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Retinal Pigment Epithelium Cell Development: Extrapolating Basic Biology to Stem Cell Research. Biomedicines 2023; 11:biomedicines11020310. [PMID: 36830851 PMCID: PMC9952929 DOI: 10.3390/biomedicines11020310] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
The retinal pigment epithelium (RPE) forms an important cellular monolayer, which contributes to the normal physiology of the eye. Damage to the RPE leads to the development of degenerative diseases, such as age-related macular degeneration (AMD). Apart from acting as a physical barrier between the retina and choroidal blood vessels, the RPE is crucial in maintaining photoreceptor (PR) and visual functions. Current clinical intervention to treat early stages of AMD includes stem cell-derived RPE transplantation, which is still in its early stages of evolution. Therefore, it becomes essential to derive RPEs which are functional and exhibit features as observed in native human RPE cells. The conventional strategy is to use the knowledge obtained from developmental studies using various animal models and stem cell-based exploratory studies to understand RPE biogenies and developmental trajectory. This article emphasises such studies and aims to present a comprehensive understanding of the basic biology, including the genetics and molecular pathways of RPE development. It encompasses basic developmental biology and stem cell-based developmental studies to uncover RPE differentiation. Knowledge of the in utero developmental cues provides an inclusive methodology required for deriving RPEs using stem cells.
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2
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Pandey RS, Krebs MP, Bolisetty MT, Charette JR, Naggert JK, Robson P, Nishina PM, Carter GW. Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium. Int J Mol Sci 2022; 23:10419. [PMID: 36142331 PMCID: PMC9499471 DOI: 10.3390/ijms231810419] [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: 06/18/2022] [Revised: 08/09/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Transcriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease. However, available evidence points to RPE cell heterogeneity within native tissue, which adds complexity to global transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2667 and 2846 RPE cells. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell populations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1-2% of total cells) exhibited the hallmarks of stem and/or progenitor (SP) cells. Placing C1-6 along a pseudotime axis suggested a relative decrease in melanogenesis and SP gene expression and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means clustering of all detected transcripts identified additional expression patterns that may advance the understanding of RPE SP cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.
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Affiliation(s)
- Ravi S. Pandey
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Mark P. Krebs
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mohan T. Bolisetty
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | | | | | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Patsy M. Nishina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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3
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Kanaan R, Medlej-Hashim M, Jounblat R, Pilecki B, Sorensen GL. Microfibrillar-associated protein 4 in health and disease. Matrix Biol 2022; 111:1-25. [DOI: 10.1016/j.matbio.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/04/2022] [Accepted: 05/24/2022] [Indexed: 10/18/2022]
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4
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van der Sande E, Haarman AEG, Quint WH, Tadema KCD, Meester-Smoor MA, Kamermans M, De Zeeuw CI, Klaver CCW, Winkelman BHJ, Iglesias AI. The Role of GJD2(Cx36) in Refractive Error Development. Invest Ophthalmol Vis Sci 2022; 63:5. [PMID: 35262731 PMCID: PMC8934558 DOI: 10.1167/iovs.63.3.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Refractive errors are common eye disorders characterized by a mismatch between the focal power of the eye and its axial length. An increased axial length is a common cause of the refractive error myopia (nearsightedness). The substantial increase in myopia prevalence over the last decades has raised public health concerns because myopia can lead to severe ocular complications later in life. Genomewide association studies (GWAS) have made considerable contributions to the understanding of the genetic architecture of refractive errors. Among the hundreds of genetic variants identified, common variants near the gap junction delta-2 (GJD2) gene have consistently been reported as one of the top hits. GJD2 encodes the connexin 36 (Cx36) protein, which forms gap junction channels and is highly expressed in the neural retina. In this review, we provide current evidence that links GJD2(Cx36) to the development of myopia. We summarize the gap junctional communication in the eye and the specific role of GJD2(Cx36) in retinal processing of visual signals. Finally, we discuss the pathways involving dopamine and gap junction phosphorylation and coupling as potential mechanisms that may explain the role of GJD2(Cx36) in refractive error development.
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Affiliation(s)
- Emilie van der Sande
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
| | - Annechien E. G. Haarman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wim H. Quint
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Kirke C. D. Tadema
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, 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
| | - Maarten Kamermans
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
- Department of Biomedical Physics and Biomedical Photonics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Chris I. De Zeeuw
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
- Department of Neuroscience, 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, Switzerland
| | - Beerend H. J. Winkelman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - 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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5
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Differential gene expression of the healthy conjunctiva during the day. Cont Lens Anterior Eye 2021; 45:101494. [PMID: 34315655 DOI: 10.1016/j.clae.2021.101494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
PURPOSE To determine if there is diurnal variation in gene expression in normal healthy conjunctival cells. METHODS Bulbar conjunctival swab samples were collected from four healthy subjects in the morning and evening of the same day. The two swab samples were taken from one eye of each participant, with a minimum of five hours gap between the two samples. RNA was extracted and analysed using RNA sequencing (RNA-Seq). RESULTS A total of 121 genes were differentially expressed between the morning and the evening conjunctival samples, of which 94 genes were upregulated in the morning, and 27 genes were upregulated in the evening. Many of the genes that were upregulated in the morning were involved in defence, cell turnover and regulation of gene expression, while the genes upregulated in the evening were involved in signalling and mucin production. CONCLUSIONS This study has identified several genes whose expression changes over the course of the day. Knowledge of diurnal variations of conjunctival gene expression provides an insight into the regulatory status of the healthy eye and provides a baseline for examining changes during ocular surface disease.
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Johari YB, Mercer AC, Liu Y, Brown AJ, James DC. Design of synthetic promoters for controlled expression of therapeutic genes in retinal pigment epithelial cells. Biotechnol Bioeng 2021; 118:2001-2015. [PMID: 33580508 DOI: 10.1002/bit.27713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 11/10/2022]
Abstract
Age-related macular degeneration (AMD) associated with dysfunction of retinal pigment epithelial (RPE) cells is the most common cause of untreatable blindness. To advance gene therapy as a viable treatment for AMD there is a need for technologies that enable controlled, RPE-specific expression of therapeutic genes. Here we describe design, construction and testing of compact synthetic promoters with a pre-defined transcriptional activity and RPE cell specificity. Initial comparative informatic analyses of RPE and photoreceptor (PR) cell transcriptomic data identified conserved and overrepresented transcription factor regulatory elements (TFREs, 8-19 bp) specifically associated with transcriptionally active RPE genes. Both RPE-specific TFREs and those derived from the generically active cytomegalovirus-immediate early (CMV-IE) promoter were then screened in vitro to identify sequence elements able to control recombinant gene transcription in model induced pluripotent stem (iPS)-derived and primary human RPE cells. Two libraries of heterotypic synthetic promoters varying in predicted RPE specificity and transcriptional activity were designed de novo using combinations of up to 20 discrete TFREs in series (323-602 bp) and their transcriptional activity in model RPE cells was compared to that of the endogenous BEST1 promoter (661 bp, plus an engineered derivative) and the highly active generic CMV-IE promoter (650 bp). Synthetic promoters with a highpredicted specificity, comprised predominantly of endogenous TFREs exhibited a range of activities up to 8-fold that of the RPE-specific BEST1 gene promoter. Moreover, albeit at a lower predicted specificity, synthetic promoter transcriptional activity in model RPE cells was enhanced beyond that of the CMV-IE promoter when viral elements were utilized in combination with endogenous RPE-specific TFREs, with a reduction in promoter size of 15%. Taken together, while our data reveal an inverse relationship between synthetic promoter activity and cell-type specificity, cell context-specific control of recombinant gene transcriptional activity may be achievable.
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Affiliation(s)
- Yusuf B Johari
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Andrew C Mercer
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Ye Liu
- Research and Early Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
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Voigt AP, Whitmore SS, Lessing ND, DeLuca AP, Tucker BA, Stone EM, Mullins RF, Scheetz TE. Spectacle: An interactive resource for ocular single-cell RNA sequencing data analysis. Exp Eye Res 2020; 200:108204. [PMID: 32910939 DOI: 10.1016/j.exer.2020.108204] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/06/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
Single-cell RNA sequencing has revolutionized ocular gene expression studies. This technology has enabled researchers to identify expression signatures for rare cell types and characterize how gene expression changes across biological conditions, such as topographic region or disease status. However, sharing single-cell RNA sequencing results remains a major obstacle, particular for individuals without a computational background. To address these limitations, we developed Spectacle, an interactive web-based resource for exploring previously published single-cell RNA sequencing data from ocular studies. Spectacle is powered by a locally developed R package, cellcuratoR, which utilizes the Shiny framework in R to generate interactive visualizations for single-cell expression data. Spectacle contains five pre-processed ocular single-cell RNA sequencing data sets and is accessible via the web at OcularGeneExpression.org/singlecell. With Spectacle, users can interactively identify which cell types express a gene of interest, detect transcriptomic subpopulations within a cell type, and perform highly flexible differential expression analyses. The freely-available Spectacle system reduces the bioinformatic barrier for interacting with rich single-cell RNA sequencing studies from ocular tissues, making it easy to quickly identify cell types that express a gene of interest.
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Affiliation(s)
- Andrew P Voigt
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - S Scott Whitmore
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas D Lessing
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Adam P DeLuca
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Budd A Tucker
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Edwin M Stone
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Robert F Mullins
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Todd E Scheetz
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA.
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8
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Dhirachaikulpanich D, Li X, Porter LF, Paraoan L. Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration. Front Cell Dev Biol 2020; 8:808. [PMID: 32984320 PMCID: PMC7480186 DOI: 10.3389/fcell.2020.00808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
We report for the first time an integrated transcriptomic analysis of RPE/choroid dysfunction in AMD (mixed stages) based on combining data from publicly available microarray (GSE29801) and RNAseq (GSE135092) datasets aimed at increasing the ability and power of detection of differentially expressed genes and AMD-associated pathways. The analysis approach employed an integrating quantitative method designed to eliminate bias among different transcriptomic studies. The analysis highlighted 764 meta-genes (366 downregulated and 398 upregulated) in macular AMD RPE/choroid and 445 meta-genes (244 downregulated and 201 upregulated) in non-macular AMD RPE/choroid. Of these, 731 genes were newly detected as differentially expressed (DE) genes in macular AMD RPE/choroid and 434 genes in non-macular AMD RPE/choroid compared with controls. Over-representation analysis of KEGG pathways associated with these DE genes mapped revealed two most significantly associated biological processes in macular RPE/choroid in AMD, namely the neuroactive ligand-receptor interaction pathway (represented by 30 DE genes) and the extracellular matrix-receptor interaction signaling pathway (represented by 12 DE genes). Furthermore, protein-protein interaction (PPI) network identified two central hub genes involved in the control of cell proliferation/differentiation processes, HDAC1 and CDK1. Overall, the analysis provided novel insights for broadening the exploration of AMD pathogenesis by extending the number of molecular determinants and functional pathways that underpin AMD-associated RPE/choroid dysfunction.
