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Wang S, Tong S, Jin X, Li N, Dang P, Sui Y, Liu Y, Wang D. Single-cell RNA sequencing analysis of the retina under acute high intraocular pressure. Neural Regen Res 2024; 19:2522-2531. [PMID: 38526288 PMCID: PMC11090430 DOI: 10.4103/1673-5374.389363] [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: 05/24/2023] [Revised: 07/27/2023] [Accepted: 09/13/2023] [Indexed: 03/26/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202419110-00032/figure1/v/2024-03-08T184507Z/r/image-tiff High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases, yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown. Rat models of acute hypertension ocular pressure were established by injection of cross-linked hyaluronic acid hydrogel (Healaflow®). Single-cell RNA sequencing was then used to describe the cellular composition and molecular profile of the retina following high intraocular pressure. Our results identified a total of 12 cell types, namely retinal pigment epithelial cells, rod-photoreceptor cells, bipolar cells, Müller cells, microglia, cone-photoreceptor cells, retinal ganglion cells, endothelial cells, retinal progenitor cells, oligodendrocytes, pericytes, and fibroblasts. The single-cell RNA sequencing analysis of the retina under acute high intraocular pressure revealed obvious changes in the proportions of various retinal cells, with ganglion cells decreased by 23%. Hematoxylin and eosin staining and TUNEL staining confirmed the damage to retinal ganglion cells under high intraocular pressure. We extracted data from retinal ganglion cells and analyzed the retinal ganglion cell cluster with the most distinct expression. We found upregulation of the B3gat2 gene, which is associated with neuronal migration and adhesion, and downregulation of the Tsc22d gene, which participates in inhibition of inflammation. This study is the first to reveal molecular changes and intercellular interactions in the retina under high intraocular pressure. These data contribute to understanding of the molecular mechanism of retinal injury induced by high intraocular pressure and will benefit the development of novel therapies.
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Affiliation(s)
- Shaojun Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Siti Tong
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Xin Jin
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Na Li
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Pingxiu Dang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Yang Sui
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Ying Liu
- Department of Ophthalmology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Dajiang Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
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2
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Yuan X, Li W, Liu Q, Long Q, Yan Q, Zhang P. Genomic characteristics of adipose-derived stromal cells induced into neurons based on single-cell RNA sequencing. Heliyon 2024; 10:e33079. [PMID: 38984299 PMCID: PMC11231542 DOI: 10.1016/j.heliyon.2024.e33079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024] Open
Abstract
Adipose-derived stromal cells (ADSCs) can be induced to differentiate into neurons, representing the most promising avenue for cell therapy. However, the molecular mechanism and genomic characteristics of the differentiation of ADSCs into neurons remain poorly understood. In this study, cells from the adult ADSCs group, induction 1h, 3h, 5h, 6h, and 8h groups were selected for single-cell RNA sequencing (scRNA-Seq). Samples from these seven-time points were sequenced and analyzed. The expression of neuron marker genes, including NES, MAP2, TMEM59L, PTK2B, CHN1, DNM1, NRSN2, FBLN2, SCAMP1, SLC1A1, DLG4, CDK5, and ENO2, was found to be low in the ADSCs group, but highly expressed in differentiated cell clusters. The expression of stem cell marker genes, including CCND1, IL1B, MMP1, MMP3, MYO10, and BMP2, was the highest in the ADSCs cluster. This expression decreased significantly with the extension of induction time. Gene ontology (GO) enrichment analysis of upregulated genes in the induced samples showed that the biological processes related to neuronal differentiation and development, such as neuronal differentiation, projection, and apoptosis, were significantly upregulated with a longer induction time during cell cluster differentiation. The results of the cell communication analysis demonstrated the gradual formation of complex neural network connections between ADSC-derived neurons through receptor and ligand pairs at 5h after the induction of differentiation.
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Affiliation(s)
- Xiaodong Yuan
- Department of Neurology of Kailuan General Hospital Affiliated North China University of Science and Technology, China
- Hebei Provincial Key Laboratory of Neurobiological Function, China
| | - Wen Li
- Department of Neurology of Kailuan General Hospital Affiliated North China University of Science and Technology, China
- Hebei Provincial Key Laboratory of Neurobiological Function, China
| | - Qing Liu
- Department of Neurology of Kailuan General Hospital Affiliated North China University of Science and Technology, China
- Hebei Provincial Key Laboratory of Neurobiological Function, China
| | - Qingxi Long
- Department of Neurology of Kailuan General Hospital Affiliated North China University of Science and Technology, China
- Hebei Provincial Key Laboratory of Neurobiological Function, China
| | - Qi Yan
- Department of Neurology of Kailuan General Hospital Affiliated North China University of Science and Technology, China
- Hebei Provincial Key Laboratory of Neurobiological Function, China
| | - Pingshu Zhang
- Department of Neurology of Kailuan General Hospital Affiliated North China University of Science and Technology, China
- Hebei Provincial Key Laboratory of Neurobiological Function, China
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3
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Mehta K, Daghsni M, Raeisossadati R, Xu Z, Davis E, Naidich A, Wang B, Tao S, Pi S, Chen W, Kostka D, Liu S, Gross JM, Kuwajima T, Aldiri I. A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis. Cell Rep 2024; 43:114291. [PMID: 38823017 PMCID: PMC11238474 DOI: 10.1016/j.celrep.2024.114291] [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: 11/15/2023] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024] Open
Abstract
Atoh7 is transiently expressed in retinal progenitor cells (RPCs) and is required for retinal ganglion cell (RGC) differentiation. In humans, a deletion in a distal non-coding regulatory region upstream of ATOH7 is associated with optic nerve atrophy and blindness. Here, we functionally interrogate the significance of the Atoh7 regulatory landscape to retinogenesis in mice. Deletion of the Atoh7 enhancer structure leads to RGC deficiency, optic nerve hypoplasia, and retinal blood vascular abnormalities, phenocopying inactivation of Atoh7. Further, loss of the Atoh7 remote enhancer impacts ipsilaterally projecting RGCs and disrupts proper axonal projections to the visual thalamus. Deletion of the Atoh7 remote enhancer is also associated with the dysregulation of axonogenesis genes, including the derepression of the axon repulsive cue Robo3. Our data provide insights into how Atoh7 enhancer elements function to promote RGC development and optic nerve formation and highlight a key role of Atoh7 in the transcriptional control of axon guidance molecules.
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Affiliation(s)
- Kamakshi Mehta
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marwa Daghsni
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Reza Raeisossadati
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Zhongli Xu
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Emily Davis
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Abigail Naidich
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Bingjie Wang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Shiyue Tao
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Wei Chen
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Dennis Kostka
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M Gross
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Takaaki Kuwajima
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Issam Aldiri
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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4
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Luo Z, Shah S, Tanasa B, Chang KC, Goldberg JL. Gene regulatory roles of growth and differentiation factors in retinal development. iScience 2024; 27:110100. [PMID: 38947520 PMCID: PMC11214324 DOI: 10.1016/j.isci.2024.110100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/06/2024] [Accepted: 05/22/2024] [Indexed: 07/02/2024] Open
Abstract
Retinal ganglion cell (RGC) differentiation is tightly controlled by extrinsic and intrinsic factors. Growth and differentiation factor 15 (GDF-15) promotes RGC differentiation, opposite to GDF-11 which inhibits RGC differentiation, both in the mouse retina and in human stem cells. To deepen our understanding of how these two closely related molecules confer opposing effects on retinal development, here we assess the transcriptional profiles of mouse retinal progenitors exposed to exogenous GDF-11 or -15. We find a dichotomous effect of GDF-15 on RGC differentiation, decreasing RGCs expressing residual pro-proliferative genes and increasing RGCs expressing non-proliferative genes, suggestive of greater RGC maturation. Furthermore, GDF-11 promoted the differentiation of photoreceptors and amacrine cells. These data enhance our understanding of the mechanisms underlying the differentiation of RGCs and photoreceptors from retinal progenitors and suggest new approaches to the optimization of protocols for the differentiation of these cell types.
