: 32668775 PMCID: PMC7408925 DOI: 10.3390/jcm9072224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/28/2020] [Accepted: 07/07/2020] [Indexed: 12/26/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited retinal dystrophy (IRD) with a prevalence of 1:4000, characterized by initial rod photoreceptor loss and subsequent cone photoreceptor loss with accompanying nyctalopia, visual field deficits, and visual acuity loss. A diversity of causative mutations have been described with autosomal dominant, autosomal recessive, and X-linked inheritance and sporadic mutations. The diversity of mutations makes gene therapy challenging, highlighting the need for mutation-agnostic treatments. Neural leucine zipper (NRL) and NR2E3 are factors important for rod photoreceptor cell differentiation and homeostasis. Germline mutations in NRL or NR2E3 leads to a loss of rods and an increased number of cones with short wavelength opsin in both rodents and humans. Multiple groups have demonstrated that inhibition of NRL or NR2E3 activity in the mature retina could endow rods with certain properties of cones, which prevents cell death in multiple rodent RP models with diverse mutations. In this review, we summarize the literature on NRL and NR2E3, therapeutic strategies of NRL/NR2E3 modulation in preclinical RP models, as well as future directions of research. In summary, inhibition of the NRL/NR2E3 pathway represents an intriguing mutation agnostic and disease-modifying target for the treatment of RP.
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8
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Chen Y, Wang H, Jiang Y, Zhang X, Wang Q. Transcriptional profiling to identify the key genes and pathways of pterygium. PeerJ 2020; 8:e9056. [PMID: 32411530 PMCID: PMC7204871 DOI: 10.7717/peerj.9056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/03/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose Pterygium results from a variety of biological pathways that are involved in the formation of ocular surface diseases. However, the exact pathogenesis of pterygium is still unclear. Our study focused on gene expression profiles to better understand the potential mechanisms of pterygium. Methods RNA sequencing experiments were performed on clinical pterygium tissues and normal conjunctival tissues. To identify the hub genes for the development of pterygium, we further conducted weighted gene co-expression network analysis (WGCNA). qRT-PCR was utilized to validate the dysregulation of the most significant differentially expressed genes (DEGs) and key hub genes in the independent subjects. Results A total of 339 DEGs (P-adjusted < 0.05 and log2 fold change [log2FC] ≥ 1.0) were obtained that reached statistical significance with p-values < 0.05. Among them, 200 DEGs were upregulated; these genes were mainly associated with the extracellular matrix and with cell adhesion or migration. In contrast, the 139 downregulated genes were enriched for endocrine and inflammation pathways. With regard to WGCNA, five modules were assigned based on the DEG profiles, and the biological functions of each module were verified with previously published GO terms. The functions included ECM-receptor interactions, the PI3K-Akt signalling pathway and an endoplasmic reticulum (ER)-related pathway. The five hub genes with the highest connectivity in each module and the five most significant DEGs showed dysregulated expression in the independent cohort samples. Conclusions RNA sequencing and WGCNA provided novel insights into the potential regulatory mechanisms of pterygium. The identified DEGs and hub genes, which were classified into two groups according to different functions or signalings, may provide important references for further research on the molecular biology of pterygium.
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Affiliation(s)
- Yihui Chen
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haoyu Wang
- Department of Dermatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaping Jiang
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoyan Zhang
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qingzhong Wang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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9
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Kallman A, Capowski EE, Wang J, Kaushik AM, Jansen AD, Edwards KL, Chen L, Berlinicke CA, Joseph Phillips M, Pierce EA, Qian J, Wang TH, Gamm DM, Zack DJ. Investigating cone photoreceptor development using patient-derived NRL null retinal organoids. Commun Biol 2020; 3:82. [PMID: 32081919 PMCID: PMC7035245 DOI: 10.1038/s42003-020-0808-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/21/2020] [Indexed: 12/22/2022] Open
Abstract
Photoreceptor loss is a leading cause of blindness, but mechanisms underlying photoreceptor degeneration are not well understood. Treatment strategies would benefit from improved understanding of gene-expression patterns directing photoreceptor development, as many genes are implicated in both development and degeneration. Neural retina leucine zipper (NRL) is critical for rod photoreceptor genesis and degeneration, with NRL mutations known to cause enhanced S-cone syndrome and retinitis pigmentosa. While murine Nrl loss has been characterized, studies of human NRL can identify important insights for human retinal development and disease. We utilized iPSC organoid models of retinal development to molecularly define developmental alterations in a human model of NRL loss. Consistent with the function of NRL in rod fate specification, human retinal organoids lacking NRL develop S-opsin dominant photoreceptor populations. We report generation of two distinct S-opsin expressing populations in NRL null retinal organoids and identify MEF2C as a candidate regulator of cone development. Kallman et al. showed the effect of Nrl in human PSC-derived retinal organoids. Using histological and single cell transcriptomics, they identified an intermediate “cod” subpopulation in the predominant S-opsin population. Their findings provide important insights for human retinal development and degeneration.