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Affiliation(s)
- Dhanach Dhirachaikulpanich
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom.,Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xin Li
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Louise F Porter
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Luminita Paraoan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
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9
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Identification of Key Genes and Pathways Associated with Age-Related Macular Degeneration. J Ophthalmol 2020; 2020:2714746. [PMID: 32904543 PMCID: PMC7456487 DOI: 10.1155/2020/2714746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/16/2020] [Accepted: 07/28/2020] [Indexed: 01/27/2023] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of severe, permanent vision loss among the elderly in the developed world. The cellular and molecular pathogenesis of initiation and development of AMD remain poorly delineated. The limited resources of the human AMD RPE/choroid tissues impeded the extensive study of the disease. To better understand the molecular and pathway changes in human AMD RPE/choroid tissues, we searched the literature and found three independent studies using high-throughput technology to analyze gene expression in 54 human AMD RPE/choroid tissues and 46 age-matched healthy controls. We downloaded these data, pooled them together, and reanalyzed the difference between molecular and pathways by the Ingenuity Pathway Analysis (IPA) database. Totally, 353 differentially expressed genes (DEGs) were identified, among which 181 genes were downregulated and 172 genes were upregulated in RPE/choroid of AMD patients. Furthermore, several significantly enriched biological processes, including cancer, organismal injury and abnormalities, and ophthalmic disease, were identified associated with these DEGs. By analysis of canonical pathway, the phototransduction pathway and atherosclerosis signaling were the top two significant canonical pathways altered in RPE/choroid tissues in human AMD. As expected, several ophthalmic disease-related molecules, including RHO, PDE6A, 3',5'-cyclic-GMP phosphodiesterase, and G protein alpha, were in the central nodes of disease network. The bioinformatics technology combined with the existing high-throughput data was applied to evaluate the underlying key genes and pathways in human AMD tissues, which may predict downstream and upstream biological processes and identify potential therapeutic intervention targets in human AMD.
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10
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Voigt AP, Whitmore SS, Mulfaul K, Chirco KR, Giacalone JC, Flamme-Wiese MJ, Stockman A, Stone EM, Tucker BA, Scheetz TE, Mullins RF. Bulk and single-cell gene expression analyses reveal aging human choriocapillaris has pro-inflammatory phenotype. Microvasc Res 2020; 131:104031. [PMID: 32531351 DOI: 10.1016/j.mvr.2020.104031] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022]
Abstract
The human choroidal vasculature is subject to age-related structural and gene expression changes implicated in age-related macular degeneration (AMD). In this study, we performed both bulk and single-cell RNA sequencing on infant (n = 4 for bulk experiments, n = 2 for single-cell experiments) and adult (n = 13 for bulk experiments, n = 6 for single-cell experiments) human donors to characterize how choroidal gene expression changes with age. Differential expression analysis revealed that aged choroidal samples were enriched in genes encoding pro-inflammatory transcription factors and leukocyte transendothelial cell migration adhesion proteins. Such genes were observed to be differentially expressed specifically within choroidal endothelial cells at the single-cell level. Immunohistochemistry experiments support transcriptional findings that CD34 is elevated in infant choriocapillaris endothelial cells while ICAM-1 is enriched in adults. These results suggest several potential drivers of the pro-inflammatory vascular phenotype observed with advancing age.
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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, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - S Scott Whitmore
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Kelly Mulfaul
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Kathleen R Chirco
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Joseph C Giacalone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Miles J Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Adam Stockman
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Iowa Lions Eye Bank, Coralville, IA 52241, United States of America
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States of America; Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, United States of America.
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11
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Pool FM, Kiel C, Serrano L, Luthert PJ. Repository of proposed pathways and protein-protein interaction networks in age-related macular degeneration. NPJ Aging Mech Dis 2020; 6:2. [PMID: 31934346 PMCID: PMC6946811 DOI: 10.1038/s41514-019-0039-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/18/2019] [Indexed: 12/21/2022] Open
Abstract
Age-related macular degeneration (AMD) is one of the commonest causes of sight loss in the elderly population and to date there is no intervention that slows or prevents early AMD disease progressing to blinding neovascularization or geographic atrophy. AMD is a complex disease and factors proposed to contribute to the development and progression of disease include aging, genetics, epigenetics, oxidative stress, pro-inflammatory state, and life-style factors such as smoking, alcohol, and high fat diet. Here, we generate a knowledge repository of pathways and protein–protein interaction (PPI) networks likely to be implicated in AMD pathogenesis, such as complement activation, lipid trafficking and metabolism, vitamin A cycle, oxidative stress, proteostasis, bioenergetics, autophagy/mitophagy, extracellular matrix (ECM) turnover, and choroidal vascular dropout. Two disctinct clusters ermerged from the networks for parainflamation and ECM homeostasis, which may represent two different disease modules underlying AMD pathology. Our analyses also suggest that the disease manifests primarily in RPE/choroid and less in neural retina. The use of standardized syntax when generating maps of these biological processes (SBGN standard) and networks (PSI standard) enables visualization of complex information in graphical programs such as CellDesigner and Cytoscape and enhances reusability and extension of data. The ability to focus onto subnetworks, multiple visualizations and simulation options will enable the AMD research community to computationally model subnetworks or to test experimentally new hypotheses arising from connectivities in the AMD pathway map.
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Affiliation(s)
- Fran M Pool
- 1UCL Institute of Ophthalmology, and NIHR Moorfields Biomedical Research Centre, University College London, 11-43 Bath Street, London, EC1V 9EL UK
| | - Christina Kiel
- 2Systems Biology Ireland & Charles Institute of Dermatology & School of Medicine, University College Dublin, Belfield Dublin, 4 Ireland
| | - Luis Serrano
- 3Centre for Genomic Regulation (CRG), Systems Biology Programme. The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003 Spain.,4Universitat Pompeu Fabra (UPF), Barcelona, 08003 Spain.,5Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona, 08010 Spain
| | - Philip J Luthert
- 1UCL Institute of Ophthalmology, and NIHR Moorfields Biomedical Research Centre, University College London, 11-43 Bath Street, London, EC1V 9EL UK
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12
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On the origin of proteins in human drusen: The meet, greet and stick hypothesis. Prog Retin Eye Res 2018; 70:55-84. [PMID: 30572124 DOI: 10.1016/j.preteyeres.2018.12.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/12/2022]
Abstract
Retinal drusen formation is not only a clinical hallmark for the development of age-related macular degeneration (AMD) but also for other disorders, such as Alzheimer's disease and renal diseases. The initiation and growth of drusen is poorly understood. Attention has focused on lipids and minerals, but relatively little is known about the origin of drusen-associated proteins and how they are retained in the space between the basal lamina of the retinal pigment epithelium and the inner collagenous layer space (sub-RPE-BL space). While some authors suggested that drusen proteins are mainly derived from cellular debris from processed photoreceptor outer segments and the RPE, others suggest a choroidal cell or blood origin. Here, we reviewed and supplemented the existing literature on the molecular composition of the retina/choroid complex, to gain a more complete understanding of the sources of proteins in drusen. These "drusenomics" studies showed that a considerable proportion of currently identified drusen proteins is uniquely originating from the blood. A smaller, but still large fraction of drusen proteins comes from both blood and/or RPE. Only a small proportion of drusen proteins is uniquely derived from the photoreceptors or choroid. We next evaluated how drusen components may "meet, greet and stick" to each other and/or to structures like hydroxyapatite spherules to form macroscopic deposits in the sub-RPE-BL space. Finally, we discuss implications of our findings with respect to the previously proposed homology between drusenogenesis in AMD and plaque formation in atherosclerosis.
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13
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Curcio CA. Antecedents of Soft Drusen, the Specific Deposits of Age-Related Macular Degeneration, in the Biology of Human Macula. Invest Ophthalmol Vis Sci 2018; 59:AMD182-AMD194. [PMID: 30357337 PMCID: PMC6733529 DOI: 10.1167/iovs.18-24883] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AMD pathobiology was irreversibly changed by the recent discovery of extracellular cholesterol-containing deposits in the subretinal space, between the photoreceptors and retinal pigment epithelium (RPE), called subretinal drusenoid deposits (SDDs). SDDs strikingly mirror the topography of rod photoreceptors in human macula, raising the question of whether an equivalent process results in a deposition related to foveal cones. Herein we propose that AMD's pathognomonic lesion-soft drusen and basal linear deposit (BLinD, same material, diffusely distributed)-is the leading candidate. Epidemiologic, clinical, and histologic data suggest that these deposits are most abundant in the central macula, under the fovea. Strong evidence presented in a companion article supports the idea that the dominant ultrastructural component is large apolipoprotein B,E-containing lipoproteins, constitutively secreted by RPE. Lipoprotein fatty acids are dominated by linoleate (implicating diet) rather than docosahexaenoate (implicating photoreceptors); we seek within the retina cellular relationships and dietary drivers to explain soft druse topography. The delivery of xanthophyll pigments to highly evolved and numerous Müller cells in the human fovea, through RPE, is one strong candidate, because Müller cells are the main reservoir of these pigments, which replenish from diet. We propose that the evolution of neuroglial relations and xanthophyll delivery that underlie exquisite human foveal vision came with a price, that is, soft drusen and sequela, long after our reproductive years.
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Affiliation(s)
- Christine A Curcio
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
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14
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Moran J, G Sanderson K, Maynes J, Vig A, Batmanabane V, Kannu P, Tavares E, Vincent A, Héon E. IFT80 mutations cause a novel complex ciliopathy phenotype with retinal degeneration. Clin Genet 2018; 94:368-372. [PMID: 29923190 DOI: 10.1111/cge.13408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/29/2018] [Accepted: 06/14/2018] [Indexed: 01/26/2023]
Abstract
Ciliopathies, a growing pleotropic class of diseases due to mutations in genes that play an important role in primary cilia function. These highly conserved organelles are key to cell signaling. We now know, that mutations in one gene may lead to more than one ciliopathy phenotype and that one ciliopathy phenotype may be due to mutations in more than one gene. We studied the case of a female child with a novel ciliopathy phenotype and identified two novel mutations in the gene IFT80. Previously, mutations in IFT80 have been associated with a very narrow rib cage and failure of the lungs. Bone anomalies are also part of this IFT80-condition but with no vision problems documented. Our case had none of the features known to be associated with IFT80 mutations and had retinal degeneration (RD). This work broadens the IFT80-phenotype spectrum and also shows RD can be a feature of many ciliopathies.
