1
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Zhang L, Cavallini M, Wang J, Xin R, Zhang Q, Feng G, Sanes JR, Peng YR. Evolutionary and developmental specialization of foveal cell types in the marmoset. Proc Natl Acad Sci U S A 2024; 121:e2313820121. [PMID: 38598343 PMCID: PMC11032471 DOI: 10.1073/pnas.2313820121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high-throughput single-cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all their foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia (MG), among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for MG in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution.
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Affiliation(s)
- Lin Zhang
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Martina Cavallini
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Junqiang Wang
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Ruiqi Xin
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
| | - Qiangge Zhang
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Yi-Rong Peng
- Department of Ophthalmology and Stein Eye Institute, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA90095
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2
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Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Comprehensive single-cell atlas of the mouse retina. bioRxiv 2024:2024.01.24.577060. [PMID: 38328114 PMCID: PMC10849744 DOI: 10.1101/2024.01.24.577060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cellular heterogeneity at the single-cell resolution by classifying and characterizing cell types in multiple tissues and species. While several mouse retinal scRNA-seq reference datasets have been published, each dataset either has a relatively small number of cells or is focused on specific cell classes, and thus is suboptimal for assessing gene expression patterns across all retina types at the same time. To establish a unified and comprehensive reference for the mouse retina, we first generated the largest retinal scRNA-seq dataset to date, comprising approximately 190,000 single cells from C57BL/6J mouse whole retinas. This dataset was generated through the targeted enrichment of rare population cells via antibody-based magnetic cell sorting. By integrating this new dataset with public datasets, we conducted an integrated analysis to construct the Mouse Retina Cell Atlas (MRCA) for wild-type mice, which encompasses over 330,000 single cells. The MRCA characterizes 12 major classes and 138 cell types. It captured consensus cell type characterization from public datasets and identified additional new cell types. To facilitate the public use of the MRCA, we have deposited it in CELLxGENE, UCSC Cell Browser, and the Broad Single Cell Portal for visualization and gene expression exploration. The comprehensive MRCA serves as an easy-to-use, one-stop data resource for the mouse retina communities.
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Affiliation(s)
- Jin Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jongsu Choi
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Justin Ma
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shahil Pema
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02130, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin J. Frankfort
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nicholas M. Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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3
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Hamel AR, Yan W, Rouhana JM, Monovarfeshani A, Jiang X, Mehta PA, Advani J, Luo Y, Liang Q, Rajasundaram S, Shrivastava A, Duchinski K, Mantena S, Wang J, van Zyl T, Pasquale LR, Swaroop A, Gharahkhani P, Khawaja AP, MacGregor S, Chen R, Vitart V, Sanes JR, Wiggs JL, Segrè AV. Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma. Nat Commun 2024; 15:396. [PMID: 38195602 PMCID: PMC10776627 DOI: 10.1038/s41467-023-44380-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
Primary open-angle glaucoma (POAG), characterized by retinal ganglion cell death, is a leading cause of irreversible blindness worldwide. However, its molecular and cellular causes are not well understood. Elevated intraocular pressure (IOP) is a major risk factor, but many patients have normal IOP. Colocalization and Mendelian randomization analysis of >240 POAG and IOP genome-wide association study (GWAS) loci and overlapping expression and splicing quantitative trait loci (e/sQTLs) in 49 GTEx tissues and retina prioritizes causal genes for 60% of loci. These genes are enriched in pathways implicated in extracellular matrix organization, cell adhesion, and vascular development. Analysis of single-nucleus RNA-seq of glaucoma-relevant eye tissues reveals that the POAG and IOP colocalizing genes and genome-wide associations are enriched in specific cell types in the aqueous outflow pathways, retina, optic nerve head, peripapillary sclera, and choroid. This study nominates IOP-dependent and independent regulatory mechanisms, genes, and cell types that may contribute to POAG pathogenesis.
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Affiliation(s)
- Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Wenjun Yan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - John M Rouhana
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aboozar Monovarfeshani
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Xinyi Jiang
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MA, USA
| | - Yuyang Luo
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Qingnan Liang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Skanda Rajasundaram
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Centre for Evidence-Based Medicine, University of Oxford, Oxford, UK
- Faculty of Medicine, Imperial College London, London, UK
| | - Arushi Shrivastava
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Katherine Duchinski
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics (BIG) PhD Program, Harvard Medical School, Boston, MA, USA
| | - Sreekar Mantena
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Jiali Wang
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Tavé van Zyl
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Ophthalmology and Visual Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MA, USA
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4029, Australia
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4029, Australia
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Janey L Wiggs
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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4
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Zhang L, Cavallini M, Wang J, Xin R, Zhang Q, Feng G, Sanes JR, Peng YR. Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset. bioRxiv 2023:2023.12.10.570996. [PMID: 38106142 PMCID: PMC10723441 DOI: 10.1101/2023.12.10.570996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing to profile retinal cells of the common marmoset ( Callithrix jacchus ), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all its foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia, among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for Müller glia in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution. Significance statement The sharpness of our eyesight hinges on a tiny retinal region known as the fovea. The fovea is pivotal for primate vision and is susceptible to diseases like age-related macular degeneration. We studied the fovea in the marmoset-a primate with ancient evolutionary ties. Our data illustrated the cellular and molecular composition of its fovea across different developmental ages. Our findings highlighted a profound cellular consistency among marmosets, humans, and macaques, emphasizing the value of marmosets in visual research and the study of visual diseases.
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Hahn J, Monavarfeshani A, Qiao M, Kao AH, Kölsch Y, Kumar A, Kunze VP, Rasys AM, Richardson R, Wekselblatt JB, Baier H, Lucas RJ, Li W, Meister M, Trachtenberg JT, Yan W, Peng YR, Sanes JR, Shekhar K. Evolution of neuronal cell classes and types in the vertebrate retina. Nature 2023; 624:415-424. [PMID: 38092908 PMCID: PMC10719112 DOI: 10.1038/s41586-023-06638-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/13/2023] [Indexed: 12/17/2023]
Abstract
The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates2. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.
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Affiliation(s)
- Joshua Hahn
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Aboozar Monavarfeshani
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Mu Qiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- LinkedIn, Mountain View, CA, USA
| | - Allison H Kao
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yvonne Kölsch
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Ayush Kumar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Vincent P Kunze
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ashley M Rasys
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Rose Richardson
- Division of Neuroscience and Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Joseph B Wekselblatt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Herwig Baier
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Robert J Lucas
- Division of Neuroscience and Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Markus Meister
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Joshua T Trachtenberg
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Wenjun Yan
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yi-Rong Peng
- Department of Ophthalmology, Stein Eye Institute, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Joshua R Sanes
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- Helen Wills Neuroscience Institute,Vision Science Graduate Group, University of California, Berkeley, Berkeley, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Center for Computational Biology, Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, USA.
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
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Tai WL, Cho KS, Kriukov E, Ashok A, Wang X, Monavarfeshani A, Yan W, Li Y, Guan T, Sanes JR, Baranov P, Chen DF. Suppressing DNMT3a Alleviates the Intrinsic Epigenetic Barrier for Optic Nerve Regeneration and Restores Vision in Adult Mice. bioRxiv 2023:2023.11.17.567614. [PMID: 38014168 PMCID: PMC10680854 DOI: 10.1101/2023.11.17.567614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The limited regenerative potential of the optic nerve in adult mammals presents a major challenge for restoring vision after optic nerve trauma or disease. The mechanisms of this regenerative failure are not fully understood1,2. Here, through small-molecule and genetic screening for epigenetic modulators3, we identify DNA methyltransferase 3a (DNMT3a) as a potent inhibitor of axon regeneration in mouse and human retinal explants. Selective suppression of DNMT3a in retinal ganglion cells (RGCs) by gene targeting or delivery of shRNA leads to robust, full-length regeneration of RGC axons through the optic nerve and restoration of vision in adult mice after nerve crush injury. Genome-wide bisulfite and transcriptome profiling in combination with single nucleus RNA-sequencing of RGCs revealed selective DNA demethylation and reactivation of genetic programs supporting neuronal survival and axonal growth/regeneration by DNMT3a deficiency. This was accompanied by the suppression of gene networks associated with apoptosis and inflammation. Our results identify DNMT3a as the central orchestrator of an RGC-intrinsic mechanism that limits optic nerve regeneration. Suppressing DNMT3a expression in RGCs unlocks the epigenetic switch for optic nerve regeneration and presents a promising therapeutic avenue for effectively reversing vision loss resulted from optic nerve trauma or diseases.
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Affiliation(s)
- Wai Lydia Tai
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kin-Sang Cho
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Emil Kriukov
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Ajay Ashok
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Xuejian Wang
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Aboozar Monavarfeshani
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, MA, USA
| | - Wenjun Yan
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, MA, USA
| | - Yingqian Li
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Timothy Guan
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Joshua R Sanes
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, MA, USA
| | - Petr Baranov
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Dong Feng Chen
- Schepens Eye Research Institute of Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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7
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Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z, Colborn SLZ, Cortez BS, Owen LA, Tran NM, Shekhar K, Sanes JR, Stout JT, Chen S, Li Y, DeAngelis MM, Theis FJ, Chen R. Integrated multi-omics single cell atlas of the human retina. Res Sq 2023:rs.3.rs-3471275. [PMID: 38014002 PMCID: PMC10680922 DOI: 10.21203/rs.3.rs-3471275/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here, we present an integrated multimodal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types. Engaging the retina community, we annotated each cluster, refined the Cell Ontology for the retina, identified distinct marker genes, and characterized cis-regulatory elements and gene regulatory networks (GRNs) for these cell types. Our analysis uncovered intriguing differences in transcriptome, chromatin, and GRNs across cell types. In addition, we modeled changes in gene expression and chromatin openness across gender and age. This integrated atlas also enabled the fine-mapping of GWAS and eQTL variants. Accessible through interactive browsers, this multimodal cross-donor and cross-lab HRCA, can facilitate a better understanding of retinal function and pathology.
