151
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Yan W, Peng YR, van Zyl T, Regev A, Shekhar K, Juric D, Sanes JR. Cell Atlas of The Human Fovea and Peripheral Retina. Sci Rep 2020; 10:9802. [PMID: 32555229 PMCID: PMC7299956 DOI: 10.1038/s41598-020-66092-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/12/2020] [Indexed: 01/28/2023] Open
Abstract
Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral retina of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and non-neuronal cells. Nearly all types are shared between the two retinal regions, but there are notable differences in gene expression and proportions between foveal and peripheral cohorts of shared types. We then used the human retinal atlas to map expression of 636 genes implicated as causes of or risk factors for blinding diseases. Many are expressed in striking cell class-, type-, or region-specific patterns. Finally, we compared gene expression signatures of cell types between human and the cynomolgus macaque monkey, Macaca fascicularis. We show that over 90% of human types correspond transcriptomically to those previously identified in macaque, and that expression of disease-related genes is largely conserved between the two species. These results validate the use of the macaque for modeling blinding disease, and provide a foundation for investigating molecular mechanisms underlying visual processing.
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Affiliation(s)
- Wenjun Yan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA
| | - Yi-Rong Peng
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA
- Department of Ophthalmology, Stein Eye Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Tavé van Zyl
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA, 02114, USA
| | - Aviv Regev
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140; and Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Karthik Shekhar
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140; and Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Chemical and Biomolecular Engineering and Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA.
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152
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VanderWall KB, Huang KC, Pan Y, Lavekar SS, Fligor CM, Allsop AR, Lentsch KA, Dang P, Zhang C, Tseng HC, Cummins TR, Meyer JS. Retinal Ganglion Cells With a Glaucoma OPTN(E50K) Mutation Exhibit Neurodegenerative Phenotypes when Derived from Three-Dimensional Retinal Organoids. Stem Cell Reports 2020; 15:52-66. [PMID: 32531194 PMCID: PMC7363877 DOI: 10.1016/j.stemcr.2020.05.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/18/2022] Open
Abstract
Retinal ganglion cells (RGCs) serve as the connection between the eye and the brain, with this connection disrupted in glaucoma. Numerous cellular mechanisms have been associated with glaucomatous neurodegeneration, and useful cellular models of glaucoma allow for the precise analysis of degenerative phenotypes. Human pluripotent stem cells (hPSCs) serve as powerful tools for studying human disease, particularly cellular mechanisms underlying neurodegeneration. Thus, efforts focused upon hPSCs with an E50K mutation in the Optineurin (OPTN) gene, a leading cause of inherited forms of glaucoma. CRISPR/Cas9 gene editing introduced the OPTN(E50K) mutation into existing lines of hPSCs, as well as generating isogenic controls from patient-derived lines. RGCs differentiated from OPTN(E50K) hPSCs exhibited numerous neurodegenerative deficits, including neurite retraction, autophagy dysfunction, apoptosis, and increased excitability. These results demonstrate the utility of OPTN(E50K) RGCs as an in vitro model of neurodegeneration, with the opportunity to develop novel therapeutic approaches for glaucoma.
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Affiliation(s)
- Kirstin B VanderWall
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Kang-Chieh Huang
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Yanling Pan
- Indiana BioMedical Gateway Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sailee S Lavekar
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Clarisse M Fligor
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Anna R Allsop
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Kelly A Lentsch
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Pengtao Dang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Henry C Tseng
- Duke Eye Center and Department of Ophthalmology, Duke University Medical Center, Durham, NC 27710, USA
| | - Theodore R Cummins
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jason S Meyer
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Ophthalmology, Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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153
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Kruczek K, Swaroop A. Pluripotent stem cell-derived retinal organoids for disease modeling and development of therapies. Stem Cells 2020; 38:1206-1215. [PMID: 32506758 PMCID: PMC7586922 DOI: 10.1002/stem.3239] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 02/06/2023]
Abstract
Retinal diseases constitute a genetically and phenotypically diverse group of clinical conditions leading to vision impairment or blindness with limited treatment options. Advances in reprogramming of somatic cells to induced pluripotent stem cells and generation of three‐dimensional organoids resembling the native retina offer promising tools to interrogate disease mechanisms and evaluate potential therapies for currently incurable retinal neurodegeneration. Next‐generation sequencing, single‐cell analysis, advanced electrophysiology, and high‐throughput screening approaches are expected to greatly expand the utility of stem cell‐derived retinal cells and organoids for developing personalized treatments. In this review, we discuss the current status and future potential of combining retinal organoids as human models with recent technologies to advance the development of gene, cell, and drug therapies for retinopathies.
