1
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Cullen PF, Gammerdinger WJ, Ho Sui SJ, Mazumder AG, Sun D. Transcriptional profiling of retinal astrocytes identifies a specific marker and points to functional specialization. Glia 2024. [PMID: 38785355 DOI: 10.1002/glia.24571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/19/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Astrocyte heterogeneity is an increasingly prominent research topic, and studies in the brain have demonstrated substantial variation in astrocyte form and function, both between and within regions. In contrast, retinal astrocytes are not well understood and remain incompletely characterized. Along with optic nerve astrocytes, they are responsible for supporting retinal ganglion cell axons and an improved understanding of their role is required. We have used a combination of microdissection and Ribotag immunoprecipitation to isolate ribosome-associated mRNA from retinal astrocytes and investigate their transcriptome, which we also compared to astrocyte populations in the optic nerve. Astrocytes from these regions are transcriptionally distinct, and we identified retina-specific astrocyte genes and pathways. Moreover, although they share much of the "classical" gene expression patterns of astrocytes, we uncovered unexpected variation, including in genes related to core astrocyte functions. We additionally identified the transcription factor Pax8 as a highly specific marker of retinal astrocytes and demonstrated that these astrocytes populate not only the retinal surface, but also the prelaminar region at the optic nerve head. These findings are likely to contribute to a revised understanding of the role of astrocytes in the retina.
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Affiliation(s)
- Paul F Cullen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - William J Gammerdinger
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Shannan J Ho Sui
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Arpan Guha Mazumder
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Sun
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
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2
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Liu D, Webber HC, Bian F, Xu Y, Prakash M, Feng X, Yang M, Yang H, You IJ, Li L, Liu L, Liu P, Huang H, Chang CY, Liu L, Shah SH, Torre AL, Welsbie DS, Sun Y, Duan X, Goldberg JL, Braun M, Lansky Z, Hu Y. Optineurin-facilitated axonal mitochondria delivery promotes neuroprotection and axon regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587832. [PMID: 38617277 PMCID: PMC11014509 DOI: 10.1101/2024.04.02.587832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Optineurin (OPTN) mutations are linked to amyotrophic lateral sclerosis (ALS) and normal tension glaucoma (NTG), but a relevant animal model is lacking, and the molecular mechanisms underlying neurodegeneration are unknown. We found that OPTN C-terminus truncation (OPTN∆C) causes late-onset neurodegeneration of retinal ganglion cells (RGCs), optic nerve (ON), and spinal cord motor neurons, preceded by a striking decrease of axonal mitochondria. Surprisingly, we discover that OPTN directly interacts with both microtubules and the mitochondrial transport complex TRAK1/KIF5B, stabilizing them for proper anterograde axonal mitochondrial transport, in a C-terminus dependent manner. Encouragingly, overexpressing OPTN/TRAK1/KIF5B reverses not only OPTN truncation-induced, but also ocular hypertension-induced neurodegeneration, and promotes striking ON regeneration. Therefore, in addition to generating new animal models for NTG and ALS, our results establish OPTN as a novel facilitator of the microtubule-dependent mitochondrial transport necessary for adequate axonal mitochondria delivery, and its loss as the likely molecular mechanism of neurodegeneration.
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Affiliation(s)
- Dong Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Hannah C. Webber
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Fuyun Bian
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yangfan Xu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Manjari Prakash
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Xue Feng
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Ming Yang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Hang Yang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - In-Jee You
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Liang Li
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Liping Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Pingting Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Haoliang Huang
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Chien-Yi Chang
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Liang Liu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sahil H Shah
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA; USA
| | - Derek S. Welsbie
- Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA; USA
| | - Yang Sun
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Xin Duan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA; USA
| | - Jeffrey Louis Goldberg
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Marcus Braun
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Zdenek Lansky
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czechia
| | - Yang Hu
- Spencer Center for Vision Research, Department of Ophthalmology, Byers Eye Institute at Stanford University School of Medicine, Palo Alto, CA 94304, USA
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3
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Salkar A, Wall RV, Basavarajappa D, Chitranshi N, Parilla GE, Mirzaei M, Yan P, Graham S, You Y. Glial Cell Activation and Immune Responses in Glaucoma: A Systematic Review of Human Postmortem Studies of the Retina and Optic Nerve. Aging Dis 2024:AD.2024.0103. [PMID: 38502591 DOI: 10.14336/ad.2024.0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/03/2024] [Indexed: 03/21/2024] Open
Abstract
Although researched extensively the understanding regarding mechanisms underlying glaucoma pathogenesis remains limited. Further, the exact mechanism behind neuronal death remains elusive. The role of neuroinflammation in retinal ganglion cell (RGC) death has been prominently theorised. This review provides a comprehensive summary of neuroinflammatory responses in glaucoma. A systematic search of Medline and Embase for articles published up to 8th March 2023 yielded 32 studies using post-mortem tissues from glaucoma patients. The raw data were extracted from tables and text to calculate the standardized mean differences (SMDs). These studies utilized post-mortem tissues from glaucoma patients, totalling 490 samples, compared with 380 control samples. Among the included studies, 27 reported glial cell activation based on changes to cellular morphology and molecular staining. Molecular changes were predominantly attributed to astrocytes (62.5%) and microglia (15.6%), with some involvement of Muller cells. These glial cell changes included amoeboid microglial cells with increased CD45 or HLA-DR intensity and hypertrophied astrocytes with increased glial fibrillary acidic protein labelling. Further, changes to extracellular matrix proteins like collagen, galectin, and tenascin-C suggested glial cells' influence on structural changes in the optic nerve head. The activation of DAMPs-driven immune response and the classical complement cascade was reported and found to be associated with activated glial cells in glaucomatous tissue. Increased pro-inflammatory markers such as interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) were also linked to glial cells. Glial cell activation was also associated with mitochondrial, vascular, metabolic and antioxidant component disruptions. Association of the activated glial cells with pro-inflammatory responses, dysregulation of homeostatic components and antigen presentation indicates that glial cell responses influence glaucoma progression. However, the exact mechanism triggering these responses and underlying interactions remains unexplored. This necessitates further research using human samples for an increased understanding of the precise role of neuroinflammation in glaucoma progression.
