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Hernández-Núñez I, Clark BS. Experimental Framework for Assessing Mouse Retinal Regeneration Through Single-Cell RNA-Sequencing. Methods Mol Biol 2025; 2848:117-134. [PMID: 39240520 DOI: 10.1007/978-1-0716-4087-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Retinal degenerative diseases including age-related macular degeneration and glaucoma are estimated to currently affect more than 14 million people in the United States, with an increased prevalence of retinal degenerations in aged individuals. An expanding aged population who are living longer forecasts an increased prevalence and economic burden of visual impairments. Improvements to visual health and treatment paradigms for progressive retinal degenerations slow vision loss. However, current treatments fail to remedy the root cause of visual impairments caused by retinal degenerations-loss of retinal neurons. Stimulation of retinal regeneration from endogenous cellular sources presents an exciting treatment avenue for replacement of lost retinal cells. In multiple species including zebrafish and Xenopus, Müller glial cells maintain a highly efficient regenerative ability to reconstitute lost cells throughout the organism's lifespan, highlighting potential therapeutic avenues for stimulation of retinal regeneration in humans. Here, we describe how the application of single-cell RNA-sequencing (scRNA-seq) has enhanced our understanding of Müller glial cell-derived retinal regeneration, including the characterization of gene regulatory networks that facilitate/inhibit regenerative responses. Additionally, we provide a validated experimental framework for cellular preparation of mouse retinal cells as input into scRNA-seq experiments, including insights into experimental design and analyses of resulting data.
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Affiliation(s)
- Ismael Hernández-Núñez
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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2
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Li B, Chang FY, Wan Z, Giauque NA, Addo EK, Bernstein PS. Imaging macular carotenoids and their related proteins in the human retina with confocal resonance Raman and fluorescence microscopy. Exp Eye Res 2024; 247:110043. [PMID: 39151780 PMCID: PMC11412777 DOI: 10.1016/j.exer.2024.110043] [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: 04/06/2024] [Revised: 07/31/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024]
Abstract
Lutein and zeaxanthin are highly concentrated at the central region of the human retina, forming a distinct yellow spot known as the macula lutea. The delivery and retention of the macular pigment carotenoids in the macula lutea involves many proteins, but their exact roles remain incompletely understood. In our study, we examined the distribution of the twelve known macular carotenoid-related proteins within the human macula and the underlying retinal pigment epithelium (RPE) using both fluorescence and Raman modes on our confocal resonance Raman microscope. Additionally, we assessed protein and gene expression through Western blot analysis and a single-cell RNA sequencing database. Our findings revealed that GSTP1, BCO2, and Aster-B exhibited distribution patterns similar to the macular carotenoids, with higher expression levels within the macular region compared to the periphery, while SR-BI and ABCA1 did not exhibit specific distribution patterns within the macula or RPE. Interestingly, LIPC, SR-BI's partner, accumulated specifically in the sub-foveal RPE. All three of these carotenoid transport proteins were found to be highly expressed in the RPE. These results offer valuable insights into the roles these proteins play in the formation of the macula lutea.
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Affiliation(s)
- Binxing Li
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Utah, Salt Lake City, UT, 84132, USA.
| | - Fu-Yen Chang
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Utah, Salt Lake City, UT, 84132, USA
| | - Zihe Wan
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Utah, Salt Lake City, UT, 84132, USA
| | - Nathan A Giauque
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Utah, Salt Lake City, UT, 84132, USA
| | - Emmanuel K Addo
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Utah, Salt Lake City, UT, 84132, USA
| | - Paul S Bernstein
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Utah, Salt Lake City, UT, 84132, USA.
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3
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Lim EW, Fallon RJ, Bates C, Ideguchi Y, Nagasaki T, Handzlik MK, Joulia E, Bonelli R, Green CR, Ansell BRE, Kitano M, Polis I, Roberts AJ, Furuya S, Allikmets R, Wallace M, Friedlander M, Metallo CM, Gantner ML. Serine and glycine physiology reversibly modulate retinal and peripheral nerve function. Cell Metab 2024:S1550-4131(24)00323-1. [PMID: 39191258 DOI: 10.1016/j.cmet.2024.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/11/2024] [Accepted: 07/30/2024] [Indexed: 08/29/2024]
Abstract
Metabolic homeostasis is maintained by redundant pathways to ensure adequate nutrient supply during fasting and other stresses. These pathways are regulated locally in tissues and systemically via the liver, kidney, and circulation. Here, we characterize how serine, glycine, and one-carbon (SGOC) metabolism fluxes across the eye, liver, and kidney sustain retinal amino acid levels and function. Individuals with macular telangiectasia (MacTel), an age-related retinal disease with reduced circulating serine and glycine, carrying deleterious alleles in SGOC metabolic enzymes exhibit an exaggerated reduction in circulating serine. A Phgdh+/- mouse model of this haploinsufficiency experiences accelerated retinal defects upon dietary serine/glycine restriction, highlighting how otherwise silent haploinsufficiencies can impact retinal health. We demonstrate that serine-associated retinopathy and peripheral neuropathy are reversible, as both are restored in mice upon serine supplementation. These data provide molecular insights into the genetic and metabolic drivers of neuro-retinal dysfunction while highlighting therapeutic opportunities to ameliorate this pathogenesis.
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Affiliation(s)
- Esther W Lim
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Regis J Fallon
- Lowy Medical Research Institute, La Jolla, CA 92037, USA
| | - Caleb Bates
- Lowy Medical Research Institute, La Jolla, CA 92037, USA
| | | | | | - Michal K Handzlik
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emeline Joulia
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Roberto Bonelli
- Lowy Medical Research Institute, La Jolla, CA 92037, USA; Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Courtney R Green
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Brendan R E Ansell
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Maki Kitano
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ilham Polis
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Shigeki Furuya
- Department of Bioscience and Biotechnology, Kyushu University, Fukuoka 812-0053, Japan
| | | | - Martina Wallace
- School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Martin Friedlander
- Lowy Medical Research Institute, La Jolla, CA 92037, USA; The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christian M Metallo
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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Shayler DW, Stachelek K, Cambier L, Lee S, Bai J, Reid MW, Weisenberger DJ, Bhat B, Aparicio JG, Kim Y, Singh M, Bay M, Thornton ME, Doyle EK, Fouladian Z, Erberich SG, Grubbs BH, Bonaguidi MA, Craft CM, Singh HP, Cobrinik D. Identification and characterization of early human photoreceptor states and cell-state-specific retinoblastoma-related features. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.28.530247. [PMID: 38915659 PMCID: PMC11195049 DOI: 10.1101/2023.02.28.530247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Human cone photoreceptors differ from rods and serve as the retinoblastoma cell-of-origin, yet the developmental basis for their distinct behaviors is poorly understood. Here, we used deep full-length single-cell RNA-sequencing to distinguish post-mitotic cone and rod developmental states and identify cone-specific features that contribute to retinoblastomagenesis. The analyses revealed early post-mitotic cone- and rod-directed populations characterized by higher THRB or NRL regulon activities, an immature photoreceptor precursor population with concurrent cone and rod gene and regulon expression, and distinct early and late cone and rod maturation states distinguished by maturation-associated declines in RAX regulon activity. Unexpectedly, both L/M cone and rod precursors co-expressed NRL and THRB RNAs, yet they differentially expressed functionally antagonistic NRL and THRB isoforms and prematurely terminated THRB transcripts. Early L/M cone precursors exhibited successive expression of several lncRNAs along with MYCN, which composed the seventh most L/M-cone-specific regulon, and SYK, which contributed to the early cone precursors' proliferative response to RB1 loss. These findings reveal previously unrecognized photoreceptor precursor states and a role for early cone-precursor-intrinsic SYK expression in retinoblastoma initiation.
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Affiliation(s)
- Dominic W.H. Shayler
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Development, Stem Cell, and Regenerative Medicine Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kevin Stachelek
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Linda Cambier
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Sunhye Lee
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Jinlun Bai
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Development, Stem Cell, and Regenerative Medicine Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark W. Reid
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bhavana Bhat
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Jennifer G. Aparicio
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Yeha Kim
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Mitali Singh
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Maxwell Bay
- Development, Stem Cell, and Regenerative Medicine Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew E. Thornton
- Maternal-Fetal Medicine Division of the Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eamon K. Doyle
- Department of Radiology and The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zachary Fouladian
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Development, Stem Cell, and Regenerative Medicine Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephan G. Erberich
- Department of Radiology and The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brendan H. Grubbs
- Maternal-Fetal Medicine Division of the Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael A. Bonaguidi
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Development, Stem Cell, and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheryl Mae Craft
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hardeep P. Singh
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Cobrinik
- The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Salzman MM, Takimoto T, Foster ML, Mowat FM. Differential gene expression between central and peripheral retinal regions in dogs and comparison with humans. Exp Eye Res 2024; 245:109980. [PMID: 38914302 PMCID: PMC11250724 DOI: 10.1016/j.exer.2024.109980] [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: 02/12/2024] [Revised: 06/09/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
The dog retina contains a central macula-like region, and there are reports of central retinal disorders in dogs with shared genetic etiologies with humans. Defining central/peripheral gene expression profiles may provide insight into the suitability of dogs as models for human disorders. We determined central/peripheral posterior eye gene expression profiles in dogs and interrogated inherited retinal and macular disease-associated genes for differential expression between central and peripheral regions. Bulk tissue RNA sequencing was performed on 8 mm samples of the dog central and superior peripheral regions, sampling retina and retinal pigmented epithelium/choroid separately. Reads were mapped to CanFam3.1, read counts were analyzed to determine significantly differentially expressed genes (DEGs). A similar analytic pipeline was used with a published bulk-tissue RNA sequencing human dataset. Pathways and processes involved in significantly DEGs were identified (Database for Annotation, Visualization and Integrated Discovery). Dogs and humans shared the extent and direction of central retinal differential gene expression, with multiple shared biological pathways implicated in differential expression. Many genes implicated in heritable retinal disorders in dogs and humans were differentially expressed between central and periphery. Approximately half of genes associated with human age-related macular degeneration were differentially expressed in human and dog tissues. We have identified similarities and differences in central/peripheral gene expression profiles between dogs and humans which can be applied to further define the relevance of dogs as models for human retinal disorders.
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Affiliation(s)
- Michele M Salzman
- Dept. Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, USA
| | - Tetsuya Takimoto
- Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, USA; Division of Gene Regulation, Division of Data Science, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
| | - Melanie L Foster
- Dept. Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Freya M Mowat
- Dept. Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, USA; Dept. Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA; Dept. Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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6
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Hu H, Liu F, Gao P, Huang Y, Jia D, Reilly J, Chen X, Han Y, Sun K, Luo J, Li P, Zhang Z, Wang Q, Lu Q, Luo D, Shu X, Tang Z, Liu M, Ren X. Cross-species single-cell landscapes identify the pathogenic gene characteristics of inherited retinal diseases. Front Genet 2024; 15:1409016. [PMID: 39055259 PMCID: PMC11269129 DOI: 10.3389/fgene.2024.1409016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/30/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Inherited retinal diseases (IRDs) affect ∼4.5 million people worldwide. Elusive pathogenic variants in over 280 genes are associated with one or more clinical forms of IRDs. It is necessary to understand the complex interaction among retinal cell types and pathogenic genes by constructing a regulatory network. In this study, we attempt to establish a panoramic expression view of the cooperative work in retinal cells to understand the clinical manifestations and pathogenic bases underlying IRDs. Methods Single-cell RNA sequencing (scRNA-seq) data on the retinas from 35 retina samples of 3 species (human, mouse, and zebrafish) including 259,087 cells were adopted to perform a comparative analysis across species. Bioinformatic tools were used to conduct weighted gene co-expression network analysis (WGCNA), single-cell regulatory network analysis, cell-cell communication analysis, and trajectory inference analysis. Results The cross-species comparison revealed shared or species-specific gene expression patterns at single-cell resolution, such as the stathmin family genes, which were highly expressed specifically in zebrafish Müller glias (MGs). Thirteen gene modules were identified, of which nine were associated with retinal cell types, and Gene Ontology (GO) enrichment of module genes was consistent with cell-specific highly expressed genes. Many IRD genes were identified as hub genes and cell-specific regulons. Most IRDs, especially the retinitis pigmentosa (RP) genes, were enriched in rod-specific regulons. Integrated expression and transcription regulatory network genes, such as congenital stationary night blindness (CSNB) genes GRK1, PDE6B, and TRPM1, showed cell-specific expression and transcription characteristics in either rods or bipolar cells (BCs). IRD genes showed evolutionary conservation (GNAT2, PDE6G, and SAG) and divergence (GNAT2, MT-ND4, and PDE6A) along the trajectory of photoreceptors (PRs) among species. In particular, the Leber congenital amaurosis (LCA) gene OTX2 showed high expression at the beginning of the trajectory of both PRs and BCs. Conclusion We identified molecular pathways and cell types closely connected with IRDs, bridging the gap between gene expression, genetics, and pathogenesis. The IRD genes enriched in cell-specific modules and regulons suggest that these diseases share common etiological bases. Overall, mining of interspecies transcriptome data reveals conserved transcriptomic features of retinas across species and promising applications in both normal retina anatomy and retina pathology.