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Affiliation(s)
- Kamil Kruczek
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
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154
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Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. Dev Cell 2020; 53:473-491.e9. [PMID: 32386599 DOI: 10.1016/j.devcel.2020.04.009] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/05/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023]
Abstract
The development of single-cell RNA sequencing (scRNA-seq) has allowed high-resolution analysis of cell-type diversity and transcriptional networks controlling cell-fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-seq analysis on 16 time points from developing retina as well as four early stages of retinal organoid differentiation. We identified evolutionarily conserved patterns of gene expression during retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we identified gene-expression differences between developing macula and periphery and between distinct populations of horizontal cells. We also identified species-specific patterns of gene expression during human and mouse retinal development. Finally, we identified an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development and may help guide the design of cell-based therapies for treating retinal dystrophies.
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155
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Zhang S, Markey M, Pena CD, Venkatesh T, Vazquez M. A Micro-Optic Stalk (μOS) System to Model the Collective Migration of Retinal Neuroblasts. MICROMACHINES 2020; 11:mi11040363. [PMID: 32244321 PMCID: PMC7230939 DOI: 10.3390/mi11040363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/18/2022]
Abstract
Contemporary regenerative therapies have introduced stem-like cells to replace damaged neurons in the visual system by recapitulating critical processes of eye development. The collective migration of neural stem cells is fundamental to retinogenesis and has been exceptionally well-studied using the fruit fly model of Drosophila Melanogaster. However, the migratory behavior of its retinal neuroblasts (RNBs) has been surprisingly understudied, despite being critical to retinal development in this invertebrate model. The current project developed a new microfluidic system to examine the collective migration of RNBs extracted from the developing visual system of Drosophila as a model for the collective motile processes of replacement neural stem cells. The system scales with the microstructure of the Drosophila optic stalk, which is a pre-cursor to the optic nerve, to produce signaling fields spatially comparable to in vivo RNB stimuli. Experiments used the micro-optic stalk system, or μOS, to demonstrate the preferred sizing and directional migration of collective, motile RNB groups in response to changes in exogenous concentrations of fibroblast growth factor (FGF), which is a key factor in development. Our data highlight the importance of cell-to-cell contacts in enabling cell cohesion during collective RNB migration and point to the unexplored synergy of invertebrate cell study and microfluidic platforms to advance regenerative strategies.
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Affiliation(s)
- Stephanie Zhang
- Department of Biomedical Engineering, Binghamton University, 4400 Vestal Pkwy E, Binghamton, NY 13902, USA;
| | - Miles Markey
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Rd, Piscataway, NJ 08854, USA;
| | - Caroline D. Pena
- Department of Biomedical Engineering, City College of New York, New York City, NY 10031, USA;
| | - Tadmiri Venkatesh
- Department of Biology, City College of New York, New York City, NY 10031, USA;
| | - Maribel Vazquez
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Rd, Piscataway, NJ 08854, USA;
- Correspondence:
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156
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Markitantova Y, Simirskii V. Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes. Int J Mol Sci 2020; 21:E1602. [PMID: 32111086 PMCID: PMC7084737 DOI: 10.3390/ijms21051602] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Retinal development is under the coordinated control of overlapping networks of signaling pathways and transcription factors. The paper was conceived as a review of the data and ideas that have been formed to date on homeobox genes mutations that lead to the disruption of eye organogenesis and result in inherited eye/retinal diseases. Many of these diseases are part of the same clinical spectrum and have high genetic heterogeneity with already identified associated genes. We summarize the known key regulators of eye development, with a focus on the homeobox genes associated with monogenic eye diseases showing retinal manifestations. Recent advances in the field of genetics and high-throughput next-generation sequencing technologies, including single-cell transcriptome analysis have allowed for deepening of knowledge of the genetic basis of inherited retinal diseases (IRDs), as well as improve their diagnostics. We highlight some promising avenues of research involving molecular-genetic and cell-technology approaches that can be effective for IRDs therapy. The most promising neuroprotective strategies are aimed at mobilizing the endogenous cellular reserve of the retina.
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