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Affiliation(s)
- Ziming Luo
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sahil Shah
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Bogdan Tanasa
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Kun-Che Chang
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jeffrey L. Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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5
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Dorgau B, Collin J, Rozanska A, Zerti D, Unsworth A, Crosier M, Hussain R, Coxhead J, Dhanaseelan T, Patel A, Sowden JC, FitzPatrick DR, Queen R, Lako M. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina. Nat Commun 2024; 15:3567. [PMID: 38670973 PMCID: PMC11053058 DOI: 10.1038/s41467-024-47933-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: 07/11/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids.
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Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Darin Zerti
- Biosciences Institute, Newcastle University, Newcastle, UK
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Moira Crosier
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Aara Patel
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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6
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Zhang L, Cavallini M, Wang J, Xin R, Zhang Q, Feng G, Sanes JR, Peng YR. Evolutionary and developmental specialization of foveal cell types in the marmoset. Proc Natl Acad Sci U S A 2024; 121:e2313820121. [PMID: 38598343 PMCID: PMC11032471 DOI: 10.1073/pnas.2313820121] [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: 08/11/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high-throughput single-cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all their foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia (MG), among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for MG in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution.
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Affiliation(s)
- Lin Zhang
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Martina Cavallini
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Junqiang Wang
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Ruiqi Xin
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Qiangge Zhang
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Yi-Rong Peng
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
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7
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Fritzsch B, Glover JC. Gene networks and the evolution of olfactory organs, eyes, hair cells and motoneurons: a view encompassing lancelets, tunicates and vertebrates. Front Cell Dev Biol 2024; 12:1340157. [PMID: 38533086 PMCID: PMC10963430 DOI: 10.3389/fcell.2024.1340157] [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: 11/17/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Key developmental pathways and gene networks underlie the formation of sensory cell types and structures involved in chemosensation, vision and mechanosensation, and of the efferents these sensory inputs can activate. We describe similarities and differences in these pathways and gene networks in selected species of the three main chordate groups, lancelets, tunicates, and vertebrates, leading to divergent development of olfactory receptors, eyes, hair cells and motoneurons. The lack of appropriately posited expression of certain transcription factors in lancelets and tunicates prevents them from developing vertebrate-like olfactory receptors and eyes, although they generate alternative structures for chemosensation and vision. Lancelets and tunicates lack mechanosensory cells associated with the sensation of acoustic stimuli, but have gravisensitive organs and ciliated epidermal sensory cells that may (and in some cases clearly do) provide mechanosensation and thus the capacity to respond to movement relative to surrounding water. Although functionally analogous to the vertebrate vestibular apparatus and lateral line, homology is questionable due to differences in the expression of the key transcription factors Neurog and Atoh1/7, on which development of vertebrate hair cells depends. The vertebrate hair cell-bearing inner ear and lateral line thus likely represent major evolutionary advances specific to vertebrates. Motoneurons develop in vertebrates under the control of the ventral signaling molecule hedgehog/sonic hedgehog (Hh,Shh), against an opposing inhibitory effect mediated by dorsal signaling molecules. Many elements of Shh-signaling and downstream genes involved in specifying and differentiating motoneurons are also exhibited by lancelets and tunicates, but the repertoire of MNs in vertebrates is broader, indicating greater diversity in motoneuron differentiation programs.
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Affiliation(s)
- Bernd Fritzsch
- Department of Biological Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Joel C. Glover
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Laboratory of Neural Development and Optical Recording (NDEVOR), Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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8
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Lei Q, Xiang K, Cheng L, Xiang M. Human retinal organoids with an OPA1 mutation are defective in retinal ganglion cell differentiation and function. Stem Cell Reports 2024; 19:68-83. [PMID: 38101398 PMCID: PMC10828684 DOI: 10.1016/j.stemcr.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
Autosomal dominant optic atrophy (ADOA), mostly caused by heterozygous OPA1 mutations and characterized by retinal ganglion cell (RGC) loss and optic nerve degeneration, is one of the most common types of inherited optic neuropathies. Previous work using a two-dimensional (2D) differentiation model of induced pluripotent stem cells (iPSCs) has investigated ADOA pathogenesis but failed to agree on the effect of OPA1 mutations on RGC differentiation. Here, we use 3D retinal organoids capable of mimicking in vivo retinal development to resolve the issue. We generated isogenic iPSCs carrying the hotspot OPA1 c.2708_2711delTTAG mutation and found that the mutant variant caused defective initial and terminal differentiation and abnormal electrophysiological properties of organoid-derived RGCs. Moreover, this variant inhibits progenitor proliferation and results in mitochondrial dysfunction. These data demonstrate that retinal organoids coupled with gene editing serve as a powerful tool to definitively identify disease-related phenotypes and provide valuable resources to further investigate ADOA pathogenesis and screen for ADOA therapeutics.
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Affiliation(s)
- Qiannan Lei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Kangjian Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Lin Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China; Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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9
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Zhang L, Cavallini M, Wang J, Xin R, Zhang Q, Feng G, Sanes JR, Peng YR. Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570996. [PMID: 38106142 PMCID: PMC10723441 DOI: 10.1101/2023.12.10.570996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing to profile retinal cells of the common marmoset ( Callithrix jacchus ), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all its foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia, among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for Müller glia in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution. Significance statement The sharpness of our eyesight hinges on a tiny retinal region known as the fovea. The fovea is pivotal for primate vision and is susceptible to diseases like age-related macular degeneration. We studied the fovea in the marmoset-a primate with ancient evolutionary ties. Our data illustrated the cellular and molecular composition of its fovea across different developmental ages. Our findings highlighted a profound cellular consistency among marmosets, humans, and macaques, emphasizing the value of marmosets in visual research and the study of visual diseases.
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10
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Lo J, Mehta K, Dhillon A, Huang YK, Luo Z, Nam MH, Al Diri I, Chang KC. Therapeutic strategies for glaucoma and optic neuropathies. Mol Aspects Med 2023; 94:101219. [PMID: 37839232 PMCID: PMC10841486 DOI: 10.1016/j.mam.2023.101219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Glaucoma is a neurodegenerative eye disease that causes permanent vision impairment. The main pathological characteristics of glaucoma are retinal ganglion cell (RGC) loss and optic nerve degeneration. Glaucoma can be caused by elevated intraocular pressure (IOP), although some cases are congenital or occur in patients with normal IOP. Current glaucoma treatments rely on medicine and surgery to lower IOP, which only delays disease progression. First-line glaucoma medicines are supported by pharmacotherapy advancements such as Rho kinase inhibitors and innovative drug delivery systems. Glaucoma surgery has shifted to safer minimally invasive (or microinvasive) glaucoma surgery, but further trials are needed to validate long-term efficacy. Further, growing evidence shows that adeno-associated virus gene transduction and stem cell-based RGC replacement therapy hold potential to treat optic nerve fiber degeneration and glaucoma. However, better understanding of the regulatory mechanisms of RGC development is needed to provide insight into RGC differentiation from stem cells and help choose target genes for viral therapy. In this review, we overview current progress in RGC development research, optic nerve fiber regeneration, and human stem cell-derived RGC differentiation and transplantation. We also provide an outlook on perspectives and challenges in the field.
