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A cell-ECM mechanism for connecting the ipsilateral eye to the brain. Proc Natl Acad Sci U S A 2021; 118:2104343118. [PMID: 34654745 PMCID: PMC8545493 DOI: 10.1073/pnas.2104343118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Distinct features of the visual world are transmitted from the retina to the brain through anatomically segregated circuits. Despite this being an organizing principle of visual pathways in mammals, we lack an understanding of the signaling mechanisms guiding axons of different types of retinal neurons into segregated layers of brain regions. We explore this question by identifying how axons from the ipsilateral retina innervate a specific lamina of the superior colliculus. Our studies reveal a unique cell–extracellular matrix recognition mechanism that specifies precise targeting of these axons to the superior colliculus. Loss of this mechanism not only resulted in the absence of this eye-specific visual circuit, but it led to an impairment of innate predatory visual behavior as well. Information about features in the visual world is parsed by circuits in the retina and is then transmitted to the brain by distinct subtypes of retinal ganglion cells (RGCs). Axons from RGC subtypes are stratified in retinorecipient brain nuclei, such as the superior colliculus (SC), to provide a segregated relay of parallel and feature-specific visual streams. Here, we sought to identify the molecular mechanisms that direct the stereotyped laminar targeting of these axons. We focused on ipsilateral-projecting subtypes of RGCs (ipsiRGCs) whose axons target a deep SC sublamina. We identified an extracellular glycoprotein, Nephronectin (NPNT), whose expression is restricted to this ipsiRGC-targeted sublamina. SC-derived NPNT and integrin receptors expressed by ipsiRGCs are both required for the targeting of ipsiRGC axons to the deep sublamina of SC. Thus, a cell–extracellular matrix (ECM) recognition mechanism specifies precise laminar targeting of ipsiRGC axons and the assembly of eye-specific parallel visual pathways.
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Ayupe AC, Beckedorff F, Levay K, Yon B, Salgueiro Y, Shiekhattar R, Park KK. Identification of long noncoding RNAs in injury-resilient and injury-susceptible mouse retinal ganglion cells. BMC Genomics 2021; 22:741. [PMID: 34649511 PMCID: PMC8518251 DOI: 10.1186/s12864-021-08050-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Emerging evidence indicates that long noncoding RNAs (lncRNAs) are important regulators of various biological processes, and their expression can be altered following certain pathological conditions, including central nervous system injury. Retinal ganglion cells (RGCs), whose axons form the optic nerve, are a heterogeneous population of neurons with more than 40 molecularly distinct subtypes in mouse. While most RGCs, including the ON-OFF direction-selective RGCs (ooDSGCs), are vulnerable to axonal injury, a small population of RGCs, including the intrinsically photosensitive RGCs (ipRGCs), are more resilient. RESULTS By performing systematic analyses on RNA-sequencing data, here we identify lncRNAs that are expressed in ooDSGCs and ipRGCs with and without axonal injury. Our results reveal a repertoire of different classes of lncRNAs, including long intergenic noncoding RNAs and antisense ncRNAs that are differentially expressed between these RGC types. Strikingly, we also found dozens of lncRNAs whose expressions are altered markedly in response to axonal injury, some of which are expressed exclusively in either one of the types. Moreover, analyses into these lncRNAs unraveled their neighboring coding genes, many of which encode transcription factors and signaling molecules, suggesting that these lncRNAs may act in cis to regulate important biological processes in these neurons. Lastly, guilt-by-association analysis showed that lncRNAs are correlated with apoptosis associated genes, suggesting potential roles for these lncRNAs in RGC survival. CONCLUSIONS Overall, the results of this study reveal RGC type-specific expression of lncRNAs and provide a foundation for future investigation of the function of lncRNAs in regulating neuronal type specification and survival.
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Affiliation(s)
- Ana C Ayupe
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, 1095 NW 14th Ter, FL, 33136, Miami, USA.
| | - Felipe Beckedorff
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, University of Miami Miller School of Medicine, Room 719, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Konstantin Levay
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, 1095 NW 14th Ter, FL, 33136, Miami, USA
| | - Benito Yon
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, 1095 NW 14th Ter, FL, 33136, Miami, USA
| | - Yadira Salgueiro
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, 1095 NW 14th Ter, FL, 33136, Miami, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, University of Miami Miller School of Medicine, Room 719, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Kevin K Park
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, 1095 NW 14th Ter, FL, 33136, Miami, USA.
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103
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van der Heide CJ, Meyer KJ, Hedberg-Buenz A, Pellack D, Pomernackas N, Mercer HE, Anderson MG. Quantification and image-derived phenotyping of retinal ganglion cell nuclei in the nee mouse model of congenital glaucoma. Exp Eye Res 2021; 212:108774. [PMID: 34597676 PMCID: PMC8608716 DOI: 10.1016/j.exer.2021.108774] [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: 04/14/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/31/2022]
Abstract
The nee mouse model exhibits characteristic features of congenital glaucoma, a common cause of childhood blindness. The current study of nee mice had two components. First, the time course of neurodegeneration in nee retinal flat-mounts was studied over time using a retinal ganglion cell (RGC)-marker, BRN3A; a pan-nuclear marker, TO-PRO-3; and H&E staining. Based on segmentation of nuclei using ImageJ and RetFM-J, this analysis identified a rapid loss of BRN3A+ nuclei from 4 to 15 weeks of age, with the first statistically significant difference in average density compared to age-matched controls detected in 8-week-old cohorts (49% reduction in nee). Consistent with a model of glaucoma, no reductions in BRN3A- nuclei were detected, but the combined analysis indicated that some RGCs lost BRN3A marker expression prior to actual cell loss. These results have a practical application in the design of experiments using nee mice to study mechanisms or potential therapies for congenital glaucoma. The second component of the study pertains to a discovery-based analysis of the large amount of image data with 748,782 segmented retinal nuclei. Using the automatedly collected region of interest feature data captured by ImageJ, we tested whether RGC density of glaucomatous mice was significantly correlated to average nuclear area, perimeter, Feret diameter, or MinFeret diameter. These results pointed to two events influencing nuclear size. For variations in RGC density above approximately 3000 nuclei/mm2 apparent spreading was observed, in which BRN3A- nuclei-regardless of genotype-became slightly larger as RGC density decreased. This same spreading occurred in BRN3A+ nuclei of wild-type mice. For variation in RGC density below 3000 nuclei/mm2, which only occurred in glaucomatous nee mutants, BRN3A+ nuclei became smaller as disease was progressively severe. These observations have relevance to defining RGCs of relatively higher sensitivity to glaucomatous cell death and the nuclear dynamics occurring during their demise.
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Affiliation(s)
- Carly J van der Heide
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd., Iowa City, IA, 52242, USA.
| | - Kacie J Meyer
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd., Iowa City, IA, 52242, USA.
| | - Adam Hedberg-Buenz
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd., Iowa City, IA, 52242, USA; VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, 601 Hwy 6 West (151), Iowa City, IA, 52246, USA.
| | - Danielle Pellack
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd., Iowa City, IA, 52242, USA.
| | - Nicholas Pomernackas
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd., Iowa City, IA, 52242, USA.
| | - Hannah E Mercer
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd., Iowa City, IA, 52242, USA.
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd., Iowa City, IA, 52242, USA; VA Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, 601 Hwy 6 West (151), Iowa City, IA, 52246, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, 200 Hawkins Dr., Iowa City, IA, 52242, USA.
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104
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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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105
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Muzyka VV, Badea TC. Genetic interplay between transcription factor Pou4f1/Brn3a and neurotrophin receptor Ret in retinal ganglion cell type specification. Neural Dev 2021; 16:5. [PMID: 34548095 PMCID: PMC8454062 DOI: 10.1186/s13064-021-00155-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/05/2021] [Indexed: 12/15/2022] Open
Abstract
Background While the transcriptional code governing retinal ganglion cell (RGC) type specification begins to be understood, its interplay with neurotrophic signaling is largely unexplored. In mice, the transcription factor Brn3a/Pou4f1 is expressed in most RGCs, and is required for the specification of RGCs with small dendritic arbors. The Glial Derived Neurotrophic Factor (GDNF) receptor Ret is expressed in a subset of RGCs, including some expressing Brn3a, but its role in RGC development is not defined. Methods Here we use combinatorial genetic experiments using conditional knock-in reporter alleles at the Brn3a and Ret loci, in combination with retina- or Ret specific Cre drivers, to generate complete or mosaic genetic ablations of either Brn3a or Ret in RGCs. We then use sparse labelling to investigate Brn3a and Ret gene dosage effects on RGC dendritic arbor morphology. In addition, we use immunostaining and/or gene expression profiling by RNASeq to identify transcriptional targets relevant for the potential Brn3a-Ret interaction in RGC development. Results We find that mosaic gene dosage manipulation of the transcription factor Brn3a/Pou4f1 in neurotrophic receptor Ret heterozygote RGCs results in altered cell fate decisions and/or morphological dendritic defects. Specific RGC types are lost if Brn3a is ablated during embryogenesis and only mildly affected by postnatal Brn3a ablation. Sparse but not complete Brn3a heterozygosity combined with complete Ret heterozygosity has striking effects on RGC type distribution. Brn3a only mildly modulates Ret transcription, while Ret knockouts exhibit slightly skewed Brn3a and Brn3b expression during development that is corrected by adult age. Brn3a loss of function modestly but significantly affects distribution of Ret co-receptors GFRα1-3, and neurotrophin receptors TrkA and TrkC in RGCs. Conclusions Based on these observations, we propose that Brn3a and Ret converge onto developmental pathways that control RGC type specification, potentially through a competitive mechanism requiring signaling from the surrounding tissue. Supplementary Information The online version contains supplementary material available at 10.1186/s13064-021-00155-z.
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Affiliation(s)
- Vladimir Vladimirovich Muzyka
- Retinal Circuit Development & Genetics Unit, Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, NIH, Bethesda, MD, USA. .,Institute of Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia.
| | - Tudor Constantin Badea
- Retinal Circuit Development & Genetics Unit, Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, NIH, Bethesda, MD, USA. .,Research and Development Institute, School of Medicine, Transilvania University of Brasov, Brasov, Romania.
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106
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Rochon PL, Theriault C, Rangel Olguin AG, Krishnaswamy A. The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges. eLife 2021; 10:e70870. [PMID: 34545809 PMCID: PMC8514235 DOI: 10.7554/elife.70870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/11/2021] [Indexed: 01/10/2023] Open
Abstract
Nearly 50 different mouse retinal ganglion cell (RGC) types sample the visual scene for distinct features. RGC feature selectivity arises from their synapses with a specific subset of amacrine (AC) and bipolar cell (BC) types, but how RGC dendrites arborize and collect input from these specific subsets remains poorly understood. Here we examine the hypothesis that RGCs employ molecular recognition systems to meet this challenge. By combining calcium imaging and type-specific histological stains, we define a family of circuits that express the recognition molecule Sidekick-1 (Sdk1), which include a novel RGC type (S1-RGC) that responds to local edges. Genetic and physiological studies revealed that Sdk1 loss selectively disrupts S1-RGC visual responses, which result from a loss of excitatory and inhibitory inputs and selective dendritic deficits on this neuron. We conclude that Sdk1 shapes dendrite growth and wiring to help S1-RGCs become feature selective.