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Affiliation(s)
- J Moran
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada
| | - K G Sanderson
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada
| | - J Maynes
- Department of Anesthesia and Pain Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - A Vig
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, SickKids and University of Toronto, Toronto, Ontario, Canada
| | - V Batmanabane
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, SickKids and University of Toronto, Toronto, Ontario, Canada
| | - P Kannu
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada.,Division of Clinical Genetics, Department of Pediatrics, SickKids and University of Toronto, Toronto, Ontario, Canada
| | - E Tavares
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada
| | - A Vincent
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, SickKids and University of Toronto, Toronto, Ontario, Canada
| | - E Héon
- Program of Genetics and Genomic Biology, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, SickKids and University of Toronto, Toronto, Ontario, Canada
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15
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Bennis A, Jacobs JG, Catsburg LAE, Ten Brink JB, Koster C, Schlingemann RO, van Meurs J, Gorgels TGMF, Moerland PD, Heine VM, Bergen AA. Stem Cell Derived Retinal Pigment Epithelium: The Role of Pigmentation as Maturation Marker and Gene Expression Profile Comparison with Human Endogenous Retinal Pigment Epithelium. Stem Cell Rev Rep 2018; 13:659-669. [PMID: 28730556 PMCID: PMC5602068 DOI: 10.1007/s12015-017-9754-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In age-related macular degeneration (AMD) the retinal pigment epithelium (RPE) deteriorates, leading to photoreceptor decay and severe vision loss. New therapeutic strategies aim at RPE replacement by transplantation of pluripotent stem cell (PSC)-derived RPE. Several protocols to generate RPE have been developed where appearance of pigmentation is commonly used as indicator of RPE differentiation and maturation. It is, however, unclear how different pigmentation stages reflect developmental stages and functionality of PSC-derived RPE cells. We generated human embryonic stem cell-derived RPE (hESC-RPE) cells and investigated their gene expression profiles at early pigmentation (EP) and late pigmentation (LP) stages. In addition, we compared the hESC-RPE samples with human endogenous RPE. We used a common reference design microarray (44 K). Our analysis showed that maturing hESC-RPE, upon acquiring pigmentation, expresses markers specific for human RPE. Interestingly, our analysis revealed that EP and LP hESC-RPE do not differ much in gene expression. Our data further showed that pigmented hESC-RPE has a significant lower expression than human endogenous RPE in the visual cycle and oxidative stress pathways. In contrast, we observed a significantly higher expression of pathways related to the process adhesion-to-polarity model that is typical of developing epithelial cells. We conclude that, in vitro, the first appearance of pigmentation hallmarks differentiated RPE. However, further increase in pigmentation does not result in much significant gene expression changes and does not add important RPE functionalities. Consequently, our results suggest that the time span for obtaining differentiated hESC-RPE cells, that are suitable for transplantation, may be greatly reduced.
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Affiliation(s)
- A Bennis
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - J G Jacobs
- Department of Pediatrics/Child Neurology, VU University Medical Center, Amsterdam, The Netherlands
| | - L A E Catsburg
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - J B Ten Brink
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - C Koster
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - R O Schlingemann
- Ocular Angiogenesis Group, AMC, Amsterdam, The Netherlands.,Department of Ophthalmology, AMC, Amsterdam, The Netherlands.,Department of Cell Biology and Histology, AMC, Amsterdam, The Netherlands
| | - J van Meurs
- Rotterdam Eye Hospital, Amsterdam, The Netherlands
| | - T G M F Gorgels
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.,University Eye Clinic Maastricht, MUMC+, Amsterdam, The Netherlands
| | - P D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, AMC, Amsterdam, The Netherlands
| | - V M Heine
- Department of Pediatrics/Child Neurology, VU University Medical Center, Amsterdam, The Netherlands. .,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands.
| | - A A Bergen
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands. .,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands. .,Department of Ophthalmology, AMC, Amsterdam, The Netherlands.
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16
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Bennis A, ten Brink JB, Moerland PD, Heine VM, Bergen AA. Comparative gene expression study and pathway analysis of the human iris- and the retinal pigment epithelium. PLoS One 2017; 12:e0182983. [PMID: 28827822 PMCID: PMC5565104 DOI: 10.1371/journal.pone.0182983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/27/2017] [Indexed: 11/25/2022] Open
Abstract
Background The retinal pigment epithelium (RPE) is a neural monolayer lining the back of the eye. Degeneration of the RPE leads to severe vision loss in, so far incurable, diseases such as age-related macular degeneration and some forms of retinitis pigmentosa. A promising future replacement therapy may be autologous iris epithelial cell transdifferentiation into RPE in vitro and, subsequently, transplantation. In this study we compared the gene expression profiles of the iris epithelium (IE) and the RPE. Methods We collected both primary RPE- and IE cells from 5 freshly frozen human donor eyes, using respectively laser dissection microscopy and excision. We performed whole-genome expression profiling using 44k Agilent human microarrays. We investigated the gene expression profiles on both gene and functional network level, using R and the knowledge database Ingenuity. Results The major molecular pathways related to the RPE and IE were quite similar and yielded basic neuro-epithelial cell functions. Nonetheless, we also found major specific differences: For example, genes and molecular pathways, related to the visual cycle and retinol biosynthesis are significantly higher expressed in the RPE than in the IE. Interestingly, Wnt and aryl hydrocarbon receptor (AhR-) signaling pathways are much higher expressed in the IE than in the RPE, suggesting, respectively, a possible pluripotent and high detoxification state of the IE. Conclusions This study provides a valuation of the similarities and differences between the expression profiles of the RPE and IE. Our data combined with that of the literature, represent a most comprehensive perspective on transcriptional variation, which may support future research in the development of therapeutic transplantation of IE.
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Affiliation(s)
- Anna Bennis
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Vivi M. Heine
- Department of Pediatrics / Child Neurology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Centre, Amsterdam, The Netherlands
- * E-mail:
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17
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Hughes AE, Bridgett S, Meng W, Li M, Curcio CA, Stambolian D, Bradley DT. Sequence and Expression of Complement Factor H Gene Cluster Variants and Their Roles in Age-Related Macular Degeneration Risk. Invest Ophthalmol Vis Sci 2017; 57:2763-9. [PMID: 27196323 PMCID: PMC4884056 DOI: 10.1167/iovs.15-18744] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Purpose To investigate how potentially functional genetic variants are coinherited on each of four common complement factor H (CFH) and CFH-related gene haplotypes and to measure expression of these genes in eye and liver tissues. Methods We sequenced the CFH region in four individuals (one homozygote for each of four common CFH region haplotypes) to identify all genetic variants. We studied associations between the haplotypes and AMD phenotypes in 2157 cases and 1150 controls. We examined RNA-seq profiles in macular and peripheral retina and retinal pigment epithelium/choroid/sclera (RCS) from eight eye donors and three liver samples. Results The haplotypic coinheritance of potentially functional variants (including missense variants, novel splice sites, and the CFHR3–CFHR1 deletion) was described for the four common haplotypes. Expression of the short and long CFH transcripts differed markedly between the retina and liver. We found no expression of any of the five CFH-related genes in the retina or RCS, in contrast to the liver, which is the main source of the circulating proteins. Conclusions We identified all genetic variants on common CFH region haplotypes and described their coinheritance. Understanding their functional effects will be key to developing and stratifying AMD therapies. The small scale of our expression study prevented us from investigating the relationships between CFH region haplotypes and their expression, and it will take time and collaboration to develop epidemiologic-scale studies. However, the striking difference between systemic and ocular expression of complement regulators shown in this study suggests important implications for the development of intraocular and systemic treatments.
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Affiliation(s)
- Anne E Hughes
- Formerly of Centre for Public Health Queen's University Belfast, Belfast, United Kingdom
| | - Stephen Bridgett
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Weihua Meng
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Christine A Curcio
- Department of Ophthalmology, University of Alabama, Birmingham, Alabama, United States
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Declan T Bradley
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
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18
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Sachdeva MM, Eliott D. Stem Cell-Based Therapy for Diseases of the Retinal Pigment Epithelium: From Bench to Bedside. Semin Ophthalmol 2016; 31:25-9. [PMID: 26959126 DOI: 10.3109/08820538.2015.1115253] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Age-related macular degeneration (AMD) represents a leading cause of blindness in the elderly, and Stargardt's macular dystrophy (SMD) is the most common form of juvenile-onset macular degeneration. Dry AMD and SMD share an underlying pathophysiology, namely dysfunction and ultimately loss of the retinal pigment epithelium (RPE), suggesting that RPE transplantation may offer a potential treatment strategy for both patient populations. Stem cells have emerged as a promising source of replacement RPE. During the past 15 years, extraordinary strides have been made in the identification, characterization, and differentiation of stem cells. Recently, this large body of basic science and preclinical research has been translated to patient care with the publication of results from Phase 1/2 trials demonstrating safety of transplantation of human embryonic stem cell (hESC)-derived RPE into patients with AMD and SMD. While significant challenges remain before dry AMD and SMD become treatable diseases, the goal has become more tangible.
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Affiliation(s)
- Mira M Sachdeva
- a Harvard Medical School, Massachusetts Eye and Ear Infirmary , Boston , Massachusetts , USA
| | - Dean Eliott
- a Harvard Medical School, Massachusetts Eye and Ear Infirmary , Boston , Massachusetts , USA
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19
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Chen W, Xia X, Song N, Wang Y, Zhu H, Deng W, Kong Q, Pan X, Qin C. Cross-Species Analysis of Gene Expression and Function in Prefrontal Cortex, Hippocampus and Striatum. PLoS One 2016; 11:e0164295. [PMID: 27716781 PMCID: PMC5055290 DOI: 10.1371/journal.pone.0164295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 09/22/2016] [Indexed: 01/08/2023] Open
Abstract
Background Mouse has been extensively used as a tool for investigating the onset and development of human neurological disorders. As a first step to construct a transgenic mouse model of human brain lesions, it is of fundamental importance to clarify the similarity and divergence of genetic background between non-diseased human and mouse brain tissues. Methods We systematically compared, based on large scale integrated microarray data, the transcriptomes of three anatomically distinct brain regions; prefrontal cortex (PFC), hippocampus (HIP) and striatum (STR), across human and mouse. The widely used DAVID web server was used to decipher the biological functions of the highly expressed genes that were identified using a previously reported approach. Venn analysis was used to depict the overlapping ratios of the notably enriched biological process (BP) terms (one-tailed Fisher’s exact test and Benjamini correction; adjusted p < 0.01) between two brain tissues. GOSemSim, an R package, was selected to perform GO semantic similarity analysis. Next, we adjusted signal intensities of orthologous genes by the total signals in all samples within species, and used one minus Pearson’s correlation coefficient to assess the expression distance. Hierarchical clustering and principal component analysis (PCA) were selected for expression pattern analysis. Lineage specific expressed orthologous genes were identified by comparison of the most extreme sub-datasets across species and further verified using reverse transcription PCR (RT-PCR) and quantitative real-time PCR (qRT-PCR). Results We found that the number of the significantly enriched BP terms of the highly expressed genes in human brain regions is larger than that in mouse corresponding brain regions. The mainly involved BP terms in human brain tissues associated with protein-membrane targeting and selenium metabolism are species-specific. The overlapping ratios of all the significantly enriched BP terms between any two brain tissues across species are lower than that within species, but the pairwise semantic similarities are very high between any two brain tissues from either human or mouse. Hierarchical clustering analysis shows the biological functions of the highly expressed genes in brain tissues are more consistent within species than interspecies; whereas it shows the expression patterns of orthologous genes are evidently conserved between human and mouse equivalent brain tissues. In addition, we identified four orthologous genes (COX5B, WIF1, SLC4A10 and PLA2G7) that are species-specific, which have been widely studied and confirmed to be closely linked with neuro- physiological and pathological functions. Conclusion Our study highlights the similarities and divergences in gene function and expression between human and mouse corresponding brain regions, including PFC, HIP and STR.