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Affiliation(s)
- Jung Lo
- Department of Ophthalmology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Kamakshi Mehta
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Armaan Dhillon
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Yu-Kai Huang
- Department of Neurosurgery, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Ziming Luo
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Mi-Hyun Nam
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Issam Al Diri
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA.
| | - Kun-Che Chang
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA; Department of Neurobiology, Center of Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
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11
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Celotto L, Rost F, Machate A, Bläsche J, Dahl A, Weber A, Hans S, Brand M. Single-cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration. eLife 2023; 12:RP86507. [PMID: 37988404 PMCID: PMC10662954 DOI: 10.7554/elife.86507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
In the lesioned zebrafish retina, Müller glia produce multipotent retinal progenitors that generate all retinal neurons, replacing lost cell types. To study the molecular mechanisms linking Müller glia reactivity to progenitor production and neuronal differentiation, we used single-cell RNA sequencing of Müller glia, progenitors and regenerated progeny from uninjured and light-lesioned retinae. We discover an injury-induced Müller glia differentiation trajectory that leads into a cell population with a hybrid identity expressing marker genes of Müller glia and progenitors. A glial self-renewal and a neurogenic trajectory depart from the hybrid cell population. We further observe that neurogenic progenitors progressively differentiate to generate retinal ganglion cells first and bipolar cells last, similar to the events observed during retinal development. Our work provides a comprehensive description of Müller glia and progenitor transcriptional changes and fate decisions in the regenerating retina, which are key to tailor cell differentiation and replacement therapies for retinal dystrophies in humans.
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Affiliation(s)
- Laura Celotto
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Fabian Rost
- Technische Universität Dresden, DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Anja Machate
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Juliane Bläsche
- Technische Universität Dresden, DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Andreas Dahl
- Technische Universität Dresden, DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Anke Weber
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Stefan Hans
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Michael Brand
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
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12
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Soucy JR, Aguzzi EA, Cho J, Gilhooley MJ, Keuthan C, Luo Z, Monavarfeshani A, Saleem MA, Wang XW, Wohlschlegel J, Baranov P, Di Polo A, Fortune B, Gokoffski KK, Goldberg JL, Guido W, Kolodkin AL, Mason CA, Ou Y, Reh TA, Ross AG, Samuels BC, Welsbie D, Zack DJ, Johnson TV. Retinal ganglion cell repopulation for vision restoration in optic neuropathy: a roadmap from the RReSTORe Consortium. Mol Neurodegener 2023; 18:64. [PMID: 37735444 PMCID: PMC10514988 DOI: 10.1186/s13024-023-00655-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Retinal ganglion cell (RGC) death in glaucoma and other optic neuropathies results in irreversible vision loss due to the mammalian central nervous system's limited regenerative capacity. RGC repopulation is a promising therapeutic approach to reverse vision loss from optic neuropathies if the newly introduced neurons can reestablish functional retinal and thalamic circuits. In theory, RGCs might be repopulated through the transplantation of stem cell-derived neurons or via the induction of endogenous transdifferentiation. The RGC Repopulation, Stem Cell Transplantation, and Optic Nerve Regeneration (RReSTORe) Consortium was established to address the challenges associated with the therapeutic repair of the visual pathway in optic neuropathy. In 2022, the RReSTORe Consortium initiated ongoing international collaborative discussions to advance the RGC repopulation field and has identified five critical areas of focus: (1) RGC development and differentiation, (2) Transplantation methods and models, (3) RGC survival, maturation, and host interactions, (4) Inner retinal wiring, and (5) Eye-to-brain connectivity. Here, we discuss the most pertinent questions and challenges that exist on the path to clinical translation and suggest experimental directions to propel this work going forward. Using these five subtopic discussion groups (SDGs) as a framework, we suggest multidisciplinary approaches to restore the diseased visual pathway by leveraging groundbreaking insights from developmental neuroscience, stem cell biology, molecular biology, optical imaging, animal models of optic neuropathy, immunology & immunotolerance, neuropathology & neuroprotection, materials science & biomedical engineering, and regenerative neuroscience. While significant hurdles remain, the RReSTORe Consortium's efforts provide a comprehensive roadmap for advancing the RGC repopulation field and hold potential for transformative progress in restoring vision in patients suffering from optic neuropathies.
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Affiliation(s)
- Jonathan R Soucy
- Department of Ophthalmology, Schepens Eye Research Institute of Mass. Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Erika A Aguzzi
- The Institute of Ophthalmology, University College London, London, England, UK
| | - Julie Cho
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael James Gilhooley
- The Institute of Ophthalmology, University College London, London, England, UK
- Moorfields Eye Hospital, London, England, UK
| | - Casey Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ziming Luo
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Meher A Saleem
- Bascom Palmer Eye Institute, University of Miami Health System, Miami, FL, USA
| | - Xue-Wei Wang
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Petr Baranov
- Department of Ophthalmology, Schepens Eye Research Institute of Mass. Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Adriana Di Polo
- Department of Neuroscience, University of Montreal, Montreal, QC, Canada
- University of Montreal Hospital Research Centre, Montreal, QC, Canada
| | - Brad Fortune
- Discoveries in Sight Research Laboratories, Devers Eye Institute and Legacy Research Institute, Legacy Health, Portland, OR, USA
| | - Kimberly K Gokoffski
- Department of Ophthalmology, Roski Eye Institute, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey L Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - William Guido
- Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Alex L Kolodkin
- The Solomon H Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carol A Mason
- Departments of Pathology and Cell Biology, Neuroscience, and Ophthalmology, College of Physicians and Surgeons, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Yvonne Ou
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Ahmara G Ross
- Departments of Ophthalmology and Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian C Samuels
- Department of Ophthalmology and Visual Sciences, Callahan Eye Hospital, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Derek Welsbie
- Shiley Eye Institute and Viterbi Family Department of Ophthalmology, University of California, San Diego, CA, USA
| | - Donald J Zack
- Glaucoma Center of Excellence, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, 21287 MD, USA
- Departments of Neuroscience, Molecular Biology & Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas V Johnson
- Departments of Neuroscience, Molecular Biology & Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Cellular & Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, 21287 MD, USA.