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Affiliation(s)
- Alyssa Kallman
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | - Jie Wang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, USA
| | - Alex D Jansen
- Waisman Center, University of Wisconsin-Madison, Madison, USA
| | | | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, USA
| | - Cynthia A Berlinicke
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - M Joseph Phillips
- Waisman Center, University of Wisconsin-Madison, Madison, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Boston, USA
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
| | - David M Gamm
- Waisman Center, University of Wisconsin-Madison, Madison, USA. .,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, USA. .,Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, USA.
| | - Donald J Zack
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA. .,Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, USA. .,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA. .,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA.
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10
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Perez-Cervantes C, Smith LA, Nadadur RD, Hughes AEO, Wang S, Corbo JC, Cepko C, Lonfat N, Moskowitz IP. Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types. Development 2020; 147:dev184432. [PMID: 31915147 PMCID: PMC7033740 DOI: 10.1242/dev.184432] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
Identification of cell type-specific cis-regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) NrlNrl-dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel Nrl-dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.
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Affiliation(s)
- Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Linsin A Smith
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rangarajan D Nadadur
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sui Wang
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Constance Cepko
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicolas Lonfat
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
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11
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Javed A, Mattar P, Lu S, Kruczek K, Kloc M, Gonzalez-Cordero A, Bremner R, Ali RR, Cayouette M. Pou2f1 and Pou2f2 cooperate to control the timing of cone photoreceptor production in the developing mouse retina. Development 2020; 147:dev.188730. [DOI: 10.1242/dev.188730] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022]
Abstract
Multipotent retinal progenitor cells (RPCs) generate various cell types in a precise chronological order, but how exactly cone photoreceptor production is restricted to early stages remains unclear. Here, we show that the POU-homeodomain factors Pou2f1/Pou2f2, the homologs of Drosophila temporal identity factors nub/pdm2, regulate the timely production of cones in mice. Forcing sustained expression of Pou2f1 or Pou2f2 in RPCs expands the period of cone production, whereas misexpression in late-stage RPCs triggers ectopic cone production at the expense of late-born fates. Mechanistically, we report that Pou2f1 induces Pou2f2 expression, which binds to a POU motif in the promoter of the rod-inducing factor Nrl to repress its expression. Conversely, conditional inactivation of Pou2f2 in RPCs increases Nrl expression and reduces cone production. Finally, we provide evidence that Pou2f1 is part of a cross-regulatory cascade with the other temporal identity factors Ikzf1 and Casz1. These results uncover Pou2f1/2 as regulators of the temporal window for cone genesis and, given their widespread expression in the nervous system, raise the possibility of a general role in temporal patterning.
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Affiliation(s)
- Awais Javed
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montreal (IRCM), Canada
- Molecular Biology Program, Université de Montréal, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montreal (IRCM), Canada
| | - Suying Lu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada. Department of Ophthalmology and Vision Science, Department of Lab Medicine and Pathobiology, University of Toronto
| | | | | | | | - Rod Bremner
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada. Department of Ophthalmology and Vision Science, Department of Lab Medicine and Pathobiology, University of Toronto
| | - Robin R. Ali
- UCL Institute of Ophthalmology, London, UK
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montreal (IRCM), Canada
- Molecular Biology Program, Université de Montréal, Canada
- Department of Medicine, Université de Montréal, Canada
- Department of Anatomy and Cell Biology; Division of Experimental Medicine, McGill University, Canada
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12
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Wan Y, Liu X, Zheng D, Wang Y, Chen H, Zhao X, Liang G, Yu D, Gan L. Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing. BMC Genomics 2019; 20:559. [PMID: 31286854 PMCID: PMC6615288 DOI: 10.1186/s12864-019-5903-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Background A great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, the biological roles of lncRNAs in the mouse retina remains largely unknown due to the lack of a comprehensive annotation of lncRNAs expressed in the retina. Results In this study, we applied the long-reads sequencing strategy to unravel the transcriptomes of developing mouse retinas and identified a total of 940 intergenic lncRNAs (lincRNAs) in embryonic and neonatal retinas, including about 13% of them were transcribed from unannotated gene loci. Subsequent analysis revealed that function of lincRNAs expressed in mouse retinas were closely related to the physiological roles of this tissue, including 90 lincRNAs that were differentially expressed after the functional loss of key regulators of retinal ganglion cell (RGC) differentiation. In situ hybridization results demonstrated the enrichment of three class IV POU-homeobox genes adjacent lincRNAs (linc-3a, linc-3b and linc-3c) in ganglion cell layer and indicated they were potentially RGC-specific. Conclusions In summary, this study systematically annotated the lincRNAs expressed in embryonic and neonatal mouse retinas and implied their crucial regulatory roles in retinal development such as RGC differentiation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5903-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ying Wan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | - Xiaoyang Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | | | - Yuying Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | - Huan Chen
- Key Laboratory of microbiological technology and Bioinformatics in Zhejiang Province, Hangzhou, China
| | - Xiaofeng Zhao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China
| | - Guoqing Liang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China. .,Zhejiang Key Laboratory of Organ Development and Regeneration, Hangzhou Normal University, Hangzhou, China.
| | - Lin Gan
- Department of Ophthalmology and Flaum Eye Institute, University of Rochester, Rochester, NY, 14642, USA.