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Affiliation(s)
- Wei Chen
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
| | - Xiayu Xia
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
| | - Nan Song
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
| | - Ying Wang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
| | - Hua Zhu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
| | - Wei Deng
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
| | - Qi Kong
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
| | - Xianmin Pan
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
- Ministry of Education, The Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Chuan Qin
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, P.R. China
- * E-mail:
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20
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Shutova MV, Surdina AV, Ischenko DS, Naumov VA, Bogomazova AN, Vassina EM, Alekseev DG, Lagarkova MA, Kiselev SL. An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion. Cell Cycle 2016; 15:986-97. [PMID: 26919644 PMCID: PMC4889246 DOI: 10.1080/15384101.2016.1152425] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the 3 germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the "gold standard" of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, 3 types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and 3 pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that 5 iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of "the best iPSC line" selection and confirmed it on an independent dataset.
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Affiliation(s)
- Maria V. Shutova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia V. Surdina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry S. Ischenko
- Research Institute of Physical Chemical Medicine, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | | | - Ekaterina M. Vassina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry G. Alekseev
- Research Institute of Physical Chemical Medicine, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maria A. Lagarkova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Institute of Physical Chemical Medicine, Moscow, Russia
- Kazan Federal University, Kremlevskaya, Russia
| | - Sergey L Kiselev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Kazan Federal University, Kremlevskaya, Russia
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21
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Bergen AA, Kaing S, ten Brink JB, Gorgels TG, Janssen SF. Gene expression and functional annotation of human choroid plexus epithelium failure in Alzheimer's disease. BMC Genomics 2015; 16:956. [PMID: 26573292 PMCID: PMC4647590 DOI: 10.1186/s12864-015-2159-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/27/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common form of dementia. AD has a multifactorial disease etiology and is currently untreatable. Multiple genes and molecular mechanisms have been implicated in AD, including ß-amyloid deposition in the brain, neurofibrillary tangle accumulation of hyper-phosphorylated Tau, synaptic failure, oxidative stress and inflammation. Relatively little is known about the role of the blood-brain barriers, especially the blood-cerebrospinal fluid barrier (BCSFB), in AD. The BCSFB is involved in cerebrospinal fluid (CSF) production, maintenance of brain homeostasis and neurodegenerative disorders. RESULTS Using an Agilent platform with common reference design, we performed a large scale gene expression analysis and functional annotation of the Choroid Plexus Epithelium (CPE), which forms the BCSFB. We obtained 2 groups of freshly frozen Choroid Plexus (CP) of 7 human donor brains each, with and without AD: Braak stages (0-1) and (5-6). We cut CP cryo-sections and isolated RNA from cresyl-violet stained, laser dissected CPE cells. Gene expression results were analysed with T-tests (R) and the knowledge-database Ingenuity. We found statistically significantly altered gene expression data sets, biological functions, canonical pathways, molecular networks and functionalities in AD-affected CPE. We observed specific cellular changes due to increased oxidative stress, such as the unfolded protein response, E1F2 and NRF2 signalling and the protein ubiquitin pathway. Most likely, the AD-affected BCSFB barrier becomes more permeable due to downregulation of CLDN5. Finally, our data also predicted down regulation of the glutathione mediated detoxification pathway and the urea cycle in the AD CPE, which suggest that the CPE sink action may be impaired. Remarkably, the expression of a number of genes known to be involved in AD, such as APP, PSEN1, PSEN2, TTR and CLU is moderate to high and remains stable in both healthy and affected CPE. Literature labelling of our new functional molecular networks confirmed multiple previous (molecular) observations in the AD literature and revealed many new ones. CONCLUSIONS We conclude that CPE failure in AD exists. Combining our data with those of the literature, we propose the following chronological and overlapping chain of events: increased Aß burden on CPE; increased oxidative stress in CPE; despite continuous high expression of TTR: decreased capability of CPE to process amyloid; (pro-) inflammatory and growth factor signalling by CPE; intracellular ubiquitin involvement, remodelling of CPE tight junctions and, finally, cellular atrophy. Our data corroborates the hypothesis that increased BCSFB permeability, especially loss of selective CLDN5-mediated paracellular transport, altered CSF production and CPE sink action, as well as loss of CPE mediated macrophage recruitment contribute to the pathogenesis of AD.
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Affiliation(s)
- Arthur A Bergen
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, AMC, Meibergdreef 9, 1105 AZ AMC, Amsterdam, The Netherlands. .,The Netherlands Institute for Neurosciences (NIN-KNAW), Amsterdam, The Netherlands.
| | - Sovann Kaing
- The Netherlands Institute for Neurosciences (NIN-KNAW), Amsterdam, The Netherlands
| | - Jacoline B ten Brink
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, AMC, Meibergdreef 9, 1105 AZ AMC, Amsterdam, The Netherlands
| | | | - Theo G Gorgels
- The Netherlands Institute for Neurosciences (NIN-KNAW), Amsterdam, The Netherlands.,University Eye Clinic Maastricht, MUMC, Maastricht, The Netherlands
| | - Sarah F Janssen
- The Netherlands Institute for Neurosciences (NIN-KNAW), Amsterdam, The Netherlands.,Department of Ophthalmology, VUMC, Amsterdam, The Netherlands
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22
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Bennis A, Gorgels TGMF, ten Brink JB, van der Spek PJ, Bossers K, Heine VM, Bergen AA. Comparison of Mouse and Human Retinal Pigment Epithelium Gene Expression Profiles: Potential Implications for Age-Related Macular Degeneration. PLoS One 2015; 10:e0141597. [PMID: 26517551 PMCID: PMC4627757 DOI: 10.1371/journal.pone.0141597] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 10/09/2015] [Indexed: 11/26/2022] Open
Abstract
Background The human retinal pigment epithelium (RPE) plays an important role in the pathogenesis of age related macular degeneration (AMD). AMD is the leading cause of blindness worldwide. There is currently no effective treatment available. Preclinical studies in AMD mouse models are essential to develop new therapeutics. This requires further in-depth knowledge of the similarities and differences between mouse and human RPE. Methods We performed a microarray study to identify and functionally annotate RPE specific gene expression in mouse and human RPE. We used a meticulous method to determine C57BL/6J mouse RPE signature genes, correcting for possible RNA contamination from its adjacent layers: the choroid and the photoreceptors. We compared the signature genes, gene expression profiles and functional annotations of the mouse and human RPE. Results We defined sets of mouse (64), human (171) and mouse–human interspecies (22) RPE signature genes. Not unexpectedly, our gene expression analysis and comparative functional annotation suggested that, in general, the mouse and human RPE are very similar. For example, we found similarities for general features, like “organ development” and “disorders related to neurological tissue”. However, detailed analysis of the molecular pathways and networks associated with RPE functions, suggested also multiple species-specific differences, some of which may be relevant for the development of AMD. For example, CFHR1, most likely the main complement regulator in AMD pathogenesis was highly expressed in human RPE, but almost absent in mouse RPE. Furthermore, functions assigned to mouse and human RPE expression profiles indicate (patho-) biological differences related to AMD, such as oxidative stress, Bruch’s membrane, immune-regulation and outer blood retina barrier. Conclusion These differences may be important for the development of new therapeutic strategies and translational studies in age-related macular degeneration.
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Affiliation(s)
- Anna Bennis
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Theo G. M. F. Gorgels
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Peter J. van der Spek
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Koen Bossers
- Laboratory for Neuroregeneration, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Vivi M. Heine
- Department of Pediatrics / Child Neurology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Centre, Amsterdam, The Netherlands
- * E-mail:
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Dong Y, Li ZD, Fang XY, Shi XF, Chen S, Tang X. Association between SERPING1 rs2511989 polymorphism and age-related macular degeneration: Meta-analysis. Int J Ophthalmol 2015; 8:385-94. [PMID: 25938061 DOI: 10.3980/j.issn.2222-3959.2015.02.31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/19/2014] [Indexed: 11/02/2022] Open
Abstract
AIM To investigate the association between SERPING1 rs2511989 (G>A) polymorphism and age-related macular degeneration (AMD). METHODS A number of electronic databases (up to July 15, 2014) were searched independently by two investigators. A Meta-analysis was performed on the association between SERPING1 rs2511989 polymorphism and AMD. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were estimated. RESULTS Eight studies with 16 cohorts consisting of 9163 cases and 6813 controls were included in this Meta-analysis. There was no significant association between rs2511989 polymorphism and AMD under all genetic models in overall estimates (A vs G: OR= 0.938, 95%CI =0.858-1.025; AA vs GG:OR =0.871, 95%CI =0.719-1.056; AG vs GG: OR =0.944, 95%CI =0.845-1.054; AA+AG vs GG: OR =0.927, 95% CI =0.823-1.044; AA vs AG+GG: OR =0.890, 95%CI =0.780-1.034). Cumulative Meta-analyses also showed a trend of no association between rs2511989 polymorphism and AMD as information accumulated by year. Subgroup analysis and Meta-regression analysis indicated that age-matching status was the main source of heterogeneity. Sensitivity analysis found the results in overall comparisons and subgroup comparisons of white subjects under the allele model were found to have significantly statistical differences after studies deviating from Hardy-Weinberg equilibrium (HWE) were excluded (overall: OR=0.918, 95%CI = 0.844-0.999, P =0.049; whites: OR =0.901, 95%CI = 0.817-0.994, P =0.038). However, the results were not sufficiently robust for further sensitivity analysis and statistical differences disappeared on applying Bonferroni correction (with a significance level set at 0.05/25). CONCLUSION This Meta-analysis indicates that SERPING1 rs2511989 polymorphism and AMD tend to have no association with each other. Age matching status is a big confounding factor, and more studies with subtle designs are warranted in future.