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Affiliation(s)
- Jin Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Jun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Ignacio L Ibarra
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Malte D Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Lung Health & Immunity, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Jiaxiong Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States
| | - Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States
| | - Zhen Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | | | | | - Leah A Owen
- John A. Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States
| | - Nicholas M Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Center for Computational Biology; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California, United States
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - J Timothy Stout
- Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, Texas, United States
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, United States
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Margaret M DeAngelis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, United States
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States
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8
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Hellevik AM, Mardoum P, Hahn J, Kölsch Y, D’Orazi FD, Suzuki SC, Godinho L, Lawrence O, Rieke F, Shekhar K, Sanes JR, Baier H, Baden T, Wong RO, Yoshimatsu T. Ancient origin of the rod bipolar cell pathway in the vertebrate retina. Res Sq 2023:rs.3.rs-3411693. [PMID: 37886445 PMCID: PMC10602083 DOI: 10.21203/rs.3.rs-3411693/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Vertebrates rely on rod photoreceptors for vision in low-light conditions. Mammals have a specialized downstream circuit for rod signaling called the primary rod pathway, which comprises specific cell types and wiring patterns that are thought to be unique to this lineage. Thus, it has been long assumed that the primary rod pathway evolved in mammals. Here, we challenge this view by demonstrating that the mammalian primary rod pathway is conserved in zebrafish, which diverged from extant mammals ~400 million years ago. Using single-cell RNA-sequencing, we identified two bipolar cell (BC) types in zebrafish that are related to mammalian rod BCs (RBCs) of the primary rod pathway. By combining electrophysiology, histology, and ultrastructural reconstruction of the zebrafish RBCs, we found that, like mammalian RBCs, both zebrafish RBC types connect with all rods in their dendritic territory, and provide output largely onto amacrine cells. The wiring pattern of the amacrine cells post-synaptic to one RBC type is strikingly similar to that of mammalian RBCs, suggesting that the cell types and circuit design of the primary rod pathway have emerged before the divergence of teleost fish and amniotes. The second RBC type, which forms separate pathways, is either lost in mammals or emerged in fish.
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Affiliation(s)
- Ayana M Hellevik
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Philip Mardoum
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Joshua Hahn
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Vision Sciences Graduate Program; California Institute of Quantitative Biosciences (QB3), University of California Berkley, Berkeley, CA 94720, USA
| | - Yvonne Kölsch
- Department of Molecular & Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Max Planck Institute for Biological Intelligence, Department Genes – Circuits – Behavior, 82152 Martinsried, Germany
| | - Florence D D’Orazi
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Sachihiro C. Suzuki
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Leanne Godinho
- Institute of Neuronal Cell Biology, Technische Universität München, 80802 Munich, Germany
| | - Owen Lawrence
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
- Vision Science Center, University of Washington, Seattle, WA 98195, USA
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Vision Sciences Graduate Program; California Institute of Quantitative Biosciences (QB3), University of California Berkley, Berkeley, CA 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joshua R Sanes
- Department of Molecular & Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Herwig Baier
- Max Planck Institute for Biological Intelligence, Department Genes – Circuits – Behavior, 82152 Martinsried, Germany
| | - Tom Baden
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, 72076, Germany
| | - Rachel O Wong
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Takeshi Yoshimatsu
- Department of Ophthalmology & Visual Sciences, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
- BioRTC, Yobe State University, Damatsuru, Yobe 620101, Nigeria
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9
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Hellevik AM, Mardoum P, Hahn J, Kölsch Y, D’Orazi FD, Suzuki SC, Godinho L, Lawrence O, Rieke F, Shekhar K, Sanes JR, Baier H, Baden T, Wong RO, Yoshimatsu T. Ancient origin of the rod bipolar cell pathway in the vertebrate retina. bioRxiv 2023:2023.09.12.557433. [PMID: 37771914 PMCID: PMC10525478 DOI: 10.1101/2023.09.12.557433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Vertebrates rely on rod photoreceptors for vision in low-light conditions1. Mammals have a specialized downstream circuit for rod signaling called the primary rod pathway, which comprises specific cell types and wiring patterns that are thought to be unique to this lineage2-6. Thus, it has been long assumed that the primary rod pathway evolved in mammals3,5-7. Here, we challenge this view by demonstrating that the mammalian primary rod pathway is conserved in zebrafish, which diverged from extant mammals ~400 million years ago. Using single-cell RNA-sequencing, we identified two bipolar cell (BC) types in zebrafish that are related to mammalian rod BCs (RBCs) of the primary rod pathway. By combining electrophysiology, histology, and ultrastructural reconstruction of the zebrafish RBCs, we found that, like mammalian RBCs8, both zebrafish RBC types connect with all rods and red-cones in their dendritic territory, and provide output largely onto amacrine cells. The wiring pattern of the amacrine cells post-synaptic to one RBC type is strikingly similar to that of mammalian RBCs. This suggests that the cell types and circuit design of the primary rod pathway may have emerged before the divergence of teleost fish and amniotes (mammals, bird, reptiles). The second RBC type in zebrafish, which forms separate pathways from the first RBC type, is either lost in mammals or emerged in fish to serve yet unknown roles.
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Affiliation(s)
- Ayana M Hellevik
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Philip Mardoum
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Joshua Hahn
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Vision Sciences Graduate Program; California Institute of Quantitative Biosciences (QB3), University of California Berkley, Berkeley, CA 94720, USA
| | - Yvonne Kölsch
- Department of Molecular & Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Max Planck Institute for Biological Intelligence, Department Genes – Circuits – Behavior, 82152 Martinsried, Germany
| | - Florence D D’Orazi
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Sachihiro C. Suzuki
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Leanne Godinho
- Institute of Neuronal Cell Biology, Technische Universität München, 80802 Munich, Germany
| | - Owen Lawrence
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
- Vision Science Center, University of Washington, Seattle, WA 98195, USA
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Vision Sciences Graduate Program; California Institute of Quantitative Biosciences (QB3), University of California Berkley, Berkeley, CA 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joshua R Sanes
- Department of Molecular & Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Herwig Baier
- Max Planck Institute for Biological Intelligence, Department Genes – Circuits – Behavior, 82152 Martinsried, Germany
| | - Tom Baden
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, 72076, Germany
| | - Rachel O Wong
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Takeshi Yoshimatsu
- Department of Ophthalmology & Visual Sciences, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
- BioRTC, Yobe State University, Damatsuru, Yobe 620101, Nigeria
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10
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Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye. Proc Natl Acad Sci U S A 2023; 120:e2306153120. [PMID: 37566633 PMCID: PMC10450437 DOI: 10.1073/pnas.2306153120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/29/2023] [Indexed: 08/13/2023] Open
Abstract
Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here, we used high-throughput single-nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in six extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases-for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ~151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the data presented here complete a "Version 1" cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as the neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
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Affiliation(s)
- Aboozar Monavarfeshani
- Center for Brain Science, Harvard University, Cambridge, MA02138
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Christian Pappas
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Kenechukwu A. Odenigbo
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA02115
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA02142
| | - Tavé van Zyl
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT065101
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT84132
- Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT84132
| | - Joshua R. Sanes
- Center for Brain Science, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
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11
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Monavarfeshani A, Yan W, Pappas C, Odenigbo KA, He Z, Segrè AV, van Zyl T, Hageman GS, Sanes JR. Transcriptomic Analysis of the Ocular Posterior Segment Completes a Cell Atlas of the Human Eye. bioRxiv 2023:2023.04.26.538447. [PMID: 37162855 PMCID: PMC10168356 DOI: 10.1101/2023.04.26.538447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Although the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here we used high-throughput single nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in the extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases - for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ∼151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the new data complete a "Version 1" cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.
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Affiliation(s)
- Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Equal contributions
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Equal contributions
| | - Christian Pappas
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Kenechukwu A. Odenigbo
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
| | - Ayellet V. Segrè
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Tavé van Zyl
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Present address: Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT 06510
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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12
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Hahn J, Monavarfeshani A, Qiao M, Kao A, Kölsch Y, Kumar A, Kunze VP, Rasys AM, Richardson R, Baier H, Lucas RJ, Li W, Meister M, Trachtenberg JT, Yan W, Peng YR, Sanes JR, Shekhar K. Evolution of neuronal cell classes and types in the vertebrate retina. bioRxiv 2023:2023.04.07.536039. [PMID: 37066415 PMCID: PMC10104162 DOI: 10.1101/2023.04.07.536039] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Muller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.