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107
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Fague L, Liu YA, Marsh-Armstrong N. The basic science of optic nerve regeneration. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1276. [PMID: 34532413 PMCID: PMC8421956 DOI: 10.21037/atm-20-5351] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/15/2021] [Indexed: 12/25/2022]
Abstract
Diverse insults to the optic nerve result in partial to total vision loss as the axons of retinal ganglion cells are destroyed. In glaucoma, axons are injured at the optic nerve head; in other optic neuropathies, axons can be damaged along the entire visual pathway. In all cases, as mammals cannot regenerate injured central nervous system cells, once the axons are lost, vision loss is irreversible. However, much has been learned about how retinal ganglion cells respond to axon injuries, and many of these crucial discoveries offer hope for future regenerative therapies. Here we review the current understanding regarding the temporal progression of axonal degeneration. We summarize known survival and regenerative mechanisms in mammals, including specific signaling pathways, key transcription factors, and reprogramming genes. We cover mechanisms intrinsic to retinal ganglion cells as well as their interactions with myeloid and glial cell populations in the retina and optic nerve that affect survival and regeneration. Finally, we highlight some non-mammalian species that are able to regenerate their retinal ganglion cell axons after injury, as understanding these successful regenerative responses may be essential to the rational design of future clinical interventions to regrow the optic nerve. In the end, a combination of many different molecular and cellular interventions will likely be the only way to achieve functional recovery of vision and restore quality of life to millions of patients around the world.
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Affiliation(s)
- Lindsay Fague
- UC Davis Eye Center, Department of Ophthalmology & Vision Science, University of California, Davis, Sacramento, CA, USA
| | - Yin Allison Liu
- UC Davis Eye Center, Department of Ophthalmology & Vision Science, University of California, Davis, Sacramento, CA, USA
| | - Nicholas Marsh-Armstrong
- UC Davis Eye Center, Department of Ophthalmology & Vision Science, University of California, Davis, Sacramento, CA, USA
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108
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Lux UT, Ehrenberg J, Joachimsthaler A, Atorf J, Pircher B, Reim K, Kremers J, Gießl A, Brandstätter JH. Cell Types and Synapses Expressing the SNARE Complex Regulating Proteins Complexin 1 and Complexin 2 in Mammalian Retina. Int J Mol Sci 2021; 22:ijms22158131. [PMID: 34360929 PMCID: PMC8348166 DOI: 10.3390/ijms22158131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Complexins (Cplxs) 1 to 4 are components of the presynaptic compartment of chemical synapses where they regulate important steps in synaptic vesicle exocytosis. In the retina, all four Cplxs are present, and while we know a lot about Cplxs 3 and 4, little is known about Cplxs 1 and 2. Here, we performed in situ hybridization experiments and bioinformatics and exploited Cplx 1 and Cplx 2 single-knockout mice combined with immunocytochemistry and light microscopy to characterize in detail the cell type and synapse-specific distribution of Cplx 1 and Cplx 2. We found that Cplx 2 and not Cplx 1 is the main isoform expressed in normal and displaced amacrine cells and ganglion cells in mouse retinae and that amacrine cells seem to operate with a single Cplx isoform at their conventional chemical synapses. Surprising was the finding that retinal function, determined with electroretinographic recordings, was altered in Cplx 1 but not Cplx 2 single-knockout mice. In summary, the results provide an important basis for future studies on the function of Cplxs 1 and 2 in the processing of visual signals in the mammalian retina.
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Affiliation(s)
- Uwe Thorsten Lux
- Division of Animal Physiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany; (U.T.L.); (J.E.); (B.P.)
| | - Johanna Ehrenberg
- Division of Animal Physiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany; (U.T.L.); (J.E.); (B.P.)
| | - Anneka Joachimsthaler
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.J.); (J.A.); (J.K.); (A.G.)
| | - Jenny Atorf
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.J.); (J.A.); (J.K.); (A.G.)
| | - Bianca Pircher
- Division of Animal Physiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany; (U.T.L.); (J.E.); (B.P.)
| | - Kerstin Reim
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany;
| | - Jan Kremers
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.J.); (J.A.); (J.K.); (A.G.)
| | - Andreas Gießl
- Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (A.J.); (J.A.); (J.K.); (A.G.)
| | - Johann Helmut Brandstätter
- Division of Animal Physiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany; (U.T.L.); (J.E.); (B.P.)
- Correspondence:
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109
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Abstract
The damage or loss of retinal ganglion cells (RGCs) and their axons accounts for the visual functional defects observed after traumatic injury, in degenerative diseases such as glaucoma, or in compressive optic neuropathies such as from optic glioma. By using optic nerve crush injury models, recent studies have revealed the cellular and molecular logic behind the regenerative failure of injured RGC axons in adult mammals and suggested several strategies with translational potential. This review summarizes these findings and discusses challenges for developing clinically applicable neural repair strategies.
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Affiliation(s)
- Philip R Williams
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Larry I Benowitz
- Laboratories for Neuroscience Research in Neurosurgery, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Neurosurgery, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jeffrey L Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California 94303, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA
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110
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Pita-Thomas W, Gonçalves TM, Kumar A, Zhao G, Cavalli V. Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration. Sci Rep 2021; 11:14924. [PMID: 34290335 PMCID: PMC8295311 DOI: 10.1038/s41598-021-94341-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/05/2021] [Indexed: 11/21/2022] Open
Abstract
Retinal Ganglion Cells (RGCs) lose their ability to grow axons during development. Adult RGCs thus fail to regenerate their axons after injury, leading to vision loss. To uncover mechanisms that promote regeneration of RGC axons, we identified transcription factors (TF) and open chromatin regions that are enriched in rat embryonic RGCs (high axon growth capacity) compared to postnatal RGCs (low axon growth capacity). We found that developmental stage-specific gene expression changes correlated with changes in promoter chromatin accessibility. Binding motifs for TFs such as CREB, CTCF, JUN and YY1 were enriched in the regions of the chromatin that were more accessible in embryonic RGCs. Proteomic analysis of purified rat RGC nuclei confirmed the expression of TFs with potential role in axon growth such as CREB, CTCF, YY1, and JUND. The CREB/ATF binding motif was widespread at the open chromatin region of known pro-regenerative TFs, supporting a role of CREB in regulating axon regeneration. Consistently, overexpression of CREB fused to the VP64 transactivation domain in mouse RGCs promoted axon regeneration after optic nerve injury. Our study provides a map of the chromatin accessibility during RGC development and highlights that TF associated with developmental axon growth can stimulate axon regeneration in mature RGC.
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Affiliation(s)
- Wolfgang Pita-Thomas
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO, 63110, USA
| | | | - Ajeet Kumar
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Guoyan Zhao
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO, 63110, USA. .,Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - Valeria Cavalli
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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111
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Do JL, Allahwerdy S, David RCC, Weinreb RN, Tuszynski MH, Welsbie DS. Optic Nerve Engraftment of Neural Stem Cells. Invest Ophthalmol Vis Sci 2021; 62:30. [PMID: 34283208 PMCID: PMC8300061 DOI: 10.1167/iovs.62.9.30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Purpose To evaluate the integrative potential of neural stem cells (NSCs) with the visual system and characterize effects on the survival and axonal regeneration of axotomized retinal ganglion cells (RGCs). Methods For in vitro studies, primary, postnatal rat RGCs were directly cocultured with human NSCs or cultured in NSC-conditioned media before their survival and neurite outgrowth were assessed. For in vivo studies, human NSCs were transplanted into the transected rat optic nerve, and immunohistology of the retina and optic nerve was performed to evaluate RGC survival, RGC axon regeneration, and NSC integration with the injured visual system. Results Increased neurite outgrowth was observed in RGCs directly cocultured with NSCs. NSC-conditioned media demonstrated a dose-dependent effect on RGC survival and neurite outgrowth in culture. NSCs grafted into the lesioned optic nerve modestly improved RGC survival following an optic nerve transection (593 ± 164 RGCs/mm2 vs. 199 ± 58 RGCs/mm2; P < 0.01). Additionally, RGC axonal regeneration following an optic nerve transection was modestly enhanced by NSCs transplanted at the lesion site (61.6 ± 8.5 axons vs. 40.3 ± 9.1 axons, P < 0.05). Transplanted NSCs also differentiated into neurons, received synaptic inputs from regenerating RGC axons, and extended axons along the transected optic nerve to incorporate with the visual system. Conclusions Human NSCs promote the modest survival and axonal regeneration of axotomized RGCs that is partially mediated by diffusible NSC-derived factors. Additionally, NSCs integrate with the injured optic nerve and have the potential to form neuronal relays to restore retinofugal connections.
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Affiliation(s)
- Jiun L Do
- Hamilton Glaucoma Center, Shiley Eye Institute and Viterbi Family Department of Ophthalmology, University of California San Diego, La Jolla, California, United States
| | - Salam Allahwerdy
- Hamilton Glaucoma Center, Shiley Eye Institute and Viterbi Family Department of Ophthalmology, University of California San Diego, La Jolla, California, United States
| | - Ryan Caezar C David
- Hamilton Glaucoma Center, Shiley Eye Institute and Viterbi Family Department of Ophthalmology, University of California San Diego, La Jolla, California, United States
| | - Robert N Weinreb
- Hamilton Glaucoma Center, Shiley Eye Institute and Viterbi Family Department of Ophthalmology, University of California San Diego, La Jolla, California, United States
| | - Mark H Tuszynski
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States.,Veterans Administration Medical Center, San Diego, California, United States
| | - Derek S Welsbie
- Hamilton Glaucoma Center, Shiley Eye Institute and Viterbi Family Department of Ophthalmology, University of California San Diego, La Jolla, California, United States
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Chen CK, Kiyama T, Weber N, Whitaker CM, Pan P, Badea TC, Massey SC, Mao CA. Characterization of Tbr2-expressing retinal ganglion cells. J Comp Neurol 2021; 529:3513-3532. [PMID: 34245014 DOI: 10.1002/cne.25208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/27/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022]
Abstract
The mammalian retina contains more than 40 retinal ganglion cell (RGC) subtypes based on their unique morphologies, functions, and molecular profiles. Among them, intrinsically photosensitive RGCs (ipRGCs) are the first specified RGC type emerging from a common retinal progenitor pool during development. Previous work has shown that T-box transcription factor T-brain 2 (Tbr2) is essential for the formation and maintenance of ipRGCs, and that Tbr2-expressing RGCs activate Opn4 expression upon native ipRGC ablation, suggesting that Tbr2+ RGCs contain a reservoir for ipRGCs. However, the identity of Tbr2+ RGCs has not been fully vetted. Here, using genetic sparse labeling and single cell recording, we showed that Tbr2-expressing retinal neurons include RGCs and a subset of GABAergic displaced amacrine cells (dACs). Most Tbr2+ RGCs are intrinsically photosensitive and morphologically resemble native ipRGCs with identical retinofugal projections. Tbr2+ RGCs also include a unique and rare Pou4f1-expressing OFF RGC subtype. Using a loss-of-function strategy, we have further demonstrated that Tbr2 is essential for the survival of these RGCs and dACs, as well as maintaining the expression of Opn4. These data set a strong foundation to study how Tbr2 regulates ipRGC development and survival, as well as the expression of molecular machinery regulating intrinsic photosensitivity.