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Affiliation(s)
- Yi Dong
- Tianjin Medical University, Tianjin 300070, China ; Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Ze-Dong Li
- Tianjin Medical University, Tianjin 300070, China ; Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Xin-Yu Fang
- Department of Epidemiology and Statistics, School of Public Health, Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Xue-Feng Shi
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Song Chen
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Xin Tang
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
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Tian L, Kazmierkiewicz KL, Bowman AS, Li M, Curcio CA, Stambolian DE. Transcriptome of the human retina, retinal pigmented epithelium and choroid. Genomics 2015; 105:253-64. [PMID: 25645700 DOI: 10.1016/j.ygeno.2015.01.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 10/24/2022]
Abstract
The retina and its adjacent supporting tissues - retinal pigmented epithelium (RPE) and choroid - are critical structures in human eyes required for normal visual perception. Abnormal changes in these layers have been implicated in diseases such as age-related macular degeneration and glaucoma. With the advent of high-throughput methods, such as serial analysis of gene expression, cDNA microarray, and RNA sequencing, there is unprecedented opportunity to facilitate our understanding of the normal retina, RPE, and choroid. This information can be used to identify dysfunction in age-related macular degeneration and glaucoma. In this review, we describe the current status in our understanding of these transcriptomes through the use of high-throughput techniques.
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Affiliation(s)
- Lifeng Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa 19104, USA.
| | | | - Anita S Bowman
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pa 19104, USA.
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pa 19104, USA.
| | - Christine A Curcio
- Department of Ophthalmology, University of Alabama School of Medicine, Birmingham, Al 35294, USA.
| | - Dwight E Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pa 19104, USA.
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Kawa MP, Machalinska A, Roginska D, Machalinski B. Complement system in pathogenesis of AMD: dual player in degeneration and protection of retinal tissue. J Immunol Res 2014; 2014:483960. [PMID: 25276841 PMCID: PMC4168147 DOI: 10.1155/2014/483960] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/18/2014] [Accepted: 08/01/2014] [Indexed: 12/25/2022] Open
Abstract
Age-related macular degeneration (AMD) is the most common cause of blindness among the elderly, especially in Western countries. Although the prevalence, risk factors, and clinical course of the disease are well described, its pathogenesis is not entirely elucidated. AMD is associated with a variety of biochemical abnormalities, including complement components deposition in the retinal pigment epithelium-Bruch's membrane-choriocapillaris complex. Although the complement system (CS) is increasingly recognized as mediating important roles in retinal biology, its particular role in AMD pathogenesis has not been precisely defined. Unrestricted activation of the CS following injury may directly damage retinal tissue and recruit immune cells to the vicinity of active complement cascades, therefore detrimentally causing bystander damage to surrounding cells and tissues. On the other hand, recent evidence supports the notion that an active complement pathway is a necessity for the normal maintenance of the neurosensory retina. In this scenario, complement activation appears to have beneficial effect as it promotes cell survival and tissue remodeling by facilitating the rapid removal of dying cells and resulting cellular debris, thus demonstrating anti-inflammatory and neuroprotective activities. In this review, we discuss both the beneficial and detrimental roles of CS in degenerative retina, focusing on the diverse aspects of CS functions that may promote or inhibit macular disease.
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Affiliation(s)
- Milosz P. Kawa
- Department of General Pathology, Pomeranian Medical University, Al. Powstancow Wlkp. 72, 70-111 Szczecin, Poland
| | - Anna Machalinska
- Department of Ophthalmology, Pomeranian Medical University, Al. Powstancow Wlkp. 72, 70-111 Szczecin, Poland
- Department of Histology and Embryology, Pomeranian Medical University, Al. Powstancow Wlkp. 72, 70-111 Szczecin, Poland
| | - Dorota Roginska
- Department of General Pathology, Pomeranian Medical University, Al. Powstancow Wlkp. 72, 70-111 Szczecin, Poland
| | - Boguslaw Machalinski
- Department of General Pathology, Pomeranian Medical University, Al. Powstancow Wlkp. 72, 70-111 Szczecin, Poland
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Janssen SF, Gorgels TG, Ten Brink JB, Jansonius NM, Bergen AA. Gene expression-based comparison of the human secretory neuroepithelia of the brain choroid plexus and the ocular ciliary body: potential implications for glaucoma. Fluids Barriers CNS 2014; 11:2. [PMID: 24472183 PMCID: PMC3909915 DOI: 10.1186/2045-8118-11-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/26/2014] [Indexed: 11/19/2022] Open
Abstract
Background The neuroepithelia of the choroid plexus (CP) in the brain and the ciliary body (CB) of the eye have common embryological origins and share similar micro-structure and functions. The CP epithelium (CPE) and the non-pigmented epithelium (NPE) of the CB produce the cerebrospinal fluid (CSF) and the aqueous humor (AH) respectively. Production and outflow of the CSF determine the intracranial pressure (ICP); production and outflow of the AH determine the intraocular pressure (IOP). Together, the IOP and ICP determine the translaminar pressure on the optic disc which may be involved in the pathophysiology of primary open angle glaucoma (POAG). The aim of this study was to compare the molecular machinery of the secretory neuroepithelia of the CP and CB (CPE versus NPE) and to determine their potential role in POAG. Methods We compared the transcriptomes and functional annotations of healthy human CPE and NPE. Microarray and bioinformatic studies were performed using an Agilent platform and the Ingenuity Knowledge Database (IPA). Results Based on gene expression profiles, we found many similar functions for the CPE and NPE including molecular transport, neurological disease processes, and immunological functions. With commonly-used selection criteria (fold-change > 2.5, p-value < 0.05), 14% of the genes were expressed significantly differently between CPE and NPE. When we used stricter selection criteria (fold-change > 5, p-value < 0.001), still 4.5% of the genes were expressed differently, which yielded specific functions for the CPE (ciliary movement and angiogenesis/hematopoiesis) and for the NPE (neurodevelopmental properties). Apart from a few exceptions (e.g. SLC12A2, SLC4A4, SLC4A10, KCNA5, and SCN4B), all ion transport protein coding genes involved in CSF and AH production had similar expression profiles in CPE and NPE. Three POAG disease genes were expressed significantly higher in the CPE than the NPE, namely CDH1, CDKN2B and SIX1. Conclusions The transcriptomes of the CPE and NPE were less similar than we previously anticipated. High expression of CSF/AH production genes and candidate POAG disease genes in the CPE and NPE suggest that both might be involved in POAG.
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Affiliation(s)
| | | | | | | | - Arthur Ab Bergen
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, Amsterdam 1105 BA, The Netherlands.
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27
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Janssen SF, van der Spek SJF, ten Brink JB, Essing AHW, Gorgels TGMF, van der Spek PJ, Jansonius NM, Bergen AAB. Gene expression and functional annotation of the human and mouse choroid plexus epithelium. PLoS One 2013; 8:e83345. [PMID: 24391755 PMCID: PMC3877019 DOI: 10.1371/journal.pone.0083345] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 11/01/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The choroid plexus epithelium (CPE) is a lobed neuro-epithelial structure that forms the outer blood-brain barrier. The CPE protrudes into the brain ventricles and produces the cerebrospinal fluid (CSF), which is crucial for brain homeostasis. Malfunction of the CPE is possibly implicated in disorders like Alzheimer disease, hydrocephalus or glaucoma. To study human genetic diseases and potential new therapies, mouse models are widely used. This requires a detailed knowledge of similarities and differences in gene expression and functional annotation between the species. The aim of this study is to analyze and compare gene expression and functional annotation of healthy human and mouse CPE. METHODS We performed 44k Agilent microarray hybridizations with RNA derived from laser dissected healthy human and mouse CPE cells. We functionally annotated and compared the gene expression data of human and mouse CPE using the knowledge database Ingenuity. We searched for common and species specific gene expression patterns and function between human and mouse CPE. We also made a comparison with previously published CPE human and mouse gene expression data. RESULTS Overall, the human and mouse CPE transcriptomes are very similar. Their major functionalities included epithelial junctions, transport, energy production, neuro-endocrine signaling, as well as immunological, neurological and hematological functions and disorders. The mouse CPE presented two additional functions not found in the human CPE: carbohydrate metabolism and a more extensive list of (neural) developmental functions. We found three genes specifically expressed in the mouse CPE compared to human CPE, being ACE, PON1 and TRIM3 and no human specifically expressed CPE genes compared to mouse CPE. CONCLUSION Human and mouse CPE transcriptomes are very similar, and display many common functionalities. Nonetheless, we also identified a few genes and pathways which suggest that the CPE between mouse and man differ with respect to transport and metabolic functions.
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Affiliation(s)
- Sarah F. Janssen
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
- * E-mail:
| | - Sophie J. F. van der Spek
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Anke H. W. Essing
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Theo G. M. F. Gorgels
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Peter J. van der Spek
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nomdo M. Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arthur A. B. Bergen
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Centre (AMC), Amsterdam, The Netherlands
- Department of Clinical Genetics, Academic Medical Centre (AMC), Amsterdam, The Netherlands
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Janssen SF, Gorgels TG, Ramdas WD, Klaver CC, van Duijn CM, Jansonius NM, Bergen AA. The vast complexity of primary open angle glaucoma: Disease genes, risks, molecular mechanisms and pathobiology. Prog Retin Eye Res 2013; 37:31-67. [DOI: 10.1016/j.preteyeres.2013.09.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/26/2013] [Accepted: 09/03/2013] [Indexed: 12/21/2022]
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Janssen SF, Gorgels TG, van der Spek PJ, Jansonius NM, Bergen AA. In silico analysis of the molecular machinery underlying aqueous humor production: potential implications for glaucoma. J Clin Bioinforma 2013; 3:21. [PMID: 24165276 PMCID: PMC3875900 DOI: 10.1186/2043-9113-3-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 10/23/2013] [Indexed: 12/03/2022] Open
Abstract
Background The ciliary body epithelia (CBE) of the eye produce the aqueous humor (AH). The equilibrium between the AH production by the CBE and the outflow through the trabecular meshwork ultimately determines the intraocular pressure (IOP). An increased IOP is a major risk factor for primary open angle glaucoma (POAG). This study aims to elucidate the molecular machinery of the most important function of the CBE: the AH production and composition, and aims to find possible new molecular clues for POAG and AH production-lowering drugs. Methods We performed a gene expression analysis of the non-pigmented (NPE) and pigmented epithelia (PE) of the human CBE of post mortem eyes. We used 44 k Agilent microarrays against a common reference design. Functional annotations were performed with the Ingenuity knowledge database. Results We built a molecular model of AH production by combining previously published physiological data with our current genomic expression data. Next, we investigated molecular CBE transport features which might influence AH composition. These features included caveolin- and clathrin vesicle-mediated transport of large biomolecules, as well as a range of substrate specific transporters. The presence of these transporters implies that, for example, immunoglobins, thyroid hormone, prostaglandins, cholesterol and vitamins can be secreted by the CBE along with the AH. In silico, we predicted some of the molecular apical interactions between the NPE and PE, the side where the two folded epithelia face each other. Finally, we found high expression of seven POAG disease genes in the plasma membrane of extracellular space of the CBE, namely APOE, CAV1, COL8A2, EDNRA, FBN1, RFTN1 and TLR4 and we found possible new targets for AH lowering drugs in the AH. Conclusions The CBE expresses many transporters, which account for AH production and/or composition. Some of these entries have also been associated with POAG. We hypothesize that the CBE may play a more prominent role than currently thought in the pathogenesis of POAG, for example by changing the composition of AH.