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Affiliation(s)
- Joshua Hahn
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aboozar Monavarfeshani
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, MA 02138, USA
| | - Mu Qiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Allison Kao
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, MA 02138, USA
| | - Yvonne Kölsch
- Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ayush Kumar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vincent P Kunze
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ashley M. Rasys
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | - Rose Richardson
- Division of Neuroscience and Centre for Biological Timing, Faculty of Biology Medicine & Health, University of Manchester, Upper Brook Street, Manchester M13 9PT, UK
| | - Herwig Baier
- Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Robert J. Lucas
- Division of Neuroscience and Centre for Biological Timing, Faculty of Biology Medicine & Health, University of Manchester, Upper Brook Street, Manchester M13 9PT, UK
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Markus Meister
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joshua T. Trachtenberg
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Wenjun Yan
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, MA 02138, USA
| | - Yi-Rong Peng
- Department of Ophthalmology, Stein Eye Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095 United States
| | - Joshua R. Sanes
- Department of Cellular and Molecular Biology, Center for Brain Science, Harvard University, MA 02138, USA
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Vision Science Graduate Group, Center for Computational Biology, Biophysics Graduate Group, California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley CA 94720, USA
- Faculty Scientist, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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13
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Benhar I, Ding J, Yan W, Whitney IE, Jacobi A, Sud M, Burgin G, Shekhar K, Tran NM, Wang C, He Z, Sanes JR, Regev A. Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury. Nat Immunol 2023; 24:700-713. [PMID: 36807640 DOI: 10.1038/s41590-023-01437-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/13/2023] [Indexed: 02/22/2023]
Abstract
Non-neuronal cells are key to the complex cellular interplay that follows central nervous system insult. To understand this interplay, we generated a single-cell atlas of immune, glial and retinal pigment epithelial cells from adult mouse retina before and at multiple time points after axonal transection. We identified rare subsets in naive retina, including interferon (IFN)-response glia and border-associated macrophages, and delineated injury-induced changes in cell composition, expression programs and interactions. Computational analysis charted a three-phase multicellular inflammatory cascade after injury. In the early phase, retinal macroglia and microglia were reactivated, providing chemotactic signals concurrent with infiltration of CCR2+ monocytes from the circulation. These cells differentiated into macrophages in the intermediate phase, while an IFN-response program, likely driven by microglia-derived type I IFN, was activated across resident glia. The late phase indicated inflammatory resolution. Our findings provide a framework to decipher cellular circuitry, spatial relationships and molecular interactions following tissue injury.
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Affiliation(s)
- Inbal Benhar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jiarui Ding
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenjun Yan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Irene E Whitney
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Anne Jacobi
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Malika Sud
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace Burgin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karthik Shekhar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemical and Biomolecular Engineering, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas M Tran
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
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14
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Tian F, Cheng Y, Zhou S, Wang Q, Monavarfeshani A, Gao K, Jiang W, Kawaguchi R, Wang Q, Tang M, Donahue R, Meng H, Zhang Y, Jacobi A, Yan W, Yin J, Cai X, Yang Z, Hegarty S, Stanicka J, Dmitriev P, Taub D, Zhu J, Woolf CJ, Sanes JR, Geschwind DH, He Z. Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells. Neuron 2023; 111:444. [PMID: 36731430 PMCID: PMC9984249 DOI: 10.1016/j.neuron.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhigang He
- Correspondence: (J.R.S.), (D.H.G.), (Z.H.)
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15
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Liu A, Milner ES, Peng YR, Blume HA, Brown MC, Bryman GS, Emanuel AJ, Morquette P, Viet NM, Sanes JR, Gamlin PD, Do MTH. Encoding of environmental illumination by primate melanopsin neurons. Science 2023; 379:376-381. [PMID: 36701440 PMCID: PMC10445534 DOI: 10.1126/science.ade2024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/21/2022] [Indexed: 01/27/2023]
Abstract
Light regulates physiology, mood, and behavior through signals sent to the brain by intrinsically photosensitive retinal ganglion cells (ipRGCs). How primate ipRGCs sense light is unclear, as they are rare and challenging to target for electrophysiological recording. We developed a method of acute identification within the live, ex vivo retina. Using it, we found that ipRGCs of the macaque monkey are highly specialized to encode irradiance (the overall intensity of illumination) by blurring spatial, temporal, and chromatic features of the visual scene. We describe mechanisms at the molecular, cellular, and population scales that support irradiance encoding across orders-of-magnitude changes in light intensity. These mechanisms are conserved quantitatively across the ~70 million years of evolution that separate macaques from mice.
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Affiliation(s)
- Andreas Liu
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
| | - Elliott S. Milner
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
- Present address: Sainsbury Wellcome Centre for Neural Circuits and Behavior, University College London, 25 Howland Street, London, W1T 4JG, UK
| | - Yi-Rong Peng
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Present address: Department of Ophthalmology, Stein Eye Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Hannah A. Blume
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
| | - Michael C. Brown
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
| | - Gregory S. Bryman
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
- Present address: Merck & Co., Inc., 320 Bent St, Cambridge, MA 02141, USA
| | - Alan J. Emanuel
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
- Present address: Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA, 02115, USA
| | - Philippe Morquette
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
| | - Nguyen-Minh Viet
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
| | - Joshua R. Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Paul D. Gamlin
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Tri H. Do
- F. M. Kirby Neurobiology Center and Department of Neurology, Boston Children’s Hospital and Harvard Medical School. Boston, MA 02115, USA
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16
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Whitney IE, Butrus S, Dyer MA, Rieke F, Sanes JR, Shekhar K. Vision-Dependent and -Independent Molecular Maturation of Mouse Retinal Ganglion Cells. Neuroscience 2023; 508:153-173. [PMID: 35870562 PMCID: PMC10809145 DOI: 10.1016/j.neuroscience.2022.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/20/2022] [Accepted: 07/13/2022] [Indexed: 01/17/2023]
Abstract
The development and connectivity of retinal ganglion cells (RGCs), the retina's sole output neurons, are patterned by activity-independent transcriptional programs and activity-dependent remodeling. To inventory the molecular correlates of these influences, we applied high-throughput single-cell RNA sequencing (scRNA-seq) to mouse RGCs at six embryonic and postnatal ages. We identified temporally regulated modules of genes that correlate with, and likely regulate, multiple phases of RGC development, ranging from differentiation and axon guidance to synaptic recognition and refinement. Some of these genes are expressed broadly while others, including key transcription factors and recognition molecules, are selectively expressed by one or a few of the 45 transcriptomically distinct types defined previously in adult mice. Next, we used these results as a foundation to analyze the transcriptomes of RGCs in mice lacking visual experience due to dark rearing from birth or to mutations that ablate either bipolar or photoreceptor cells. 98.5% of visually deprived (VD) RGCs could be unequivocally assigned to a single RGC type based on their transcriptional profiles, demonstrating that visual activity is dispensable for acquisition and maintenance of RGC type identity. However, visual deprivation significantly reduced the transcriptomic distinctions among RGC types, implying that activity is required for complete RGC maturation or maintenance. Consistent with this notion, transcriptomic alternations in VD RGCs significantly overlapped with gene modules found in developing RGCs. Our results provide a resource for mechanistic analyses of RGC differentiation and maturation, and for investigating the role of activity in these processes.
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Affiliation(s)
- Irene E Whitney
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Karthik Shekhar
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Helen Wills Neuroscience Institute, California Institute for Quantitative Biosciences, QB3, Center for Computational Biology, University of California, Berkeley, CA 94720, USA; Biological Systems Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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17
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Tian F, Cheng Y, Zhou S, Wang Q, Monavarfeshani A, Gao K, Jiang W, Kawaguchi R, Wang Q, Tang M, Donahue R, Meng H, Zhang Y, Jacobi A, Yan W, Yin J, Cai X, Yang Z, Hegarty S, Stanicka J, Dmitriev P, Taub D, Zhu J, Woolf CJ, Sanes JR, Geschwind DH, He Z. Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells. Neuron 2022; 110:2607-2624.e8. [PMID: 35767995 PMCID: PMC9391318 DOI: 10.1016/j.neuron.2022.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/10/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023]
Abstract
Regulatory programs governing neuronal death and axon regeneration in neurodegenerative diseases remain poorly understood. In adult mice, optic nerve crush (ONC) injury by severing retinal ganglion cell (RGC) axons results in massive RGC death and regenerative failure. We performed an in vivo CRISPR-Cas9-based genome-wide screen of 1,893 transcription factors (TFs) to seek repressors of RGC survival and axon regeneration following ONC. In parallel, we profiled the epigenetic and transcriptional landscapes of injured RGCs by ATAC-seq and RNA-seq to identify injury-responsive TFs and their targets. These analyses converged on four TFs as critical survival regulators, of which ATF3/CHOP preferentially regulate pathways activated by cytokines and innate immunity and ATF4/C/EBPγ regulate pathways engaged by intrinsic neuronal stressors. Manipulation of these TFs protects RGCs in a glaucoma model. Our results reveal core transcription programs that transform an initial axonal insult into a degenerative process and suggest novel strategies for treating neurodegenerative diseases.
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Affiliation(s)
- Feng Tian
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Yuyan Cheng
- Departments of Neurology, Psychiatry and Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-1761, USA
| | - Songlin Zhou
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Qianbin Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Aboozar Monavarfeshani
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Kun Gao
- Departments of Neurology, Psychiatry and Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-1761, USA
| | - Weiqian Jiang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Riki Kawaguchi
- Departments of Neurology, Psychiatry and Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-1761, USA
| | - Qing Wang
- Departments of Neurology, Psychiatry and Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-1761, USA
| | - Mingjun Tang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Ryan Donahue
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Huyan Meng
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Yu Zhang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Anne Jacobi
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Wenjun Yan
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Jiani Yin
- Departments of Neurology, Psychiatry and Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-1761, USA
| | - Xinyi Cai
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Zhiyun Yang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Shane Hegarty
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Joanna Stanicka
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Phillip Dmitriev
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Daniel Taub
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Junjie Zhu
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Daniel H Geschwind
- Departments of Neurology, Psychiatry and Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-1761, USA.