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Affiliation(s)
- Hualei Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jamas Reilly
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pei Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zuxiao Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Daji Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinhua Shu
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Xu Y, Tummala SR, Chen X, Vardi N. VDAC in Retinal Health and Disease. Biomolecules 2024; 14:654. [PMID: 38927058 PMCID: PMC11201675 DOI: 10.3390/biom14060654] [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: 04/18/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The retina, a tissue of the central nervous system, is vital for vision as its photoreceptors capture light and transform it into electrical signals, which are further processed before they are sent to the brain to be interpreted as images. The retina is unique in that it is continuously exposed to light and has the highest metabolic rate and demand for energy amongst all the tissues in the body. Consequently, the retina is very susceptible to oxidative stress. VDAC, a pore in the outer membrane of mitochondria, shuttles metabolites between mitochondria and the cytosol and normally protects cells from oxidative damage, but when a cell's integrity is greatly compromised it initiates cell death. There are three isoforms of VDAC, and existing evidence indicates that all three are expressed in the retina. However, their precise localization and function in each cell type is unknown. It appears that most retinal cells express substantial amounts of VDAC2 and VDAC3, presumably to protect them from oxidative stress. Photoreceptors express VDAC2, HK2, and PKM2-key proteins in the Warburg pathway that also protect these cells. Consistent with its role in initiating cell death, VDAC is overexpressed in the retinal degenerative diseases retinitis pigmentosa, age related macular degeneration (AMD), and glaucoma. Treatment with antioxidants or inhibiting VDAC oligomerization reduced its expression and improved cell survival. Thus, VDAC may be a promising therapeutic candidate for the treatment of these diseases.
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Affiliation(s)
- Ying Xu
- Guangdong Key Laboratory of Non-Human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (Y.X.); (X.C.)
| | - Shanti R. Tummala
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Xiongmin Chen
- Guangdong Key Laboratory of Non-Human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (Y.X.); (X.C.)
| | - Noga Vardi
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA
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8
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Chen J, Curcio CA, Crosson JN. Shotgun lipidomics of human subretinal fluids under rod-dominant retina reveals cone-dominated lipids. Exp Eye Res 2024; 240:109807. [PMID: 38278468 DOI: 10.1016/j.exer.2024.109807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Subretinal fluid (SRF) accumulates between photoreceptor outer segments and retinal pigment epithelium during rhegmatogenous retinal detachment. Biomolecular components such as lipids originate from cells surrounding the SRF. Knowledge of the composition of these molecules in SRF potentially provides mechanistic insight into the physiologic transfer of lipids between retinal tissue compartments. Using mass spectrometry and tandem mass spectrometry analysis on an electrospray ionization quadrupole-time-of-flight mass spectrometer, we identified a total of 115 lipid molecular species of 11 subclasses and 9 classes in two samples from two patients with rhegmatogenous retinal detachment. These included 47 glycerophosphocholines, 6 glycerophosphoethanolamines, 1 glycerophosphoinositol, 18 sphingomyelins, 9 cholesteryl esters, free cholesterol, 3 ceramides, 22 triacylglycerols and 8 free fatty acids. Glycerophosphocholines were of the highest intensity. By minimizing the formation of different adduct forms or clustering ions of different adducts, we determined the relative intensity of lipid molecular species within the same subclasses. The profiles were compared with those of retinal cells available in the published literature. The glycerophosphocholine profile of SRF was similar to that of cone outer segments, suggesting that outer segment degradation products are constitutively released into the interphotoreceptor matrix, appearing in SRF during detachment. This hypothesis was supported by the retinal distributions of corresponding lipid synthases' mRNA expression obtained from an online resource based on publicly available single-cell sequencing data. In contrast, based on lipid profiles and relevant gene expression in this study, the sources of free cholesterol and cholesteryl esters in SRF appeared more ambiguous, possibly reflecting that outer retina takes up plasma lipoproteins. Further studies to identify and quantify lipids in SRF will help better understand etiology of diseases relevant to outer retina.
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Affiliation(s)
- Jianzhong Chen
- Center for Biotechnology & Genomic Medicine, Medical College of Georgia, Augusta University, GA, United States; Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, GA, United States; Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Christine A Curcio
- Department of Ophthalmology and Visual Sciences, The University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Jason N Crosson
- Department of Ophthalmology and Visual Sciences, The University of Alabama at Birmingham, Birmingham, AL, United States
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9
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Rzhanova LA, Markitantova YV, Aleksandrova MA. Recent Achievements in the Heterogeneity of Mammalian and Human Retinal Pigment Epithelium: In Search of a Stem Cell. Cells 2024; 13:281. [PMID: 38334673 PMCID: PMC10854871 DOI: 10.3390/cells13030281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Retinal pigment epithelium (RPE) cells are important fundamentally for the development and function of the retina. In this regard, the study of the morphological and molecular properties of RPE cells, as well as their regenerative capabilities, is of particular importance for biomedicine. However, these studies are complicated by the fact that, despite the external morphological similarity of RPE cells, the RPE is a population of heterogeneous cells, the molecular genetic properties of which have begun to be revealed by sequencing methods only in recent years. This review carries out an analysis of the data from morphological and molecular genetic studies of the heterogeneity of RPE cells in mammals and humans, which reveals the individual differences in the subpopulations of RPE cells and the possible specificity of their functions. Particular attention is paid to discussing the properties of "stemness," proliferation, and plasticity in the RPE, which may be useful for uncovering the mechanisms of retinal diseases associated with pathologies of the RPE and finding new ways of treating them.
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Affiliation(s)
| | - Yuliya V. Markitantova
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (L.A.R.); (M.A.A.)
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10
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Krueger MR, Fishman-Williams E, Simó S, Tarantal AF, La Torre A. Expression patterns of CYP26A1, FGF8, CDKN1A, and NPVF in the developing rhesus monkey retina. Differentiation 2024; 135:100743. [PMID: 38147763 PMCID: PMC10868720 DOI: 10.1016/j.diff.2023.100743] [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: 11/07/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/28/2023]
Abstract
The fovea centralis (fovea) is a specialized region of the primate retina that plays crucial roles in high-resolution visual acuity and color perception. The fovea is characterized by a high density of cone photoreceptors and no rods, and unique anatomical properties that contribute to its remarkable visual capabilities. Early histological analyses identified some of the key events that contribute to foveal development, but the mechanisms that direct the specification of this area are not understood. Recently, the expression of the retinoic acid-metabolizing enzyme CYP26A1 has become a hallmark of some of the retinal specializations found in vertebrates, including the primate fovea and the high-acuity area in avian species. In chickens, the retinoic acid pathway regulates the expression of FGF8 to then direct the development of a rod-free area. Similarly, high levels of CYP26A1, CDKN1A, and NPVF expression have been observed in the primate macula using transcriptomic approaches. However, which retinal cells express these genes and their expression dynamics in the developing primate eye remain unknown. Here, we systematically characterize the expression patterns of CYP26A1, FGF8, CDKN1A, and NPVF during the development of the rhesus monkey retina, from early stages of development in the first trimester until the third trimester (near term). Our data suggest that some of the markers previously proposed to be fovea-specific are not enriched in the progenitors of the rhesus monkey fovea. In contrast, CYP26A1 is expressed at high levels in the progenitors of the fovea, while it localizes in a subpopulation of macular Müller glia cells later in development. Together these data provide invaluable insights into the expression dynamics of several molecules in the nonhuman primate retina and highlight the developmental advancement of the foveal region.
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Affiliation(s)
- Miranda R Krueger
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, 95616, United States
| | - Elizabeth Fishman-Williams
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, 95616, United States
| | - Sergi Simó
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, 95616, United States
| | - Alice F Tarantal
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, 95616, United States; Department of Pediatrics, University of California, Davis, Davis, CA, 95616, United States; California National Primate Research Center, University of California, Davis, Davis, CA, 95616, United States
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, 95616, United States.
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11
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Rasys AM, Wegerski A, Trainor PA, Hufnagel RB, Menke DB, Lauderdale JD. Dynamic changes in ocular shape during human development and its implications for retina fovea formation. Bioessays 2024; 46:e2300054. [PMID: 38037292 DOI: 10.1002/bies.202300054] [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: 03/27/2023] [Revised: 10/10/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
The human fovea is known for its distinctive pit-like appearance, which results from the displacement of retinal layers superficial to the photoreceptors cells. The photoreceptors are found at high density within the foveal region but not the surrounding retina. Efforts to elucidate the mechanisms responsible for these unique features have ruled out cell death as an explanation for pit formation and changes in cell proliferation as the cause of increased photoreceptor density. These findings have led to speculation that mechanical forces acting within and on the retina during development underly the formation of foveal architecture. Here we review eye morphogenesis and retinal remodeling in human embryonic development. Our meta-analysis of the literature suggests that fovea formation is a protracted process involving dynamic changes in ocular shape that start early and continue throughout most of human embryonic development. From these observations, we propose a new model for fovea development.
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Affiliation(s)
- Ashley M Rasys
- Department of Cellular Biology, The University of Georgia, Athens, Georgia, USA
| | - Andrew Wegerski
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
- Department of Anatomy & Cell Biology, The University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Douglas B Menke
- Department of Genetics, The University of Georgia, Athens, Georgia, USA
| | - James D Lauderdale
- Department of Cellular Biology, The University of Georgia, Athens, Georgia, USA
- Neuroscience Division of the Biomedical and Health Sciences Institute, The University of Georgia, Athens, Georgia, USA
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12
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Sbornova I, van der Sande E, Milosavljevic S, Amurrio E, Burbano SD, Das PK, Do HH, Fisher JL, Kargbo P, Patel J, Porcher L, De Zeeuw CI, Meester-Smoor MA, Winkelman BHJ, Klaver CCW, Pocivavsek A, Kelly MP. The Sleep Quality- and Myopia-Linked PDE11A-Y727C Variant Impacts Neural Physiology by Reducing Catalytic Activity and Altering Subcellular Compartmentalization of the Enzyme. Cells 2023; 12:2839. [PMID: 38132157 PMCID: PMC10742168 DOI: 10.3390/cells12242839] [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: 11/17/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Recently, a Y727C variant in the dual-specific 3',5'-cyclic nucleotide phosphodiesterase 11A (PDE11A-Y727C) was linked to increased sleep quality and reduced myopia risk in humans. Given the well-established role that the PDE11 substrates cAMP and cGMP play in eye physiology and sleep, we determined if (1) PDE11A protein is expressed in the retina or other eye segments in mice, (2) PDE11A-Y7272C affects catalytic activity and/or subcellular compartmentalization more so than the nearby suicide-associated PDE11A-M878V variant, and (3) Pde11a deletion alters eye growth or sleep quality in male and female mice. Western blots show distinct protein expression of PDE11A4, but not PDE11A1-3, in eyes of Pde11a WT, but not KO mice, that vary by eye segment and age. In HT22 and COS-1 cells, PDE11A4-Y727C reduces PDE11A4 catalytic activity far more than PDE11A4-M878V, with both variants reducing PDE11A4-cAMP more so than PDE11A4-cGMP activity. Despite this, Pde11a deletion does not alter age-related changes in retinal or lens thickness or axial length, nor vitreous or anterior chamber depth. Further, Pde11a deletion only minimally changes refractive error and sleep quality. That said, both variants also dramatically alter the subcellular compartmentalization of human and mouse PDE11A4, an effect occurring independently of dephosphorylating PDE11A4-S117/S124 or phosphorylating PDE11A4-S162. Rather, re-compartmentalization of PDE11A4-Y727C is due to the loss of the tyrosine changing how PDE11A4 is packaged/repackaged via the trans-Golgi network. Therefore, the protective impact of the Y727C variant may reflect a gain-of-function (e.g., PDE11A4 displacing another PDE) that warrants further investigation in the context of reversing/preventing sleep disturbances or myopia.