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Affiliation(s)
- Ching-Kang Chen
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA
| | - Takae Kiyama
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
| | - Nicole Weber
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA
| | - Christopher M Whitaker
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
| | - Ping Pan
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
| | - Tudor C Badea
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.,Research and Development Institute, Transilvania University of Brasov, School of Medicine, Brasov, Romania
| | - Stephen C Massey
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA.,The MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Chai-An Mao
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA.,The MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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113
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Vidal-Villegas B, Di Pierdomenico J, Gallego-Ortega A, Galindo-Romero C, Martínez-de-la-Casa JM, García-Feijoo J, Villegas-Pérez MP, Vidal-Sanz M. Systemic treatment with 7,8-Dihydroxiflavone activates TtkB and affords protection of two different retinal ganglion cell populations against axotomy in adult rats. Exp Eye Res 2021; 210:108694. [PMID: 34245756 DOI: 10.1016/j.exer.2021.108694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/26/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022]
Abstract
PURPOSE To analyze responses of different RGC populations to left intraorbital optic nerve transection (IONT) and intraperitoneal (i.p.) treatment with 7,8-Dihydroxyflavone (DHF), a potent selective TrkB agonist. METHODS Adult albino Sprague-Dawley rats received, following IONT, daily i.p. injections of vehicle (1%DMSO in 0.9%NaCl) or DHF. Group-1 (n = 58) assessed at 7days (d) the optimal DHF amount (1-25 mg/kg). Group-2, using freshly dissected naïve or treated retinas (n = 28), investigated if DHF treatment was associated with TrkB activation using Western-blotting at 1, 3 or 7d. Group-3 (n = 98) explored persistence of protection and was analyzed at survival intervals from 7 to 60d after IONT. Groups 2-3 received daily i.p. vehicle or DHF (5 mg/kg). Retinal wholemounts were immunolabelled for Brn3a and melanopsin to identify Brn3a+RGCs and m+RGCs, respectively. RESULTS Optimal neuroprotection was achieved with 5 mg/kg DHF and resulted in TrkB phosphorylation. The percentage of surviving Brn3a+RGCs in vehicle treated rats was 60, 28, 18, 13, 12 or 8% of the original value at 7, 10, 14, 21, 30 or 60d, respectively, while in DHF treated retinas was 94, 70, 64, 17, 10 or 9% at the same time intervals. The percentages of m+RGCs diminished by 7d-13%, and recovered by 14d-38% in vehicle-treated and to 48% in DHF-treated retinas, without further variations. CONCLUSIONS DHF neuroprotects Brn3a + RGCs and m + RGCs; its protective effects for Brn3a+RGCs are maximal at 7 days but still significant at 21d, whereas for m+RGCs neuroprotection was significant at 14d and permanent.
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Affiliation(s)
- Beatriz Vidal-Villegas
- Servicio de Oftalmología, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; Departamento de Oftalmología, Universidad de Murcia e Instituto Murciano de Investigación Biosanitaria (IMIB) Virgen de la Arrixaca. Campus de CC de la Salud, 30120, El Palmar, Murcia, Spain
| | - Johnny Di Pierdomenico
- Departamento de Oftalmología, Universidad de Murcia e Instituto Murciano de Investigación Biosanitaria (IMIB) Virgen de la Arrixaca. Campus de CC de la Salud, 30120, El Palmar, Murcia, Spain
| | - Alejandro Gallego-Ortega
- Departamento de Oftalmología, Universidad de Murcia e Instituto Murciano de Investigación Biosanitaria (IMIB) Virgen de la Arrixaca. Campus de CC de la Salud, 30120, El Palmar, Murcia, Spain
| | - Caridad Galindo-Romero
- Departamento de Oftalmología, Universidad de Murcia e Instituto Murciano de Investigación Biosanitaria (IMIB) Virgen de la Arrixaca. Campus de CC de la Salud, 30120, El Palmar, Murcia, Spain
| | - Jose M Martínez-de-la-Casa
- Servicio de Oftalmología, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - Julian García-Feijoo
- Servicio de Oftalmología, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - María P Villegas-Pérez
- Servicio de Oftalmología, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; Departamento de Oftalmología, Universidad de Murcia e Instituto Murciano de Investigación Biosanitaria (IMIB) Virgen de la Arrixaca. Campus de CC de la Salud, 30120, El Palmar, Murcia, Spain
| | - Manuel Vidal-Sanz
- Departamento de Oftalmología, Universidad de Murcia e Instituto Murciano de Investigación Biosanitaria (IMIB) Virgen de la Arrixaca. Campus de CC de la Salud, 30120, El Palmar, Murcia, Spain.
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114
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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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115
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Mead B, Kerr A, Nakaya N, Tomarev SI. miRNA Changes in Retinal Ganglion Cells after Optic Nerve Crush and Glaucomatous Damage. Cells 2021; 10:1564. [PMID: 34206213 PMCID: PMC8305746 DOI: 10.3390/cells10071564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022] Open
Abstract
The purpose of this study was to characterize the miRNA profile of purified retinal ganglion cells (RGC) from healthy and diseased rat retina. Diseased retina includes those after a traumatic optic nerve crush (ONC), and after ocular hypertension/glaucoma. Rats were separated into four groups: healthy/intact, 7 days after laser-induced ocular hypertension, 2 days after traumatic ONC, and 7 days after ONC. RGC were purified from rat retina using microbeads conjugated to CD90.1/Thy1. RNA were sequenced using Next Generation Sequencing. Over 100 miRNA were identified that were significantly different in diseased retina compared to healthy retina. Considerable differences were seen in the miRNA expression of RGC 7 days after ONC, whereas after 2 days, few changes were seen. The miRNA profiles of RGC 7 days after ONC and 7 days after ocular hypertension were similar, but discrete miRNA differences were still seen. Candidate mRNA showing different levels of expression after retinal injury were manipulated in RGC cultures using mimics/AntagomiRs. Of the five candidate miRNA identified and subsequently tested for therapeutic efficacy, miR-194 inhibitor and miR-664-2 inhibitor elicited significant RGC neuroprotection, whereas miR-181a mimic and miR-181d-5p mimic elicited significant RGC neuritogenesis.
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Affiliation(s)
- Ben Mead
- School of Optometry and Vision Sciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Alicia Kerr
- Section of Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (A.K.); (N.N.)
| | - Naoki Nakaya
- Section of Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (A.K.); (N.N.)
| | - Stanislav I. Tomarev
- Section of Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (A.K.); (N.N.)
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116
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Development of the vertebrate retinal direction-selective circuit. Dev Biol 2021; 477:273-283. [PMID: 34118273 DOI: 10.1016/j.ydbio.2021.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/17/2021] [Accepted: 06/04/2021] [Indexed: 01/13/2023]
Abstract
The vertebrate retina contains an array of neural circuits that detect distinct features in visual space. Direction-selective (DS) circuits are an evolutionarily conserved retinal circuit motif - from zebrafish to rodents to primates - specialized for motion detection. During retinal development, neuronal subtypes that wire DS circuits form exquisitely precise connections with each other to shape the output of retinal ganglion cells tuned for specific speeds and directions of motion. In this review, we follow the chronology of DS circuit development in the vertebrate retina, including the cellular, molecular, and activity-dependent mechanisms that regulate the formation of DS circuits, from cell birth and migration to synapse formation and refinement. We highlight recent findings that identify genetic programs critical for specifying neuronal subtypes within DS circuits and molecular interactions essential for responses along the cardinal axes of motion. Finally, we discuss the roles of DS circuits in visual behavior and in certain human visual disease conditions. As one of the best-characterized circuits in the vertebrate retina, DS circuits represent an ideal model system for studying the development of neural connectivity at the level of individual genes, cells, and behavior.
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117
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Axonopathy precedes cell death in ocular damage mediated by blast exposure. Sci Rep 2021; 11:11774. [PMID: 34083587 PMCID: PMC8175471 DOI: 10.1038/s41598-021-90412-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injuries (TBI) of varied types are common across all populations and can cause visual problems. For military personnel in combat settings, injuries from blast exposures (bTBI) are prevalent and arise from a myriad of different situations. To model these diverse conditions, we are one of several groups modeling bTBI using mice in varying ways. Here, we report a refined analysis of retinal ganglion cell (RGC) damage in male C57BL/6J mice exposed to a blast-wave in an enclosed chamber. Ganglion cell layer thickness, RGC density (BRN3A and RBPMS immunoreactivity), cellular density of ganglion cell layer (hematoxylin and eosin staining), and axon numbers (paraphenylenediamine staining) were quantified at timepoints ranging from 1 to 17-weeks. RNA sequencing was performed at 1-week and 5-weeks post-injury. Earliest indices of damage, evident by 1-week post-injury, are a loss of RGC marker expression, damage to RGC axons, and increase in glial markers expression. Blast exposure caused a loss of RGC somas and axons—with greatest loss occurring by 5-weeks post-injury. While indices of glial involvement are prominent early, they quickly subside as RGCs are lost. The finding that axonopathy precedes soma loss resembles pathology observed in mouse models of glaucoma, suggesting similar mechanisms.
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118
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Wang J, Struebing FL, Geisert EE. Commonalities of optic nerve injury and glaucoma-induced neurodegeneration: Insights from transcriptome-wide studies. Exp Eye Res 2021; 207:108571. [PMID: 33844961 PMCID: PMC9890784 DOI: 10.1016/j.exer.2021.108571] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 02/03/2023]
Abstract
Glaucoma is a collection of diseases that lead to an irreversible vision loss due to damage of retinal ganglion cells (RGCs). Although the underlying events leading to RGC death are not fully understood, recent research efforts are beginning to define the genetic changes that play a critical role in the initiation and progression of glaucomatous injury and RGC death. Several genetic and experimental animal models have been developed to mimic glaucomatous neurodegeneration. These models differ in many respects but all result in the loss of RGCs. Assessing transcriptional changes across different models could provide a more complete perspective on the molecular drivers of RGC degeneration. For the past several decades, changes in the retinal transcriptome during neurodegeneration process were defined using microarray methods, RNA sequencing and now single cell RNA sequencing. It is understood that these methods have strengths and weaknesses due to technical differences and variations in the analytical tools used. In this review, we focus on the use of transcriptome-wide expression profiling of the changes occurring as RGCs are lost across different glaucoma models. Commonalities of optic nerve crush and glaucoma-induced neurodegeneration are identified and discussed.