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13
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Wong NK, Yip SP, Huang CL. Establishing Functional Retina in a Dish: Progress and Promises of Induced Pluripotent Stem Cell-Based Retinal Neuron Differentiation. Int J Mol Sci 2023; 24:13652. [PMID: 37686457 PMCID: PMC10487913 DOI: 10.3390/ijms241713652] [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: 08/03/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
The human eye plays a critical role in vision perception, but various retinal degenerative diseases such as retinitis pigmentosa (RP), glaucoma, and age-related macular degeneration (AMD) can lead to vision loss or blindness. Although progress has been made in understanding retinal development and in clinical research, current treatments remain inadequate for curing or reversing these degenerative conditions. Animal models have limited relevance to humans, and obtaining human eye tissue samples is challenging due to ethical and legal considerations. Consequently, researchers have turned to stem cell-based approaches, specifically induced pluripotent stem cells (iPSCs), to generate distinct retinal cell populations and develop cell replacement therapies. iPSCs offer a novel platform for studying the key stages of human retinogenesis and disease-specific mechanisms. Stem cell technology has facilitated the production of diverse retinal cell types, including retinal ganglion cells (RGCs) and photoreceptors, and the development of retinal organoids has emerged as a valuable in vitro tool for investigating retinal neuron differentiation and modeling retinal diseases. This review focuses on the protocols, culture conditions, and techniques employed in differentiating retinal neurons from iPSCs. Furthermore, it emphasizes the significance of molecular and functional validation of the differentiated cells.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
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14
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Bosze B, Suarez-Navarro J, Cajias I, Brzezinski IV JA, Brown NL. Notch pathway mutants do not equivalently perturb mouse embryonic retinal development. PLoS Genet 2023; 19:e1010928. [PMID: 37751417 PMCID: PMC10522021 DOI: 10.1371/journal.pgen.1010928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023] Open
Abstract
In the vertebrate eye, Notch ligands, receptors, and ternary complex components determine the destiny of retinal progenitor cells in part by regulating Hes effector gene activity. There are multiple paralogues for nearly every node in this pathway, which results in numerous instances of redundancy and compensation during development. To dissect such complexity at the earliest stages of eye development, we used seven germline or conditional mutant mice and two spatiotemporally distinct Cre drivers. We perturbed the Notch ternary complex and multiple Hes genes to understand if Notch regulates optic stalk/nerve head development; and to test intracellular pathway components for their Notch-dependent versus -independent roles during retinal ganglion cell and cone photoreceptor competence and fate acquisition. We confirmed that disrupting Notch signaling universally blocks progenitor cell growth, but delineated specific pathway components that can act independently, such as sustained Hes1 expression in the optic stalk/nerve head. In retinal progenitor cells, we found that among the genes tested, they do not uniformly suppress retinal ganglion cell or cone differentiation; which is not due differences in developmental timing. We discovered that shifts in the earliest cell fates correlate with expression changes for the early photoreceptor factor Otx2, but not with Atoh7, a factor required for retinal ganglion cell formation. During photoreceptor genesis we also better defined multiple and simultaneous activities for Rbpj and Hes1 and identify redundant activities that occur downstream of Notch. Given its unique roles at the retina-optic stalk boundary and cone photoreceptor genesis, our data suggest Hes1 as a hub where Notch-dependent and -independent inputs converge.
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Affiliation(s)
- Bernadett Bosze
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Julissa Suarez-Navarro
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Illiana Cajias
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Joseph A. Brzezinski IV
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Nadean L. Brown
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
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15
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Gong J, Gong Y, Zou T, Zeng Y, Yang C, Mo L, Kang J, Fan X, Xu H, Yang J. A controllable perfusion microfluidic chip for facilitating the development of retinal ganglion cells in human retinal organoids. LAB ON A CHIP 2023; 23:3820-3836. [PMID: 37496497 DOI: 10.1039/d3lc00054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Retinal organoids (ROs) derived from human pluripotent stem cells (hPSCs) have become a promising model in vitro to recapitulate human retinal development, which can be further employed to explore the mechanisms of retinal diseases. However, the current culture systems for ROs lack physiologically relevant microenvironments, such as controllable mechano-physiological cues and dynamic feedback between cells and the extracellular matrix (ECM), which limits the accurate control of RO development. Therefore, we designed a controllable perfusion microfluidic chip (CPMC) with the advantages of precisely controlling fluidic shear stress (FSS) and oxygen concentration distribution in a human embryonic stem cell (hESC)-derived RO culture system. We found that ROs cultured under this system allow for expanding the retinal progenitor cell (RPC) pool, orchestrating the retinal ganglion cell (RGC) specification, and axon growth without disturbing the spatial and temporal patterning events at the early stage of RO development. Furthermore, RNA sequencing data revealed that the activation of voltage-gated ion channels and the increased expression of ECM components synergistically improve the growth of ROs and facilitate the differentiation of RGCs. This study elaborates on the advantages of the designed CPMC to promote RO growth and provide a controllable and reliable platform for the efficient maturity of RGCs in the ROs, promising applications in modeling RGC-related disorders, drug screening, and cell transplantation.
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Affiliation(s)
- Jing Gong
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Yu Gong
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Ting Zou
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Yuxiao Zeng
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Cao Yang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Lingyue Mo
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Jiahui Kang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Xiaotang Fan
- Department of Military Cognitive Psychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, 40038, China.
| | - Haiwei Xu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
| | - Jun Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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16
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Peng YR. Cell-type specification in the retina: Recent discoveries from transcriptomic approaches. Curr Opin Neurobiol 2023; 81:102752. [PMID: 37499619 DOI: 10.1016/j.conb.2023.102752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
Understanding the formation of the complex nervous system hinges on decoding the mechanism that specifies a vast array of neuronal types, each endowed with a unique morphology, physiology, and connectivity. As a pivotal step towards addressing this problem, seminal work has been devoted to characterizing distinct neuronal types. In recent years, high-throughput, single-cell transcriptomic methods have enabled a rapid inventory of cell types in various regions of the nervous system, with the retina exhibiting complete molecular characterization across many vertebrate species. This invaluable resource has furnished a fresh perspective for investigating the molecular principles of cell-type specification, thereby advancing our understanding of retinal development. Accordingly, this review focuses on the most recent transcriptomic characterizations of retinal cells, with a particular focus on amacrine cells and retinal ganglion cells. These investigations have unearthed new insights into their cell-type specification.
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Affiliation(s)
- Yi-Rong Peng
- Department of Ophthalmology and Stein Eye Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA.
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17
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Guo L, Xie X, Wang J, Xiao H, Li S, Xu M, Quainoo E, Koppaka R, Zhuo J, Smith SB, Gan L. Inducible Rbpms-CreER T2 Mouse Line for Studying Gene Function in Retinal Ganglion Cell Physiology and Disease. Cells 2023; 12:1951. [PMID: 37566030 PMCID: PMC10416940 DOI: 10.3390/cells12151951] [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: 06/20/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Retinal ganglion cells (RGCs) are the sole output neurons conveying visual stimuli from the retina to the brain, and dysfunction or loss of RGCs is the primary determinant of visual loss in traumatic and degenerative ocular conditions. Currently, there is a lack of RGC-specific Cre mouse lines that serve as invaluable tools for manipulating genes in RGCs and studying the genetic basis of RGC diseases. The RNA-binding protein with multiple splicing (RBPMS) is identified as the specific marker of all RGCs. Here, we report the generation and characterization of a knock-in mouse line in which a P2A-CreERT2 coding sequence is fused in-frame to the C-terminus of endogenous RBPMS, allowing for the co-expression of RBPMS and CreERT2. The inducible Rbpms-CreERT2 mice exhibited a high recombination efficiency in activating the expression of the tdTomato reporter gene in nearly all adult RGCs as well as in differentiated RGCs starting at E13.5. Additionally, both heterozygous and homozygous Rbpms-CreERT2 knock-in mice showed no detectable defect in the retinal structure, visual function, and transcriptome. Together, these results demonstrated that the Rbpms-CreERT2 knock-in mouse can serve as a powerful and highly desired genetic tool for lineage tracing, genetic manipulation, retinal physiology study, and ocular disease modeling in RGCs.