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Affiliation(s)
- Irina Sbornova
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Emilie van der Sande
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Meibergdreef 47, 1105 AZ Amsterdam, The Netherlands
| | - Snezana Milosavljevic
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina School of Medicine, Garners Ferry Rd., Columbia, SC 29209, USA
| | - Elvis Amurrio
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Steven D. Burbano
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Prosun K. Das
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Helen H. Do
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Janet L. Fisher
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina School of Medicine, Garners Ferry Rd., Columbia, SC 29209, USA
| | - Porschderek Kargbo
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Janvi Patel
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Latarsha Porcher
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
| | - Chris I. De Zeeuw
- The Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Meibergdreef 47, 1105 AZ Amsterdam, The Netherlands
- Department of Neuroscience, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
| | - Magda A. Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
| | - Beerend H. J. Winkelman
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Meibergdreef 47, 1105 AZ Amsterdam, The Netherlands
- Department of Neuroscience, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, 3015 CN Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology, Mittlere Strasse 91, 4070 Basel, Switzerland
| | - Ana Pocivavsek
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina School of Medicine, Garners Ferry Rd., Columbia, SC 29209, USA
| | - Michy P. Kelly
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA (P.K.D.); (J.P.)
- Center for Research on Aging, University of Maryland School of Medicine, 20 Penn St., Baltimore, MD 21201, USA
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13
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Sbornova I, van der Sande E, Milosavljevic S, Amurrio E, Burbano SD, Das P, Do H, Fisher JL, Kargbo P, Patel J, Porcher L, De Zeeuw CI, Meester-Smoor MA, Winkelman BH, Klaver CC, Pocivavsek A, Kelly MP. The sleep quality- and myopia-linked PDE11A-Y727C variant impacts neural physiology by reducing catalytic activity and altering subcellular compartmentalization of the enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567422. [PMID: 38014312 PMCID: PMC10680747 DOI: 10.1101/2023.11.16.567422] [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
Recently, a Y727C variant in the dual-specific 3',5'-cyclic nucleotide phosphodiesterase 11A (PDE11A-Y727C) was linked to increased sleep quality and reduced myopia risk in humans. Given the well-established role that the PDE11 substrates cAMP and cGMP play in eye physiology and sleep, we determined if 1) PDE11A protein is expressed in the retina or other eye segments in mouse, 2) PDE11A-Y7272C affects catalytic activity and/or subcellular compartmentalization more so than the nearby suicide-associated PDE11A-M878V variant, and 3) Pde11a deletion alters eye growth or sleep quality in male and female mice. Western blots show distinct protein expression of PDE11A4, but not PDE11A1-3, in eyes of Pde11a WT-but not KO mice-that vary by eye segment and age. In HT22 and COS-1 cells, PDE11A4-Y727C reduces PDE11A4 catalytic activity far more than PDE11A4-M878V, with both variants reducing PDE11A4-cAMP more so than PDE11A4-cGMP activity. Despite this, Pde11a deletion does not alter age-related changes in retinal or lens thickness, axial length, nor vitreous or anterior chamber depth. Further, Pde11a deletion only minimally changes refractive error and sleep quality. That said, both variants also dramatically alter the subcellular compartmentalization of human and mouse PDE11A4, an effect occurring independently of dephosphorylating PDE11A4-S117/S124 or phosphorylating PDE11A4-S162. Rather, re-compartmentalization of PDE11A4-Y727C is due to the loss of the tyrosine changing how PDE11A4 is packaged/repackaged via the trans-Golgi network. Therefore, the protective impact of the Y727C variant may reflect a gain-of-function (e.g., PDE11A4 displacing another PDE) that warrants further investigation in the context of reversing/preventing sleep disturbances or myopia.
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Affiliation(s)
- Irina Sbornova
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Emilie van der Sande
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Meibergdreef 47, Amsterdam, The Netherlands
| | - Snezana Milosavljevic
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina School of Medicine, Garners Ferry Rd, Columbia, SC
| | - Elvis Amurrio
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Steven D. Burbano
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Prosun Das
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Helen Do
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Janet L. Fisher
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina School of Medicine, Garners Ferry Rd, Columbia, SC
| | - Porschderek Kargbo
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Janvi Patel
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Latarsha Porcher
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
| | - Chris I. De Zeeuw
- The Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Meibergdreef 47, Amsterdam, The Netherlands
- Department of Neuroscience, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
| | - Beerend H.J. Winkelman
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Meibergdreef 47, Amsterdam, The Netherlands
- Department of Neuroscience, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
| | - Caroline C.W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Wytemaweg 40, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology, Mittlere Strasse 91, Basel, Switzerland
| | - Ana Pocivavsek
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina School of Medicine, Garners Ferry Rd, Columbia, SC
| | - Michy P. Kelly
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
- Center for Research on Aging, University of Maryland School of Medicine, 20 Penn St, Baltimore, MD 21201
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14
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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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15
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Wolf J, Rasmussen DK, Sun YJ, Vu JT, Wang E, Espinosa C, Bigini F, Chang RT, Montague AA, Tang PH, Mruthyunjaya P, Aghaeepour N, Dufour A, Bassuk AG, Mahajan VB. Liquid-biopsy proteomics combined with AI identifies cellular drivers of eye aging and disease in vivo. Cell 2023; 186:4868-4884.e12. [PMID: 37863056 PMCID: PMC10720485 DOI: 10.1016/j.cell.2023.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/26/2023] [Accepted: 09/13/2023] [Indexed: 10/22/2023]
Abstract
Single-cell analysis in living humans is essential for understanding disease mechanisms, but it is impractical in non-regenerative organs, such as the eye and brain, because tissue biopsies would cause serious damage. We resolve this problem by integrating proteomics of liquid biopsies with single-cell transcriptomics from all known ocular cell types to trace the cellular origin of 5,953 proteins detected in the aqueous humor. We identified hundreds of cell-specific protein markers, including for individual retinal cell types. Surprisingly, our results reveal that retinal degeneration occurs in Parkinson's disease, and the cells driving diabetic retinopathy switch with disease stage. Finally, we developed artificial intelligence (AI) models to assess individual cellular aging and found that many eye diseases not associated with chronological age undergo accelerated molecular aging of disease-specific cell types. Our approach, which can be applied to other organ systems, has the potential to transform molecular diagnostics and prognostics while uncovering new cellular disease and aging mechanisms.
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Affiliation(s)
- Julian Wolf
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Ditte K Rasmussen
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Young Joo Sun
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Jennifer T Vu
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Elena Wang
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fabio Bigini
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Robert T Chang
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Artis A Montague
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Peter H Tang
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA; Retina Consultants of Minnesota, Edina, MN 55435, USA
| | - Prithvi Mruthyunjaya
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine Dufour
- Departments of Physiology and Pharmacology & Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alexander G Bassuk
- Departments of Pediatrics and Neurology, The Iowa Neuroscience Institute (INI), University of Iowa, Iowa City, IA 52242, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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16
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Voigt AP, Mullin NK, Navratil EM, Flamme-Wiese MJ, Lin LC, Scheetz TE, Han IC, Stone EM, Tucker BA, Mullins RF. Gene Expression Within a Human Choroidal Neovascular Membrane Using Spatial Transcriptomics. Invest Ophthalmol Vis Sci 2023; 64:40. [PMID: 37878301 PMCID: PMC10615143 DOI: 10.1167/iovs.64.13.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/07/2023] [Indexed: 10/26/2023] Open
Abstract
Purpose Macular neovascularization is a relatively common and potentially visually devastating complication of age-related macular degeneration. In macular neovascularization, pathologic angiogenesis can originate from either the choroid or the retina, but we have limited understanding of how different cell types become dysregulated in this dynamic process. Methods To study how gene expression is altered in focal areas of pathology, we performed spatial RNA sequencing on a human donor eye with macular neovascularization as well as a healthy control donor. We performed differential expression to identify genes enriched within the area of macular neovascularization and used deconvolution algorithms to predict the originating cell type of these dysregulated genes. Results Within the area of neovascularization, endothelial cells demonstrated increased expression of genes related to Rho family GTPase signaling and integrin signaling. Likewise, VEGF and TGFB1 were identified as potential upstream regulators that could drive the observed gene expression changes produced by endothelial and retinal pigment epithelium cells in the macular neovascularization donor. These spatial gene expression profiles were compared to previous single-cell gene expression experiments in human age-related macular degeneration as well as a model of laser-induced neovascularization in mice. As a secondary aim, we investigated regional gene expression patterns within the macular neural retina and between the macular and peripheral choroid. Conclusions Overall, this study spatially analyzes gene expression across the retina, retinal pigment epithelium, and choroid in health and describes a set of candidate molecules that become dysregulated in macular neovascularization.
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Affiliation(s)
- Andrew P. Voigt
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Nathaniel K. Mullin
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Emma M. Navratil
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Miles J. Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Li-Chun Lin
- University of Iowa Neuroscience Institute, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Ian C. Han
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Budd A. Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
| | - Robert F. Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, Iowa, United States
- Institute for Vision Research, the University of Iowa, Iowa City, Iowa, United States
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17
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Lyu P, Zhai Y, Li T, Qian J. CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server. Bioinformatics 2023; 39:btad521. [PMID: 37610325 PMCID: PMC10477937 DOI: 10.1093/bioinformatics/btad521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/17/2023] [Accepted: 08/22/2023] [Indexed: 08/24/2023] Open
Abstract
MOTIVATION Single-cell sequencing technology has become a routine in studying many biological problems. A core step of analyzing single-cell data is the assignment of cell clusters to specific cell types. Reference-based methods are proposed for predicting cell types for single-cell clusters. However, the scalability and lack of preprocessed reference datasets prevent them from being practical and easy to use. RESULTS Here, we introduce a reference-based cell annotation web server, CellAnn, which is super-fast and easy to use. CellAnn contains a comprehensive reference database with 204 human and 191 mouse single-cell datasets. These reference datasets cover 32 organs. Furthermore, we developed a cluster-to-cluster alignment method to transfer cell labels from the reference to the query datasets, which is superior to the existing methods with higher accuracy and higher scalability. Finally, CellAnn is an online tool that integrates all the procedures in cell annotation, including reference searching, transferring cell labels, visualizing results, and harmonizing cell annotation labels. Through the user-friendly interface, users can identify the best annotation by cross-validating with multiple reference datasets. We believe that CellAnn can greatly facilitate single-cell sequencing data analysis. AVAILABILITY AND IMPLEMENTATION The web server is available at www.cellann.io, and the source code is available at https://github.com/Pinlyu3/CellAnn_shinyapp.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Yijie Zhai
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218, United States
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
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18
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Madadi Y, Monavarfeshani A, Chen H, Stamer WD, Williams RW, Yousefi S. Artificial Intelligence Models for Cell Type and Subtype Identification Based on Single-Cell RNA Sequencing Data in Vision Science. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2837-2852. [PMID: 37294649 PMCID: PMC10631573 DOI: 10.1109/tcbb.2023.3284795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various tissues. However, scRNA-seq based identification of discrete cell-types is still labor intensive and depends on prior molecular knowledge. Artificial intelligence has provided faster, more accurate, and user-friendly approaches for cell-type identification. In this review, we discuss recent advances in cell-type identification methods using artificial intelligence techniques based on single-cell and single-nucleus RNA sequencing data in vision science. The main purpose of this review paper is to assist vision scientists not only to select suitable datasets for their problems, but also to be aware of the appropriate computational tools to perform their analysis. Developing novel methods for scRNA-seq data analysis remains to be addressed in future studies.