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Affiliation(s)
- Jiaxing Wang
- Emory Eye Center, Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
| | - Felix L. Struebing
- Center for Neuropathology and Prion Research, Ludwig Maximilian University of Munich, Germany,Department for Translational Brain Research, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Eldon E. Geisert
- Emory Eye Center, Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA,Corresponding author: (E.E. Geisert)
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119
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Fligor CM, Lavekar SS, Harkin J, Shields PK, VanderWall KB, Huang KC, Gomes C, Meyer JS. Extension of retinofugal projections in an assembled model of human pluripotent stem cell-derived organoids. Stem Cell Reports 2021; 16:2228-2241. [PMID: 34115986 PMCID: PMC8452489 DOI: 10.1016/j.stemcr.2021.05.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 01/31/2023] Open
Abstract
The development of the visual system involves the coordination of spatial and temporal events to specify the organization of varied cell types, including the elongation of axons from retinal ganglion cells (RGCs) to post-synaptic targets in the brain. Retinal organoids recapitulate many features of retinal development, yet have lacked downstream targets into which RGC axons extend, limiting the ability to model projections of the human visual system. To address these issues, retinal organoids were generated and organized into an in vitro assembloid model of the visual system with cortical and thalamic organoids. RGCs responded to environmental cues and extended axons deep into assembloids, modeling the projections of the visual system. In addition, RGC survival was enhanced in long-term assembloids, overcoming prior limitations of retinal organoids in which RGCs are lost. Overall, these approaches will facilitate studies of human visual system development, as well as diseases or injuries to this critical pathway. Human stem cell-derived RGC axons respond to target-derived cues Assembloids were generated between retinal, thalamic, and cortical organoids Retinofugal projections robustly extend toward thalamic targets
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Affiliation(s)
- Clarisse M Fligor
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Sailee S Lavekar
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Jade Harkin
- Interdisciplinary Biomedical Research Gateway Program, Indiana University School of Medicine, Indianapolis IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis IN, USA
| | - Priya K Shields
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Kirstin B VanderWall
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Kang-Chieh Huang
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Cátia Gomes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis IN, USA
| | - Jason S Meyer
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis IN, USA; Department of Ophthalmology, Indiana University School of Medicine, Indianapolis IN, USA.
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120
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Hilla AM, Baehr A, Leibinger M, Andreadaki A, Fischer D. CXCR4/CXCL12-mediated entrapment of axons at the injury site compromises optic nerve regeneration. Proc Natl Acad Sci U S A 2021; 118:e2016409118. [PMID: 34011605 PMCID: PMC8166183 DOI: 10.1073/pnas.2016409118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Regenerative failure in the mammalian optic nerve is generally attributed to axotomy-induced retinal ganglion cell (RGC) death, an insufficient intrinsic regenerative capacity, and an extrinsic inhibitory environment. Here, we show that a chemoattractive CXCL12/CXCR4-dependent mechanism prevents the extension of growth-stimulated axons into the distal nerve. The chemokine CXCL12 is chemoattractive toward axonal growth cones in an inhibitory environment, and these effects are entirely abolished by the specific knockout of its receptor, CXCR4 (CXCR4-/-), in cultured regenerating RGCs. Notably, 8% of naïve RGCs express CXCL12 and transport the chemokine along their axons in the nerve. Thus, axotomy causes its release at the injury site. However, most osteopontin-positive α-RGCs, the main neuronal population that survives optic nerve injury, express CXCR4 instead. Thus, CXCL12-mediated attraction prevents growth-stimulated axons from regenerating distally in the nerve, indicated by axons returning to the lesion site. Accordingly, specific depletion of CXCR4 in RGC reduces aberrant axonal growth and enables long-distance regeneration. Likewise, CXCL12 knockout in RGCs fully mimics these CXCR4-/- effects. Thus, active CXCL12/CXCR4-mediated entrapment of regenerating axons to the injury site contributes to regenerative failure in the optic nerve.
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Affiliation(s)
- Alexander M Hilla
- Department of Cell Physiology, Faculty of Biology and Biotechnology, Ruhr University, 44780 Bochum, Germany
| | - Annemarie Baehr
- Department of Cell Physiology, Faculty of Biology and Biotechnology, Ruhr University, 44780 Bochum, Germany
| | - Marco Leibinger
- Department of Cell Physiology, Faculty of Biology and Biotechnology, Ruhr University, 44780 Bochum, Germany
| | - Anastasia Andreadaki
- Department of Cell Physiology, Faculty of Biology and Biotechnology, Ruhr University, 44780 Bochum, Germany
| | - Dietmar Fischer
- Department of Cell Physiology, Faculty of Biology and Biotechnology, Ruhr University, 44780 Bochum, Germany
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121
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Gu L, Kwong JM, Caprioli J, Piri N. Loss of Rbfox1 Does Not Affect Survival of Retinal Ganglion Cells Injured by Optic Nerve Crush. Front Neurosci 2021; 15:687690. [PMID: 34108862 PMCID: PMC8180555 DOI: 10.3389/fnins.2021.687690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Rbfox1 is a multifunctional RNA binding protein that regulates alternative splicing, transcription, mRNA stability and translation. Its roles in neurogenesis and neuronal functions are well established. Recent studies also implicate Rbfox1 in the regulation of gene networks that support cell survival during stress. We have earlier characterized the expression of Rbfox1 in amacrine and retinal ganglion cells (RGCs) and showed that deletion of Rbfox1 in adult animals results in depth perception deficiency. The current study investigates the effect of Rbfox1 downregulation on survival of RGCs injured by optic nerve crush (ONC). Seven days after ONC, animals sustained severe degeneration of RGC axons in the optic nerve and significant loss of RGC somas. Semi-quantitative grading of optic nerve damage in control + ONC, control + tamoxifen + ONC, and Rbfox1 -/- + ONC groups ranged from 4.6 to 4.8 on a scale of 1 (normal; no degenerated axons were noted) to 5 (total degeneration; all axons showed degenerated organelles, axonal content, and myelin sheath), indicating a severe degeneration. Among these three ONC groups, no statistical significance was observed when any two groups were compared. The number of RGC somas were quantitatively analyzed in superior, inferior, nasal and temporal retinal quadrants at 0.5, 1, and 1.5 mm from the center of the optic disc. The average RGC densities (cells/mm2) were: control 6,438 ± 1,203; control + ONC 2,779 ± 573; control + tamoxifen 6,163 ± 861; control + tamoxifen + ONC 2,573 ± 555; Rbfox1 -/- 6,437 ± 893; and Rbfox1 -/- + ONC 2,537 ± 526. The RGC loss in control + ONC, control + tamoxifen + ONC and Rbfox1 -/- + ONC was 57% (P = 1.44954E-42), 58% (P = 1.37543E-57) and 61% (P = 5.552E-59) compared to RGC numbers in the relevant uninjured groups, respectively. No statistically significant difference was observed between any two groups of uninjured animals or between any two ONC groups. Our data indicate that Rbfox1-mediated pathways have no effect on survival of RGCs injured by ONC.
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Affiliation(s)
- Lei Gu
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jacky M Kwong
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Joseph Caprioli
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Natik Piri
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, United States
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122
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Wilkison SJ, Bright CL, Vancini R, Song DJ, Bomze HM, Cartoni R. Local Accumulation of Axonal Mitochondria in the Optic Nerve Glial Lamina Precedes Myelination. Front Neuroanat 2021; 15:678501. [PMID: 34093141 PMCID: PMC8173055 DOI: 10.3389/fnana.2021.678501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Mitochondria are essential for neurons and must be optimally distributed along their axon to fulfill local functions. A high density of mitochondria has been observed in retinal ganglion cell (RGC) axons of an unmyelinated region of the optic nerve, called the glial lamina (GL) in mouse (lamina cribrosa in human). In glaucoma, the world's leading cause of irreversible blindness, the GL is the epicenter of RGC degeneration and is connected to mitochondrial dysfunction. It is generally accepted that the local accumulation of mitochondria in the GL is established due to the higher energy requirement of unmyelinated axons. Here we revisit the connection between mitochondrial positioning and myelin in RGC axons. We show that the high density of mitochondria in the GL is restricted to larger axons and is established before myelination. Thus, contrary to a longstanding belief in the field, the myelination pattern is not responsible for the establishment of the local accumulation of mitochondria in GL axons. Our findings open new research avenues likely critical to understanding the pathophysiology of glaucoma.
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Affiliation(s)
- Samantha J Wilkison
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States.,Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States
| | - Cora L Bright
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States.,Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States
| | - Ricardo Vancini
- Department of Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Daniel J Song
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States.,Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States
| | - Howard M Bomze
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States.,Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States
| | - Romain Cartoni
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States.,Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States
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123
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Dou S, Wang Q, Qi X, Zhang B, Jiang H, Chen S, Duan H, Lu Y, Dong J, Cao Y, Xie L, Zhou Q, Shi W. Molecular identity of human limbal heterogeneity involved in corneal homeostasis and privilege. Ocul Surf 2021; 21:206-220. [PMID: 33964410 DOI: 10.1016/j.jtos.2021.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/10/2021] [Accepted: 04/24/2021] [Indexed: 12/20/2022]
Abstract
PURPOSE The corneal limbus maintains the homeostasis, immune and angiogenic privilege of cornea. This study aimed to depict the landscape of human limbal tissues by single-cell RNA sequencing (scRNA-seq). METHODS Single cells of human limbus collected from donor corneas were subjected to 10x scRNA-seq, followed by clustering cell types through the t-distributed stochastic neighbor embedding (t-SNE) and unbiased computational informatic analysis. Immunofluorescent staining was performed using human corneas to validate the analysis results. RESULTS 47,627 cells acquired from six human limbal tissues were collected and subjected to scRNA-seq. 14 distinct clusters were identified and 8 cell types were annotated with representative markers. In-depth dissection revealed three limbal epithelial cell subtypes and refined the X-Y-Z hypothesis of corneal epithelial maintenance. We further unveiled two cell states with higher stemness (TP63+ and CCL20+ cells), and two other differentiated cell states (GPHA2+ and KRT6B + cells) in homeostatic limbal stem/progenitor cells (LSPCs) that differ in transcriptional profiles. Cell-cell communication analysis revealed the central role of LSPCs and their bidirectional regulation with various niche cells. Moreover, comparative analysis between limbus and skin deciphered the pivotal contribution of limbal immune cells, vascular and lymphatic endothelial cells to corneal immune and angiogenic privilege. CONCLUSIONS The human limbus atlas provided valuable resources and foundations for understanding corneal biology, disease and potential interventions.
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Affiliation(s)
- Shengqian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Qun Wang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Xia Qi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Bin Zhang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Hui Jiang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Shengwen Chen
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Haoyun Duan
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Yao Lu
- OE Biotech Co., Ltd, Shanghai, Shanghai, China
| | | | - Yihai Cao
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Lixin Xie
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Qingjun Zhou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China.
| | - Weiyun Shi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China; Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China; Eye Hospital of Shandong First Medical University, Jinan, China.