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Affiliation(s)
- Luming Guo
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Xiaoling Xie
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jing Wang
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Haiyan Xiao
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Shuchun Li
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Mei Xu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Ebenezer Quainoo
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Rithwik Koppaka
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jiaping Zhuo
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Sylvia B. Smith
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Lin Gan
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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18
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Zhang H, Guo Y, Yang Y, Wang Y, Zhang Y, Zhuang J, Zhang Y, Shen M, Zhao J, Zhang R, Qiu Y, Li S, Hu J, Li W, Wu J, Xu H, Fliesler SJ, Liao Y, Liu Z. MAP4Ks inhibition promotes retinal neuron regeneration from Müller glia in adult mice. NPJ Regen Med 2023; 8:36. [PMID: 37443319 DOI: 10.1038/s41536-023-00310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Mammalian Müller glia (MG) possess limited regenerative capacities. However, the intrinsic capacity of mammalian MG to transdifferentiate to generate mature neurons without transgenic manipulations remains speculative. Here we show that MAP4K4, MAP4K6 and MAP4K7, which are conserved Misshapen subfamily of ste20 kinases homologs, repress YAP activity in mammalian MG and therefore restrict their ability to be reprogrammed. However, by treating with a small molecule inhibitor of MAP4K4/6/7, mouse MG regain their ability to proliferate and enter into a retinal progenitor cell (RPC)-like state after NMDA-induced retinal damage; such plasticity was lost in YAP knockout MG. Moreover, spontaneous trans-differentiation of MG into retinal neurons expressing both amacrine and retinal ganglion cell (RGC) markers occurs after inhibitor withdrawal. Taken together, these findings suggest that MAP4Ks block the reprogramming capacity of MG in a YAP-dependent manner in adult mammals, which provides a novel avenue for the pharmaceutical induction of retinal regeneration in vivo.
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Affiliation(s)
- Houjian Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
- Xiamen University Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, China
- Department of Ophthalmology, the First Affiliated Hospital of University of South China, Hengyang, Hunan, 421001, China
| | - Yuli Guo
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
- Xiamen University Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, China
- Department of Ophthalmology, the First Affiliated Hospital of University of South China, Hengyang, Hunan, 421001, China
| | - Yaqiong Yang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yuqian Wang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Youwen Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jingbin Zhuang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yuting Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Mei Shen
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jiankai Zhao
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Rongrong Zhang
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yan Qiu
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Shiying Li
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jiaoyue Hu
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Wei Li
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jianfeng Wu
- Laboratory animal research center, Xiamen University, Xiamen, Fujian, 361102, China
| | - Haiwei Xu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China
| | - Steven J Fliesler
- Departments of Ophthalmology and Biochemistry and Neuroscience Graduate School, Jacobs School of Medicine and Biomedical Sciences, SUNY- University at Buffalo, Buffalo, NY, USA
- Research Service, VA Western New York Healthcare System, Buffalo, NY, USA
| | - Yi Liao
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Zuguo Liu
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science; Fujian Engineering and Research Center of Eye Regenerative Medicine; Eye Institute of Xiamen University; School of Medicine, Xiamen University, Xiamen, Fujian, 361005, China.
- Xiamen University Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, China.
- Department of Ophthalmology, the First Affiliated Hospital of University of South China, Hengyang, Hunan, 421001, China.
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19
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Li R, Liu J, Yi P, Yang X, Chen J, Zhao C, Liao X, Wang X, Xu Z, Lu H, Li H, Zhang Z, Liu X, Xiang J, Hu K, Qi H, Yu J, Yang P, Hou S. Integrative Single-Cell Transcriptomics and Epigenomics Mapping of the Fetal Retina Developmental Dynamics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206623. [PMID: 37017569 DOI: 10.1002/advs.202206623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/24/2023] [Indexed: 06/04/2023]
Abstract
The underlying mechanisms that determine gene expression and chromatin accessibility in retinogenesis are poorly understood. Herein, single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin sequencing are performed on human embryonic eye samples obtained 9-26 weeks after conception to explore the heterogeneity of retinal progenitor cells (RPCs) and neurogenic RPCs. The differentiation trajectory from RPCs to 7 major types of retinal cells are verified. Subsequently, diverse lineage-determining transcription factors are identified and their gene regulatory networks are refined at the transcriptomic and epigenomic levels. Treatment of retinospheres, with the inhibitor of RE1 silencing transcription factor, X5050, induces more neurogenesis with the regular arrangement, and a decrease in Müller glial cells. The signatures of major retinal cells and their correlation with pathogenic genes associated with multiple ocular diseases, including uveitis and age-related macular degeneration are also described. A framework for the integrated exploration of single-cell developmental dynamics of the human primary retina is provided.
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Affiliation(s)
- Ruonan Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Jiangyi Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, P. R. China
| | - Xianli Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, P. R. China
| | - Jun Chen
- Department of Obstetrics, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401147, P. R. China
| | - Chenyang Zhao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Xingyun Liao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, P. R. China
| | - Xiaotang Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Zongren Xu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
| | - Huiping Lu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Hongshun Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Zhi Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Xianyang Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Junjie Xiang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Ke Hu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Hongbo Qi
- Department of Obstetrics, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401147, P. R. China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, P. R. China
- The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100005, P. R. China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Ophthalmology, Chongqing, 400016, P. R. China
- Chongqing Eye Institute, Chongqing, 400016, P. R. China
- Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, 400016, P. R. China
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, 100730, P. R. China
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20
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Ferrena A, Zhang X, Shrestha R, Zheng D, Liu W. Six3 and Six6 jointly regulate the identities and developmental trajectories of multipotent retinal progenitor cells in the mouse retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539288. [PMID: 37205402 PMCID: PMC10187238 DOI: 10.1101/2023.05.03.539288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Formation, maintenance, and differentiation of tissue-specific progenitor cells are fundamental tasks during organogenesis. Retinal development is an excellent model for dissecting these processes; mechanisms of retinal differentiation can be harnessed for retinal regeneration toward curing blindness. Using single-cell RNA sequencing of embryonic mouse eye cups in which transcription factor Six3 was conditionally inactivated in peripheral retinas on top of germline deletion of its close paralog Six6 ("DKO"), we identified cell clusters and then inferred developmental trajectories in the integrated dataset. In control retinas, naïve retinal progenitor cells had two major trajectories leading to ciliary margin cells and retinal neurons, respectively. The ciliary margin trajectory was directly from naïve retinal progenitor cells at G1 phase, and the retinal neuron trajectory was through a neurogenic state marked by Atoh7 expression. Upon Six3 and Six6 dual deficiency, both naïve and neurogenic retinal progenitor cells were defective. Ciliary margin differentiation was enhanced, and multi-lineage retinal differentiation was disrupted. An ectopic neuronal trajectory lacking the Atoh7+ state led to ectopic neurons. Differential expression analysis not only confirmed previous phenotype studies but also identified novel candidate genes regulated by Six3/Six6 . Six3 and Six6 were jointly required for balancing the opposing gradients of the Fgf and Wnt signaling in the central-peripheral patterning of the eye cups. Taken together, we identify transcriptomes and developmental trajectories jointly regulated by Six3 and Six6, providing deeper insight into molecular mechanisms underlying early retinal differentiation.