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19
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Ramsay E, Lajunen T, Bhattacharya M, Reinisalo M, Rilla K, Kidron H, Terasaki T, Urtti A. Selective drug delivery to the retinal cells: Biological barriers and avenues. J Control Release 2023; 361:1-19. [PMID: 37481214 DOI: 10.1016/j.jconrel.2023.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/09/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
Retinal drug delivery is a challenging, but important task, because most retinal diseases are still without any proper therapy. Drug delivery to the retina is hampered by the anatomical and physiological barriers resulting in minimal bioavailability after topical ocular and systemic administrations. Intravitreal injections are current method-of-choice in retinal delivery, but these injections show short duration of action for small molecules and low target bioavailability for many protein, gene based drugs and nanomedicines. State-of-art delivery systems are based on prolonged retention, controlled drug release and physical features (e.g. size and charge). However, drug delivery to the retina is not cell-specific and these approaches do not facilitate intracellular delivery of modern biological drugs (e.g. intracellular proteins, RNA based medicines, gene editing). In this focused review we highlight biological factors and mechanisms that form the basis for the selective retinal drug delivery systems in the future. Therefore, we are presenting current knowledge related to retinal membrane transporters, receptors and targeting ligands in relation to nanomedicines, conjugates, extracellular vesicles, and melanin binding. These issues are discussed in the light of retinal structure and cell types as well as future prospects in the field. Unlike in some other fields of targeted drug delivery (e.g. cancer research), selective delivery technologies have been rarely studied, even though cell targeted delivery may be even more feasible after local administration into the eye.
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Affiliation(s)
- Eva Ramsay
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 University of Helsinki, Finland
| | - Tatu Lajunen
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 University of Helsinki, Finland; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Madhushree Bhattacharya
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 University of Helsinki, Finland
| | - Mika Reinisalo
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Kirsi Rilla
- School of Medicine, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Heidi Kidron
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 University of Helsinki, Finland
| | - Tetsuya Terasaki
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Arto Urtti
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 University of Helsinki, Finland; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland.
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20
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Park SY, Ter-Saakyan S, Faraci G, Lee HY. Immune cell identifier and classifier (ImmunIC) for single cell transcriptomic readouts. Sci Rep 2023; 13:12093. [PMID: 37495649 PMCID: PMC10372073 DOI: 10.1038/s41598-023-39282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/22/2023] [Indexed: 07/28/2023] Open
Abstract
Single cell RNA sequencing has a central role in immune profiling, identifying specific immune cells as disease markers and suggesting therapeutic target genes of immune cells. Immune cell-type annotation from single cell transcriptomics is in high demand for dissecting complex immune signatures from multicellular blood and organ samples. However, accurate cell type assignment from single-cell RNA sequencing data alone is complicated by a high level of gene expression heterogeneity. Many computational methods have been developed to respond to this challenge, but immune cell annotation accuracy is not highly desirable. We present ImmunIC, a simple and robust tool for immune cell identification and classification by combining marker genes with a machine learning method. With over two million immune cells and half-million non-immune cells from 66 single cell RNA sequencing studies, ImmunIC shows 98% accuracy in the identification of immune cells. ImmunIC outperforms existing immune cell classifiers, categorizing into ten immune cell types with 92% accuracy. We determine peripheral blood mononuclear cell compositions of severe COVID-19 cases and healthy controls using previously published single cell transcriptomic data, permitting the identification of immune cell-type specific differential pathways. Our publicly available tool can maximize the utility of single cell RNA profiling by functioning as a stand-alone bioinformatic cell sorter, advancing cell-type specific immune profiling for the discovery of disease-specific immune signatures and therapeutic targets.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Sonia Ter-Saakyan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA.
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21
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Mullin NK, Voigt AP, Flamme-Wiese MJ, Liu X, Riker MJ, Varzavand K, Stone EM, Tucker BA, Mullins RF. Multimodal single-cell analysis of nonrandom heteroplasmy distribution in human retinal mitochondrial disease. JCI Insight 2023; 8:e165937. [PMID: 37289546 PMCID: PMC10443808 DOI: 10.1172/jci.insight.165937] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
Variants within the high copy number mitochondrial genome (mtDNA) can disrupt organelle function and lead to severe multisystem disease. The wide range of manifestations observed in patients with mitochondrial disease results from varying fractions of abnormal mtDNA molecules in different cells and tissues, a phenomenon termed heteroplasmy. However, the landscape of heteroplasmy across cell types within tissues and its influence on phenotype expression in affected patients remains largely unexplored. Here, we identify nonrandom distribution of a pathogenic mtDNA variant across a complex tissue using single-cell RNA-Seq, mitochondrial single-cell ATAC sequencing, and multimodal single-cell sequencing. We profiled the transcriptome, chromatin accessibility state, and heteroplasmy in cells from the eyes of a patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and from healthy control donors. Utilizing the retina as a model for complex multilineage tissues, we found that the proportion of the pathogenic m.3243A>G allele was neither evenly nor randomly distributed across diverse cell types. All neuroectoderm-derived neural cells exhibited a high percentage of the mutant variant. However, a subset of mesoderm-derived lineage, namely the vasculature of the choroid, was near homoplasmic for the WT allele. Gene expression and chromatin accessibility profiles of cell types with high and low proportions of m.3243A>G implicate mTOR signaling in the cellular response to heteroplasmy. We further found by multimodal single-cell sequencing of retinal pigment epithelial cells that a high proportion of the pathogenic mtDNA variant was associated with transcriptionally and morphologically abnormal cells. Together, these findings show the nonrandom nature of mitochondrial variant partitioning in human mitochondrial disease and underscore its implications for mitochondrial disease pathogenesis and treatment.
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Affiliation(s)
- Nathaniel K. Mullin
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Andrew P. Voigt
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Miles J. Flamme-Wiese
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Xiuying Liu
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Megan J. Riker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Katayoun Varzavand
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Edwin M. Stone
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Budd A. Tucker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Robert F. Mullins
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
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22
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Chen K, Wang Y, Huang Y, Liu X, Tian X, Yang Y, Dong A. Cross-species scRNA-seq reveals the cellular landscape of retina and early alterations in type 2 diabetes mice. Genomics 2023; 115:110644. [PMID: 37279838 DOI: 10.1016/j.ygeno.2023.110644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/08/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) analysis have provided an unprecedented resolution for the studies on diabetic retinopathy (DR). However, the early changes in the retina in diabetes remain unclear. A total of 8 human and mouse scRNA-seq datasets, containing 276,402 cells were analyzed individually to comprehensively delineate the retinal cell atlas. The neural retinas were isolated from the type 2 diabetes (T2D) and control mice, and scRNA-seq analysis was conducted to evaluate the early effects of diabetes on the retina. Bipolar cell (BC) heterogeneity were identified. We found some stable BCs across multiple datasets, and explored their biological functions. A new RBC subtype (Car8_RBC) in the mouse retina was validated using the multi-color immunohistochemistry. AC149090.1 was significantly upregulated in the rod cells, ON cone BCs (CBCs), OFF CBCs, and RBCs in T2D mice. Additionally, the interneurons, especially BCs, were the most vulnerable cells to diabetes by integrating scRNA-seq and genome-wide association studies (GWAS) analyses. In conclusion, this study delineated a cross-species retinal cell atlas and uncovered the early pathological alterations in the retina of T2D mice.
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Affiliation(s)
- Kai Chen
- Department of General Surgery, Peking University First Hospital, Beijing 100034, China
| | - Yinhao Wang
- Department of Ophthalmology, First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 310003, China
| | - Youyuan Huang
- Department of Endocrinology, Peking University First Hospital, Beijing 100034, China
| | - Xinxin Liu
- Department of General Surgery, Peking University First Hospital, Beijing 100034, China
| | - Xiaodong Tian
- Department of General Surgery, Peking University First Hospital, Beijing 100034, China.
| | - Yinmo Yang
- Department of General Surgery, Peking University First Hospital, Beijing 100034, China.
| | - Aimei Dong
- Department of Endocrinology, Peking University First Hospital, Beijing 100034, China; Department of General Practice, Peking University First Hospital, Beijing 100034, China.
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23
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Vöcking O, Famulski JK. Single cell transcriptome analyses of the developing zebrafish eye- perspectives and applications. Front Cell Dev Biol 2023; 11:1213382. [PMID: 37457291 PMCID: PMC10346855 DOI: 10.3389/fcell.2023.1213382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
Within a relatively short period of time, single cell transcriptome analyses (SCT) have become increasingly ubiquitous with transcriptomic research, uncovering plentiful details that boost our molecular understanding of various biological processes. Stemming from SCT analyses, the ever-growing number of newly assigned genetic markers increases our understanding of general function and development, while providing opportunities for identifying genes associated with disease. SCT analyses have been carried out using tissue from numerous organisms. However, despite the great potential of zebrafish as a model organism, other models are still preferably used. In this mini review, we focus on eye research as an example of the advantages in using zebrafish, particularly its usefulness for single cell transcriptome analyses of developmental processes. As studies have already shown, the unique opportunities offered by zebrafish, including similarities to the human eye, in combination with the possibility to analyze and extract specific cells at distinct developmental time points makes the model a uniquely powerful one. Particularly the practicality of collecting large numbers of embryos and therefore isolation of sufficient numbers of developing cells is a distinct advantage compared to other model organisms. Lastly, the advent of highly efficient genetic knockouts methods offers opportunities to characterize target gene function in a more cost-efficient way. In conclusion, we argue that the use of zebrafish for SCT approaches has great potential to further deepen our molecular understanding of not only eye development, but also many other organ systems.
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Affiliation(s)
| | - Jakub K. Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
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24
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Voigt AP, Mullin NK, Navratil EM, Flamme-Wiese MJ, Lin LC, Scheetz TE, Han IC, Stone EM, Tucker BA, Mullins RF. GENE EXPRESSION WITHIN A HUMAN CHOROIDAL NEOVASCULAR MEMBRANE USING SPATIAL TRANSCRIPTOMICS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.544770. [PMID: 37398429 PMCID: PMC10312719 DOI: 10.1101/2023.06.16.544770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Macular neovascularization is a relatively common and potentially visually devastating complication of age-related macular degeneration. In macular neovascularization, pathologic angiogenesis can originate from either the choroid or the retina, but we have limited understanding of how different cell types become dysregulated in this dynamic process. In this study, we performed spatial RNA sequencing on a human donor eye with macular neovascularization as well as a healthy control donor. We identified genes enriched within the area of macular neovascularization and used deconvolution algorithms to predict the originating cell type of these dysregulated genes. Within the area of neovascularization, endothelial cells were predicted to increase expression of genes related to Rho family GTPase signaling and integrin signaling. Likewise, VEGF and TGFB1 were identified as potential upstream regulators that could drive the observed gene expression changes produced by endothelial and retinal pigment epithelium cells in the macular neovascularization donor. These spatial gene expression profiles were compared to previous single-cell gene expression experiments in human age-related macular degeneration as well as a model of laser-induced neovascularization in mice. As a secondary aim, we also investigated spatial gene expression patterns within the macular neural retina and between the macular and peripheral choroid. We recapitulated previously described regional-specific gene expression patterns across both tissues. Overall, this study spatially analyzes gene expression across the retina, retinal pigment epithelium, and choroid in health and describes a set of candidate molecules that become dysregulated in macular neovascularization.
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Affiliation(s)
- Andrew P. Voigt
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Nathaniel K. Mullin
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Emma M. Navratil
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Miles J. Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Li-Chun Lin
- University of Iowa Neuroscience Institute, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
| | - Todd E. Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Ian C. Han
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Edwin M. Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Budd A. Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
| | - Robert F. Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242
- Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242
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25
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Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543087. [PMID: 37398481 PMCID: PMC10312535 DOI: 10.1101/2023.05.31.543087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA-seq multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10x methods produce highly concordant cell class compositions and then expand sci-Plex to analyze the cell class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to six weeks later. Our data show sci-Plex's potential to dramatically scale-up the analysis of treatment conditions on relevant human models.