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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18
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Jacobi A, Tran NM, Yan W, Benhar I, Tian F, Schaffer R, He Z, Sanes JR. Overlapping transcriptional programs promote survival and axonal regeneration of injured retinal ganglion cells. Neuron 2022; 110:2625-2645.e7. [PMID: 35767994 PMCID: PMC9391321 DOI: 10.1016/j.neuron.2022.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 12/12/2022]
Abstract
Injured neurons in the adult mammalian central nervous system often die and seldom regenerate axons. To uncover transcriptional pathways that could ameliorate these disappointing responses, we analyzed three interventions that increase survival and regeneration of mouse retinal ganglion cells (RGCs) following optic nerve crush (ONC) injury, albeit not to a clinically useful extent. We assessed gene expression in each of 46 RGC types by single-cell transcriptomics following ONC and treatment. We also compared RGCs that regenerated with those that survived but did not regenerate. Each intervention enhanced survival of most RGC types, but type-independent axon regeneration required manipulation of multiple pathways. Distinct computational methods converged on separate sets of genes selectively expressed by RGCs likely to be dying, surviving, or regenerating. Overexpression of genes associated with the regeneration program enhanced both survival and axon regeneration in vivo, indicating that mechanistic analysis can be used to identify novel therapeutic strategies.
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Affiliation(s)
- Anne Jacobi
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Nicholas M Tran
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Wenjun Yan
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Inbal Benhar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Feng Tian
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Rebecca Schaffer
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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19
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van Zyl T, Yan W, McAdams AM, Monavarfeshani A, Hageman GS, Sanes JR. Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types. Proc Natl Acad Sci U S A 2022; 119:e2200914119. [PMID: 35858321 PMCID: PMC9303934 DOI: 10.1073/pnas.2200914119] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
The anterior segment of the eye consists of the cornea, iris, ciliary body, crystalline lens, and aqueous humor outflow pathways. Together, these tissues are essential for the proper functioning of the eye. Disorders of vision have been ascribed to defects in all of them; some disorders, including glaucoma and cataract, are among the most prevalent causes of blindness in the world. To characterize the cell types that compose these tissues, we generated an anterior segment cell atlas of the human eye using high-throughput single-nucleus RNA sequencing (snRNAseq). We profiled 195,248 nuclei from nondiseased anterior segment tissues of six human donors, identifying >60 cell types. Many of these cell types were discrete, whereas others, especially in the lens and cornea, formed continua corresponding to known developmental transitions that persist in adulthood. Having profiled each tissue separately, we performed an integrated analysis of the entire anterior segment, revealing that some cell types are unique to a single structure, whereas others are shared across tissues. The integrated cell atlas was then used to investigate cell type-specific expression patterns of more than 900 human ocular disease genes identified through either Mendelian inheritance patterns or genome-wide association studies.
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Affiliation(s)
- Tavé van Zyl
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Alexi M. McAdams
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Aboozar Monavarfeshani
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Boston Children’s Hospital, F.M. Kirby Neurobiology Center, Boston, MA 02115
| | - Gregory S. Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84132
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132
| | - Joshua R. Sanes
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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20
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Shekhar K, Whitney IE, Butrus S, Peng YR, Sanes JR. Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types. eLife 2022; 11:e73809. [PMID: 35191836 PMCID: PMC8956290 DOI: 10.7554/elife.73809] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
The genesis of broad neuronal classes from multipotential neural progenitor cells has been extensively studied, but less is known about the diversification of a single neuronal class into multiple types. We used single-cell RNA-seq to study how newly born (postmitotic) mouse retinal ganglion cell (RGC) precursors diversify into ~45 discrete types. Computational analysis provides evidence that RGC transcriptomic type identity is not specified at mitotic exit, but acquired by gradual, asynchronous restriction of postmitotic multipotential precursors. Some types are not identifiable until a week after they are generated. Immature RGCs may be specified to project ipsilaterally or contralaterally to the rest of the brain before their type identity emerges. Optimal transport inference identifies groups of RGC precursors with largely nonoverlapping fates, distinguished by selectively expressed transcription factors that could act as fate determinants. Our study provides a framework for investigating the molecular diversification of discrete types within a neuronal class.
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Affiliation(s)
- Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Center for Computational Biology; California Institute for Quantitative Biosciences, QB3, University of California, BerkeleyBerkeleyUnited States
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Broad Institute of Harvard and MITCambridgeUnited States
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Irene E Whitney
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Center for Computational Biology; California Institute for Quantitative Biosciences, QB3, University of California, BerkeleyBerkeleyUnited States
| | - Yi-Rong Peng
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Department of Ophthalmology, Stein Eye Institute, UCLA David Geffen School of MedicineLos AngelesUnited States
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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21
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Affiliation(s)
- Seth Blackshaw
- Departments of Neuroscience.,Neurology, and.,Ophthalmology.,Institute for Cell Engineering, and.,Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joshua R Sanes
- Center for Brain Science and.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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22
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Yamagata M, Sanes JR. CRISPR-mediated Labeling of Cells in Chick Embryos Based on Selectively Expressed Genes. Bio Protoc 2021; 11:e4105. [PMID: 34458399 PMCID: PMC8376491 DOI: 10.21769/bioprotoc.4105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
The abilities to mark and manipulate specific cell types are essential for an increasing number of functional, structural, molecular, and developmental analyses in model organisms. In a few species, this can be accomplished by germline transgenesis; in other species, other methods are needed to selectively label somatic cells based on the genes that they express. Here, we describe a method for CRISPR-based somatic integration of reporters or Cre recombinase into specific genes in the chick genome, followed by visualization of cells in the retina and midbrain. Loci are chosen based on an RNA-seq-based cell atlas. Reporters can be soluble to visualize the morphology of individual cells or appended to the encoded protein to assess subcellular localization. We call the method eCHIKIN for electroporation- and CRISPR-mediated Homology-instructed Knock-IN.
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Affiliation(s)
- Masahito Yamagata
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138, USA
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23
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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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24
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Lindborg JA, Tran NM, Chenette DM, DeLuca K, Foli Y, Kannan R, Sekine Y, Wang X, Wollan M, Kim IJ, Sanes JR, Strittmatter SM. Optic nerve regeneration screen identifies multiple genes restricting adult neural repair. Cell Rep 2021; 34:108777. [PMID: 33657370 PMCID: PMC8009559 DOI: 10.1016/j.celrep.2021.108777] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/21/2020] [Accepted: 01/29/2021] [Indexed: 12/22/2022] Open
Abstract
Adult mammalian central nervous system (CNS) trauma interrupts neural networks and, because axonal regeneration is minimal, neurological deficits persist. Repair via axonal growth is limited by extracellular inhibitors and cell-autonomous factors. Based on results from a screen in vitro, we evaluate nearly 400 genes through a large-scale in vivo regeneration screen. Suppression of 40 genes using viral-driven short hairpin RNAs (shRNAs) promotes retinal ganglion cell (RGC) axon regeneration after optic nerve crush (ONC), and most are validated by separate CRISPR-Cas9 editing experiments. Expression of these axon-regeneration-suppressing genes is not significantly altered by axotomy. Among regeneration-limiting genes, loss of the interleukin 22 (IL-22) cytokine allows an early, yet transient, inflammatory response in the retina after injury. Reduced IL-22 drives concurrent activation of signal transducer and activator of transcription 3 (Stat3) and dual leucine zipper kinase (DLK) pathways and upregulation of multiple neuron-intrinsic regeneration-associated genes (RAGs). Including IL-22, our screen identifies dozens of genes that limit CNS regeneration. Suppression of these genes in the context of axonal damage could support improved neural repair.
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Affiliation(s)
- Jane A Lindborg
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Nicholas M Tran
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Devon M Chenette
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Kristin DeLuca
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Yram Foli
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Ramakrishnan Kannan
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Yuichi Sekine
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Xingxing Wang
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Marius Wollan
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA
| | - In-Jung Kim
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Stephen M Strittmatter
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT 06536, USA.
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25
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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: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Armañanzas R, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano-Houzel S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Chameh HM, Mohapatra AN, Munguba H, Nedergaard M, Němec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann RH, Serrano-Saiz E, Staiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Wozny C, Wuttke TV, Liu Y, Yuan J, Zeng H, Lein E. A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci 2021; 23:1456-1468. [PMID: 32839617 PMCID: PMC7683348 DOI: 10.1038/s41593-020-0685-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.