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124
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Haverkamp S, Albert L, Balaji V, Němec P, Dedek K. Expression of cell markers and transcription factors in the avian retina compared with that in the marmoset retina. J Comp Neurol 2021; 529:3171-3193. [PMID: 33834511 DOI: 10.1002/cne.25154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
In the vertebrate retina, amacrine and ganglion cells represent the most diverse cell classes. They can be classified into different cell types by several features, such as morphology, light responses, and gene expression profile. Although birds possess high visual acuity (similar to primates that we used here for comparison) and tetrachromatic color vision, data on the expression of transcription factors in retinal ganglion cells of birds are largely missing. In this study, we tested various transcription factors, known to label subpopulations of cells in mammalian retinae, in two avian species: the common buzzard (Buteo buteo), a raptor with exceptional acuity, and the domestic pigeon (Columba livia domestica), a good navigator and widely used model for visual cognition. Staining for the transcription factors Foxp2, Satb1 and Satb2 labeled most ganglion cells in the avian ganglion cell layer. CtBP2 was established as marker for displaced amacrine cells, which allowed us to reliably distinguish ganglion cells from displaced amacrine cells and assess their densities in buzzard and pigeon. When we additionally compared the temporal and central fovea of the buzzard with the fovea of primates, we found that the cellular organization in the pits was different in primates and raptors. In summary, we demonstrate that the expression of transcription factors is a defining feature of cell types not only in the retina of mammals but also in the retina of birds. The markers, which we have established, may provide useful tools for more detailed studies on the retinal circuitry of these highly visual animals.
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Affiliation(s)
- Silke Haverkamp
- Department of Computational Neuroethology, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - László Albert
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Vaishnavi Balaji
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Pavel Němec
- Department of Zoology, Charles University, Prague, Czech Republic
| | - Karin Dedek
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany.,Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
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125
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Johnson KP, Fitzpatrick MJ, Zhao L, Wang B, McCracken S, Williams PR, Kerschensteiner D. Cell-type-specific binocular vision guides predation in mice. Neuron 2021; 109:1527-1539.e4. [PMID: 33784498 PMCID: PMC8112612 DOI: 10.1016/j.neuron.2021.03.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/09/2021] [Accepted: 03/05/2021] [Indexed: 12/20/2022]
Abstract
Predators use vision to hunt, and hunting success is one of evolution's main selection pressures. However, how viewing strategies and visual systems are adapted to predation is unclear. Tracking predator-prey interactions of mice and crickets in 3D, we find that mice trace crickets with their binocular visual fields and that monocular mice are poor hunters. Mammalian binocular vision requires ipsi- and contralateral projections of retinal ganglion cells (RGCs) to the brain. Large-scale single-cell recordings and morphological reconstructions reveal that only a small subset (9 of 40+) of RGC types in the ventrotemporal mouse retina innervate ipsilateral brain areas (ipsi-RGCs). Selective ablation of ipsi-RGCs (<2% of RGCs) in the adult retina drastically reduces the hunting success of mice. Stimuli based on ethological observations indicate that five ipsi-RGC types reliably signal prey. Thus, viewing strategies align with a spatially restricted and cell-type-specific set of ipsi-RGCs that supports binocular vision to guide predation.
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Affiliation(s)
- Keith P Johnson
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Graduate Program in Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Fitzpatrick
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Graduate Program in Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lei Zhao
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bing Wang
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sean McCracken
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip R Williams
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel Kerschensteiner
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA.
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126
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Advances in Regeneration of Retinal Ganglion Cells and Optic Nerves. Int J Mol Sci 2021; 22:ijms22094616. [PMID: 33924833 PMCID: PMC8125313 DOI: 10.3390/ijms22094616] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
Glaucoma, the second leading cause of blindness worldwide, is an incurable neurodegenerative disorder due to the dysfunction of retinal ganglion cells (RGCs). RGCs function as the only output neurons conveying the detected light information from the retina to the brain, which is a bottleneck of vision formation. RGCs in mammals cannot regenerate if injured, and RGC subtypes differ dramatically in their ability to survive and regenerate after injury. Recently, novel RGC subtypes and markers have been uncovered in succession. Meanwhile, apart from great advances in RGC axon regeneration, some degree of experimental RGC regeneration has been achieved by the in vitro differentiation of embryonic stem cells and induced pluripotent stem cells or in vivo somatic cell reprogramming, which provides insights into the future therapy of myriad neurodegenerative disorders. Further approaches to the combination of different factors will be necessary to develop efficacious future therapeutic strategies to promote ultimate axon and RGC regeneration and functional vision recovery following injury.
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127
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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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128
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Mure LS. Intrinsically Photosensitive Retinal Ganglion Cells of the Human Retina. Front Neurol 2021; 12:636330. [PMID: 33841306 PMCID: PMC8027232 DOI: 10.3389/fneur.2021.636330] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Light profoundly affects our mental and physical health. In particular, light, when not delivered at the appropriate time, may have detrimental effects. In mammals, light is perceived not only by rods and cones but also by a subset of retinal ganglion cells that express the photopigment melanopsin that renders them intrinsically photosensitive (ipRGCs). ipRGCs participate in contrast detection and play critical roles in non-image-forming vision, a set of light responses that include circadian entrainment, pupillary light reflex (PLR), and the modulation of sleep/alertness, and mood. ipRGCs are also found in the human retina, and their response to light has been characterized indirectly through the suppression of nocturnal melatonin and PLR. However, until recently, human ipRGCs had rarely been investigated directly. This gap is progressively being filled as, over the last years, an increasing number of studies provided descriptions of their morphology, responses to light, and gene expression. Here, I review the progress in our knowledge of human ipRGCs, in particular, the different morphological and functional subtypes described so far and how they match the murine subtypes. I also highlight questions that remain to be addressed. Investigating ipRGCs is critical as these few cells play a major role in our well-being. Additionally, as ipRGCs display increased vulnerability or resilience to certain disorders compared to conventional RGCs, a deeper knowledge of their function could help identify therapeutic approaches or develop diagnostic tools. Overall, a better understanding of how light is perceived by the human eye will help deliver precise light usage recommendations and implement light-based therapeutic interventions to improve cognitive performance, mood, and life quality.
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Affiliation(s)
- Ludovic S Mure
- Institute of Physiology, University of Bern, Bern, Switzerland.,Department of Neurology, Zentrum für Experimentelle Neurologie, Inselspital University Hospital Bern, Bern, Switzerland
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129
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Xia F, Ha Y, Shi S, Li Y, Li S, Luisi J, Kayed R, Motamedi M, Liu H, Zhang W. Early alterations of neurovascular unit in the retina in mouse models of tauopathy. Acta Neuropathol Commun 2021; 9:51. [PMID: 33762004 PMCID: PMC7992935 DOI: 10.1186/s40478-021-01149-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/06/2021] [Indexed: 02/07/2023] Open
Abstract
The retina, as the only visually accessible tissue in the central nervous system, has attracted significant attention for evaluating it as a biomarker for neurodegenerative diseases. Yet, most of studies focus on characterizing the loss of retinal ganglion cells (RGCs) and degeneration of their axons. There is no integrated analysis addressing temporal alterations of different retinal cells in the neurovascular unit (NVU) in particular retinal vessels. Here we assessed NVU changes in two mouse models of tauopathy, P301S and P301L transgenic mice overexpressing the human tau mutated gene, and evaluated the therapeutic effects of a tau oligomer monoclonal antibody (TOMA). We found that retinal edema and breakdown of blood-retina barrier were observed at the very early stage of tauopathy. Leukocyte adhesion/infiltration, and microglial recruitment/activation were constantly increased in the retinal ganglion cell layer of tau transgenic mice at different ages, while Müller cell gliosis was only detected in relatively older tau mice. Concomitantly, the number and function of RGCs progressively decreased during aging although they were not considerably altered in the very early stage of tauopathy. Moreover, intrinsically photosensitive RGCs appeared more sensitive to tauopathy. Remarkably, TOMA treatment in young tau transgenic mice significantly attenuated vascular leakage, inflammation and RGC loss. Our data provide compelling evidence that abnormal tau accumulation can lead to pathology in the retinal NVU, and vascular alterations occur more manifest and earlier than neurodegeneration in the retina. Oligomeric tau-targeted immunotherapy has the potential to treat tau-induced retinopathies. These data suggest that retinal NVU may serve as a potential biomarker for diagnosis and staging of tauopathy as well as a platform to study the molecular mechanisms of neurodegeneration.
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Affiliation(s)
- Fan Xia
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
| | - Yonju Ha
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
| | - Shuizhen Shi
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
| | - Yi Li
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
| | - Shengguo Li
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
| | - Jonathan Luisi
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX USA
| | - Rakez Kayed
- Department of Neurology, University of Texas Medical Branch, Galveston, TX USA
| | - Massoud Motamedi
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
| | - Hua Liu
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
| | - Wenbo Zhang
- Department of Ophthalmology and Visual Sciences, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0144 USA
- Departments of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555 USA
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130
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You M, Rong R, Zeng Z, Li H, Xia X, Ji D. Single-cell RNA sequencing: A new opportunity for retinal research. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1652. [PMID: 33754496 DOI: 10.1002/wrna.1652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/08/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a technology for single-cell transcriptome analysis that can be used to characterize complex dynamics of various retinal cell types. It provides deep scrutiny into the gene expression character of diverse cell types, lending insight into all the biological processes being carried out. The scRNA-seq is an alternative to regular RNA-seq, which does not achieve cellular heterogeneity. The retina, is a part of the central nervous system (CNS) and consists of six types of neurons and several types of glial cells. Studying retinal cell heterogeneity is important for understanding retinal diseases. Currently, scRNA-seq is employed to assess retina development and retinal disease pathogenesis and has improved our understanding of the relationship between the retina, its visual pathways, and the brain. Moreover, this technology provides new ideas on the sensitivity and molecular mechanisms of cell subtypes involved in retinal-related diseases. The application of scRNA-seq technology has given us a deeper understanding of the latest advancements and challenges in retinal development and diseases. We advocate scRNA-seq as one of the important tools for developing novel therapies for retinal diseases. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA in Disease and Development > RNA in Development RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Mengling You
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Rong Rong
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Zhou Zeng
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Haibo Li
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Xiaobo Xia
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Dan Ji
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
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131
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Calvo L, Ronshaugen M, Pettini T. smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods. Commun Biol 2021; 4:352. [PMID: 33742105 PMCID: PMC7979837 DOI: 10.1038/s42003-021-01803-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/03/2021] [Indexed: 01/01/2023] Open
Abstract
Recently, advances in fluorescent in-situ hybridization techniques and in imaging technology have enabled visualization and counting of individual RNA molecules in single cells. This has greatly enhanced the resolution in our understanding of transcriptional processes. Here, we adapt a recently published smiFISH protocol (single-molecule inexpensive fluorescent in-situ hybridization) to whole embryos across a range of arthropod model species, and also to non-embryonic tissues. Using multiple fluorophores with distinct spectra and white light laser confocal imaging, we simultaneously detect and separate single RNAs from up to eight different genes in a whole embryo. We also combine smiFISH with cell membrane immunofluorescence, and present an imaging and analysis pipeline for 3D cell segmentation and single-cell RNA counting in whole blastoderm embryos. Finally, using whole embryo single-cell RNA count data, we propose two alternative single-cell variability measures to the commonly used Fano factor, and compare the capacity of these three measures to address different aspects of single-cell expression variability. Here, the authors combine single-molecule inexpensive FISH (smiFISH) with cell membrane immunofluorescence and mathematical methods to enable whole embryo segmentation in 3D image stacks and mRNA quantification of multiple genes in each cell of the embryo.