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13
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Garafalo AV, Calzetti G, Cideciyan AV, Roman AJ, Saxena S, Sumaroka A, Choi W, Wright AF, Jacobson SG. Cone Vision Changes in the Enhanced S-Cone Syndrome Caused by NR2E3 Gene Mutations. Invest Ophthalmol Vis Sci 2019; 59:3209-3219. [PMID: 29971438 DOI: 10.1167/iovs.18-24518] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To determine the progression of cone vision loss in patients with recessive disease from NR2E3 gene mutations. Methods Patients with NR2E3 mutations (n = 37) were studied as a retrospective observational case series clinically and with chromatic static perimetry. Patients were investigated cross-sectionally, and a subset was followed longitudinally. Results Patients showed a range of visual acuities; there was no clear relationship to age. With kinetic perimetry (V4e target), a full field could be retained over many years. Other patients showed progression from a full field, with or without pericentral scotomas, to a small central island. Three patterns of S-cone function were defined, based on percentage of hypersensitive S-cone loci in the field. From occupying most of the visual field, hyperfunctioning S-cone loci could diminish in percent, remaining largely in the periphery. Normal S-cone functioning then dominates, followed by the appearance of an annular region of abnormal S-cone loci approximately 10° to 40° from the fovea. Overall, S-cone sensitivity declined 2.6 times faster than L/M-cone sensitivity. Conclusions Murine proof-of-concept studies suggest that clinical trials of patients with NR2E3 mutations may be forthcoming. Patterns of S-cone hyperfunction across the field would serve as a means to categorize patients as entry criteria or cohort selection in clinical trials. S-cone perimetry can be measured in the clinic and would be the logical efficacy monitor for therapeutic strategies. Given further understanding of the natural history of the disease, targeting the annular region of S-cone dysfunction for a focal therapy or for monitoring in a retina-wide intervention warrants consideration.
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Affiliation(s)
- Alexandra V Garafalo
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Giacomo Calzetti
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Artur V Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Alejandro J Roman
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Supna Saxena
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Alexander Sumaroka
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Windy Choi
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Alan F Wright
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel G Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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14
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Non-coding RNAs in retinal development and function. Hum Genet 2018; 138:957-971. [DOI: 10.1007/s00439-018-1931-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/24/2018] [Indexed: 12/12/2022]
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15
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Generation of a rod-specific NRL reporter line in human pluripotent stem cells. Sci Rep 2018; 8:2370. [PMID: 29402929 PMCID: PMC5799252 DOI: 10.1038/s41598-018-20813-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/24/2018] [Indexed: 12/18/2022] Open
Abstract
Reporter lines generated in human pluripotent stem cells can be highly useful for the analysis of specific cell types and lineages in live cultures. We created the first human rod reporter line using CRISPR/Cas9 genome editing to replace one allele of the Neural Retina Leucine zipper (NRL) gene with an eGFP transgene in the WA09 human embryonic stem cell (hESC) line. After confirming successful targeting, three-dimensional optic vesicle structures were produced to examine reporter specificity and to track rod differentiation in culture. The NRL+/eGFP hESC line robustly and exclusively labeled the entirety of rods throughout differentiation, eventually revealing highly mature structural features. This line provides a valuable tool for studying human rod development and disease and testing therapeutic strategies for retinitis pigmentosa.
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16
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Zelinger L, Swaroop A. RNA Biology in Retinal Development and Disease. Trends Genet 2018; 34:341-351. [PMID: 29395379 DOI: 10.1016/j.tig.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 02/06/2023]
Abstract
For decades, RNA has served in a supporting role between the genetic carrier (DNA) and the functional molecules (proteins). It is finally time for RNA to take center stage in all aspects of biology. The retina provides a unique opportunity to dissect the molecular underpinnings of neuronal diversity and disease. Transcriptome profiles of the retina and its resident cell types have unraveled unique features of the RNA landscape. The discovery of distinct RNA molecules and the recognition that RNA processing is a major cause of retinal neurodegeneration have prompted the design of biomarkers and novel therapeutic paradigms. We review here RNA biology as it pertains to the retina, emphasizing new avenues for investigations in development and disease.
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Affiliation(s)
- Lina Zelinger
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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