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Affiliation(s)
| | | | | | | | - Detlev Arendt
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ruben Armañanzas
- George Mason University, Fairfax, VA, USA.,BrainScope Company Inc., Bethesda, MD, USA
| | | | | | - Vahid Bokharaie
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | | | | | - Marco Capogna
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - YoonJeung Chang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | - Richárd Fiáth
- Research Centre for Natural Sciences, Budapest, Hungary
| | | | | | - Xuefan Gao
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Parviz Ghaderi
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | | | - Kenta Hagihara
- Friedrich Miescher Institute for Biological Research, Basel, Switzerland
| | | | | | | | - Markus M Hilscher
- Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | | | | | - Josh Huang
- Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
| | - Rafiq Huda
- WM Keck Center for Collaborative Neuroscience, Department of Cell Biology and Neuroscience, Rutgers University - New Brunswick, Piscataway, NJ, USA
| | | | - Ole Kiehn
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | | | - Eric S Kuebler
- Robarts Research Institute, Western University, London, Ontario, Canada
| | | | | | | | | | - Jan H Lui
- Stanford University, Stanford, CA, USA
| | | | | | - Julio Martinez-Trujillo
- Schulich School of Medicine and Dentistry, Departments of Physiology, Pharmacology and Psychiatry, University of Western Ontario, London, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | | | | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA.,Department of Pathology, University of California, San Diego, CA, USA
| | | | - Jochen F Staiger
- Institute for Neuroanatomy, University of Göttingen, Göttingen, Germany
| | | | | | | | | | | | - Christian Wozny
- University of Strathclyde, Glasgow, UK.,MSH Medical School, Hamburg, Germany
| | - Thomas V Wuttke
- Departments of Neurosurgery and of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Yong Liu
- University of Copenhagen, Copenhagen, Denmark
| | - Juan Yuan
- Karolinska Institutet, Stockholm, Sweden
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
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27
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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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28
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Nakanishi K, Niida H, Tabata H, Ito T, Hori Y, Hattori M, Johmura Y, Yamada C, Ueda T, Takeuchi K, Yamada K, Nagata KI, Wakamatsu N, Kishi M, Pan YA, Ugawa S, Shimada S, Sanes JR, Higashi Y, Nakanishi M. Isozyme-Specific Role of SAD-A in Neuronal Migration During Development of Cerebral Cortex. Cereb Cortex 2020; 29:3738-3751. [PMID: 30307479 DOI: 10.1093/cercor/bhy253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 08/18/2018] [Indexed: 11/13/2022] Open
Abstract
SAD kinases regulate presynaptic vesicle clustering and neuronal polarization. A previous report demonstrated that Sada-/- and Sadb-/- double-mutant mice showed perinatal lethality with a severe defect in axon/dendrite differentiation, but their single mutants did not. These results indicated that they were functionally redundant. Surprisingly, we show that on a C57BL/6N background, SAD-A is essential for cortical development whereas SAD-B is dispensable. Sada-/- mice died within a few days after birth. Their cortical lamination pattern was disorganized and radial migration of cortical neurons was perturbed. Birth date analyses with BrdU and in utero electroporation using pCAG-EGFP vector showed a delayed migration of cortical neurons to the pial surface in Sada-/- mice. Time-lapse imaging of these mice confirmed slow migration velocity in the cortical plate. While the neurites of hippocampal neurons in Sada-/- mice could ultimately differentiate in culture to form axons and dendrites, the average length of their axons was shorter than that of the wild type. Thus, analysis on a different genetic background than that used initially revealed a nonredundant role for SAD-A in neuronal migration and differentiation.
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Affiliation(s)
- Keiko Nakanishi
- Department of Perinatology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan.,Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Japan
| | - Hiroyuki Niida
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan.,Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hidenori Tabata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Tsuyoshi Ito
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Yuki Hori
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Madoka Hattori
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Yoshikazu Johmura
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan.,Division of Cancer Cell Biology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Chisato Yamada
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Takashi Ueda
- Department of Anatomy and Neuroscience, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Kosei Takeuchi
- Department of Medical Biology, Aichi Medical University, Nagakute, Aichi, Japan
| | - Kenichiro Yamada
- Department of Genetics, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Nobuaki Wakamatsu
- Department of Genetics, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Masashi Kishi
- Neuroscience Laboratory, Research Institute, Nozaki Tokushukai Hospital, Daito, Osaka, Japan
| | - Y Albert Pan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA.,Developmental and Translational Neurobiology Center, Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | - Shinya Ugawa
- Department of Anatomy and Neuroscience, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Shoichi Shimada
- Department of Anatomy and Neuroscience, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan.,Department of Neuroscience and Cell Biology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yujiro Higashi
- Department of Perinatology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Makoto Nakanishi
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan.,Division of Cancer Cell Biology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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29
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Yan W, Laboulaye MA, Tran NM, Whitney IE, Benhar I, Sanes JR. Mouse Retinal Cell Atlas: Molecular Identification of over Sixty Amacrine Cell Types. J Neurosci 2020; 40:5177-5195. [PMID: 32457074 PMCID: PMC7329304 DOI: 10.1523/jneurosci.0471-20.2020] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 02/01/2023] Open
Abstract
Amacrine cells (ACs) are a diverse class of interneurons that modulate input from photoreceptors to retinal ganglion cells (RGCs), rendering each RGC type selectively sensitive to particular visual features, which are then relayed to the brain. While many AC types have been identified morphologically and physiologically, they have not been comprehensively classified or molecularly characterized. We used high-throughput single-cell RNA sequencing to profile >32,000 ACs from mice of both sexes and applied computational methods to identify 63 AC types. We identified molecular markers for each type and used them to characterize the morphology of multiple types. We show that they include nearly all previously known AC types as well as many that had not been described. Consistent with previous studies, most of the AC types expressed markers for the canonical inhibitory neurotransmitters GABA or glycine, but several expressed neither or both. In addition, many expressed one or more neuropeptides, and two expressed glutamatergic markers. We also explored transcriptomic relationships among AC types and identified transcription factors expressed by individual or multiple closely related types. Noteworthy among these were Meis2 and Tcf4, expressed by most GABAergic and most glycinergic types, respectively. Together, these results provide a foundation for developmental and functional studies of ACs, as well as means for genetically accessing them. Along with previous molecular, physiological, and morphologic analyses, they establish the existence of at least 130 neuronal types and nearly 140 cell types in the mouse retina.SIGNIFICANCE STATEMENT The mouse retina is a leading model for analyzing the development, structure, function, and pathology of neural circuits. A complete molecular atlas of retinal cell types provides an important foundation for these studies. We used high-throughput single-cell RNA sequencing to characterize the most heterogeneous class of retinal interneurons, amacrine cells, identifying 63 distinct types. The atlas includes types identified previously as well as many novel types. We provide evidence for the use of multiple neurotransmitters and neuropeptides, and identify transcription factors expressed by groups of closely related types. Combining these results with those obtained previously, we proposed that the mouse retina contains ∼130 neuronal types and is therefore comparable in complexity to other regions of the brain.
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Affiliation(s)
- Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Mallory A Laboulaye
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Nicholas M Tran
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Irene E Whitney
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Inbal Benhar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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30
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Abstract
Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral retina of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and non-neuronal cells. Nearly all types are shared between the two retinal regions, but there are notable differences in gene expression and proportions between foveal and peripheral cohorts of shared types. We then used the human retinal atlas to map expression of 636 genes implicated as causes of or risk factors for blinding diseases. Many are expressed in striking cell class-, type-, or region-specific patterns. Finally, we compared gene expression signatures of cell types between human and the cynomolgus macaque monkey, Macaca fascicularis. We show that over 90% of human types correspond transcriptomically to those previously identified in macaque, and that expression of disease-related genes is largely conserved between the two species. These results validate the use of the macaque for modeling blinding disease, and provide a foundation for investigating molecular mechanisms underlying visual processing.
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Affiliation(s)
- Wenjun Yan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA
| | - Yi-Rong Peng
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA
- Department of Ophthalmology, Stein Eye Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Tavé van Zyl
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA, 02114, USA
| | - Aviv Regev
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140; and Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Karthik Shekhar
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140; and Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Chemical and Biomolecular Engineering and Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA.
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31
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van Zyl T, Yan W, McAdams A, Peng YR, Shekhar K, Regev A, Juric D, Sanes JR. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis. Proc Natl Acad Sci U S A 2020; 117:10339-10349. [PMID: 32341164 PMCID: PMC7229661 DOI: 10.1073/pnas.2001250117] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Increased intraocular pressure (IOP) represents a major risk factor for glaucoma, a prevalent eye disease characterized by death of retinal ganglion cells; lowering IOP is the only proven treatment strategy to delay disease progression. The main determinant of IOP is the equilibrium between production and drainage of aqueous humor, with compromised drainage generally viewed as the primary contributor to dangerous IOP elevations. Drainage occurs through two pathways in the anterior segment of the eye called conventional and uveoscleral. To gain insights into the cell types that comprise these pathways, we used high-throughput single-cell RNA sequencing (scRNAseq). From ∼24,000 single-cell transcriptomes, we identified 19 cell types with molecular markers for each and used histological methods to localize each type. We then performed similar analyses on four organisms used for experimental studies of IOP dynamics and glaucoma: cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa), and mouse (Mus musculus). Many human cell types had counterparts in these models, but differences in cell types and gene expression were evident. Finally, we identified the cell types that express genes implicated in glaucoma in all five species. Together, our results provide foundations for investigating the pathogenesis of glaucoma and for using model systems to assess mechanisms and potential interventions.