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Affiliation(s)
- Amy Tresenrider
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Kiara C. Eldred
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Sophia Cuschieri
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Dawn Hoffer
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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26
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Koch NA, Sonnenberg L, Hedrich UBS, Lauxmann S, Benda J. Loss or gain of function? Effects of ion channel mutations on neuronal firing depend on the neuron type. Front Neurol 2023; 14:1194811. [PMID: 37292138 PMCID: PMC10244640 DOI: 10.3389/fneur.2023.1194811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Clinically relevant mutations to voltage-gated ion channels, called channelopathies, alter ion channel function, properties of ionic currents, and neuronal firing. The effects of ion channel mutations are routinely assessed and characterized as loss of function (LOF) or gain of function (GOF) at the level of ionic currents. However, emerging personalized medicine approaches based on LOF/GOF characterization have limited therapeutic success. Potential reasons are among others that the translation from this binary characterization to neuronal firing is currently not well-understood-especially when considering different neuronal cell types. In this study, we investigate the impact of neuronal cell type on the firing outcome of ion channel mutations. Methods To this end, we simulated a diverse collection of single-compartment, conductance-based neuron models that differed in their composition of ionic currents. We systematically analyzed the effects of changes in ion current properties on firing in different neuronal types. Additionally, we simulated the effects of known mutations in KCNA1 gene encoding the KV1.1 potassium channel subtype associated with episodic ataxia type 1 (EA1). Results These simulations revealed that the outcome of a given change in ion channel properties on neuronal excitability depends on neuron type, i.e., the properties and expression levels of the unaffected ionic currents. Discussion Consequently, neuron-type specific effects are vital to a full understanding of the effects of channelopathies on neuronal excitability and are an important step toward improving the efficacy and precision of personalized medicine approaches.
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Affiliation(s)
- Nils A. Koch
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Bernstein Center for Computational Neuroscience Tübingen, Tübingen, Germany
| | - Lukas Sonnenberg
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Bernstein Center for Computational Neuroscience Tübingen, Tübingen, Germany
| | - Ulrike B. S. Hedrich
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Stephan Lauxmann
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Jan Benda
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Bernstein Center for Computational Neuroscience Tübingen, Tübingen, Germany
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27
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Rämö JT, Abner E, van Dijk EHC, Wang X, Brinks J, Nikopensius T, Nõukas M, Marjonen H, Silander K, Jukarainen S, Kiiskinen T, Choi SH, Kajanne R, Mehtonen J, Palta P, Lubitz SA, Kaarniranta K, Sobrin L, Kurki M, Yzer S, Ellinor PT, Esko T, Daly MJ, den Hollander AI, Palotie A, Turunen JA, Boon CJF, Rossin EJ. Overlap of Genetic Loci for Central Serous Chorioretinopathy With Age-Related Macular Degeneration. JAMA Ophthalmol 2023; 141:449-457. [PMID: 37079300 PMCID: PMC10119776 DOI: 10.1001/jamaophthalmol.2023.0706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/12/2023] [Indexed: 04/21/2023]
Abstract
Importance Central serous chorioretinopathy (CSC) is a serous maculopathy of unknown etiology. Two of 3 previously reported CSC genetic risk loci are also associated with AMD. Improved understanding of CSC genetics may broaden our understanding of this genetic overlap and unveil mechanisms in both diseases. Objective To identify novel genetic risk factors for CSC and compare genetic risk factors for CSC and AMD. Design, Setting, and Participants Using International Classification of Diseases, Ninth (ICD-9) and Tenth (ICD-10) Revision code-based inclusion and exclusion criteria, patients with CSC and controls were identified in both the FinnGen study and the Estonian Biobank (EstBB). Also included in a meta-analysis were previously reported patients with chronic CSC and controls. Data were analyzed from March 1 to September 31, 2022. Main Outcomes and Measures Genome-wide association studies (GWASs) were performed in the biobank-based cohorts followed by a meta-analysis of all cohorts. The expression of genes prioritized by the polygenic priority score and nearest-gene methods were assessed in cultured choroidal endothelial cells and public ocular single-cell RNA sequencing data sets. The predictive utility of polygenic scores (PGSs) for CSC and AMD were evaluated in the FinnGen study. Results A total of 1176 patients with CSC and 526 787 controls (312 162 female [59.3%]) were included in this analysis: 552 patients with CSC and 343 461 controls were identified in the FinnGen study, 103 patients with CSC and 178 573 controls were identified in the EstBB, and 521 patients with chronic CSC and 3577 controls were included in a meta-analysis. Two previously reported CSC risk loci were replicated (near CFH and GATA5) and 3 novel loci were identified (near CD34/46, NOTCH4, and PREX1). The CFH and NOTCH4 loci were associated with AMD but in the opposite direction. Prioritized genes showed increased expression in cultured choroidal endothelial cells compared with other genes in the loci (median [IQR] of log 2 [counts per million], 7.3 [0.6] vs 4.7 [3.7]; P = .004) and were differentially expressed in choroidal vascular endothelial cells in single-cell RNA sequencing data (mean [SD] fold change, 2.05 [0.38] compared with other cell types; P < 7.1 × 10-20). A PGS for AMD was predictive of reduced CSC risk (odds ratio, 0.76; 95% CI, 0.70-0.83 per +1 SD in AMD-PGS; P = 7.4 × 10-10). This association may have been mediated by loci containing complement genes. Conclusions and Relevance In this 3-cohort genetic association study, 5 genetic risk loci for CSC were identified, highlighting a likely role for genes involved in choroidal vascular function and complement regulation. Results suggest that polygenic AMD risk was associated with reduced risk of CSC and that this genetic overlap was largely due to loci containing complement genes.
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Affiliation(s)
- Joel T. Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Massachusetts Eye and Ear, Boston
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Erik Abner
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Xin Wang
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Joost Brinks
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Margit Nõukas
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Heidi Marjonen
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kaisa Silander
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sakari Jukarainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Biostatistics, Boston University, Boston, Massachusetts
| | - Risto Kajanne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Juha Mehtonen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Steven A. Lubitz
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Kai Kaarniranta
- Department of Ophthalmology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Lucia Sobrin
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston
| | - Mitja Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Suzanne Yzer
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Tõnu Esko
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mark J. Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Anneke I. den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Genomics Research Center, AbbVie, Cambridge, Massachusetts
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology, Massachusetts General Hospital, Boston
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Joni A. Turunen
- Folkhälsan Research Center, Biomedicum, Helsinki, Finland
- Department of Ophthalmology, University of Helsinki, Helsinki, Finland
| | - Camiel J. F. Boon
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Elizabeth J. Rossin
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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Haarman AE, Klaver CC, Tedja MS, Roosing S, Astuti G, Gilissen C, Hoefsloot LH, van Tienhoven M, Brands T, Magielsen FJ, Eussen BH, de Klein A, Brosens E, Verhoeven VJ. Identification of rare variants involved in high myopia unraveled by whole genome sequencing. OPHTHALMOLOGY SCIENCE 2023; 3:100303. [DOI: 10.1016/j.xops.2023.100303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023]
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29
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Srivastava D, Yadav RP, Singh S, Boyd K, Artemyev NO. Unique interface and dynamics of the complex of HSP90 with a specialized cochaperone AIPL1. Structure 2023; 31:309-317.e5. [PMID: 36657440 PMCID: PMC9992320 DOI: 10.1016/j.str.2022.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/06/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023]
Abstract
Photoreceptor phosphodiesterase PDE6 is central for visual signal transduction. Maturation of PDE6 depends on a specialized chaperone complex of HSP90 with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1). Disruption of PDE6 maturation underlies a severe form of retina degeneration. Here, we report a 3.9 Å cryoelectron microscopy (cryo-EM) structure of the complex of HSP90 with AIPL1. This structure reveals a unique interaction of the FK506-binding protein (FKBP)-like domain of AIPL1 with HSP90 at its dimer interface. Unusually, the N terminus AIPL1 inserts into the HSP90 lumen in a manner that was observed previously for HSP90 clients. Deletion of the 7 N-terminal residues of AIPL1 decreased its ability to cochaperone PDE6. Multi-body refinement of the cryo-EM data indicated large swing-like movements of AIPL1-FKBP. Modeling the complex of HSP90 with AIPL1 using crosslinking constraints indicated proximity of the mobile tetratricopeptide repeat (TPR) domain with the C-terminal domain of HSP90. Our study establishes a framework for future structural studies of PDE6 maturation.
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Affiliation(s)
- Dhiraj Srivastava
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Ravi P Yadav
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Sneha Singh
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kimberly Boyd
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
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30
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Quint WH, Tadema KCD, Kokke NCCJ, Meester-Smoor MA, Miller AC, Willemsen R, Klaver CCW, Iglesias AI. Post-GWAS screening of candidate genes for refractive error in mutant zebrafish models. Sci Rep 2023; 13:2017. [PMID: 36737489 PMCID: PMC9898536 DOI: 10.1038/s41598-023-28944-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Genome-wide association studies (GWAS) have dissected numerous genetic factors underlying refractive errors (RE) such as myopia. Despite significant insights into understanding the genetic architecture of RE, few studies have validated and explored the functional role of candidate genes within these loci. To functionally follow-up on GWAS and characterize the potential role of candidate genes on the development of RE, we prioritized nine genes (TJP2, PDE11A, SHISA6, LAMA2, LRRC4C, KCNQ5, GNB3, RBFOX1, and GRIA4) based on biological and statistical evidence; and used CRISPR/cas9 to generate knock-out zebrafish mutants. These mutant fish were screened for abnormalities in axial length by spectral-domain optical coherence tomography and refractive status by eccentric photorefraction at the juvenile (2 months) and adult (4 months) developmental stage. We found a significantly increased axial length and myopic shift in refractive status in three of our studied mutants, indicating a potential involvement of the human orthologs (LAMA2, LRRC4C, and KCNQ5) in myopia development. Further, in-situ hybridization studies showed that all three genes are expressed throughout the zebrafish retina. Our zebrafish models provide evidence of a functional role of these three genes in refractive error development and offer opportunities to elucidate pathways driving the retina-to-sclera signaling cascade that leads to myopia.
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Affiliation(s)
- Wim H Quint
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Kirke C D Tadema
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Nina C C J Kokke
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, USA
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Adriana I Iglesias
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
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31
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Kaplan L, Drexler C, Pfaller AM, Brenna S, Wunderlich KA, Dimitracopoulos A, Merl-Pham J, Perez MT, Schlötzer-Schrehardt U, Enzmann V, Samardzija M, Puig B, Fuchs P, Franze K, Hauck SM, Grosche A. Retinal regions shape human and murine Müller cell proteome profile and functionality. Glia 2023; 71:391-414. [PMID: 36334068 DOI: 10.1002/glia.24283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022]
Abstract
The human macula is a highly specialized retinal region with pit-like morphology and rich in cones. How Müller cells, the principal glial cell type in the retina, are adapted to this environment is still poorly understood. We compared proteomic data from cone- and rod-rich retinae from human and mice and identified different expression profiles of cone- and rod-associated Müller cells that converged on pathways representing extracellular matrix and cell adhesion. In particular, epiplakin (EPPK1), which is thought to play a role in intermediate filament organization, was highly expressed in macular Müller cells. Furthermore, EPPK1 knockout in a human Müller cell-derived cell line led to a decrease in traction forces as well as to changes in cell size, shape, and filopodia characteristics. We here identified EPPK1 as a central molecular player in the region-specific architecture of the human retina, which likely enables specific functions under the immense mechanical loads in vivo.