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Affiliation(s)
- Llilians Calvo
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Matthew Ronshaugen
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Tom Pettini
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK.
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132
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Retinal Genomic Fabric Remodeling after Optic Nerve Injury. Genes (Basel) 2021; 12:genes12030403. [PMID: 33799827 PMCID: PMC7999523 DOI: 10.3390/genes12030403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and analyzed the data from the genomic fabric paradigm (GFP) to bring additional insights into the molecular mechanisms of the retinal remodeling after induction of RGC degeneration. GFP considers three independent characteristics for the expression of each gene: level, variability, and correlation with each other gene. Thus, the 17,657 quantified genes in our study generated a total of 155,911,310 values to analyze. This represents 8830x more data per condition than a traditional transcriptomic analysis. ONC led to a 57% reduction in RGC numbers as detected by retrograde labeling with 1,1'-dioctadecyl-3,3,3,3'-tetramethylindocarbocyanine perchlorate (DiI). We observed a higher relative expression variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Predicted protein-protein interaction (PPI) analysis with STRING revealed axon and neuron projection as mostly decreased processes, consistent with RGC degeneration. Conversely, immune response PPIs were found among upregulated genes. Enrichment analysis showed that complement cascade and Notch signaling pathway, as well as oxidative stress and kit receptor pathway were affected after ONC. To expand our studies of altered molecular pathways, we examined the pairwise coordination of gene expressions within each pathway and within the entire transcriptome using Pearson correlations. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles mainly in complement cascade and Notch signaling pathway. This deep bioinformatic study provided novel insights beyond the regulation of individual gene expression and disclosed changes in the control of expression of complement cascade and Notch signaling functional pathways that may be relevant for both RGC degeneration and remodeling of the retinal tissue after ONC.
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133
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Oswald J, Kegeles E, Minelli T, Volchkov P, Baranov P. Transplantation of miPSC/mESC-derived retinal ganglion cells into healthy and glaucomatous retinas. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 21:180-198. [PMID: 33816648 PMCID: PMC7994731 DOI: 10.1016/j.omtm.2021.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/06/2021] [Indexed: 12/11/2022]
Abstract
Optic neuropathies, including glaucoma, are a group of neurodegenerative diseases, characterized by the progressive loss of retinal ganglion cells (RGCs), leading to irreversible vision loss. While previous studies demonstrated the potential to replace RGCs with primary neurons from developing mouse retinas, their use is limited clinically. We demonstrate successful transplantation of mouse induced pluripotent stem cell (miPSC)/mouse embryonic stem cell (mESC)-derived RGCs into healthy and glaucomatous mouse retinas, at a success rate exceeding 65% and a donor cell survival window of up to 12 months. Transplanted Thy1-GFP+ RGCs were able to polarize within the host retina and formed axonal processes that followed host axons along the retinal surface and entered the optic nerve head. RNA sequencing of donor RGCs re-isolated from host retinas at 24 h and 1 week post-transplantation showed upregulation of cellular pathways mediating axonal outgrowth, extension, and guidance. Additionally, we provide evidence of subtype-specific diversity within miPSC-derived RGCs prior to transplantation.
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Affiliation(s)
- Julia Oswald
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Evgenii Kegeles
- Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Tomas Minelli
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Pavel Volchkov
- Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
- Research Institute of Personalized Medicine, National Center for Personalized Medicine of Endocrine Diseases, The National Medical Research Center for Endocrinology, Moscow 117036, Russia
| | - Petr Baranov
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
- Corresponding author: Petr Baranov, The Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
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Wu F, Bard JE, Kann J, Yergeau D, Sapkota D, Ge Y, Hu Z, Wang J, Liu T, Mu X. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nat Commun 2021; 12:1465. [PMID: 33674582 PMCID: PMC7935890 DOI: 10.1038/s41467-021-21704-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Atoh7 has been believed to be essential for establishing the retinal ganglion cell (RGC) lineage, and Pou4f2 and Isl1 are known to regulate RGC specification and differentiation. Here we report our further study of the roles of these transcription factors. Using bulk RNA-seq, we identify genes regulated by the three transcription factors, which expand our understanding of the scope of downstream events. Using scRNA-seq on wild-type and mutant retinal cells, we reveal a transitional cell state of retinal progenitor cells (RPCs) co-marked by Atoh7 and other genes for different lineages and shared by all early retinal lineages. We further discover the unexpected emergence of the RGC lineage in the absence of Atoh7. We conclude that competence of RPCs for different retinal fates is defined by lineage-specific genes co-expressed in the transitional state and that Atoh7 defines the RGC competence and collaborates with other factors to shepherd transitional RPCs to the RGC lineage.
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Affiliation(s)
- Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jonathan E Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Julien Kann
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Zihua Hu
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA.
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA.
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135
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Bargagna‐Mohan P, Schultz G, Rheaume B, Trakhtenberg EF, Robson P, Pal‐Ghosh S, Stepp MA, Given KS, Macklin WB, Mohan R. Corneal nonmyelinating Schwann cells illuminated by single-cell transcriptomics and visualized by protein biomarkers. J Neurosci Res 2021; 99:731-749. [PMID: 33197966 PMCID: PMC7894186 DOI: 10.1002/jnr.24757] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 10/05/2020] [Accepted: 10/25/2020] [Indexed: 12/23/2022]
Abstract
The cornea is the most innervated tissue in the human body. Myelinated axons upon inserting into the peripheral corneal stroma lose their myelin sheaths and continue into the central cornea wrapped by only nonmyelinating corneal Schwann cells (nm-cSCs). This anatomical organization is believed to be important for central vision. Here we employed single-cell RNA sequencing (scRNA-seq), microscopy, and transgenics to characterize these nm-cSCs of the central cornea. Using principal component analysis, uniform manifold approximation and projection, and unsupervised hierarchal cell clustering of scRNA-seq data derived from central corneal cells of male rabbits, we successfully identified several clusters representing different corneal cell types, including a unique cell cluster representing nm-cSCs. To confirm protein expression of cSC genes, we performed cross-species validation, employing corneal whole-mount immunostaining with confocal microscopy in mouse corneas. The expression of several representative proteins of nm-cSCs were validated. As the proteolipid protein 1 (PLP1) gene was also expressed in nm-cSCs, we explored the Plp1-eGFP transgenic reporter mouse line to visualize cSCs. Specific and efficient eGFP expression was observed in cSCs in adult mice of different ages. Of several putative cornea-specific SC genes identified, Dickkopf-related protein 1 was shown to be present in nm-cSCs. Taken together, our findings, for the first time, identify important insights and tools toward the study nm-cSCs in isolated tissue and adult animals. We expect that our results will advance the future study of nm-cSCs in applications of nerve repair, and provide a resource for the study of corneal sensory function.
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Affiliation(s)
- Paola Bargagna‐Mohan
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
| | - Gwendolyn Schultz
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
| | - Bruce Rheaume
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
| | | | - Paul Robson
- Department of Genetics & Genome SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
- The Jackson Laboratory for Genomic MedicineFarmingtonCTUSA
| | - Sonali Pal‐Ghosh
- Department of Anatomy and Regenerative BiologyGeorge Washington University Medical SchoolWashingtonDCUSA
| | - Mary Ann Stepp
- Department of Anatomy and Regenerative BiologyGeorge Washington University Medical SchoolWashingtonDCUSA
| | - Katherine S. Given
- Department of Cell and Developmental BiologyUniversity of Colorado School of MedicineAuroraCOUSA
| | - Wendy B. Macklin
- Department of Cell and Developmental BiologyUniversity of Colorado School of MedicineAuroraCOUSA
| | - Royce Mohan
- Department of NeuroscienceUniversity of Connecticut Health CenterFarmingtonCTUSA
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136
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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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137
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Rossin EJ, Sobrin L, Kim LA. Single-cell RNA sequencing: An overview for the ophthalmologist. Semin Ophthalmol 2021; 36:191-197. [PMID: 33635751 DOI: 10.1080/08820538.2021.1889615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Understanding the molecular composition of pathogenic tissues is a critical step in understanding the pathophysiology of disease and designing therapeutics. First described in 2009, single cell RNA sequencing (scRNAseq) is a methodology whereby thousands of cells are simultaneously isolated into individual micro-environments that can be altered experimentally and the genome-wide RNA expression of each cell is captured. It has undergone significant technological improvement over the last decade and gained tremendous popularity. scRNAseq is an improvement over prior pooled RNA analyses which cannot identify the cellular composition and heterogeneity of a tissue of interest. This new approach offers new opportunity for new discovery, as tissue samples can now be sub-categorized into groups of cell types based on genome-wide gene expression in an unbiased fashion. As ophthalmologists, we are uniquely positioned to obtain pathologic samples from the eye for further study. ScRNAseq has already been applied in ophthalmology to characterize retinal tissue, and it may offer the key to understanding various pathological processes in the future.
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Affiliation(s)
- Elizabeth J Rossin
- Massachusetts Eye and Ear, Harvard Medical School Department of Ophthalmology, Boston, MA, USA
| | - Lucia Sobrin
- Massachusetts Eye and Ear, Harvard Medical School Department of Ophthalmology, Boston, MA, USA
| | - Leo A Kim
- Massachusetts Eye and Ear, Harvard Medical School Department of Ophthalmology, Boston, MA, USA
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138
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Abstract
Neurons develop dendritic morphologies that bear cell type-specific features in dendritic field size and geometry, branch placement and density, and the types and distributions of synaptic contacts. Dendritic patterns influence the types and numbers of inputs a neuron receives, and the ways in which neural information is processed and transmitted in the circuitry. Even subtle alterations in dendritic structures can have profound consequences on neuronal function and are implicated in neurodevelopmental disorders. In this chapter, I review how growing dendrites acquire their exquisite patterns by drawing examples from diverse neuronal cell types in vertebrate and invertebrate model systems. Dendrite morphogenesis is shaped by intrinsic and extrinsic factors such as transcriptional regulators, guidance and adhesion molecules, neighboring cells and synaptic partners. I discuss molecular mechanisms that regulate dendrite morphogenesis with a focus on five aspects of dendrite patterning: (1) Dendritic cytoskeleton and cellular machineries that build the arbor; (2) Gene regulatory mechanisms; (3) Afferent cues that regulate dendritic arbor growth; (4) Space-filling strategies that optimize dendritic coverage; and (5) Molecular cues that specify dendrite wiring. Cell type-specific implementation of these patterning mechanisms produces the diversity of dendrite morphologies that wire the nervous system.