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Affiliation(s)
| | | | | | | | - Arthur Ab Bergen
- Department of Clinical and Molecular Ophthalmogenetics the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, the Netherlands.
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Kim BJ, Sprehe N, Morganti A, Wordinger RJ, Clark AF. The effect of postmortem time on the RNA quality of human ocular tissues. Mol Vis 2013; 19:1290-5. [PMID: 23805035 PMCID: PMC3692406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 06/07/2013] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Profiling gene expression in human ocular tissues provides invaluable information for understanding ocular biology and investigating numerous ocular diseases. Accurate measurement of gene expression requires high-quality RNA, which often is a challenge with postmortem ocular tissues. METHODS We examined the effect of various death to preservation (DP) times on the RNA quality of ten different ocular tissues. We used 16 eyes from eight different human donors. The eyes were preserved immediately in RNAlater or preserved after initial storage at 4 °C to create a range of DP times from 2 to 48 h. Ten ocular tissues were dissected from each eye. After total RNA was extracted from each dissected ocular tissue, the RNA integrity number (RIN) was determined using an Agilent Bioanalyzer. RESULTS The RIN values from corneal and trabecular meshwork tissues were significantly (p<0.05) higher than those from the ciliary body at an earlier DP time (<6 h), but were not different among all tissues after 8 h. Interestingly, the RIN values from non-vascularized tissues were significantly (p=0.0002) higher than those from vascularized ocular tissues at early DP times (<6 h). The RIN value from the cornea was significantly (p<0.05) higher at short DP times compared to longer DP times. The RIN values from corneal tissues were significantly correlated to DP time according to regression analysis (p<0.05). CONCLUSIONS In this study, we determined RNA quality from postmortem ocular tissues with various DP times. Our results emphasize the need for rapid preservation and processing of postmortem human donor eye tissues, especially for vascularized ocular tissues.
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Affiliation(s)
- Byung-Jin Kim
- Department of Cell Biology & Anatomy and The North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX
| | | | | | - Robert J. Wordinger
- Department of Cell Biology & Anatomy and The North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX
| | - Abbot F. Clark
- Department of Cell Biology & Anatomy and The North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX
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Verhoeven VJM, Hysi PG, Wojciechowski R, Fan Q, Guggenheim JA, Höhn R, MacGregor S, Hewitt AW, Nag A, Cheng CY, Yonova-Doing E, Zhou X, Ikram MK, Buitendijk GHS, McMahon G, Kemp JP, Pourcain BS, Simpson CL, Mäkelä KM, Lehtimäki T, Kähönen M, Paterson AD, Hosseini SM, Wong HS, Xu L, Jonas JB, Pärssinen O, Wedenoja J, Yip SP, Ho DWH, Pang CP, Chen LJ, Burdon KP, Craig JE, Klein BEK, Klein R, Haller T, Metspalu A, Khor CC, Tai ES, Aung T, Vithana E, Tay WT, Barathi VA, Chen P, Li R, Liao J, Zheng Y, Ong RT, Döring A, Evans DM, Timpson NJ, Verkerk AJMH, Meitinger T, Raitakari O, Hawthorne F, Spector TD, Karssen LC, Pirastu M, Murgia F, Ang W, Mishra A, Montgomery GW, Pennell CE, Cumberland PM, Cotlarciuc I, Mitchell P, Wang JJ, Schache M, Janmahasatian S, Janmahasathian S, Igo RP, Lass JH, Chew E, Iyengar SK, Gorgels TGMF, Rudan I, Hayward C, Wright AF, Polasek O, Vatavuk Z, Wilson JF, Fleck B, Zeller T, Mirshahi A, Müller C, Uitterlinden AG, Rivadeneira F, Vingerling JR, Hofman A, Oostra BA, Amin N, Bergen AAB, Teo YY, Rahi JS, Vitart V, Williams C, Baird PN, Wong TY, Oexle K, Pfeiffer N, Mackey DA, Young TL, van Duijn CM, Saw SM, Bailey-Wilson JE, Stambolian D, Klaver CC, Hammond CJ. Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Nat Genet 2013; 45:314-8. [PMID: 23396134 PMCID: PMC3740568 DOI: 10.1038/ng.2554] [Citation(s) in RCA: 336] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/16/2013] [Indexed: 02/06/2023]
Abstract
Refractive error is the most common eye disorder worldwide and is a prominent cause of blindness. Myopia affects over 30% of Western populations and up to 80% of Asians. The CREAM consortium conducted genome-wide meta-analyses, including 37,382 individuals from 27 studies of European ancestry and 8,376 from 5 Asian cohorts. We identified 16 new loci for refractive error in individuals of European ancestry, of which 8 were shared with Asians. Combined analysis identified 8 additional associated loci. The new loci include candidate genes with functions in neurotransmission (GRIA4), ion transport (KCNQ5), retinoic acid metabolism (RDH5), extracellular matrix remodeling (LAMA2 and BMP2) and eye development (SIX6 and PRSS56). We also confirmed previously reported associations with GJD2 and RASGRF1. Risk score analysis using associated SNPs showed a tenfold increased risk of myopia for individuals carrying the highest genetic load. Our results, based on a large meta-analysis across independent multiancestry studies, considerably advance understanding of the mechanisms involved in refractive error and myopia.
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Janssen SF, Gorgels TGMF, Bossers K, ten Brink JB, Essing AHW, Nagtegaal M, van der Spek PJ, Jansonius NM, Bergen AAB. Gene expression and functional annotation of the human ciliary body epithelia. PLoS One 2012; 7:e44973. [PMID: 23028713 PMCID: PMC3445623 DOI: 10.1371/journal.pone.0044973] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/15/2012] [Indexed: 12/01/2022] Open
Abstract
Purpose The ciliary body (CB) of the human eye consists of the non-pigmented (NPE) and pigmented (PE) neuro-epithelia. We investigated the gene expression of NPE and PE, to shed light on the molecular mechanisms underlying the most important functions of the CB. We also developed molecular signatures for the NPE and PE and studied possible new clues for glaucoma. Methods We isolated NPE and PE cells from seven healthy human donor eyes using laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44×k Agilent microarrays. For microarray conformations, we used a literature study, RT-PCRs, and immunohistochemical stainings. We analyzed the gene expression data with R and with the knowledge database Ingenuity. Results The gene expression profiles and functional annotations of the NPE and PE were highly similar. We found that the most important functionalities of the NPE and PE were related to developmental processes, neural nature of the tissue, endocrine and metabolic signaling, and immunological functions. In total 1576 genes differed statistically significantly between NPE and PE. From these genes, at least 3 were cell-specific for the NPE and 143 for the PE. Finally, we observed high expression in the (N)PE of 35 genes previously implicated in molecular mechanisms related to glaucoma. Conclusion Our gene expression analysis suggested that the NPE and PE of the CB were quite similar. Nonetheless, cell-type specific differences were found. The molecular machineries of the human NPE and PE are involved in a range of neuro-endocrinological, developmental and immunological functions, and perhaps glaucoma.
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Affiliation(s)
- Sarah F. Janssen
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Theo G. M. F. Gorgels
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Koen Bossers
- Laboratory for Neuroregeneration, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Anke H. W. Essing
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Martijn Nagtegaal
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Peter J. van der Spek
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nomdo M. Jansonius
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arthur A. B. Bergen
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Centre, Amsterdam, The Netherlands
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
- * E-mail:
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Montanini L, Ferrari S, Crafa P, Ghirardini S, Ponzin D, Orsoni JG, Mora P. Human RNA integrity after postmortem retinal tissue recovery. Ophthalmic Genet 2012; 34:27-31. [PMID: 22950451 DOI: 10.3109/13816810.2012.720342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To assess the parameters for postmortem retinal tissue recovery and processing that affect the quality of RNA extracted from the retina/retinal pigment epithelium (RPE) complex. METHODS RNA was extracted from retina/RPE samples. The RNA quality was determined based on qualitative/quantitative measurements made with a Bioanalyzer (Agilent) and on the expression of a long retinal gene (RPE65). After a pilot analysis on rats, ocular RNA was extracted from human donor eyeballs (group A) explanted according to conventional procedures for cornea transplantation. In a second experiment, another group of human donor eyeballs (group B) were processed in a much shorter time. The postmortem interval (T) comprised two periods: T1, the time between a donor's death and enucleation, and T2, the time between eyeball explantation and immersion of the excised retina/RPE sample in preservative solution (T = T1 + T2). RESULTS A short T2 was correlated with good quality of RNA extracted from the retina/RPE complex (p = 0.043) and successful expression of a tissue-specific gene (p = 0.007). No other parameter appeared to influence RNA quality. CONCLUSIONS The time between eyeball explantation and immersion of the retina/RPE sample in preservative solution was the chief parameter affecting the quality of RNA extracted from the retina/RPE complex.
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Affiliation(s)
- Luisa Montanini
- Institute of Ophthalmology, University of Parma, Parma, Italy.
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Common genetic determinants of intraocular pressure and primary open-angle glaucoma. PLoS Genet 2012; 8:e1002611. [PMID: 22570627 PMCID: PMC3342933 DOI: 10.1371/journal.pgen.1002611] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 02/06/2012] [Indexed: 01/11/2023] Open
Abstract
Intraocular pressure (IOP) is a highly heritable risk factor for primary open-angle glaucoma and is the only target for current glaucoma therapy. The genetic factors which determine IOP are largely unknown. We performed a genome-wide association study for IOP in 11,972 participants from 4 independent population-based studies in The Netherlands. We replicated our findings in 7,482 participants from 4 additional cohorts from the UK, Australia, Canada, and the Wellcome Trust Case-Control Consortium 2/Blue Mountains Eye Study. IOP was significantly associated with rs11656696, located in GAS7 at 17p13.1 (p = 1.4×10−8), and with rs7555523, located in TMCO1 at 1q24.1 (p = 1.6×10−8). In a meta-analysis of 4 case-control studies (total N = 1,432 glaucoma cases), both variants also showed evidence for association with glaucoma (p = 2.4×10−2 for rs11656696 and p = 9.1×10−4 for rs7555523). GAS7 and TMCO1 are highly expressed in the ciliary body and trabecular meshwork as well as in the lamina cribrosa, optic nerve, and retina. Both genes functionally interact with known glaucoma disease genes. These data suggest that we have identified two clinically relevant genes involved in IOP regulation. Glaucoma is a major eye disease in the elderly and is the second leading cause of blindness worldwide. The numerous familial glaucoma cases, as well as evidence from epidemiological and twin studies, strongly support a genetic component in developing glaucoma. However, it has proven difficult to identify the specific genes involved. Intraocular pressure (IOP) is the major risk factor for glaucoma and the only target for the current glaucoma therapy. IOP has been shown to be highly heritable. We investigated the role of common genetic variants in IOP by performing a genome-wide association study. Discovery analyses in 11,972 participants and subsequent replication analyses in a further 7,482 participants yielded two common genetic variants that were associated with IOP. The first (rs11656696) is located in GAS7 at chromosome 17, the second (rs7555523) in TMCO1 at chromosome 1. Both variants were associated with glaucoma in a meta-analysis of 4 case-control studies. GAS7 and TMCO1 are expressed in the ocular tissues that are involved in glaucoma. Both genes functionally interact with the known glaucoma disease genes. These data suggest that we have identified two genes involved in IOP regulation and glaucomatous neuropathy.