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Affiliation(s)
- Tavé van Zyl
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114;
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Alexi McAdams
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Yi-Rong Peng
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Karthik Shekhar
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Aviv Regev
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Dejan Juric
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital Cancer Center, Boston, MA 02114
| | - Joshua R Sanes
- Center for Brain Science, Harvard University, Cambridge, MA 02138;
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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32
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Luo L, Ambrozkiewicz MC, Benseler F, Chen C, Dumontier E, Falkner S, Furlanis E, Gomez AM, Hoshina N, Huang WH, Hutchison MA, Itoh-Maruoka Y, Lavery LA, Li W, Maruo T, Motohashi J, Pai ELL, Pelkey KA, Pereira A, Philips T, Sinclair JL, Stogsdill JA, Traunmüller L, Wang J, Wortel J, You W, Abumaria N, Beier KT, Brose N, Burgess HA, Cepko CL, Cloutier JF, Eroglu C, Goebbels S, Kaeser PS, Kay JN, Lu W, Luo L, Mandai K, McBain CJ, Nave KA, Prado MA, Prado VF, Rothstein J, Rubenstein JL, Saher G, Sakimura K, Sanes JR, Scheiffele P, Takai Y, Umemori H, Verhage M, Yuzaki M, Zoghbi HY, Kawabe H, Craig AM. Optimizing Nervous System-Specific Gene Targeting with Cre Driver Lines: Prevalence of Germline Recombination and Influencing Factors. Neuron 2020; 106:37-65.e5. [PMID: 32027825 PMCID: PMC7377387 DOI: 10.1016/j.neuron.2020.01.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/12/2019] [Accepted: 01/10/2020] [Indexed: 12/17/2022]
Abstract
The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and reporter expression in the mouse nervous system. However, we report varying probabilities of unexpected germline recombination in distinct Cre driver lines designed for nervous system-specific recombination. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expression in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional control elements affect germline recombination rates. Specific target loci demonstrated differential recombination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and provide guidelines to inform future research for the neuroscience and broader molecular genetics communities.
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Affiliation(s)
- Lin Luo
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Mateusz C. Ambrozkiewicz
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany,Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Fritz Benseler
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Cui Chen
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Emilie Dumontier
- Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | | | - Naosuke Hoshina
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei-Hsiang Huang
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
| | - Mary Anne Hutchison
- Synapse and Neural Circuit Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yu Itoh-Maruoka
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Laura A. Lavery
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77003, USA,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wei Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Tomohiko Maruo
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan,Department of Biochemistry, Tokushima University Graduate School of Medical Sciences, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan,Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Junko Motohashi
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kenneth A. Pelkey
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ariane Pereira
- Department of Neurobiology and Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas Philips
- Department of Neurology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jennifer L. Sinclair
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Jeff A. Stogsdill
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02139, USA
| | | | - Jiexin Wang
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joke Wortel
- Department of Functional Genomics and Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and University Medical Center Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Wenjia You
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA,Departments of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nashat Abumaria
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China,Department of Laboratory Animal Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Kevin T. Beier
- Department of Physiology and Biophysics, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Harold A. Burgess
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Constance L. Cepko
- Departments of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jean-François Cloutier
- Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Cagla Eroglu
- Department of Cell Biology, Department of Neurobiology, and Duke Institute for Brain Sciences, Regeneration Next Initiative, Duke University Medical Center, Durham, NC 27710, USA
| | - Sandra Goebbels
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Pascal S. Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy N. Kay
- Department of Neurobiology and Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wei Lu
- Synapse and Neural Circuit Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Kenji Mandai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan,Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Chris J. McBain
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Marco A.M. Prado
- Robarts Research Institute, Department of Anatomy and Cell Biology, and Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada,Brain and Mind Institute, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Vania F. Prado
- Robarts Research Institute, Department of Anatomy and Cell Biology, and Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada,Brain and Mind Institute, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Jeffrey Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John L.R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hisashi Umemori
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthijs Verhage
- Department of Functional Genomics and Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and University Medical Center Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Michisuke Yuzaki
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Huda Yahya Zoghbi
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77003, USA,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hiroshi Kawabe
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany; Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Gerontology, Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-minamimachi Chuo-ku, Kobe, Hyogo 650-0047, Japan.
| | - Ann Marie Craig
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada.
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Sanes JR, Zipursky SL. Synaptic Specificity, Recognition Molecules, and Assembly of Neural Circuits. Cell 2020; 181:536-556. [DOI: 10.1016/j.cell.2020.04.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/23/2020] [Accepted: 04/06/2020] [Indexed: 01/02/2023]
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Peng YR, James RE, Yan W, Kay JN, Kolodkin AL, Sanes JR. Binary Fate Choice between Closely Related Interneuronal Types Is Determined by a Fezf1-Dependent Postmitotic Transcriptional Switch. Neuron 2019; 105:464-474.e6. [PMID: 31812516 DOI: 10.1016/j.neuron.2019.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 02/08/2023]
Abstract
Many neuronal types occur as pairs that are similar in most respects but differ in a key feature. In some pairs of retinal neurons, called paramorphic, one member responds to increases and the other to decreases in luminance (ON and OFF responses). Here, we focused on one such pair, starburst amacrine cells (SACs), to explore how closely related neuronal types diversify. We find that ON and OFF SACs are transcriptionally distinct prior to their segregation, dendritic outgrowth, and synapse formation. The transcriptional repressor Fezf1 is selectively expressed by postmitotic ON SACs and promotes the ON fate and gene expression program while repressing the OFF fate and program. The atypical Rho GTPase Rnd3 is selectively expressed by OFF SACs and regulates their migration but is repressed by Fezf1 in ON SACs, enabling differential positioning of the two types. These results define a transcriptional program that controls diversification of a paramorphic pair.
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Affiliation(s)
- Yi-Rong Peng
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rebecca E James
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jeremy N Kay
- Departments of Ophthalmology and Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Alex L Kolodkin
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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35
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Tran NM, Shekhar K, Whitney IE, Jacobi A, Benhar I, Hong G, Yan W, Adiconis X, Arnold ME, Lee JM, Levin JZ, Lin D, Wang C, Lieber CM, Regev A, He Z, Sanes JR. Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes. Neuron 2019; 104:1039-1055.e12. [PMID: 31784286 DOI: 10.1016/j.neuron.2019.11.006] [Citation(s) in RCA: 308] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023]
Abstract
Neuronal types in the central nervous system differ dramatically in their resilience to injury or other insults. Here we studied the selective resilience of mouse retinal ganglion cells (RGCs) following optic nerve crush (ONC), which severs their axons and leads to death of ∼80% of RGCs within 2 weeks. To identify expression programs associated with differential resilience, we first used single-cell RNA-seq (scRNA-seq) to generate a comprehensive molecular atlas of 46 RGC types in adult retina. We then tracked their survival after ONC; characterized transcriptomic, physiological, and morphological changes that preceded degeneration; and identified genes selectively expressed by each type. Finally, using loss- and gain-of-function assays in vivo, we showed that manipulating some of these genes improved neuronal survival and axon regeneration following ONC. This study provides a systematic framework for parsing type-specific responses to injury and demonstrates that differential gene expression can be used to reveal molecular targets for intervention.
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Affiliation(s)
- Nicholas M Tran
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Karthik Shekhar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Irene E Whitney
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Anne Jacobi
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Inbal Benhar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Guosong Hong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Material Science and Engineering and Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xian Adiconis
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - McKinzie E Arnold
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jung Min Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joshua Z Levin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Dingchang Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles M Lieber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA and Department of Biology and Koch Institute, MIT, Cambridge, MA 02139, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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36
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Abstract
Many authors start with the figures when writing a scientific paper, but it is easier to tell a good story if you start with the Introduction and the Results, and leave the figures to later.
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Affiliation(s)
- Joshua R Sanes
- Center for Brain Science, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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37
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Hong YK, Burr EF, Sanes JR, Chen C. Heterogeneity of retinogeniculate axon arbors. Eur J Neurosci 2019; 49:948-956. [PMID: 29883007 PMCID: PMC6286704 DOI: 10.1111/ejn.13986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 01/25/2023]
Abstract
The retinogeniculate synapse transmits information from retinal ganglion cells (RGC) in the eye to thalamocortical relay neurons in the visual thalamus, the dorsal lateral geniculate nucleus (dLGN). Studies in mice have identified genetic markers for distinct classes of RGCs encoding different features of the visual space, facilitating the dissection of RGC subtype-specific physiology and anatomy. In this study, we examine the morphological properties of axon arbors of the BD-RGC class of ON-OFF direction selective cells that, by definition, exhibit a stereotypic dendritic arbor and termination pattern in the retina. We find that axon arbors from the same class of RGCs exhibit variations in their structure based on their target region of the dLGN. Our findings suggest that target regions may influence the morphologic and synaptic properties of their afferent inputs.
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Affiliation(s)
- Y. Kate Hong
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, U.S.A
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, U.S.A
| | - Eliza F. Burr
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, U.S.A
| | - Joshua R. Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, U.S.A
| | - Chinfei Chen
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, U.S.A
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39
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Yamagata M, Sanes JR. Expression and Roles of the Immunoglobulin Superfamily Recognition Molecule Sidekick1 in Mouse Retina. Front Mol Neurosci 2019; 11:485. [PMID: 30687002 PMCID: PMC6333872 DOI: 10.3389/fnmol.2018.00485] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
Processes of >100 types of interneurons (bipolar and amacrine cells) and projection neurons (retinal ganglion cells, RGCs) form specific and stereotyped patterns of connections in the inner plexiform layer (IPL) of the mouse retina. Four closely related homophilic immunoglobulin superfamily recognition molecules (Sidekick [Sdk] 1, Sdk 2, Dscam, and DscamL1) have been shown to play roles in patterning neuronal arbors and connections in chick retina, and all but Sdk1 have been shown to play related roles in mice. Here, we compare patterns of Sdk1 and Sdk2 expression in mouse retina and use genetic methods to assess roles of Sdk1. In adult retina, 3 neuronal types express sdk1 but not sdk2 at detectable levels, 5 express sdk2 but not sdk1 and 3 express both. Patterns of gene expression and protein localization at or near synapses are established during the first postnatal week. Dendrites of amacrine cells and RGCs that express sdk1 but not sdk2 arborize in the same narrow stratum in the center of the IPL. In the absence of Sdk1, this laminar restriction is degraded. Overexpression of sdk1 in developing cells that normally express sdk2 reorients their dendrites to resemble those of endogenously Sdk1-positive cells, indicating that Sdk1 plays an instructive role in patterning the IPL. Sdk1 fails to affect arbors when introduced after they are mature, suggesting that it is required to form but not maintain laminar restrictions. The effect of ectopically expressed sdk1 requires the presence of endogenous Sdk1, suggesting that the effect requires homophilic interactions among Sdk1-positive neurites. Together with previous results on Sdk2, Dscam, DscamL1, as well as the related Contactins, our results support the idea that an elaborate immunoglobulin superfamily code plays a prominent role in establishing neural circuits in the retina by means of tightly regulated cell type-specific expression and homophilically restricted intercellular interactions.