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139
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Kölsch Y, Hahn J, Sappington A, Stemmer M, Fernandes AM, Helmbrecht TO, Lele S, Butrus S, Laurell E, Arnold-Ammer I, Shekhar K, Sanes JR, Baier H. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Neuron 2021; 109:645-662.e9. [PMID: 33357413 PMCID: PMC7897282 DOI: 10.1016/j.neuron.2020.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
Retinal ganglion cells (RGCs) form an array of feature detectors, which convey visual information to central brain regions. Characterizing RGC diversity is required to understand the logic of the underlying functional segregation. Using single-cell transcriptomics, we systematically classified RGCs in adult and larval zebrafish, thereby identifying marker genes for >30 mature types and several developmental intermediates. We used this dataset to engineer transgenic driver lines, enabling specific experimental access to a subset of RGC types. Expression of one or few transcription factors often predicts dendrite morphologies and axonal projections to specific tectal layers and extratectal targets. In vivo calcium imaging revealed that molecularly defined RGCs exhibit specific functional tuning. Finally, chemogenetic ablation of eomesa+ RGCs, which comprise melanopsin-expressing types with projections to a small subset of central targets, selectively impaired phototaxis. Together, our study establishes a framework for systematically studying the functional architecture of the visual system.
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Affiliation(s)
- Yvonne Kölsch
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany; Graduate School of Systemic Neurosciences, Ludwig Maximilian University, 82152 Martinsried, Germany
| | - Joshua Hahn
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Anna Sappington
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Manuel Stemmer
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - António M Fernandes
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Thomas O Helmbrecht
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Shriya Lele
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Eva Laurell
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Irene Arnold-Ammer
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, California Institute for Quantitative Biosciences, QB3, Center for Computational Biology, UC Berkeley, Berkeley, CA 94720, USA.
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cell Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Herwig Baier
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany.
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140
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Nasir-Ahmad S, Lee SCS, Martin PR, Grünert U. Identification of retinal ganglion cell types expressing the transcription factor Satb2 in three primate species. J Comp Neurol 2021; 529:2727-2749. [PMID: 33527361 DOI: 10.1002/cne.25120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/31/2020] [Accepted: 01/25/2021] [Indexed: 12/17/2022]
Abstract
In primates, the retinal ganglion cells contributing to high acuity spatial vision (midget cells and parasol cells), and blue-yellow color vision (small bistratified cells) are well understood. Many other ganglion cell types with large dendritic fields (named wide-field ganglion cells) have been identified, but their spatial density and distribution are largely unknown. Here we took advantage of the recently established molecular diversity of ganglion cells to study wide-field ganglion cell populations in three primate species. We used antibodies against the transcription factor Special AT-rich binding protein 2 (Satb2) to explore its expression in macaque (Macaca fascicularis, M. nemestrina), human and marmoset (Callithrix jacchus) retinas. In all three species, Satb2 cells make up a low proportion (1.5-4%) of the ganglion cell population, with a slight increase from central to peripheral retina. Intracellular dye injections revealed that in macaque and human retinas, the large majority (over 80%) of Satb2 cells are inner and outer stratifying large sparse cells. By contrast, in marmoset retina the majority (over 60%) of Satb2 expressing cells were broad thorny cells, with smaller proportions of recursive bistratified (putative direction-selective), large bistratified, and outer stratifying narrow thorny cells. Our findings imply that Satb2 expression has undergone rapid species specific adaptations during primate evolution, because expression is not conserved across Old World (macaque, human) and New World (marmoset) suborders.
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Affiliation(s)
- Subha Nasir-Ahmad
- Faculty of Medicine and Health, Save Sight Institute and Discipline of Ophthalmology, The University of Sydney, Sydney, New South Wales, Australia.,Australian Research Council Centre of Excellence for Integrative Brain Function, The University of Sydney, Sydney, New South Wales, Australia
| | - Sammy C S Lee
- Faculty of Medicine and Health, Save Sight Institute and Discipline of Ophthalmology, The University of Sydney, Sydney, New South Wales, Australia.,Australian Research Council Centre of Excellence for Integrative Brain Function, The University of Sydney, Sydney, New South Wales, Australia
| | - Paul R Martin
- Faculty of Medicine and Health, Save Sight Institute and Discipline of Ophthalmology, The University of Sydney, Sydney, New South Wales, Australia.,Australian Research Council Centre of Excellence for Integrative Brain Function, The University of Sydney, Sydney, New South Wales, Australia
| | - Ulrike Grünert
- Faculty of Medicine and Health, Save Sight Institute and Discipline of Ophthalmology, The University of Sydney, Sydney, New South Wales, Australia.,Australian Research Council Centre of Excellence for Integrative Brain Function, The University of Sydney, Sydney, New South Wales, Australia
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141
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Shen LL, Mangalesh S, McGeehan B, Tai V, Sarin N, El-Dairi MA, Freedman SF, Maguire MG, Toth CA. Birth Weight Is a Significant Predictor of Retinal Nerve Fiber Layer Thickness at 36 Weeks Postmenstrual Age in Preterm Infants. Am J Ophthalmol 2021; 222:41-53. [PMID: 32891695 PMCID: PMC7930155 DOI: 10.1016/j.ajo.2020.08.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE To assess retinal nerve fiber layer (RNFL) thickness in preterm infants. DESIGN Prospective observational study. METHODS We imaged 83 awake infants (159 eyes) at 36 ± 1 weeks postmenstrual age (defined as the time elapsed between the first day of the last maternal menstrual period and the time at imaging) using a handheld optical coherence tomography (OCT) system at the bedside. Blinded graders semi-automatically segmented RNFL in the papillomacular bundle (-15 to +15° relative to the fovea-optic nerve axis). We correlated RNFL thickness and 7 characteristics of interest (sex, race, ethnicity, gestational age, birth weight, stage of retinopathy at prematurity, and presence of pre-plus or plus disease) via univariable and multivariable regressions. RESULTS RNFL was 3.4 μm thicker in the right eyes than in the left eyes (P < .001). Among 7 characteristics, birth weight was the only independent predictor of RNFL thickness (P < .001). A 250-g increase in birth weight was associated with 5.2 μm (95% confidence interval: 3.3-7.0) increase in RNFL thickness. Compared with very preterm infants, extremely preterm infants had thinner RNFL (58.0 ± 10.7 μm vs 63.4 ± 10.7 μm, P = .03), but the statistical significance disappeared after adjustment for birth weight (P = .25). RNFL thickness was 11.2 μm thinner in extremely low birth weight infants than in very low birth weight infants (55.5 ± 8.3 μm vs. 66.7 ± 10.2 μm; P < .001). The difference remained statistically significant after adjustment for gestational age. CONCLUSION Birth weight is a significant independent predictor of RNFL thickness near birth, implying that the retinal ganglion cells reserve is affected by intrauterine processes that affect birth weight.
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Affiliation(s)
- Liangbo L Shen
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shwetha Mangalesh
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brendan McGeehan
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vincent Tai
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Neeru Sarin
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Mays A El-Dairi
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sharon F Freedman
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maureen G Maguire
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cynthia A Toth
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina, USA.
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142
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Gilhooley MJ, Owen N, Moosajee M, Yu Wai Man P. From Transcriptomics to Treatment in Inherited Optic Neuropathies. Genes (Basel) 2021; 12:147. [PMID: 33499292 PMCID: PMC7912133 DOI: 10.3390/genes12020147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 02/06/2023] Open
Abstract
Inherited optic neuropathies, including Leber Hereditary Optic Neuropathy (LHON) and Dominant Optic Atrophy (DOA), are monogenetic diseases with a final common pathway of mitochondrial dysfunction leading to retinal ganglion cell (RGC) death and ultimately loss of vision. They are, therefore, excellent models with which to investigate this ubiquitous disease process-implicated in both common polygenetic ocular diseases (e.g., Glaucoma) and late-onset central nervous system neurodegenerative diseases (e.g., Parkinson disease). In recent years, cellular and animal models of LHON and DOA have matured in parallel with techniques (such as RNA-seq) to determine and analyze the transcriptomes of affected cells. This confluence leaves us at a particularly exciting time with the potential for the identification of novel pathogenic players and therapeutic targets. Here, we present a discussion of the importance of inherited optic neuropathies and how transcriptomic techniques can be exploited in the development of novel mutation-independent, neuroprotective therapies.
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Affiliation(s)
- Michael James Gilhooley
- Institute of Ophthalmology, University College London, Bath Street, London EC1V 9EL, UK; (N.O.); (M.M.); (P.Y.W.M.)
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London EC1V 2PD, UK
| | - Nicholas Owen
- Institute of Ophthalmology, University College London, Bath Street, London EC1V 9EL, UK; (N.O.); (M.M.); (P.Y.W.M.)
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, Bath Street, London EC1V 9EL, UK; (N.O.); (M.M.); (P.Y.W.M.)
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London EC1V 2PD, UK
- The Francis Crick Institute, 1 Midland Road, Somers Town, London NW1 1AT, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Patrick Yu Wai Man
- Institute of Ophthalmology, University College London, Bath Street, London EC1V 9EL, UK; (N.O.); (M.M.); (P.Y.W.M.)
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London EC1V 2PD, UK
- Department of Clinical Neurosciences, University of Cambridge, Robinson Way, Cambridge CB2 0PY, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Robinson Way, Cambridge CB2 0PY, UK
- Cambridge Eye Unit, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
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143
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Masin L, Claes M, Bergmans S, Cools L, Andries L, Davis BM, Moons L, De Groef L. A novel retinal ganglion cell quantification tool based on deep learning. Sci Rep 2021; 11:702. [PMID: 33436866 PMCID: PMC7804414 DOI: 10.1038/s41598-020-80308-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Glaucoma is a disease associated with the loss of retinal ganglion cells (RGCs), and remains one of the primary causes of blindness worldwide. Major research efforts are presently directed towards the understanding of disease pathogenesis and the development of new therapies, with the help of rodent models as an important preclinical research tool. The ultimate goal is reaching neuroprotection of the RGCs, which requires a tool to reliably quantify RGC survival. Hence, we demonstrate a novel deep learning pipeline that enables fully automated RGC quantification in the entire murine retina. This software, called RGCode (Retinal Ganglion Cell quantification based On DEep learning), provides a user-friendly interface that requires the input of RBPMS-immunostained flatmounts and returns the total RGC count, retinal area and density, together with output images showing the computed counts and isodensity maps. The counting model was trained on RBPMS-stained healthy and glaucomatous retinas, obtained from mice subjected to microbead-induced ocular hypertension and optic nerve crush injury paradigms. RGCode demonstrates excellent performance in RGC quantification as compared to manual counts. Furthermore, we convincingly show that RGCode has potential for wider application, by retraining the model with a minimal set of training data to count FluoroGold-traced RGCs.