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Bandyopadhyay M, Rohrer B. Matrix metalloproteinase activity creates pro-angiogenic environment in primary human retinal pigment epithelial cells exposed to complement. Invest Ophthalmol Vis Sci 2012; 53:1953-61. [PMID: 22408008 DOI: 10.1167/iovs.11-8638] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Mechanistic studies have shown that inflammation, complement activation, extracellular matrix (ECM) turnover, growth factor imbalance, and oxidative stress are fundamental components of age-related macular degeneration (AMD). Matrix metalloproteinases (MMPs) mediate ECM turnover but also process various bioactive molecules. Here, we tested whether complement attack on RPE monolayers changes MMP secretion and activation, thereby altering the availability of growth factors in the extracellular space. METHODS Human embryonic RPE monolayers with stable transepithelial resistance (TER) were established. Complement activation was induced with H₂O₂ and normal human serum. MMP-2/9, vascular endothelial growth factor (VEGF) and pigment epithelium-derived factor (PEDF) protein, and mRNA levels were analyzed by Western blotting, ELISA, and real-time PCR; activity of MMP-2/9 by gelatin zymography. RESULTS Complement activation resulted in a loss of TER, which required transient membrane attack complex formation, activation of the alternative pathway, and VEGF secretion and signaling. Despite the generation of reactive oxygen species, cellular integrity or intracellular adenosine triphosphate (ATP) levels were unaffected. However, expression of MMP-2/9 and their protease activity was elevated. Inhibition of MMP-2/9 activity increased PEDF and decreased VEGF levels in the apical and basal supernatants but had no effect on their expression levels. VEGF levels in the supernatant correlated with the level TER reduction. CONCLUSIONS These studies suggest that complement activation, by altering the expression and activation of MMPs, has the ability to generate a proangiogenic environment by altering the balance between VEGF and PEDF. Our findings link reported results that have been associated with AMD pathogenesis; oxidative stress; complement activation; VEGF/PEDF ratio; and MMP activity.
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Affiliation(s)
- Mausumi Bandyopadhyay
- Department of Ophthalmology, Storm Eye Institute, Medical University of South Carolina, Charleston, South Carolina, USA
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Baas DC, Ho L, Tanck MW, Fritsche LG, Merriam JE, van het Slot R, Koeleman BP, Gorgels TG, van Duijn CM, Uitterlinden AG, de Jong PT, Hofman A, ten Brink JB, Vingerling JR, Klaver CC, Dean M, Weber BHF, Allikmets R, Hageman GS, Bergen AA. Multicenter cohort association study of SLC2A1 single nucleotide polymorphisms and age-related macular degeneration. Mol Vis 2012; 18:657-74. [PMID: 22509097 PMCID: PMC3324365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 03/14/2012] [Indexed: 11/11/2022] Open
Abstract
PURPOSE Age-related macular degeneration (AMD) is a major cause of blindness in older adults and has a genetically complex background. This study examines the potential association between single nucleotide polymorphisms (SNPs) in the glucose transporter 1 (SLC2A1) gene and AMD. SLC2A1 regulates the bioavailability of glucose in the retinal pigment epithelium (RPE), which might influence oxidative stress-mediated AMD pathology. METHODS Twenty-two SNPs spanning the SLC2A1 gene were genotyped in 375 cases and 199 controls from an initial discovery cohort (the Amsterdam-Rotterdam-Netherlands study). Replication testing was performed in The Rotterdam Study (the Netherlands) and study populations from Würzburg (Germany), the Age Related Eye Disease Study (AREDS; United States), Columbia University (United States), and Iowa University (United States). Subsequently, a meta-analysis of SNP association was performed. RESULTS In the discovery cohort, significant genotypic association between three SNPs (rs3754219, rs4660687, and rs841853) and AMD was found. Replication in five large independent (Caucasian) cohorts (4,860 cases and 4,004 controls) did not yield consistent association results. The genotype frequencies for these SNPs were significantly different for the controls and/or cases among the six individual populations. Meta-analysis revealed significant heterogeneity of effect between the studies. CONCLUSIONS No overall association between SLC2A1 SNPs and AMD was demonstrated. Since the genotype frequencies for the three SLC2A1 SNPs were significantly different for the controls and/or cases between the six cohorts, this study corroborates previous evidence that population dependent genetic risk heterogeneity in AMD exists.
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Affiliation(s)
- Dominique C. Baas
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Lintje Ho
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, EMC, Rotterdam, The Netherlands
| | - Michael W.T. Tanck
- Department of Clinical Epidemiology, Biostatistics & Bioinformatics, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Lars G. Fritsche
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Joanna E. Merriam
- Department of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, NY
| | - Ruben van het Slot
- Department of Medical Genetics Research Section, Utrecht Medical Center (UMC), Utrecht, The Netherlands
| | - Bobby P.C. Koeleman
- Department of Medical Genetics Research Section, Utrecht Medical Center (UMC), Utrecht, The Netherlands
| | - Theo G.M.F. Gorgels
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Internal Medicine, EMC, Rotterdam, The Netherlands
| | - Paulus T.V.M. de Jong
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands,Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, AMC, Amsterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Johannes R. Vingerling
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, EMC, Rotterdam, The Netherlands
| | - Caroline C.W. Klaver
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, EMC, Rotterdam, The Netherlands
| | - Michael Dean
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD
| | | | - Rando Allikmets
- Department of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, NY
| | - Gregory S. Hageman
- Department of Ophthalmology and Visual Sciences, The University of Iowa, IA,Center for the Study of Macular Degeneration, University of California, Santa Barbara, CA
| | - Arthur A.B. Bergen
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands,Department of Ophthalmology, AMC, Amsterdam, The Netherlands,Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
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Baas DC, Despriet DD, Gorgels TGMF, Bergeron-Sawitzke J, Uitterlinden AG, Hofman A, van Duijn CM, Merriam JE, Smith RT, Barile GR, ten Brink JB, Vingerling JR, Klaver CCW, Allikmets R, Dean M, Bergen AAB. The ERCC6 gene and age-related macular degeneration. PLoS One 2010; 5:e13786. [PMID: 21072178 PMCID: PMC2967476 DOI: 10.1371/journal.pone.0013786] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 10/08/2010] [Indexed: 01/22/2023] Open
Abstract
Background Age-related macular degeneration (AMD) is the leading cause of irreversible visual loss in the developed countries and is caused by both environmental and genetic factors. A recent study (Tuo et al., PNAS) reported an association between AMD and a single nucleotide polymorphism (SNP) (rs3793784) in the ERCC6 (NM_000124) gene. The risk allele also increased ERCC6 expression. ERCC6 is involved in DNA repair and mutations in ERCC6 cause Cockayne syndrome (CS). Amongst others, photosensitivity and pigmentary retinopathy are hallmarks of CS. Methodology/Principal Findings Separate and combined data from three large AMD case-control studies and a prospective population-based study (The Rotterdam Study) were used to analyse the genetic association between ERCC6 and AMD (2682 AMD cases and 3152 controls). We also measured ERCC6 mRNA levels in retinal pigment epithelium (RPE) cells of healthy and early AMD affected human donor eyes. Rs3793784 conferred a small increase in risk for late AMD in the Dutch population (The Rotterdam and AMRO-NL study), but this was not replicated in two non-European studies (AREDS, Columbia University). In addition, the AMRO-NL study revealed no significant association for 9 other variants spanning ERCC6. Finally, we determined that ERCC6 expression in the human RPE did not depend on rs3793784 genotype, but, interestingly, on AMD status: Early AMD-affected donor eyes had a 50% lower ERCC6 expression than healthy donor eyes (P = 0.018). Conclusions/Significance Our meta-analysis of four Caucasian cohorts does not replicate the reported association between SNPs in ERCC6 and AMD. Nevertheless, our findings on ERCC6 expression in the RPE suggest that ERCC6 may be functionally involved in AMD. Combining our data with those of the literature, we hypothesize that the AMD-related reduced transcriptional activity of ERCC6 may be caused by diverse, small and heterogeneous genetic and/or environmental determinants.
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Affiliation(s)
- Dominique C. Baas
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Dominiek D. Despriet
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo G. M. F. Gorgels
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Julie Bergeron-Sawitzke
- Basic Science Program, Human Genetics Section, SAIC-Frederick, Frederick, Maryland, United States of America
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Joanna E. Merriam
- Department of Ophthalmology, and Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - R. Theodore Smith
- Department of Ophthalmology, and Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Gaetano R. Barile
- Department of Ophthalmology, and Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Jacoline B. ten Brink
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Johannes R. Vingerling
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C. W. Klaver
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rando Allikmets
- Department of Ophthalmology, and Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Michael Dean
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Arthur A. B. Bergen
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Solouki AM, Verhoeven VJM, van Duijn CM, Verkerk AJMH, Ikram MK, Hysi PG, Despriet DDG, van Koolwijk LM, Ho L, Ramdas WD, Czudowska M, Kuijpers RWAM, Amin N, Struchalin M, Aulchenko YS, van Rij G, Riemslag FCC, Young TL, Mackey DA, Spector TD, Gorgels TGMF, Willemse-Assink JJM, Isaacs A, Kramer R, Swagemakers SMA, Bergen AAB, van Oosterhout AALJ, Oostra BA, Rivadeneira F, Uitterlinden AG, Hofman A, de Jong PTVM, Hammond CJ, Vingerling JR, Klaver CCW. A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14. Nat Genet 2010; 42:897-901. [PMID: 20835239 PMCID: PMC4115149 DOI: 10.1038/ng.663] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 08/19/2010] [Indexed: 02/07/2023]
Abstract
Refractive errors are the most common ocular disorders worldwide and may lead to blindness. Although this trait is highly heritable, identification of susceptibility genes has been challenging. We conducted a genome-wide association study for refractive error in 5,328 individuals from a Dutch population-based study with replication in four independent cohorts (combined 10,280 individuals in the replication stage). We identified a significant association at chromosome 15q14 (rs634990, P = 2.21 × 10⁻¹⁴). The odds ratio of myopia compared to hyperopia for the minor allele (minor allele frequency = 0.47) was 1.41 (95% CI 1.16-1.70) for individuals heterozygous for the allele and 1.83 (95% CI 1.42-2.36) for individuals homozygous for the allele. The associated locus is near two genes that are expressed in the retina, GJD2 and ACTC1, and appears to harbor regulatory elements which may influence transcription of these genes. Our data suggest that common variants at 15q14 influence susceptibility for refractive errors in the general population.