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Affiliation(s)
- Masahito Yamagata
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, United States
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, United States
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40
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Laboulaye MA, Duan X, Qiao M, Whitney IE, Sanes JR. Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes and Neighboring Endogenous Genes. Front Mol Neurosci 2018; 11:385. [PMID: 30405348 PMCID: PMC6206269 DOI: 10.3389/fnmol.2018.00385] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/25/2018] [Indexed: 11/13/2022] Open
Abstract
Transgenic mouse lines are routinely employed to label and manipulate distinct cell types. The transgene generally comprises cell-type specific regulatory elements linked to a cDNA encoding a reporter or other protein. However, off-target expression seemingly unrelated to the regulatory elements in the transgene is often observed, it is sometimes suspected to reflect influences related to the site of transgene integration in the genome. To test this hypothesis, we used a proximity ligation-based method, Targeted Locus Amplification (TLA), to map the insertion sites of three well-characterized transgenes that appeared to exhibit insertion site-dependent expression in retina. The nearest endogenous genes to transgenes HB9-GFP, Mito-P, and TYW3 are Cdh6, Fat4 and Khdrbs2, respectively. For two lines, we demonstrate that expression reflects that of the closest endogenous gene (Fat4 and Cdh6), even though the distance between transgene and endogenous gene is 550 and 680 kb, respectively. In all three lines, the transgenes decrease expression of the neighboring endogenous genes. In each case, the affected endogenous gene was expressed in at least some of the cell types that the transgenic line has been used to mark and study. These results provide insights into the effects of transgenes and endogenous genes on each other's expression, demonstrate that mapping insertion site is valuable for interpreting results obtained with transgenic lines, and indicate that TLA is a reliable method for integration site discovery.
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Affiliation(s)
| | | | | | | | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
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41
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Duan X, Krishnaswamy A, Laboulaye MA, Liu J, Peng YR, Yamagata M, Toma K, Sanes JR. Cadherin Combinations Recruit Dendrites of Distinct Retinal Neurons to a Shared Interneuronal Scaffold. Neuron 2018; 99:1145-1154.e6. [PMID: 30197236 DOI: 10.1016/j.neuron.2018.08.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 12/13/2022]
Abstract
Distinct neuronal types connect in complex ways to generate functional neural circuits. The molecular diversity required to specify this connectivity could be supplied by multigene families of synaptic recognition molecules, but most studies to date have assessed just one or a few members at a time. Here, we analyze roles of cadherins (Cdhs) in formation of retinal circuits comprising eight neuronal types that inform the brain about motion in four directions. We show that at least 15 classical Cdhs are expressed by neurons in these circuits and at least 6 (Cdh6-10 and 18) act individually or in combinations to promote specific connectivity among the cells. They act in part by directing the processes of output neurons and excitatory interneurons to a cellular scaffold formed by inhibitory interneurons. Because Cdhs are expressed combinatorially by many central neurons, similar interactions could be involved in patterning circuits throughout the brain.
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Affiliation(s)
- Xin Duan
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Departments of Ophthalmology and Physiology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arjun Krishnaswamy
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Mallory A Laboulaye
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Jinyue Liu
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Yi-Rong Peng
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Masahito Yamagata
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Kenichi Toma
- Departments of Ophthalmology and Physiology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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42
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Hong G, Fu TM, Qiao M, Viveros RD, Yang X, Zhou T, Lee JM, Park HG, Sanes JR, Lieber CM. A method for single-neuron chronic recording from the retina in awake mice. Science 2018; 360:1447-1451. [PMID: 29954976 DOI: 10.1126/science.aas9160] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/26/2018] [Indexed: 12/16/2022]
Abstract
The retina, which processes visual information and sends it to the brain, is an excellent model for studying neural circuitry. It has been probed extensively ex vivo but has been refractory to chronic in vivo electrophysiology. We report a nonsurgical method to achieve chronically stable in vivo recordings from single retinal ganglion cells (RGCs) in awake mice. We developed a noncoaxial intravitreal injection scheme in which injected mesh electronics unrolls inside the eye and conformally coats the highly curved retina without compromising normal eye functions. The method allows 16-channel recordings from multiple types of RGCs with stable responses to visual stimuli for at least 2 weeks, and reveals circadian rhythms in RGC responses over multiple day/night cycles.
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Affiliation(s)
- Guosong Hong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Tian-Ming Fu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Mu Qiao
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Robert D Viveros
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Xiao Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Tao Zhou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jung Min Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Korea University, Seoul, Republic of Korea
| | - Hong-Gyu Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Korea University, Seoul, Republic of Korea
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Charles M Lieber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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43
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Cohen O, Vald L, Yamagata M, Sanes JR, Klar A. Roles of DSCAM in axonal decussation and fasciculation of chick spinal interneurons. Int J Dev Biol 2018. [PMID: 28621421 DOI: 10.1387/ijdb.160235ak] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The ventral midline of the embryonic neural tube, the floor plate, has a profound role in guiding axons during embryonic development. Floor plate-derived guidance cues attract or repel axons, depending on the neuronal subtype and developmental stage. Netrin-1 and its receptor, Deleted in Colon Carcinoma (DCC), are the key constituents of commissurral axons guidance cues toward the floor plate. Recent studies have implicated Down Syndrome Cell Adhesion Molecule (Dscam) as an additional Netrin-1 receptor. In this study, we examined the role of Dscam in guiding defined spinal dorsal interneuron populations. In vivo knockdown and ectopic expression of Dscam were performed in the dorsal dI1, dI2 and dI3 interneurons of chick embryos, by separately increasing or decreasing Dscam expression in each of these three specific interneuronal populations. Neuron-specific gain and loss of function of Dscam had no effect on the axonal trajectories of dI1-3 neurons. The commissural neurons, dI1c and dI2, crossed the midline, and the ipsilaterally projecting neurons, dI1i and dI3, projected ipsilaterally. However, the fasciculation of dI1 axons was diminished when Dscam expression was attenuated. Dscam is not required for either attraction to or repulsion from the floor plate. In contrast, Dscam is required for the fasciculation of axons, probably via homophilic interaction.
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Affiliation(s)
- Oksana Cohen
- Dept. of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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44
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Basu R, Duan X, Taylor MR, Martin EA, Muralidhar S, Wang Y, Gangi-Wellman L, Das SC, Yamagata M, West PJ, Sanes JR, Williams ME. Heterophilic Type II Cadherins Are Required for High-Magnitude Synaptic Potentiation in the Hippocampus. Neuron 2018; 98:658-668. [PMID: 29723502 DOI: 10.1016/j.neuron.2018.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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45
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Yamagata M, Duan X, Sanes JR. Cadherins Interact With Synaptic Organizers to Promote Synaptic Differentiation. Front Mol Neurosci 2018; 11:142. [PMID: 29760652 PMCID: PMC5936767 DOI: 10.3389/fnmol.2018.00142] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/09/2018] [Indexed: 01/17/2023] Open
Abstract
Classical cadherins, a set of ~20 related recognition and signaling molecules, have been implicated in many aspects of neural development, including the formation and remodeling of synapses. Mechanisms underlying some of these steps have been studied by expressing N-cadherin (cdh2), a Type 1 cadherin, in heterologous cells, but analysis is complicated because widely used lines express cdh2 endogenously. We used CRISPR-mediated gene editing to generate a Human embryonic kidney (HEK)293 variant lacking Cdh2, then compared the behavior of rodent cortical and hippocampal neurons co-cultured with parental, cdh2 mutant and cdh2-rescued 293 lines. The comparison demonstrated that Cdh2 promotes neurite branching and that it is required for three synaptic organizers, neurologin1 (NLGL1), leucine-rich repeat transmembrane protein 2 (LRRtm2), and Cell Adhesion Molecule 1 (Cadm1/SynCAM) to stimulate presynaptic differentiation, assayed by clustering of synaptic vesicles at sites of neurite-293 cell contact. Similarly, Cdh2 is required for a presynaptic organizing molecule, Neurexin1β, to promote postsynaptic differentiation in dendrites. We also show that another Type I cadherin, Cdh4, and a Type II cadherin, Cdh6, can substitute for Cdh2 in these assays. Finally, we provide evidence that the effects of cadherins require homophilic interactions between neurites and the heterologous cells. Together, these results indicate that classical cadherins act together with synaptic organizers to promote synaptic differentiation, perhaps in part by strengthening the intracellular adhesion required for the organizers to act efficiently. We propose that cadherins promote high affinity contacts between appropriate partners, which then enable synaptic differentiation.