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Affiliation(s)
- Lew Kaplan
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Corinne Drexler
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.,Vienna Biocenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anna M Pfaller
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Santra Brenna
- Neurology Department, Experimental Research in Stroke and Inflammation (ERSI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten A Wunderlich
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea Dimitracopoulos
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Juliane Merl-Pham
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Maria-Theresa Perez
- Department of Clinical Sciences, Division of Ophthalmology, Lund University, Lund, Sweden.,NanoLund, Nanometer Structure Consortium, Lund University, Lund, Sweden
| | | | - Volker Enzmann
- Department of Ophthalmology, Bern University Hospital, Inselspital, University of Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Marijana Samardzija
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Berta Puig
- Neurology Department, Experimental Research in Stroke and Inflammation (ERSI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Fuchs
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.,Institute of Medical Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Antje Grosche
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
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32
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Liu CY, Chen HH. Large-Scale Single-Nucleus RNA Sequencing Compatible with Complex Archived Samples. Methods Mol Biol 2022; 2560:333-346. [PMID: 36481908 DOI: 10.1007/978-1-0716-2651-1_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcriptome profiling at single-cell resolution allows us to identify and assess functional cell types and cellular states, including those within degenerating ocular tissues in retinitis pigmentosa. The technology is particularly valuable when studying tissues with high cellular heterogeneity, or when specific cell types are of interest. In this chapter, we introduce a detailed protocol of a medium-throughput single-nucleus RNA sequencing technique that utilizes frozen tissue as input sample. This protocol can be executed by any researcher with basic training in molecular biology techniques. With this protocol, a single experimenter can easily process two samples per day up to cDNA amplification, and library preparations can be done in batches of 8. Routinely we can obtain ~20 K nuclei per eye from 3 to 4 library preparations.
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Affiliation(s)
- Chao-Yu Liu
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu-Hsin Chen
- Department of Biomarker Discovery OMNI, Genentech , South San Francisco, CA, United States.
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33
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den Hollander AI, Mullins RF, Orozco LD, Voigt AP, Chen HH, Strunz T, Grassmann F, Haines JL, Kuiper JJW, Tumminia SJ, Allikmets R, Hageman GS, Stambolian D, Klaver CCW, Boeke JD, Chen H, Honigberg L, Katti S, Frazer KA, Weber BHF, Gorin MB. Systems genomics in age-related macular degeneration. Exp Eye Res 2022; 225:109248. [PMID: 36108770 PMCID: PMC10150562 DOI: 10.1016/j.exer.2022.109248] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 12/29/2022]
Abstract
Genomic studies in age-related macular degeneration (AMD) have identified genetic variants that account for the majority of AMD risk. An important next step is to understand the functional consequences and downstream effects of the identified AMD-associated genetic variants. Instrumental for this next step are 'omics' technologies, which enable high-throughput characterization and quantification of biological molecules, and subsequent integration of genomics with these omics datasets, a field referred to as systems genomics. Single cell sequencing studies of the retina and choroid demonstrated that the majority of candidate AMD genes identified through genomic studies are expressed in non-neuronal cells, such as the retinal pigment epithelium (RPE), glia, myeloid and choroidal cells, highlighting that many different retinal and choroidal cell types contribute to the pathogenesis of AMD. Expression quantitative trait locus (eQTL) studies in retinal tissue have identified putative causal genes by demonstrating a genetic overlap between gene regulation and AMD risk. Linking genetic data to complement measurements in the systemic circulation has aided in understanding the effect of AMD-associated genetic variants in the complement system, and supports that protein QTL (pQTL) studies in plasma or serum samples may aid in understanding the effect of genetic variants and pinpointing causal genes in AMD. A recent epigenomic study fine-mapped AMD causal variants by determing regulatory regions in RPE cells differentiated from induced pluripotent stem cells (iPSC-RPE). Another approach that is being employed to pinpoint causal AMD genes is to produce synthetic DNA assemblons representing risk and protective haplotypes, which are then delivered to cellular or animal model systems. Pinpointing causal genes and understanding disease mechanisms is crucial for the next step towards clinical translation. Clinical trials targeting proteins encoded by the AMD-associated genomic loci C3, CFB, CFI, CFH, and ARMS2/HTRA1 are currently ongoing, and a phase III clinical trial for C3 inhibition recently showed a modest reduction of lesion growth in geographic atrophy. The EYERISK consortium recently developed a genetic test for AMD that allows genotyping of common and rare variants in AMD-associated genes. Polygenic risk scores (PRS) were applied to quantify AMD genetic risk, and may aid in predicting AMD progression. In conclusion, genomic studies represent a turning point in our exploration of AMD. The results of those studies now serve as a driving force for several clinical trials. Expanding to omics and systems genomics will further decipher function and causality from the associations that have been reported, and will enable the development of therapies that will lessen the burden of AMD.
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Affiliation(s)
- Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; AbbVie, Genomics Research Center, Cambridge, MA, USA.
| | - Robert F Mullins
- The University of Iowa Institute for Vision Research, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | | | - Andrew P Voigt
- The University of Iowa Institute for Vision Research, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | | | - Tobias Strunz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | | | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands; Center of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Rando Allikmets
- Department of Ophthalmology, Columbia University, NY, USA; Department of Pathology and Cell Biology, Columbia University, NY, USA
| | - Gregory S Hageman
- Sharon Eccles Steele Center for Translational Medicine, John A. Moran Eye Center, Department of Ophthalmology & Visual Sciences, University of Utah, Salt Lake City, UT, USA
| | - Dwight Stambolian
- Departments of Ophthalmology and Human Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Caroline C W Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; Departments of Ophthalmology and Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands; Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, NY, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, NY, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Hao Chen
- Genentech, South San Francisco, CA, USA
| | | | | | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany; Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Michael B Gorin
- Departments of Ophthalmology and Human Genetics, University of California, Los Angeles, CA, USA
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34
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Xu H, Chen M. Immune response in retinal degenerative diseases - Time to rethink? Prog Neurobiol 2022; 219:102350. [PMID: 36075351 DOI: 10.1016/j.pneurobio.2022.102350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 11/30/2022]
Abstract
Retinal degeneration comprises a group of diseases whereby either the retinal neurons or the neurovascular unit degenerates leading to the loss of visual function. Although the initial cause varies in different conditions, inflammation is known to play an important role in disease pathogenesis. Recent advances in molecular and cell biology and systems biology have yielded unexpected findings, including the heterogeneity of immune cells in the degenerative retina, bidirectional neuron-microglia cross talk, and links to the gut microbiome. Here we discuss the immune response in retinal degenerative conditions, taking into account both regional (retinal) and systemic factors. We propose to classify retinal degeneration into dry and wet forms based on whether the blood-retinal barrier (BRB) is breached and fluid is accumulated in retinal parenchyma. The dry form has a relatively intact BRB and is characterised by progressive retinal thinning. Immune response to degenerative insults is dominated by the retinal defence system, which remains to be regulated by neurons. In contrast, the wet form has retinal oedema due to BRB damaged. Inflammation is executed by infiltrating immune cells as well as the retinal defence system. The gut microbiome will have easy access to the retina in wet retinal degeneration and may affect significantly retinal immune response.
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Affiliation(s)
- Heping Xu
- Aier Institute of Optometry and Vision Science, Changsha 410000, China; The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, BT9 7BL, UK.
| | - Mei Chen
- The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, BT9 7BL, UK.
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35
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Mungale A, McGaughey DM, Zhang C, Yousaf S, Liu J, Brooks BP, Maminishkis A, Fufa TD, Hufnagel RB. Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways. Front Genet 2022; 13:949449. [PMID: 36506320 PMCID: PMC9732541 DOI: 10.3389/fgene.2022.949449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022] Open
Abstract
The macula and fovea comprise a highly sensitive visual detection tissue that is susceptible to common disease processes like age-related macular degeneration (AMD). Our understanding of the molecular determinants of high acuity vision remains unclear, as few model organisms possess a human-like fovea. We explore transcription factor networks and receptor-ligand interactions to elucidate tissue interactions in the macula and peripheral retina and concomitant changes in the underlying retinal pigment epithelium (RPE)/choroid. Poly-A selected, 100 bp paired-end RNA-sequencing (RNA-seq) was performed across the macular/foveal, perimacular, and temporal peripheral regions of the neural retina and RPE/choroid tissues of four adult Rhesus macaque eyes to characterize region- and tissue-specific gene expression. RNA-seq reads were mapped to both the macaque and human genomes for maximum alignment and analyzed for differential expression and Gene Ontology (GO) enrichment. Comparison of the neural retina and RPE/choroid tissues indicated distinct, contiguously changing gene expression profiles from fovea through perimacula to periphery. Top GO enrichment of differentially expressed genes in the RPE/choroid included cell junction organization and epithelial cell development. Expression of transcriptional regulators and various disease-associated genes show distinct location-specific preference and retina-RPE/choroid tissue-tissue interactions. Regional gene expression changes in the macaque retina and RPE/choroid is greater than that found in previously published transcriptome analysis of the human retina and RPE/choroid. Further, conservation of human macula-specific transcription factor profiles and gene expression in macaque tissues suggest a conservation of programs required for retina and RPE/choroid function and disease susceptibility.
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Affiliation(s)
- Ameera Mungale
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - David M. McGaughey
- Bioinformatics Group, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Congxiao Zhang
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Sairah Yousaf
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - James Liu
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brian P. Brooks
- Pediatric, Developmental and Genetic Ophthalmology, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Arvydas Maminishkis
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Temesgen D. Fufa
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Robert B. Hufnagel
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
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36
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Becker K, Weigelt CM, Fuchs H, Viollet C, Rust W, Wyatt H, Huber J, Lamla T, Fernandez-Albert F, Simon E, Zippel N, Bakker RA, Klein H, Redemann NH. Transcriptome analysis of AAV-induced retinopathy models expressing human VEGF, TNF-α, and IL-6 in murine eyes. Sci Rep 2022; 12:19395. [PMID: 36371417 PMCID: PMC9653384 DOI: 10.1038/s41598-022-23065-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/25/2022] [Indexed: 11/14/2022] Open
Abstract
Retinopathies are multifactorial diseases with complex pathologies that eventually lead to vision loss. Animal models facilitate the understanding of the pathophysiology and identification of novel treatment options. However, each animal model reflects only specific disease aspects and understanding of the specific molecular changes in most disease models is limited. Here, we conducted transcriptome analysis of murine ocular tissue transduced with recombinant Adeno-associated viruses (AAVs) expressing either human VEGF-A, TNF-α, or IL-6. VEGF expression led to a distinct regulation of extracellular matrix (ECM)-associated genes. In contrast, both TNF-α and IL-6 led to more comparable gene expression changes in interleukin signaling, and the complement cascade, with TNF-α-induced changes being more pronounced. Furthermore, integration of single cell RNA-Sequencing data suggested an increase of endothelial cell-specific marker genes by VEGF, while TNF-α expression increased the expression T-cell markers. Both TNF-α and IL-6 expression led to an increase in macrophage markers. Finally, transcriptomic changes in AAV-VEGF treated mice largely overlapped with gene expression changes observed in the oxygen-induced retinopathy model, especially regarding ECM components and endothelial cell-specific gene expression. Altogether, our study represents a valuable investigation of gene expression changes induced by VEGF, TNF-α, and IL-6 and will aid researchers in selecting appropriate animal models for retinopathies based on their agreement with the human pathophysiology.
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Affiliation(s)
- Kolja Becker
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carina M. Weigelt
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Holger Fuchs
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Coralie Viollet
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Werner Rust
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Hannah Wyatt
- grid.420061.10000 0001 2171 7500Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jochen Huber
- grid.420061.10000 0001 2171 7500Clinical Development & Operations Corporate, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Thorsten Lamla
- grid.420061.10000 0001 2171 7500Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Francesc Fernandez-Albert
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Eric Simon
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Nina Zippel
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Remko A. Bakker
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Holger Klein
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Norbert H. Redemann
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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Bandara S, von Lintig J. Aster la vista: Unraveling the biochemical basis of carotenoid homeostasis in the human retina. Bioessays 2022; 44:e2200133. [PMID: 36127289 PMCID: PMC10044510 DOI: 10.1002/bies.202200133] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022]
Abstract
Carotenoids play pivotal roles in vision as light filters and precursor of chromophore. Many vertebrates also display the colorful pigments as ornaments in bare skin parts and feathers. Proteins involved in the transport and metabolism of these lipids have been identified including class B scavenger receptors and carotenoid cleavage dioxygenases. Recent research implicates members of the Aster protein family, also known as GRAM domain-containing (GRAMD), in carotenoid metabolism. These multi-domain proteins facilitate the intracellular movement of carotenoids from their site of cellular uptake by scavenger receptors to the site of their metabolic processing by carotenoid cleavage dioxygenases. We provide a model how the coordinated interplay of these proteins and their differential expression establishes carotenoid distribution patterns and function in tissues, with particular emphasis on the human retina.