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Affiliation(s)
- Luca Masin
- grid.5596.f0000 0001 0668 7884Department of Biology, Neural Circuit Development and Regeneration Research Group, KU Leuven, Leuven, Belgium
| | - Marie Claes
- grid.5596.f0000 0001 0668 7884Department of Biology, Neural Circuit Development and Regeneration Research Group, KU Leuven, Leuven, Belgium
| | - Steven Bergmans
- grid.5596.f0000 0001 0668 7884Department of Biology, Neural Circuit Development and Regeneration Research Group, KU Leuven, Leuven, Belgium
| | - Lien Cools
- grid.5596.f0000 0001 0668 7884Department of Biology, Neural Circuit Development and Regeneration Research Group, KU Leuven, Leuven, Belgium
| | - Lien Andries
- grid.5596.f0000 0001 0668 7884Department of Biology, Neural Circuit Development and Regeneration Research Group, KU Leuven, Leuven, Belgium
| | - Benjamin M. Davis
- grid.83440.3b0000000121901201Glaucoma and Retinal Neurodegenerative Disease Research Group, Institute of Ophthalmology, University College London, London, UK ,grid.496779.2Central Laser Facility, Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire UK
| | - Lieve Moons
- grid.5596.f0000 0001 0668 7884Department of Biology, Neural Circuit Development and Regeneration Research Group, KU Leuven, Leuven, Belgium
| | - Lies De Groef
- grid.5596.f0000 0001 0668 7884Department of Biology, Neural Circuit Development and Regeneration Research Group, KU Leuven, Leuven, Belgium
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144
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Yamagata M, Yan W, Sanes JR. A cell atlas of the chick retina based on single-cell transcriptomics. eLife 2021; 10:e63907. [PMID: 33393903 PMCID: PMC7837701 DOI: 10.7554/elife.63907] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/01/2021] [Indexed: 12/14/2022] Open
Abstract
Retinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. We used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. We identified 136 cell types plus 14 positional or developmental intermediates distributed among the six classes conserved across vertebrates - photoreceptor, horizontal, bipolar, amacrine, retinal ganglion, and glial cells. To assess morphology of molecularly defined types, we adapted a method for CRISPR-based integration of reporters into selectively expressed genes. For Müller glia, we found that transcriptionally distinct cells were regionally localized along the anterior-posterior, dorsal-ventral, and central-peripheral retinal axes. We also identified immature photoreceptor, horizontal cell, and oligodendrocyte types that persist into late embryonic stages. Finally, we analyzed relationships among chick, mouse, and primate retinal cell classes and types. Our results provide a foundation for anatomical, physiological, evolutionary, and developmental studies of the avian visual system.
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Affiliation(s)
- Masahito Yamagata
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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145
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Kim US, Mahroo OA, Mollon JD, Yu-Wai-Man P. Retinal Ganglion Cells-Diversity of Cell Types and Clinical Relevance. Front Neurol 2021; 12:661938. [PMID: 34093409 PMCID: PMC8175861 DOI: 10.3389/fneur.2021.661938] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/06/2021] [Indexed: 11/24/2022] Open
Abstract
Retinal ganglion cells (RGCs) are the bridging neurons that connect the retinal input to the visual processing centres within the central nervous system. There is a remarkable diversity of RGCs and the various subtypes have unique morphological features, distinct functions, and characteristic pathways linking the inner retina to the relevant brain areas. A number of psychophysical and electrophysiological tests have been refined to investigate this large and varied population of RGCs. Technological advances, such as high-resolution optical coherence tomography imaging, have provided additional tools to define the pattern of RGC involvement and the chronological sequence of events in both inherited and acquired optic neuropathies. The mechanistic insights gained from these studies, in particular the selective vulnerability and relative resilience of particular RGC subtypes, are of fundamental importance as they are directly relevant to the development of targeted therapies for these invariably progressive blinding diseases. This review provides a comprehensive description of the various types of RGCs, the developments in proposed methods of classification, and the current gaps in our knowledge of how these RGCs are differentially affected depending on the underlying aetiology. The synthesis of the current body of knowledge on the diversity of RGCs and the pathways that are potentially amenable to therapeutic modulation will hopefully lead to much needed effective treatments for patients with optic neuropathies.
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Affiliation(s)
- Ungsoo Samuel Kim
- Kim's Eye Hospital, Seoul, South Korea
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
- Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- *Correspondence: Ungsoo Samuel Kim
| | - Omar A. Mahroo
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Section of Ophthalmology, King's College London, St. Thomas' Hospital Campus, London, United Kingdom
| | - John D. Mollon
- Department of Psychology, University of Cambridge, Cambridge, United Kingdom
| | - Patrick Yu-Wai-Man
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
- Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
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146
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874
expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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147
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Al-Dbass A, Amina M, Al Musayeib NM, El-Anssary AA, Bhat RS, Fahmy R, Alhamdan MM, El-Ansary A. Lepidium sativum as candidate against excitotoxicity in retinal ganglion cells. Transl Neurosci 2021; 12:247-259. [PMID: 34141454 PMCID: PMC8178586 DOI: 10.1515/tnsci-2020-0174] [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: 12/09/2020] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
Glutamate excitotoxicity is considered one of the major causes of retinal ganglion cell death in many retinal diseases. Retinal ganglion cell degeneration causes severe blindness since visual signals from the eye to the brain are conducted only through retinal ganglion cells. OBJECTIVE We aimed to explore the potential ameliorative effects of L. sativum against glutamate excitotoxicity-induced retinal ganglion cell damage. METHODS Pure retinal ganglion cells were divided into a control group (untreated); L. sativum-treated groups in which retinal ganglion cells were treated with 5, 10, 50, or 100 µg/mL L. sativum seed extract for 2 h; glutamate-treated groups in which cells were treated with 5, 10, 50, or 100 µM glutamate for 48 h; and L. sativum/glutamate groups [pretreatment with L. sativum for 2 h (50 or 100 µg/mL) before glutamate treatment at 100 µM for 48 h]. Cell damage was assessed by comet assay and cell viability was by MTT test. RESULTS Tailed DNA, tail length, and tail moment of the 50 and 100 mM glutamate-treated groups were significantly greater than those of the blank control group, while the L. sativum-treated groups demonstrated nonsignificantly different tailed DNA, tail length, and tail moment compared with the blank control group, but significantly lower values compared with the glutamate-treated groups. CONCLUSION L. sativum ameliorated the cell viability in retinal ganglion cells after high-concentration glutamate exposure. L. sativum seed extracts were efficient anti-excitotoxic and antioxidant agent that might improve the clinical presentation of many neurological disorders.
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Affiliation(s)
- Abeer Al-Dbass
- Biochemistry Department, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Musarat Amina
- Department of Pharmacognosy, Pharmacy College, King Saud University, Riyadh, Saudi Arabia
| | - Nawal M. Al Musayeib
- Department of Pharmacognosy, Pharmacy College, King Saud University, Riyadh, Saudi Arabia
| | | | - Ramesa Shafi Bhat
- Biochemistry Department, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Rania Fahmy
- Department of Ophthalmology, Faculty of Medicine, Cairo University, Cairo, Egypt
- Department of Optometry, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | | | - Afaf El-Ansary
- Central Laboratory, Female Centre for Scientific and Medical Studies, King Saud University, Riyadh, Saudi Arabia
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148
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Liu L, Dong X, Tu Y, Miao G, Zhang Z, Zhang L, Wei Z, Yu D, Qiu X. Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics. MICROFLUIDICS AND NANOFLUIDICS 2021; 25:87. [PMID: 34580578 PMCID: PMC8457033 DOI: 10.1007/s10404-021-02485-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/30/2021] [Indexed: 05/14/2023]
Abstract
Single-cell nucleic acid analysis aims at discovering the genetic differences between individual cells which is well known as the cellular heterogeneity. This technology facilitates cancer diagnosis, stem cell research, immune system analysis, and other life science applications. The conventional platforms for single-cell nucleic acid analysis more rely on manual operation or bulky devices. Recently, the emerging microfluidic technology has provided a perfect platform for single-cell nucleic acid analysis with the characteristic of accurate and automatic single-cell manipulation. In this review, we briefly summarized the procedure of single-cell nucleic acid analysis including single-cell isolation, single-cell lysis, nucleic acid amplification, and genetic analysis. And then, three representative microfluidic platforms for single-cell nucleic acid analysis are concluded as valve-, microwell-, and droplet-based platforms. Furthermore, we described the state-of-the-art integrated single-cell nucleic acid analysis systems based on the three platforms. Finally, the future development and challenges of microfluidics-based single-cell nucleic acid analysis are discussed as well.
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Affiliation(s)
- Luyao Liu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Xiaobin Dong
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Yunping Tu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Zhongping Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing, 100081 China
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029 China
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
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149
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Single-cell RNA sequencing in vision research: Insights into human retinal health and disease. Prog Retin Eye Res 2020; 83:100934. [PMID: 33383180 DOI: 10.1016/j.preteyeres.2020.100934] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/03/2023]
Abstract
Gene expression provides valuable insight into cell function. As such, vision researchers have frequently employed gene expression studies to better understand retinal physiology and disease. With the advent of single-cell RNA sequencing, expression experiments provide an unparalleled resolution of information. Instead of studying aggregated gene expression across all cells in a heterogenous tissue, single-cell technology maps RNA to an individual cell, which facilitates grouping of retinal and choroidal cell types for further study. Single-cell RNA sequencing has been quickly adopted by both basic and translational vision researchers, and single-cell level gene expression has been studied in the visual systems of animal models, retinal organoids, and primary human retina, RPE, and choroid. These experiments have generated detailed atlases of gene expression and identified new retinal cell types. Likewise, single-cell RNA sequencing investigations have characterized how gene expression changes in the setting of many retinal diseases, including how choroidal endothelial cells are altered in age-related macular degeneration. In addition, this technology has allowed vision researchers to discover drivers of retinal development and model rare retinal diseases with induced pluripotent stem cells. In this review, we will overview the growing number of single-cell RNA sequencing studies in the field of vision research. We will summarize experimental considerations for designing single-cell RNA sequencing experiments and highlight important advancements in retinal, RPE, choroidal, and retinal organoid biology driven by this technology. Finally, we generalize these findings to genes involved in retinal degeneration and outline the future of single-cell expression experiments in studying retinal disease.
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150
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Raj B, Farrell JA, Liu J, El Kholtei J, Carte AN, Navajas Acedo J, Du LY, McKenna A, Relić Đ, Leslie JM, Schier AF. Emergence of Neuronal Diversity during Vertebrate Brain Development. Neuron 2020; 108:1058-1074.e6. [PMID: 33068532 PMCID: PMC8286448 DOI: 10.1016/j.neuron.2020.09.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/05/2020] [Accepted: 09/17/2020] [Indexed: 01/03/2023]
Abstract
Neurogenesis comprises many highly regulated processes including proliferation, differentiation, and maturation. However, the transcriptional landscapes underlying brain development are poorly characterized. We describe a developmental single-cell catalog of ∼220,000 zebrafish brain cells encompassing 12 stages from embryo to larva. We characterize known and novel gene markers for ∼800 clusters and provide an overview of the diversification of neurons and progenitors across these time points. We also introduce an optimized GESTALT lineage recorder that enables higher expression and recovery of Cas9-edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post-embryonic stages. Reconstruction of cell specification trajectories reveals that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis.
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Affiliation(s)
- Bushra Raj
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
| | - Jeffrey A Farrell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Unit on Cell Specification and Differentiation, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Jialin Liu
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Jakob El Kholtei
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Adam N Carte
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland; Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA
| | - Joaquin Navajas Acedo
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Lucia Y Du
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03756, USA
| | - Đorđe Relić
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), 4056 Basel, Switzerland
| | - Jessica M Leslie
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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