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Affiliation(s)
- Masahito Yamagata
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
| | - Xin Duan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
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46
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Liu J, Reggiani JDS, Laboulaye MA, Pandey S, Chen B, Rubenstein JLR, Krishnaswamy A, Sanes JR. Tbr1 instructs laminar patterning of retinal ganglion cell dendrites. Nat Neurosci 2018; 21:659-670. [PMID: 29632360 PMCID: PMC5920715 DOI: 10.1038/s41593-018-0127-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/20/2018] [Indexed: 12/20/2022]
Abstract
Visual information is delivered to the brain by >40 types of retinal ganglion cells (RGCs). Diversity in this representation arises within the inner plexiform layer (IPL), where dendrites of each RGC type are restricted to specific sublaminae, limiting the interneuronal types that can innervate them. How such dendritic restriction arises is unclear. We show that the transcription factor Tbr1 is expressed by four mouse RGC types with dendrites in the outer IPL and is required for their laminar specification. Loss of Tbr1 results in elaboration of dendrites within the inner IPL, while misexpression in other cells retargets their neurites to the outer IPL. Two transmembrane molecules, Sorcs3 and Cdh8, act as effectors of the Tbr1-controlled lamination program. However, they are expressed in just one Tbr1+ RGC type, supporting a model in which a single transcription factor implements similar laminar choices in distinct cell types by recruiting partially non-overlapping effectors.
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Affiliation(s)
- Jinyue Liu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA.,Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Jasmine D S Reggiani
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Mallory A Laboulaye
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Shristi Pandey
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Bin Chen
- Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - John L R Rubenstein
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | - Arjun Krishnaswamy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA.,Department of Physiology, McGill University, Montreal, QC, Canada
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. .,Center for Brain Science, Harvard University, Cambridge, MA, USA.
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47
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Sarin S, Zuniga-Sanchez E, Kurmangaliyev YZ, Cousins H, Patel M, Hernandez J, Zhang KX, Samuel MA, Morey M, Sanes JR, Zipursky SL. Role for Wnt Signaling in Retinal Neuropil Development: Analysis via RNA-Seq and In Vivo Somatic CRISPR Mutagenesis. Neuron 2018; 98:109-126.e8. [PMID: 29576390 DOI: 10.1016/j.neuron.2018.03.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/16/2018] [Accepted: 03/02/2018] [Indexed: 12/22/2022]
Abstract
Screens for genes that orchestrate neural circuit formation in mammals have been hindered by practical constraints of germline mutagenesis. To overcome these limitations, we combined RNA-seq with somatic CRISPR mutagenesis to study synapse development in the mouse retina. Here synapses occur between cellular layers, forming two multilayered neuropils. The outer neuropil, the outer plexiform layer (OPL), contains synapses made by rod and cone photoreceptor axons on rod and cone bipolar dendrites, respectively. We used RNA-seq to identify selectively expressed genes encoding cell surface and secreted proteins and CRISPR-Cas9 electroporation with cell-specific promoters to assess their roles in OPL development. Among the genes identified in this way are Wnt5a and Wnt5b. They are produced by rod bipolars and activate a non-canonical signaling pathway in rods to regulate early OPL patterning. The approach we use here can be applied to other parts of the brain.
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Affiliation(s)
- Sumeet Sarin
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA
| | - Elizabeth Zuniga-Sanchez
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yerbol Z Kurmangaliyev
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Henry Cousins
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA
| | - Mili Patel
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA
| | - Jeanette Hernandez
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kelvin X Zhang
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Melanie A Samuel
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA
| | - Marta Morey
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA.
| | - S Lawrence Zipursky
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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48
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Martersteck EM, Hirokawa KE, Evarts M, Bernard A, Duan X, Li Y, Ng L, Oh SW, Ouellette B, Royall JJ, Stoecklin M, Wang Q, Zeng H, Sanes JR, Harris JA. Diverse Central Projection Patterns of Retinal Ganglion Cells. Cell Rep 2017; 18:2058-2072. [PMID: 28228269 DOI: 10.1016/j.celrep.2017.01.075] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/09/2016] [Accepted: 01/27/2017] [Indexed: 11/27/2022] Open
Abstract
Understanding how >30 types of retinal ganglion cells (RGCs) in the mouse retina each contribute to visual processing in the brain will require more tools that label and manipulate specific RGCs. We screened and analyzed retinal expression of Cre recombinase using 88 transgenic driver lines. In many lines, Cre was expressed in multiple RGC types and retinal cell classes, but several exhibited more selective expression. We comprehensively mapped central projections from RGCs labeled in 26 Cre lines using viral tracers, high-throughput imaging, and a data processing pipeline. We identified over 50 retinorecipient regions and present a quantitative retina-to-brain connectivity map, enabling comparisons of target-specificity across lines. Projections to two major central targets were notably correlated: RGCs projecting to the outer shell or core regions of the lateral geniculate projected to superficial or deep layers within the superior colliculus, respectively. Retinal images and projection data are available online at http://connectivity.brain-map.org.
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Affiliation(s)
- Emily M Martersteck
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Mariah Evarts
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xin Duan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yang Li
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Seung W Oh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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49
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Lissek T, Adams M, Adelman J, Ahissar E, Akaaboune M, Akil H, al’Absi M, Arain F, Arango-Lasprilla JC, Atasoy D, Avila J, Badawi A, Bading H, Baig AM, Baleriola J, Belmonte C, Bertocchi I, Betz H, Blakemore C, Blanke O, Boehm-Sturm P, Bonhoeffer T, Bonifazi P, Brose N, Campolongo P, Celikel T, Chang CC, Chang TY, Citri A, Cline HT, Cortes JM, Cullen K, Dean K, Delgado-Garcia JM, Desroches M, Disterhoft JF, Dowling JE, Draguhn A, El-Khamisy SF, El Manira A, Enam SA, Encinas JM, Erramuzpe A, Esteban JA, Fariñas I, Fischer E, Fukunaga I, Gabilondo I, Ganten D, Gidon A, Gomez-Esteban JC, Greengard P, Grinevich V, Gruart A, Guillemin R, Hariri AR, Hassan B, Häusser M, Hayashi Y, Hussain NK, Jabbar AA, Jaber M, Jahn R, Janahi EM, Kabbaj M, Kettenmann H, Kindt M, Knafo S, Köhr G, Komai S, Krugers H, Kuhn B, Ghazal NL, Larkum ME, London M, Lutz B, Matute C, Martinez-Millan L, Maroun M, McGaugh J, Moustafa AA, Nasim A, Nave KA, Neher E, Nikolich K, Outeiro T, Palmer LM, Penagarikano O, Perez-Otano I, Pfaff DW, Poucet B, Rahman AU, Ramos-Cabrer P, Rashidy-Pour A, Roberts RJ, Rodrigues S, Sanes JR, Schaefer AT, Segal M, Segev I, Shafqat S, Siddiqui NA, Soreq H, Soriano-García E, Spanagel R, Sprengel R, Stuart G, Südhof TC, Tønnesen J, Treviño M, Uthman BM, Venter JC, Verkhratsky A, Weiss C, Wiesel TN, Yaksi E, Yizhar O, Young LJ, Young P, Zawia NH, Zugaza JL, Hasan MT. Building Bridges through Science. Neuron 2017; 96:730-735. [DOI: 10.1016/j.neuron.2017.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
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50
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Basu R, Duan X, Taylor MR, Martin EA, Muralidhar S, Wang Y, Gangi-Wellman L, Das SC, Yamagata M, West PJ, Sanes JR, Williams ME. Heterophilic Type II Cadherins Are Required for High-Magnitude Synaptic Potentiation in the Hippocampus. Neuron 2017; 96:160-176.e8. [PMID: 28957665 DOI: 10.1016/j.neuron.2017.09.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 08/03/2017] [Accepted: 09/11/2017] [Indexed: 11/26/2022]
Abstract
Hippocampal CA3 neurons form synapses with CA1 neurons in two layers, stratum oriens (SO) and stratum radiatum (SR). Each layer develops unique synaptic properties but molecular mechanisms that mediate these differences are unknown. Here, we show that SO synapses normally have significantly more mushroom spines and higher-magnitude long-term potentiation (LTP) than SR synapses. Further, we discovered that these differences require the Type II classic cadherins, cadherins-6, -9, and -10. Though cadherins typically function via trans-cellular homophilic interactions, our results suggest presynaptic cadherin-9 binds postsynaptic cadherins-6 and -10 to regulate mushroom spine density and high-magnitude LTP in the SO layer. Loss of these cadherins has no effect on the lower-magnitude LTP typically observed in the SR layer, demonstrating that cadherins-6, -9, and -10 are gatekeepers for high-magnitude LTP. Thus, Type II cadherins may uniquely contribute to the specificity and strength of synaptic changes associated with learning and memory.
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Affiliation(s)
- Raunak Basu
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Xin Duan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Department of Ophthalmology, UCSF School of Medicine, San Francisco, CA 94117, USA
| | - Matthew R Taylor
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - E Anne Martin
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Shruti Muralidhar
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Yueqi Wang
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Luke Gangi-Wellman
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sujan C Das
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Masahito Yamagata
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peter J West
- Department of Pharmacology and Toxicology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Megan E Williams
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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