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Affiliation(s)
- Sepalika Bandara
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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Völkner M, Wagner F, Steinheuer LM, Carido M, Kurth T, Yazbeck A, Schor J, Wieneke S, Ebner LJA, Del Toro Runzer C, Taborsky D, Zoschke K, Vogt M, Canzler S, Hermann A, Khattak S, Hackermüller J, Karl MO. HBEGF-TNF induce a complex outer retinal pathology with photoreceptor cell extrusion in human organoids. Nat Commun 2022; 13:6183. [PMID: 36261438 PMCID: PMC9581928 DOI: 10.1038/s41467-022-33848-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Human organoids could facilitate research of complex and currently incurable neuropathologies, such as age-related macular degeneration (AMD) which causes blindness. Here, we establish a human retinal organoid system reproducing several parameters of the human retina, including some within the macula, to model a complex combination of photoreceptor and glial pathologies. We show that combined application of TNF and HBEGF, factors associated with neuropathologies, is sufficient to induce photoreceptor degeneration, glial pathologies, dyslamination, and scar formation: These develop simultaneously and progressively as one complex phenotype. Histologic, transcriptome, live-imaging, and mechanistic studies reveal a previously unknown pathomechanism: Photoreceptor neurodegeneration via cell extrusion. This could be relevant for aging, AMD, and some inherited diseases. Pharmacological inhibitors of the mechanosensor PIEZO1, MAPK, and actomyosin each avert pathogenesis; a PIEZO1 activator induces photoreceptor extrusion. Our model offers mechanistic insights, hypotheses for neuropathologies, and it could be used to develop therapies to prevent vision loss or to regenerate the retina in patients suffering from AMD and other diseases.
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Affiliation(s)
- Manuela Völkner
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Felix Wagner
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Lisa Maria Steinheuer
- Department Computational Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Madalena Carido
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Thomas Kurth
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform Core Facility Electron Microscopy and Histology, Dresden, Germany
| | - Ali Yazbeck
- Department Computational Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jana Schor
- Department Computational Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Stephanie Wieneke
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Lynn J A Ebner
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | | | - David Taborsky
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Katja Zoschke
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Marlen Vogt
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Sebastian Canzler
- Department Computational Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Hermann
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Department of Neurology, Technische Universität Dresden, 01307, Dresden, Germany
| | - Shahryar Khattak
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform Core Facility Electron Microscopy and Histology, Dresden, Germany
| | - Jörg Hackermüller
- Department Computational Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Mike O Karl
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany.
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39
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Lehmann GL, Ginsberg M, Nolan DJ, Rodríguez C, Martínez-González J, Zeng S, Voigt AP, Mullins RF, Rafii S, Rodriguez-Boulan E, Benedicto I. Retinal Pigment Epithelium-Secreted VEGF-A Induces Alpha-2-Macroglobulin Expression in Endothelial Cells. Cells 2022; 11:2975. [PMID: 36230937 PMCID: PMC9564307 DOI: 10.3390/cells11192975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
Alpha-2-macroglobulin (A2M) is a protease inhibitor that regulates extracellular matrix (ECM) stability and turnover. Here, we show that A2M is expressed by endothelial cells (ECs) from human eye choroid. We demonstrate that retinal pigment epithelium (RPE)-conditioned medium induces A2M expression specifically in ECs. Experiments using chemical inhibitors, blocking antibodies, and recombinant proteins revealed a key role of VEGF-A in RPE-mediated A2M induction in ECs. Furthermore, incubation of ECs with RPE-conditioned medium reduces matrix metalloproteinase-2 gelatinase activity of culture supernatants, which is partially restored after A2M knockdown in ECs. We propose that dysfunctional RPE or choroidal blood vessels, as observed in retinal diseases such as age-related macular degeneration, may disrupt the crosstalk mechanism we describe here leading to alterations in the homeostasis of choroidal ECM, Bruch's membrane and visual function.
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Affiliation(s)
- Guillermo L. Lehmann
- Margaret Dyson Vision Research Institute, Department of Ophthalmology, Weill Cornell Medicine, New York, NY 10065, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | | | | | - Cristina Rodríguez
- Institut de Recerca Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José Martínez-González
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas (IIBB-CSIC), 08036 Barcelona, Spain
| | - Shemin Zeng
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA 52246, USA
| | - Andrew P. Voigt
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA 52246, USA
| | - Robert F. Mullins
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA 52246, USA
| | - Shahin Rafii
- Ansary Stem Cell Institute, Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Enrique Rodriguez-Boulan
- Margaret Dyson Vision Research Institute, Department of Ophthalmology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ignacio Benedicto
- Margaret Dyson Vision Research Institute, Department of Ophthalmology, Weill Cornell Medicine, New York, NY 10065, USA
- Departamento de Inmunología, Oftalmología y ORL, Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
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Subramanian R, Sahoo D. Boolean implication analysis of single-cell data predicts retinal cell type markers. BMC Bioinformatics 2022; 23:378. [PMID: 36114457 PMCID: PMC9482279 DOI: 10.1186/s12859-022-04915-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022] Open
Abstract
Background The retina is a complex tissue containing multiple cell types that are essential for vision. Understanding the gene expression patterns of various retinal cell types has potential applications in regenerative medicine. Retinal organoids (optic vesicles) derived from pluripotent stem cells have begun to yield insights into the transcriptomics of developing retinal cell types in humans through single cell RNA-sequencing studies. Previous methods of gene reporting have relied upon techniques in vivo using microarray data, or correlational and dimension reduction methods for analyzing single cell RNA-sequencing data computationally. We aimed to develop a state-of-the-art Boolean method that filtered out noise, could be applied to a wide variety of datasets and lent insight into gene expression over differentiation. Results Here, we present a bioinformatic approach using Boolean implication to discover genes which are retinal cell type-specific or involved in retinal cell fate. We apply this approach to previously published retina and retinal organoid datasets and improve upon previously published correlational methods. Our method improves the prediction accuracy of marker genes of retinal cell types and discovers several new high confidence cone and rod-specific genes. Conclusions The results of this study demonstrate the benefits of a Boolean approach that considers asymmetric relationships. We have shown a statistically significant improvement from correlational, symmetric methods in the prediction accuracy of retinal cell-type specific genes. Furthermore, our method contains no cell or tissue-specific tuning and hence could impact other areas of gene expression analyses in cancer and other human diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04915-4.
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Abstract
Carotenoids constitute an essential dietary component of animals and other non-carotenogenic species which use these pigments in both their modified and unmodified forms. Animals utilize uncleaved carotenoids to mitigate light damage and oxidative stress and to signal fitness and health. Carotenoids also serve as precursors of apocarotenoids including retinol, and its retinoid metabolites, which carry out essential functions in animals by forming the visual chromophore 11-cis-retinaldehyde. Retinoids, such as all-trans-retinoic acid, can also act as ligands of nuclear hormone receptors. The fact that enzymes and biochemical pathways responsible for the metabolism of carotenoids in animals bear resemblance to the ones in plants and other carotenogenic species suggests an evolutionary relationship. We will explore some of the modes of transmission of carotenoid genes from carotenogenic species to metazoans. This apparent relationship has been successfully exploited in the past to identify and characterize new carotenoid and retinoid modifying enzymes. We will review approaches used to identify putative animal carotenoid enzymes, and we will describe methods used to functionally validate and analyze the biochemistry of carotenoid modifying enzymes encoded by animals.
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Affiliation(s)
- Alexander R Moise
- Northern Ontario School of Medicine, Sudbury, ON, Canada; Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada.
| | - Sepalika Bandara
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
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42
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Lankford CK, Umino Y, Poria D, Kefalov V, Solessio E, Baker SA. Cone-Driven Retinal Responses Are Shaped by Rod But Not Cone HCN1. J Neurosci 2022; 42:4231-4249. [PMID: 35437278 PMCID: PMC9145265 DOI: 10.1523/jneurosci.2271-21.2022] [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: 11/16/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Signal integration of converging neural circuits is poorly understood. One example is in the retina where the integration of rod and cone signaling is responsible for the large dynamic range of vision. The relative contribution of rods versus cones is dictated by a complex function involving background light intensity and stimulus temporal frequency. One understudied mechanism involved in coordinating rod and cone signaling onto the shared retinal circuit is the hyperpolarization activated current (Ih) mediated by hyperpolarization-activated cyclic nucleotide-gated 1 (HCN1) channels expressed in rods and cones. Ih opposes membrane hyperpolarization driven by activation of the phototransduction cascade and modulates the strength and kinetics of the photoreceptor voltage response. We examined conditional knock-out (KO) of HCN1 from mouse rods using electroretinography (ERG). In the absence of HCN1, rod responses are prolonged in dim light which altered the response to slow modulation of light intensity both at the level of retinal signaling and behavior. Under brighter intensities, cone-driven signaling was suppressed. To our surprise, conditional KO of HCN1 from mouse cones had no effect on cone-mediated signaling. We propose that Ih is dispensable in cones because of the high level of temporal control of cone phototransduction. Thus, HCN1 is required for cone-driven retinal signaling only indirectly by modulating the voltage response of rods to limit their output.SIGNIFICANCE STATEMENT Hyperpolarization gated hyperpolarization-activated cyclic nucleotide-gated 1 (HCN1) channels carry a feedback current that helps to reset light-activated photoreceptors. Using conditional HCN1 knock-out (KO) mice we show that ablating HCN1 from rods allows rods to signal in bright light when they are normally shut down. Instead of enhancing vision this results in suppressing cone signaling. Conversely, ablating HCN1 from cones was of no consequence. This work provides novel insights into the integration of rod and cone signaling in the retina and challenges our assumptions about the role of HCN1 in cones.
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Affiliation(s)
- Colten K Lankford
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242
| | - Yumiko Umino
- Center for Vision Research, Department of Ophthalmology and Visual Sciences, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Deepak Poria
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697
| | - Vladimir Kefalov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697
- Department of Physiology and Biophysics, University of California, Irvine, California 92697
| | - Eduardo Solessio
- Center for Vision Research, Department of Ophthalmology and Visual Sciences, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Sheila A Baker
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242
- Department of Ophthalmology and Visual Sciences and Institute for Vision Research, University of Iowa, Iowa City, Iowa 52242
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43
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Single-cell characterization of malignant phenotypes and microenvironment alteration in retinoblastoma. Cell Death Dis 2022; 13:438. [PMID: 35523772 PMCID: PMC9076657 DOI: 10.1038/s41419-022-04904-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
Retinoblastoma (RB) is the most common primary intraocular malignancy of childhood. It is known that the tumor microenvironment (TME) regulates tumorigenesis and metastasis. However, how the malignant progression in RB is determined by the heterogeneity of tumor cells and TME remains uncharacterized. Here, we conducted integrative single-cell transcriptome and whole-exome sequencing analysis of RB patients with detailed pathological and clinical measurements. By single-cell transcriptomic sequencing, we profiled around 70,000 cells from tumor samples of seven RB patients. We identified that the major cell types in RB were cone precursor-like (CP-like) and MKI67+ cone precursor (MKI67+ CP) cells. By integrating copy number variation (CNV) analysis, we found that RB samples had large clonal heterogeneity, where the malignant MKI67+ CP cells had significantly larger copy number changes. Enrichment analysis revealed that the conversion of CP-like to MKI67+ CP resulted in the loss of photoreceptor function and increased cell proliferation ability. The TME in RB was composed of tumor-associated macrophages (TAMs), astrocyte-like, and cancer-associated fibroblasts (CAFs). Particularly, during the invasion process, TAMs created an immunosuppressive environment, in which the proportion of TAMs decreased, M1-type macrophage was lost, and the TAMs-related immune functions were depressed. Finally, we identified that TAMs regulated tumor cells through GRN and MIF signaling pathways, while TAMs self-regulated through inhibition of CCL and GALECTIN signaling pathways during the invasion process. Altogether, our study creates a detailed transcriptomic map of RB with single-cell characterization of malignant phenotypes and provides novel molecular insights into the occurrence and progression of RB.