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21
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Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O’Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535726. [PMID: 37066300 PMCID: PMC10104014 DOI: 10.1101/2023.04.05.535726] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Riza M. Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Truc-Mai Le
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eva K. Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Megan L. Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Olivia Fulton
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diana R. O’Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Saskia Ilcisin
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christine M. Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Kimelman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-cell genomics and Population dynamics, The Rockefeller University, New York, NY, USA
| | - Alexander F. Schier
- Biozentrum, University of Basel, Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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22
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Ge Y, Chen X, Nan N, Bard J, Wu F, Yergeau D, Liu T, Wang J, Mu X. Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res 2023; 51:2151-2176. [PMID: 36715342 PMCID: PMC10018358 DOI: 10.1093/nar/gkad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
How the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. In this study, we dissect the changes in the epigenetic landscape during early retinal cell differentiation by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages. Using CUT&Tag, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2 and Isl1, including those dependent on Atoh7, and uncover the sequential and combinatorial interactions of these factors with the epigenetic landscape to control gene expression along individual retinal cell lineages such as retinal ganglion cells (RGCs). Our results reveal a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from multipotent retinal progenitor cells (RPCs).
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xushen Chen
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Nan Nan
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jie Wang
- Correspondence may also be addressed to Jie Wang.
| | - Xiuqian Mu
- To whom correspondence should be addressed. Tel: +1 716 881 7463; Fax: +1 716 887 2991;
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23
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Li CY, Anuraga G, Chang CP, Weng TY, Hsu HP, Ta HDK, Su PF, Chiu PH, Yang SJ, Chen FW, Ye PH, Wang CY, Lai MD. Repurposing nitric oxide donating drugs in cancer therapy through immune modulation. J Exp Clin Cancer Res 2023; 42:22. [PMID: 36639681 PMCID: PMC9840268 DOI: 10.1186/s13046-022-02590-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/29/2022] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Nitric oxide-releasing drugs are used for cardiovascular diseases; however, their effects on the tumor immune microenvironment are less clear. Therefore, this study explored the impact of nitric oxide donors on tumor progression in immune-competent mice. METHODS The effects of three different nitric oxide-releasing compounds (SNAP, SNP, and ISMN) on tumor growth were studied in tumor-bearing mouse models. Three mouse tumor models were used: B16F1 melanoma and LL2 lung carcinoma in C57BL/6 mice, CT26 colon cancer in BALB/c mice, and LL2 lung carcinoma in NOD/SCID mice. After nitric oxide treatment, splenic cytokines and lymphocytes were analyzed by cytokine array and flow cytometry, and tumor-infiltrating lymphocytes in the TME were analyzed using flow cytometry and single-cell RNA sequencing. RESULTS Low doses of three exogenous nitric oxide donors inhibited tumor growth in two immunocompetent mouse models but not in NOD/SCID immunodeficient mice. Low-dose nitric oxide donors increase the levels of splenic cytokines IFN-γ and TNF-α but decrease the levels of cytokines IL-6 and IL-10, suggesting an alteration in Th2 cells. Nitric oxide donors increased the number of CD8+ T cells with activation gene signatures, as indicated by single-cell RNA sequencing. Flow cytometry analysis confirmed an increase in infiltrating CD8+ T cells and dendritic cells. The antitumor effect of nitric oxide donors was abolished by depletion of CD8+ T cells, indicating the requirement for CD8+ T cells. Tumor inhibition correlated with a decrease in a subtype of protumor macrophages and an increase in a subset of Arg1-positive macrophages expressing antitumor gene signatures. The increase in this subset of macrophages was confirmed by flow cytometry analysis. Finally, the combination of low-dose nitric oxide donor and cisplatin induced an additive cancer therapeutic effect in two immunocompetent animal models. The enhanced therapeutic effect was accompanied by an increase in the cells expressing the gene signature of NK cell. CONCLUSIONS Low concentrations of exogenous nitric oxide donors inhibit tumor growth in vivo by regulating T cells and macrophages. CD8+ T cells are essential for antitumor effects. In addition, low-dose nitric oxide donors may be combined with chemotherapeutic drugs in cancer therapy in the future.
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Affiliation(s)
- Chung-Yen Li
- College of Medicine, Institute of basic medical sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan, ROC
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya, Indonesia
| | - Chih-Peng Chang
- College of Medicine, Institute of basic medical sciences, National Cheng Kung University, Tainan, Taiwan, ROC
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Tzu-Yang Weng
- College of Medicine, Institute of basic medical sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan, ROC
| | - Pei-Fang Su
- Department of Statistics, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Pin-Hsuan Chiu
- The Center for Quantitative Sciences, Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Shiang-Jie Yang
- College of Medicine, Institute of basic medical sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Feng-Wei Chen
- College of Medicine, Institute of basic medical sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Pei-Hsuan Ye
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan, ROC.
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
| | - Ming-Derg Lai
- College of Medicine, Institute of basic medical sciences, National Cheng Kung University, Tainan, Taiwan, ROC.
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC.
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24
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Keeley PW, Patel PS, Ryu MS, Reese BE. Neurog2 regulates Isl1 to modulate horizontal cell number. Development 2023; 150:dev201315. [PMID: 36537573 PMCID: PMC10108602 DOI: 10.1242/dev.201315] [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: 09/22/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
The population sizes of different retinal cell types vary between different strains of mice, and that variation can be mapped to genomic loci in order to identify its polygenic origin. In some cases, controlling genes act independently, whereas in other instances, they exhibit epistasis. Here, we identify an epistatic interaction revealed through the mapping of quantitative trait loci from a panel of recombinant inbred strains of mice. The population of retinal horizontal cells exhibits a twofold variation in number, mapping to quantitative trait loci on chromosomes 3 and 13, where these loci are shown to interact epistatically. We identify a prospective genetic interaction underlying this, mediated by the bHLH transcription factor Neurog2, at the chromosome 3 locus, functioning to repress the LIM homeodomain transcription factor Isl1, at the chromosome 13 locus. Using single and double conditional knockout mice, we confirm the countervailing actions of each gene, and validate in vitro a crucial role for two single nucleotide polymorphisms in the 5'UTR of Isl1, one of which yields a novel E-box, mediating the repressive action of Neurog2.
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Affiliation(s)
- Patrick W. Keeley
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
| | - Pooja S. Patel
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
| | - Matthew S. Ryu
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
| | - Benjamin E. Reese
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
- Department of Psychological and Brain Sciences, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
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25
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Todd L, Jenkins W, Finkbeiner C, Hooper MJ, Donaldson PC, Pavlou M, Wohlschlegel J, Ingram N, Rieke F, Reh TA. Reprogramming Müller glia to regenerate ganglion-like cells in adult mouse retina with developmental transcription factors. SCIENCE ADVANCES 2022; 8:eabq7219. [PMID: 36417510 PMCID: PMC9683702 DOI: 10.1126/sciadv.abq7219] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/26/2022] [Indexed: 06/11/2023]
Abstract
Many neurodegenerative diseases cause degeneration of specific types of neurons. For example, glaucoma leads to death of retinal ganglion cells, leaving other neurons intact. Neurons are not regenerated in the adult mammalian central nervous system. However, in nonmammalian vertebrates, glial cells spontaneously reprogram into neural progenitors and replace neurons after injury. We have recently developed strategies to stimulate regeneration of functional neurons in the adult mouse retina by overexpressing the proneural factor Ascl1 in Müller glia. Here, we test additional transcription factors (TFs) for their ability to direct regeneration to particular types of retinal neurons. We engineered mice to express different combinations of TFs in Müller glia, including Ascl1, Pou4f2, Islet1, and Atoh1. Using immunohistochemistry, single-cell RNA sequencing, single-cell assay for transposase-accessible chromatin sequencing, and electrophysiology, we find that retinal ganglion-like cells can be regenerated in the damaged adult mouse retina in vivo with targeted overexpression of developmental retinal ganglion cell TFs.