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Affiliation(s)
- Akanksha Salkar
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
| | - Roshana Vander Wall
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
| | - Devaraj Basavarajappa
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
| | - Nitin Chitranshi
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
| | - Gabriella E Parilla
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
| | - Peng Yan
- Department of Ophthalmology & Vision Sciences, University of Toronto, Kensington Eye Institute /UHN, Canada
| | - Stuart Graham
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
| | - Yuyi You
- Department of Clinical Medicine, Faculty of Human, Health, and Medical Science, Macquarie University. Sydney, NSW, Australia
- Save Sight Institute, University of Sydney. Sydney, NSW, Australia
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4
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Guo Y, Mehrabian Z, Milbrandt J, DiAntonio A, Bernstein SL. Synergistic Protection of Retinal Ganglion Cells (RGCs) by SARM1 Inactivation with CNTF in a Rodent Model of Nonarteritic Anterior Ischemic Optic Neuropathy. Cells 2024; 13:202. [PMID: 38334594 PMCID: PMC10854792 DOI: 10.3390/cells13030202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
We evaluated whether inhibiting sterile alpha and (Toll/interleukin receptor (TIR)) motif-containing 1 (SARM1) activity protects retinal ganglion cells (RGCs) following ischemic axonopathy (rodent nonarteritic anterior ischemic optic neuropathy: rNAION) by itself and combined with ciliary neurotrophic factor (CNTF). Genetically modified SARM1(-) rats were rNAION-induced in one eye and compared against equivalently induced wild-type animals of the same background. Optic nerve (ON) diameters were quantified using optical coherence tomography (SD-OCT). RGCs were quantified 30 d post-induction using retinal stereology for Brn3a(+) nuclei. ON sections were analyzed by TEM and immunohistochemistry. SARM1(-)(-) and WT animals were then bilaterally sequentially rNAION-induced. One eye received intravitreal vehicle injection following induction; the contralateral side received CNTF and was analyzed 30 d post-induction. Inhibiting SARM1 activity suppressed axonal collapse following ischemic axonopathy. SARM1(-) animals significantly reduced RGC loss, compared with WT animals (49.4 ± 6.8% RGC loss in SARM1(-) vs. 63.6 ± 3.2% sem RGC loss in WT; Mann-Whitney one-tailed U-test, (p = 0.049)). IVT-CNTF treatment vs. IVT-vehicle in SARM1(-) animals further reduced RGC loss by 24% at 30 d post-induction, but CNTF did not, by itself, improve long-term RGC survival in WT animals compared with vehicle (Mann-Whitney one-tailed t-test; p = 0.033). While inhibiting SARM1 activity is itself neuroprotective, combining SARM1 inhibition and CNTF treatment generated a long-term, synergistic neuroprotective effect in ischemic neuropathy. Combinatorial treatments for NAION utilizing independent neuroprotective mechanisms may thus provide a greater effect than individual treatment modalities.
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Affiliation(s)
- Yan Guo
- Departments of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Y.G.); (Z.M.)
| | - Zara Mehrabian
- Departments of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Y.G.); (Z.M.)
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA;
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, MO 63110, USA;
| | - Aaron DiAntonio
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, MO 63110, USA;
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven L. Bernstein
- Departments of Ophthalmology and Visual Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Y.G.); (Z.M.)
- Anatomy and Neurobiology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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5
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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] [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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6
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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. RESEARCH SQUARE 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] [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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