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Abstract
Carotenoid pigments accumulate in specific patterns in vertebrate tissues and play important roles as colorants, chromophores, and hormone precursors. However, proteins that facilitate transportation of these lipophilic pigments within cells have not been identified. We provide evidence that Aster proteins are key components for this process and show that they bind the pigments with high affinity. We observed in mice that carotenoids accumulate in tissues that express Aster-B and this accumulation can be prevented by enzymatic turnover by the BCO2 protein. Accordingly, we found opposing expression patterns of the Aster-B protein and BCO2 in the human retina that seemingly contribute to the unique carotenoid concentration in the macula lutea. Some mammalian tissues uniquely concentrate carotenoids, but the underlying biochemical mechanism for this accumulation has not been fully elucidated. For instance, the central retina of the primate eyes displays high levels of the carotenoids, lutein, and zeaxanthin, whereas the pigments are largely absent in rodent retinas. We previously identified the scavenger receptor class B type 1 and the enzyme β-carotene-oxygenase-2 (BCO2) as key components that determine carotenoid concentration in tissues. We now provide evidence that Aster (GRAM-domain-containing) proteins, recently recognized for their role in nonvesicular cholesterol transport, engage in carotenoid metabolism. Our analyses revealed that the StART-like lipid binding domain of Aster proteins can accommodate the bulky pigments and bind them with high affinity. We further showed that carotenoids and cholesterol compete for the same binding site. We established a bacterial test system to demonstrate that the StART-like domains of mouse and human Aster proteins can extract carotenoids from biological membranes. Mice deficient for the carotenoid catabolizing enzyme BCO2 concentrated carotenoids in Aster-B protein-expressing tissues such as the adrenal glands. Remarkably, Aster-B was expressed in the human but not in the mouse retina. Within the retina, Aster-B and BCO2 showed opposite expression patterns in central versus peripheral parts. Together, our study unravels the biochemical basis for intracellular carotenoid transport and implicates Aster-B in the pathway for macula pigment concentration in the human retina.
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Amamoto R, Wallick GK, Cepko CL. Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration. eLife 2022; 11:76389. [PMID: 35315776 PMCID: PMC8940176 DOI: 10.7554/elife.76389] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/25/2022] [Indexed: 12/16/2022] Open
Abstract
Retinitis Pigmentosa (RP) is a progressive, debilitating visual disorder caused by mutations in a diverse set of genes. In both humans with RP and mouse models of RP, rod photoreceptor dysfunction leads to loss of night vision, and is followed by secondary cone photoreceptor dysfunction and degeneration, leading to loss of daylight color vision. A strategy to prevent secondary cone death could provide a general RP therapy to preserve daylight color vision regardless of the underlying mutation. In mouse models of RP, cones in the peripheral retina survive long-term, despite complete rod loss. The mechanism for such peripheral cone survival had not been explored. Here, we found that active retinoic acid (RA) signaling in peripheral Muller glia is necessary for the abnormally long survival of these peripheral cones. RA depletion by conditional knockout of RA synthesis enzymes, or overexpression of an RA degradation enzyme, abrogated the extended survival of peripheral cones. Conversely, constitutive activation of RA signaling in the central retina promoted long-term cone survival. These results indicate that RA signaling mediates the prolonged peripheral cone survival in the rd1 mouse model of retinal degeneration, and provide a basis for a generic strategy for cone survival in the many diseases that lead to loss of cone-mediated vision.
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Affiliation(s)
- Ryoji Amamoto
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Grace K Wallick
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Constance L Cepko
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, United States
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Wolf J, Boneva S, Rosmus DD, Agostini H, Schlunck G, Wieghofer P, Schlecht A, Lange C. In-Depth Molecular Profiling Specifies Human Retinal Microglia Identity. Front Immunol 2022; 13:863158. [PMID: 35371110 PMCID: PMC8971200 DOI: 10.3389/fimmu.2022.863158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 12/20/2022] Open
Abstract
Microglia are the tissue-resident macrophages of the retina and brain, being critically involved in organ development, tissue homeostasis, and response to cellular damage. Until now, little is known about the molecular signature of human retinal microglia and how it differs from the one of brain microglia and peripheral monocytes. In addition, it is not yet clear to what extent murine retinal microglia resemble those of humans, which represents an important prerequisite for translational research. The present study applies fluorescence-activated cell sorting to isolate human retinal microglia from enucleated eyes and compares their transcriptional profile with the one of whole retinal tissue, human brain microglia as well as classical, intermediate and non-classical monocytes. Finally, human retinal microglia are compared to murine retinal microglia, isolated from Cx3cr1GFP/+ mice. Whereas human retinal microglia exhibited a high grade of similarity in comparison to their counterparts in the brain, several enriched genes were identified in retinal microglia when compared to whole retinal tissue, as well as classical, intermediate, and non-classical monocytes. In relation to whole retina sequencing, several risk genes associated with age-related macular degeneration (AMD) and diabetic retinopathy (DR) were preferentially expressed in retinal microglia, indicating their potential pathophysiological involvement. Although a high degree of similarity was observed between human and murine retinal microglia, several species-specific genes were identified, which should be kept in mind when employing mouse models to investigate retinal microglia biology. In summary, this study provides detailed insights into the molecular profile of human retinal microglia, identifies a plethora of tissue-specific and species-specific genes in comparison to human brain microglia and murine retinal microglia, and thus highlights the significance of retinal microglia in human retinal diseases and for translational research approaches.
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Affiliation(s)
- Julian Wolf
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefaniya Boneva
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Hansjürgen Agostini
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Wieghofer
- Institute of Anatomy, Leipzig University, Leipzig, Germany
- Cellular Neuroanatomy, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Anja Schlecht
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University Wuerzburg, Wuerzburg, Germany
| | - Clemens Lange
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Ophtha-Lab, Department of Ophthalmology at St. Franziskus Hospital, Muenster, Germany
- *Correspondence: Clemens Lange,
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Zouache MA. Variability in Retinal Neuron Populations and Associated Variations in Mass Transport Systems of the Retina in Health and Aging. Front Aging Neurosci 2022; 14:778404. [PMID: 35283756 PMCID: PMC8914054 DOI: 10.3389/fnagi.2022.778404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Aging is associated with a broad range of visual impairments that can have dramatic consequences on the quality of life of those impacted. These changes are driven by a complex series of alterations affecting interactions between multiple cellular and extracellular elements. The resilience of many of these interactions may be key to minimal loss of visual function in aging; yet many of them remain poorly understood. In this review, we focus on the relation between retinal neurons and their respective mass transport systems. These metabolite delivery systems include the retinal vasculature, which lies within the inner portion of the retina, and the choroidal vasculature located externally to the retinal tissue. A framework for investigation is proposed and applied to identify the structures and processes determining retinal mass transport at the cellular and tissue levels. Spatial variability in the structure of the retina and changes observed in aging are then harnessed to explore the relation between variations in neuron populations and those seen among retinal metabolite delivery systems. Existing data demonstrate that the relation between inner retinal neurons and their mass transport systems is different in nature from that observed between the outer retina and choroid. The most prominent structural changes observed across the eye and in aging are seen in Bruch's membrane, which forms a selective barrier to mass transfers at the interface between the choroidal vasculature and the outer retina.
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Affiliation(s)
- Moussa A. Zouache
- John A. Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT, United States
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48
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Abstract
The retina was historically considered as an “approachable part of the brain”; advantageous, for its simplicity, to use as a model organ for deciphering cellular and molecular mechanisms underlying physiology and pathology of the nervous system. However, the most relevant discoveries arise precisely from unveiling the complexity of the retina. A complexity that partially relies on the layered organization of an extended variety of specialized neuronal and glial cellular types and subtypes. Based on functional, morphological or transcriptome data, over 40 subtypes of retinal ganglion cells or 60 subtypes of retinal amacrine cells have been described. A high degree of specialization, that may lead to segregation into functionally diverse subtypes, is also conceivable for Müller cells, a pleiotropic glial component of all vertebrate retinas. The essential role of Müller glia in retinal homeostasis maintenance involves participation in structural, metabolic and intercellular communication processes. Additionally, they are the only retinal cells that possess regenerative potential in response to injury or disease, and thus may be considered as therapeutic tools. In the assumption that functional heterogeneity might be driven by molecular heterogeneity this review aims to compile emerging evidence that could broaden our understanding of Müller cell biology and retinal physiology. Summary statement Müller glial cells exert multiple essential functions in retinal physiology and retinopathies reflecting perhaps the existence of distinct Müller cellular subpopulations. Harnessing Müller cell heterogeneity may serve to enhance new therapeutic approaches for retinal disease.
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Affiliation(s)
- Monica Lamas
- Departamento de Farmacobiología. CINVESTAV-Sede Sur. México D.F. México
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49
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Chandra B, Tung ML, Hsu Y, Scheetz T, Sheffield VC. Retinal ciliopathies through the lens of Bardet-Biedl Syndrome: Past, present and future. Prog Retin Eye Res 2021; 89:101035. [PMID: 34929400 DOI: 10.1016/j.preteyeres.2021.101035] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
The primary cilium is a highly specialized and evolutionary conserved organelle in eukaryotes that plays a significant role in cell signaling and trafficking. Over the past few decades tremendous progress has been made in understanding the physiology of cilia and the underlying pathomechanisms of various ciliopathies. Syndromic ciliopathies consist of a group of disorders caused by ciliary dysfunction or abnormal ciliogenesis. These disorders have multiorgan involvement in addition to retinal degeneration underscoring the ubiquitous distribution of primary cilia in different cell types. Genotype-phenotype correlation is often challenging due to the allelic heterogeneity and pleiotropy of these disorders. In this review, we discuss the clinical and genetic features of syndromic ciliopathies with a focus on Bardet-Biedl syndrome (BBS) as a representative disorder. We discuss the structure and function of primary cilia and their role in retinal photoreceptors. We describe the progress made thus far in understanding the functional and genetic characterization including expression quantitative trait locus (eQTL) analysis of BBS genes. In the future directions section, we discuss the emerging technologies, such as gene therapy, as well as anticipated challenges and their implications in therapeutic development for ciliopathies.
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Affiliation(s)
- Bharatendu Chandra
- Stead Family Department of Pediatrics, Division of Medical Genetics and Genomics, University of Iowa Carver College of Medicine, Iowa City, IA, USA; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Moon Ley Tung
- Stead Family Department of Pediatrics, Division of Medical Genetics and Genomics, University of Iowa Carver College of Medicine, Iowa City, IA, USA; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ying Hsu
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, Iowa City, IA, USA
| | - Todd Scheetz
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, Iowa City, IA, USA
| | - Val C Sheffield
- Stead Family Department of Pediatrics, Division of Medical Genetics and Genomics, University of Iowa Carver College of Medicine, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, Iowa City, IA, USA.
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50
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Spead O, Weaver CJ, Moreland T, Poulain FE. Live imaging of retinotectal mapping reveals topographic map dynamics and a previously undescribed role for Contactin 2 in map sharpening. Development 2021; 148:272618. [PMID: 34698769 DOI: 10.1242/dev.199584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 10/07/2021] [Indexed: 11/20/2022]
Abstract
Organization of neuronal connections into topographic maps is essential for processing information. Yet, our understanding of topographic mapping has remained limited by our inability to observe maps forming and refining directly in vivo. Here, we used Cre-mediated recombination of a new colorswitch reporter in zebrafish to generate the first transgenic model allowing the dynamic analysis of retinotectal mapping in vivo. We found that the antero-posterior retinotopic map forms early but remains dynamic, with nasal and temporal retinal axons expanding their projection domains over time. Nasal projections initially arborize in the anterior tectum but progressively refine their projection domain to the posterior tectum, leading to the sharpening of the retinotopic map along the antero-posterior axis. Finally, using a CRISPR-mediated mutagenesis approach, we demonstrate that the refinement of nasal retinal projections requires the adhesion molecule Contactin 2. Altogether, our study provides the first analysis of a topographic map maturing in real time in a live animal and opens new strategies for dissecting the molecular mechanisms underlying precise topographic mapping in vertebrates.
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Affiliation(s)
- Olivia Spead
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Cory J Weaver
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Trevor Moreland
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Fabienne E Poulain
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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