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Affiliation(s)
- Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Wesley Jenkins
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Connor Finkbeiner
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Marcus J. Hooper
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Phoebe C. Donaldson
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Marina Pavlou
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Juliette Wohlschlegel
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Norianne Ingram
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 91895, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 91895, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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26
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Yamamoto M, Ong Lee Chen A, Shinozuka T, Sasai N. The Rx transcription factor is required for determination of the retinal lineage and regulates the timing of neuronal differentiation. Dev Growth Differ 2022; 64:318-324. [PMID: 35700309 DOI: 10.1111/dgd.12796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
Understanding the molecular mechanisms leading to retinal development is of great interest for both basic scientific and clinical applications. Several signaling molecules and transcription factors involved in retinal development have been isolated and analyzed; however, determining the direct impact of the loss of a specific molecule is problematic, due to difficulties in identifying the corresponding cellular lineages in different individuals. Here, we conducted genome-wide expression analysis with embryonic stem cells devoid of the Rx gene, which encodes one of several homeobox transcription factors essential for retinal development. We performed three-dimensional differentiation of wild-type and mutant cells and compared their gene-expression profiles. The mutant tissue failed to differentiate into the retinal lineage and exhibited precocious expression of genes characteristic of neuronal cells. Together, these results suggest that Rx expression is an important biomarker of the retinal lineage and that it helps regulates appropriate differentiation stages.
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Affiliation(s)
- Maho Yamamoto
- Developmental Biomedical Science, Division of Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Japan
| | - Agnes Ong Lee Chen
- Developmental Biomedical Science, Division of Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Japan
| | - Takuma Shinozuka
- Developmental Biomedical Science, Division of Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Japan
| | - Noriaki Sasai
- Developmental Biomedical Science, Division of Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Japan
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27
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Finkbeiner C, Ortuño-Lizarán I, Sridhar A, Hooper M, Petter S, Reh TA. Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition. Cell Rep 2022; 38:110294. [DOI: 10.1016/j.celrep.2021.110294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/04/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
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28
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Construction and analysis of mRNA, lncRNA, and transcription factor regulatory networks after retinal ganglion cell injury. Exp Eye Res 2021; 215:108915. [PMID: 34971620 DOI: 10.1016/j.exer.2021.108915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/11/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
Retinal ganglion cell (RGC) injury is a critical pathological feature of several optic neurodegenerative diseases. The regulatory mechanisms underlying RGC injury remain poorly understood. Recent evidence has highlighted the important roles of long noncoding RNAs (lncRNAs) in degenerative neuropathy but few studies have focused on lncRNAs associated with RGC injury. In this study, we analyzed dysregulated lncRNAs associated with RGC injury, their potential regulatory functions, and the molecular mechanisms underlying the regulation of lncRNAs and transcription factors (TFs). We analyzed lncRNA and mRNA profiles in the GSE142881 dataset associated with RGC injury and identified 1049 differentially expressed genes (DEGs), with 18 differentially expressed (DE) TFs among 883 DE mRNAs and 312 DE lncRNAs. The predicted DE lncRNAs and DE mRNAs were used to construct a lncRNA-mRNA co-expression network. Functional enrichment analysis was performed to explore the functions of the lncRNAs and mRNAs. The co-expression network between DE lncRNAs and DE mRNAs was highly enriched in inflammatory and immune-related pathways, indicating that they play role in the process of RGC injury. Among the DE mRNAs, we screened 18 DE TFs, including activating transcription factor 3 (ATF3), associated with RGC injury. Co-expression analysis predicted that 13 lncRNAs were potential binding targets of ATF3. The screening of the potential targets of these 13 lncRNAs showed that they were also significantly enriched in functional pathways associated with inflammation and apoptosis. After analysis, we constructed the mRNA-ATF3-lncRNA regulatory network after RGCs injury. In summary, we identified the gene module associated with immune and inflammatory responses after optic nerve injury and constructed a regulatory network of lncRNA-TF-mRNA. The results indicate that lncRNAs, by binding to TFs, can regulate downstream genes and function during RGC injury. The results provide a foundation for further studies of the mechanism of RGC injury and provide insight into the clinical diagnosis and investigation direction of neurodegenerative diseases such as traumatic optic neuropathy and glaucoma.
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29
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Daghsni M, Aldiri I. Building a Mammalian Retina: An Eye on Chromatin Structure. Front Genet 2021; 12:775205. [PMID: 34764989 PMCID: PMC8576187 DOI: 10.3389/fgene.2021.775205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression by chromatin structure has been under intensive investigation, establishing nuclear organization and genome architecture as a potent and effective means of regulating developmental processes. The substantial growth in our knowledge of the molecular mechanisms underlying retinogenesis has been powered by several genome-wide based tools that mapped chromatin organization at multiple cellular and biochemical levels. Studies profiling the retinal epigenome and transcriptome have allowed the systematic annotation of putative cis-regulatory elements associated with transcriptional programs that drive retinal neural differentiation, laying the groundwork to understand spatiotemporal retinal gene regulation at a mechanistic level. In this review, we outline recent advances in our understanding of the chromatin architecture in the mammalian retina during development and disease. We focus on the emerging roles of non-coding regulatory elements in controlling retinal cell-type specific transcriptional programs, and discuss potential implications in untangling the etiology of eye-related disorders.
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Affiliation(s)
- Marwa Daghsni
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Issam Aldiri
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, United States
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30
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Xiao D, Jin K, Qiu S, Lei Q, Huang W, Chen H, Su J, Xu Q, Xu Z, Gou B, Tie X, Liu F, Liu S, Liu Y, Xiang M. In vivo Regeneration of Ganglion Cells for Vision Restoration in Mammalian Retinas. Front Cell Dev Biol 2021; 9:755544. [PMID: 34671605 PMCID: PMC8520940 DOI: 10.3389/fcell.2021.755544] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022] Open
Abstract
Glaucoma and other optic neuropathies affect millions of people worldwide, ultimately causing progressive and irreversible degeneration of retinal ganglion cells (RGCs) and blindness. Previous research into cell replacement therapy of these neurodegenerative diseases has been stalled due to the incapability for grafted RGCs to integrate into the retina and project properly along the long visual pathway. In vivo RGC regeneration would be a promising alternative approach but mammalian retinas lack regenerative capacity. It therefore has long been a great challenge to regenerate functional and properly projecting RGCs for vision restoration in mammals. Here we show that the transcription factors (TFs) Math5 and Brn3b together are able to reprogram mature mouse Müller glia (MG) into RGCs. The reprogrammed RGCs extend long axons that make appropriate intra-retinal and extra-retinal projections through the entire visual pathway to innervate both image-forming and non-image-forming brain targets. They exhibit typical neuronal electrophysiological properties and improve visual responses in RGC loss mouse models. Together, our data provide evidence that mammalian MG can be reprogrammed by defined TFs to achieve in vivo regeneration of functional RGCs as well as a promising new therapeutic approach to restore vision to patients with glaucoma and other optic neuropathies.