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Affiliation(s)
- Abbas M Solouki
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
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Wang L, Clark ME, Crossman DK, Kojima K, Messinger JD, Mobley JA, Curcio CA. Abundant lipid and protein components of drusen. PLoS One 2010; 5:e10329. [PMID: 20428236 PMCID: PMC2859054 DOI: 10.1371/journal.pone.0010329] [Citation(s) in RCA: 252] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Accepted: 03/30/2010] [Indexed: 01/24/2023] Open
Abstract
Background Drusen are extracellular lesions characteristic of aging and age-related maculopathy, a major retinal disease of the elderly. We determined the relative proportions of lipids and proteins in drusen capped with retinal pigment epithelium (RPE) and in RPE isolated from non-macular regions of 36 human retinas with grossly normal maculas obtained <6 hr after death. Methodology/Principal Findings Druse pellets were examined by light and electron microscopy. Component proteins were extracted using novel methods for preserved tissues, separated, subjected to tryptic digestion and LC-MS(MS)2 analysis using an ion trap mass spectrometer, and identified with reference to databases. Lipid classes were separated using thin layer chromatography and quantified by densitometry. Major druse components were esterified cholesterol (EC), phosphatidylcholine (PC), and protein (37.5±13.7, 36.9±12.9, and 43.0±11.5 ng/druse, respectively). Lipid-containing particles (median diameter, 77 nm) occupied 37–44% of druse volume. Major proteins include vitronectin, complement component 9, apoE, and clusterin, previously seen in drusen, and ATP synthase subunit β, scavenger receptor B2, and retinol dehydrogenase 5, previously seen in RPE. Drusen and RPE had similar protein profiles, with higher intensities and greater variability in drusen. C8, part of the complement membrane attack complex, was localized in drusen by immunofluorescence. Conclusions/Significance At least 40% of druse content is comprised by lipids dominated by EC and PC, 2 components that are potentially accounted for by just one pathway, the secretion of lipoproteins by RPE. Manipulating genes encoding apolipoprotein pathways would be a fruitful approach to producing drusen with high EC content in laboratory animals. Therapies that directly mitigate drusen should prepare for the substantial volume of neutral lipids. The catalog of major druse proteins is nearing completion.
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Affiliation(s)
- Lan Wang
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Mark E. Clark
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David K. Crossman
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Kyoko Kojima
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jeffrey D. Messinger
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - James A. Mobley
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christine A. Curcio
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Booij JC, Boon CJF, van Schooneveld MJ, ten Brink JB, Bakker A, de Jong PTVM, Hoyng CB, Bergen AAB, Klaver CCW. Course of visual decline in relation to the Best1 genotype in vitelliform macular dystrophy. Ophthalmology 2010; 117:1415-22. [PMID: 20381869 DOI: 10.1016/j.ophtha.2009.11.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 11/24/2009] [Accepted: 11/25/2009] [Indexed: 11/19/2022] Open
Abstract
PURPOSE To describe the disease course in patients with vitelliform macular dystrophy (VMD) with a Best1 mutation and to determine the association between Best1 genotype and visual prognosis. DESIGN Consecutive case series. PARTICIPANTS Fifty-three patients with VMD with Best1 mutations from 27 Dutch families, aged 11 to 87 years. METHODS Best-corrected visual acuity (VA), fundus appearance, and Arden ratio on the electro-oculogram (EOG) during clinical follow-up were assessed from medical records. Mutation analysis of the Best1 gene was performed on DNA samples using denaturing high-pressure liquid chromatography and direct sequencing. MAIN OUTCOME MEASURES Cumulative lifetime risk of visual decline below 0.5, 0.3, and 0.1 for the entire group and stratified for genotype. RESULTS Median age of onset of visual symptoms was 33 years (range: 2-78). The cumulative risk of VA below 0.5 (20/40) was 50% at 55 years and 75% at 66 years. The cumulative risk of decline less than 0.3 (20/63) was 50% by age 66 years and 75% by age 74 years. Two patients progressed to VA less than 0.1 (20/200). Fourteen different mutations were found. Most patients (96%) had missense mutations; the Thr6Pro, Ala10Val, and Tyr227Asn mutations were most common. Visual decline was significantly faster in patients with an Ala10Val mutation than either the Thr6Pro or the Tyr227Asn mutation (P=0.001). CONCLUSIONS Age of onset of visual symptoms varies greatly among patients with VMD. All patients show a gradual decrease in VA, and most progress to visual impairment at a relatively late age. Our data suggest a phenotype-genotype correlation, because the Ala10Val mutation has a more rapid disease progression than other common mutations. FINANCIAL DISCLOSURE(S) The author(s) have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Judith C Booij
- Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
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Strunnikova NV, Maminishkis A, Barb JJ, Wang F, Zhi C, Sergeev Y, Chen W, Edwards AO, Stambolian D, Abecasis G, Swaroop A, Munson PJ, Miller SS. Transcriptome analysis and molecular signature of human retinal pigment epithelium. Hum Mol Genet 2010; 19:2468-86. [PMID: 20360305 PMCID: PMC2876890 DOI: 10.1093/hmg/ddq129] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinal pigment epithelium (RPE) is a polarized cell layer critical for photoreceptor function and survival. The unique physiology and relationship to the photoreceptors make the RPE a critical determinant of human vision. Therefore, we performed a global expression profiling of native and cultured human fetal and adult RPE and determined a set of highly expressed ‘signature’ genes by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues. Using stringent selection criteria of at least 10-fold higher expression in three distinct preparations, we identified 154 RPE signature genes, which were validated by qRT-PCR analysis in RPE and in an independent set of 11 tissues. Several of the highly expressed signature genes encode proteins involved in visual cycle, melanogenesis and cell adhesion and Gene ontology analysis enabled the assignment of RPE signature genes to epithelial channels and transporters (ClCN4, BEST1, SLCA20) or matrix remodeling (TIMP3, COL8A2). Fifteen RPE signature genes were associated with known ophthalmic diseases, and 25 others were mapped to regions of disease loci. An evaluation of the RPE signature genes in a recently completed AMD genomewide association (GWA) data set revealed that TIMP3, GRAMD3, PITPNA and CHRNA3 signature genes may have potential roles in AMD pathogenesis and deserve further examination. We propose that RPE signature genes are excellent candidates for retinal diseases and for physiological investigations (e.g. dopachrome tautomerase in melanogenesis). The RPE signature gene set should allow the validation of RPE-like cells derived from human embryonic or induced pluripotent stem cells for cell-based therapies of degenerative retinal diseases.
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Affiliation(s)
- N V Strunnikova
- Ophthalmic Genetics & Visual Function Branch, NIH, Bethesda, MD 20892-2510, USA
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Booij JC, ten Brink JB, Swagemakers SMA, Verkerk AJMH, Essing AHW, van der Spek PJ, Bergen AAB. A new strategy to identify and annotate human RPE-specific gene expression. PLoS One 2010; 5:e9341. [PMID: 20479888 PMCID: PMC2866542 DOI: 10.1371/journal.pone.0009341] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 01/27/2010] [Indexed: 01/15/2023] Open
Abstract
Background To identify and functionally annotate cell type-specific gene expression in the human retinal pigment epithelium (RPE), a key tissue involved in age-related macular degeneration and retinitis pigmentosa. Methodology RPE, photoreceptor and choroidal cells were isolated from selected freshly frozen healthy human donor eyes using laser microdissection. RNA isolation, amplification and hybridization to 44 k microarrays was carried out according to Agilent specifications. Bioinformatics was carried out using Rosetta Resolver, David and Ingenuity software. Principal Findings Our previous 22 k analysis of the RPE transcriptome showed that the RPE has high levels of protein synthesis, strong energy demands, is exposed to high levels of oxidative stress and a variable degree of inflammation. We currently use a complementary new strategy aimed at the identification and functional annotation of RPE-specific expressed transcripts. This strategy takes advantage of the multilayered cellular structure of the retina and overcomes a number of limitations of previous studies. In triplicate, we compared the transcriptomes of RPE, photoreceptor and choroidal cells and we deduced RPE specific expression. We identified at least 114 entries with RPE-specific gene expression. Thirty-nine of these 114 genes also show high expression in the RPE, comparison with the literature showed that 85% of these 39 were previously identified to be expressed in the RPE. In the group of 114 RPE specific genes there was an overrepresentation of genes involved in (membrane) transport, vision and ophthalmic disease. More fundamentally, we found RPE-specific involvement in the RAR-activation, retinol metabolism and GABA receptor signaling pathways. Conclusions In this study we provide a further specification and understanding of the RPE transcriptome by identifying and analyzing genes that are specifically expressed in the RPE.
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Affiliation(s)
- Judith C. Booij
- Department of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Sigrid M. A. Swagemakers
- Department of Bioinformatics and Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
- Cancer Genomics Centre, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Anke H. W. Essing
- Department of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Peter J. van der Spek
- Department of Bioinformatics and Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Arthur A. B. Bergen
- Department of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Clinical Genetics Academic Medical Centre Amsterdam, University of Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Centre Amsterdam, University of Amsterdam, The Netherlands
- * E-mail:
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Zhu D, Deng X, Xu J, Hinton DR. What determines the switch between atrophic and neovascular forms of age related macular degeneration? - the role of BMP4 induced senescence. Aging (Albany NY) 2009; 1:740-5. [PMID: 20157553 PMCID: PMC2806048 DOI: 10.18632/aging.100078] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 08/10/2009] [Indexed: 01/11/2023]
Abstract
Age-related macular degeneration (AMD), the leading cause of blindness in the elderly, targets the retinal pigment epithelium (RPE), a monolayer of cells at the back of the eye. As AMD progresses, it can develop into two distinct forms of late AMD: "dry," atrophic AMD, characterized by RPE senescence and geographic RPE loss, and "wet," neovascular AMD, characterized by RPE activation with abnormal growth of choroidal vessels. The genetic and molecular pathways that lead to these diverse phenotypes are currently under investigation. We have found that bone morphogenetic protein-4 (BMP4) is differentially expressed in atrophic and neovascular AMD. In atrophic AMD, BMP4 is highly expressed in RPE, and mediates oxidative stress induced RPE senescencein vitro via Smad and p38 pathways. In contrast, in neovascular AMD lesions, BMP4 expression in RPE is low, possibly a result of local expression of pro-inflammatory mediators. Thus, BMP4 may be involved in the molecular switch determining which phenotypic pathway is taken in the progression of AMD.
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Affiliation(s)
- Danhong Zhu
- Arnold and Mabel Beckman Macular Research Center, Doheny Eye Institute, Los Angeles, CA 90033, USA
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