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Affiliation(s)
- Dongchang Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Kangxin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Suo Qiu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiannan Lei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wanjing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Haiqiao Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jing Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiang Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zihui Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bin Gou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoxiu Tie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Feng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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31
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Shiau F, Ruzycki PA, Clark BS. A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq. Dev Biol 2021; 478:41-58. [PMID: 34146533 PMCID: PMC8386138 DOI: 10.1016/j.ydbio.2021.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
Recent advances in high throughput single-cell RNA sequencing (scRNA-seq) technology have enabled the simultaneous transcriptomic profiling of thousands of individual cells in a single experiment. To investigate the intrinsic process of retinal development, researchers have leveraged this technology to quantify gene expression in retinal cells across development, in multiple species, and from numerous important models of human disease. In this review, we summarize recent applications of scRNA-seq and discuss how these datasets have complemented and advanced our understanding of retinal progenitor cell competence, cell fate specification, and differentiation. Finally, we also highlight the outstanding questions in the field that advances in single-cell data generation and analysis will soon be able to answer.
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Affiliation(s)
- Fion Shiau
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A Ruzycki
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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32
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Abstract
It has been known for over a century that the basic organization of the retina is conserved across vertebrates. It has been equally clear that retinal cells can be classified into numerous types, but only recently have methods been devised to explore this diversity in unbiased, scalable, and comprehensive ways. Advances in high-throughput single-cell RNA-sequencing (scRNA-seq) have played a pivotal role in this effort. In this article, we outline the experimental and computational components of scRNA-seq and review studies that have used them to generate retinal atlases of cell types in several vertebrate species. These atlases have enabled studies of retinal development, responses of retinal cells to injury, expression patterns of genes implicated in retinal disease, and the evolution of cell types. Recently, the inquiry has expanded to include the entire eye and visual centers in the brain. These studies have enhanced our understanding of retinal function and dysfunction and provided tools and insights for exploring neural diversity throughout the brain. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; and California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, USA;
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cell Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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33
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Zhang X, Mandric I, Nguyen KH, Nguyen TTT, Pellegrini M, Grove JCR, Barnes S, Yang XJ. Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development. Front Cell Dev Biol 2021; 9:653305. [PMID: 34055784 PMCID: PMC8155690 DOI: 10.3389/fcell.2021.653305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog2 in human ES cell-derived retinal organoids. Single cell transcriptome analyses identify three states of proliferating retinal progenitors: pre-neurogenic, neurogenic, and cell cycle-exiting progenitors. Each shows different expression profile of bHLH factors. The cell cycle-exiting progenitors feed into a postmitotic heterozygous neuroblast pool that gives rise to early born neuronal lineages. Elevating ATOH7 or Neurog2 expression accelerates the transition from the pre-neurogenic to the neurogenic state, and expands the exiting progenitor and neuroblast populations. In addition, ATOH7 and Neurog2 significantly, yet differentially, enhance retinal ganglion cell and cone photoreceptor production. Moreover, single cell transcriptome analyses reveal that ATOH7 and Neurog2 each assert positive autoregulation, and both suppress key bHLH factors associated with the pre-neurogenic and states and elevate bHLH factors expressed by exiting progenitors and differentiating neuroblasts. This study thus provides novel insight regarding how ATOH7 and Neurog2 impact human retinal progenitor behaviors and neuroblast fate choices.
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Affiliation(s)
- Xiangmei Zhang
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Igor Mandric
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin H Nguyen
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thao T T Nguyen
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - James C R Grove
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Steven Barnes
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Doheny Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xian-Jie Yang
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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34
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Lyu J, Mu X. Genetic control of retinal ganglion cell genesis. Cell Mol Life Sci 2021; 78:4417-4433. [PMID: 33782712 DOI: 10.1007/s00018-021-03814-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/27/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
Retinal ganglion cells (RGCs) are the only projection neurons in the neural retina. They receive and integrate visual signals from upstream retinal neurons in the visual circuitry and transmit them to the brain. The function of RGCs is performed by the approximately 40 RGC types projecting to various central brain targets. RGCs are the first cell type to form during retinogenesis. The specification and differentiation of the RGC lineage is a stepwise process; a hierarchical gene regulatory network controlling the RGC lineage has been identified and continues to be elaborated. Recent studies with single-cell transcriptomics have led to unprecedented new insights into their types and developmental trajectory. In this review, we summarize our current understanding of the functions and relationships of the many regulators of the specification and differentiation of the RGC lineage. We emphasize the roles of these key transcription factors and pathways in different developmental steps, including the transition from retinal progenitor cells (RPCs) to RGCs, RGC differentiation, generation of diverse RGC types, and central projection of the RGC axons. We discuss critical issues that remain to be addressed for a comprehensive understanding of these different aspects of RGC genesis and emerging technologies, including single-cell techniques, novel genetic tools and resources, and high-throughput genome editing and screening assays, which can be leveraged in future studies.
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Affiliation(s)
- Jianyi Lyu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA.
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35
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Brodie-Kommit J, Clark BS, Shi Q, Shiau F, Kim DW, Langel J, Sheely C, Ruzycki PA, Fries M, Javed A, Cayouette M, Schmidt T, Badea T, Glaser T, Zhao H, Singer J, Blackshaw S, Hattar S. Atoh7-independent specification of retinal ganglion cell identity. SCIENCE ADVANCES 2021; 7:7/11/eabe4983. [PMID: 33712461 PMCID: PMC7954457 DOI: 10.1126/sciadv.abe4983] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/29/2021] [Indexed: 06/11/2023]
Abstract
Retinal ganglion cells (RGCs) relay visual information from the eye to the brain. RGCs are the first cell type generated during retinal neurogenesis. Loss of function of the transcription factor Atoh7, expressed in multipotent early neurogenic retinal progenitors leads to a selective and essentially complete loss of RGCs. Therefore, Atoh7 is considered essential for conferring competence on progenitors to generate RGCs. Despite the importance of Atoh7 in RGC specification, we find that inhibiting apoptosis in Atoh7-deficient mice by loss of function of Bax only modestly reduces RGC numbers. Single-cell RNA sequencing of Atoh7;Bax-deficient retinas shows that RGC differentiation is delayed but that the gene expression profile of RGC precursors is grossly normal. Atoh7;Bax-deficient RGCs eventually mature, fire action potentials, and incorporate into retinal circuitry but exhibit severe axonal guidance defects. This study reveals an essential role for Atoh7 in RGC survival and demonstrates Atoh7-dependent and Atoh7-independent mechanisms for RGC specification.
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Affiliation(s)
| | - Brian S Clark
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Qing Shi
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Fion Shiau
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Dong Won Kim
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Langel
- National Institute of Mental Health (NIMH), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Catherine Sheely
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Philip A Ruzycki
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Michel Fries
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, QC H3C 3J7, Canada
| | - Awais Javed
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, QC H3C 3J7, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0G4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Tiffany Schmidt
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Tudor Badea
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
- Research and Development Institute, Transylvania University of Brasov, School of Medicine, Brasov, Romania
| | - Tom Glaser
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, CA, USA
| | - Haiqing Zhao
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua Singer
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Samer Hattar
- National Institute of Mental Health (NIMH), National Institutes of Health (NIH), Bethesda, MD, USA.
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