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Ptito M, Bleau M, Bouskila J. The Retina: A Window into the Brain. Cells 2021; 10:cells10123269. [PMID: 34943777 PMCID: PMC8699497 DOI: 10.3390/cells10123269] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 11/18/2021] [Indexed: 12/18/2022] Open
Affiliation(s)
- Maurice Ptito
- School of Optometry, University of Montreal, Montreal, QC H3T 1P1, Canada; (M.B.); (J.B.)
- Department of Neuroscience, Copenhagen University, 2200 Copenhagen, Denmark
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
- Correspondence:
| | - Maxime Bleau
- School of Optometry, University of Montreal, Montreal, QC H3T 1P1, Canada; (M.B.); (J.B.)
| | - Joseph Bouskila
- School of Optometry, University of Montreal, Montreal, QC H3T 1P1, Canada; (M.B.); (J.B.)
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Qiu Y, Yu P, Lin R, Fu X, Hao B, Lei B. Genome-wide retinal transcriptome analysis of endotoxin-induced uveitis in mice with next-generation sequencing. Mol Vis 2017; 23:395-406. [PMID: 28706439 PMCID: PMC5501689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 06/30/2017] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Endotoxin-induced uveitis (EIU) is a well-established mouse model for studying human acute inflammatory uveitis. The purpose of this study is to investigate the genome-wide retinal transcriptome profile of EIU. METHODS The anterior segment of the mice was examined with a slit-lamp, and clinical scores were evaluated simultaneously. The histological changes in the posterior segment of the eyes were evaluated with hematoxylin and eosin (H&E) staining. A high throughput RNA sequencing (RNA-seq) strategy using the Illumina Hiseq 2500 platform was applied to characterize the retinal transcriptome profile from lipopolysaccharide (LPS)-treated and untreated mice. The validation of the differentially expressed genes (DEGs) was analyzed with real-time PCR. RESULTS At the 24th hour after challenge, the clinical score of the LPS group was significantly higher (3.83±0.75, mean ± standard deviation [SD]) than that of the control group (0.08±0.20, mean ± SD; p<0.001). The histological evaluation showed a large number of inflammatory cells infiltrated into the vitreous cavity in the LPS group compared with the control group. A total of 478 DEGs were identified with RNA-seq. Among these genes, 406 were upregulated and 72 were downregulated in the LPS group. Gene Ontology (GO) enrichment showed three significantly enriched upregulated terms. Twenty-one upregulated and seven downregulated pathways were remarkably enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Eleven inflammatory response-, complement system-, fibrinolytic system-, and cell stress-related genes were validated to show similar results as the RNA-seq. CONCLUSIONS We first reported the retinal transcriptome profile of the EIU mouse with RNA-seq. The results indicate that the abnormal changes in the inflammatory response-, complement system-, fibrinolytic system-, and cell stress-related genes occurred concurrently in EIU. These genes may play an important role in the pathogenesis of EIU. This study will lead to a better understanding of the underlying mechanisms and shed light on discovering novel therapeutic targets for ocular inflammation.
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Affiliation(s)
- Yiguo Qiu
- Department of Ophthalmology, the First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing, China
| | - Peng Yu
- Department of Ophthalmology, the First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing, China
| | - Ru Lin
- Department of Ophthalmology, the First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing, China
| | - Xinyu Fu
- Department of Ophthalmology, the First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing, China
| | - Bingtao Hao
- Cancer Research Institute, Southern Medical University, Guangzhou, China
| | - Bo Lei
- Department of Ophthalmology, the First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing, China,Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, China
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3
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De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing. GENETICS RESEARCH INTERNATIONAL 2015; 2015:638679. [PMID: 26788372 PMCID: PMC4695645 DOI: 10.1155/2015/638679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/29/2023]
Abstract
We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.
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Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015; 46:1-30. [PMID: 25668385 PMCID: PMC4402139 DOI: 10.1016/j.preteyeres.2015.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/10/2023]
Abstract
Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.
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Affiliation(s)
- Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA.
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5
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Farkas MH, Au ED, Sousa ME, Pierce EA. RNA-Seq: Improving Our Understanding of Retinal Biology and Disease. Cold Spring Harb Perspect Med 2015; 5:a017152. [PMID: 25722474 PMCID: PMC4561396 DOI: 10.1101/cshperspect.a017152] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Over the past several years, rapid technological advances have allowed for a dramatic increase in our knowledge and understanding of the transcriptional landscape, because of the ability to study gene expression in greater depth and with more detail than previously possible. To this end, RNA-Seq has quickly become one of the most widely used methods for studying transcriptomes of tissues and individual cells. Unlike previously favored analysis methods, RNA-Seq is extremely high-throughput, and is not dependent on an annotated transcriptome, laying the foundation for novel genetic discovery. Additionally, RNA-Seq derived transcriptomes provide a basis for widening the scope of research to identify potential targets in the treatment of retinal disease.
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Affiliation(s)
- Michael H Farkas
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114
| | - Elizabeth D Au
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114
| | - Maria E Sousa
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114
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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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Goetz JJ, Farris C, Chowdhury R, Trimarchi JM. Making of a retinal cell: insights into retinal cell-fate determination. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:273-321. [PMID: 24411174 DOI: 10.1016/b978-0-12-800097-7.00007-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Understanding the process by which an uncommitted dividing cell produces particular specialized cells within a tissue remains a fundamental question in developmental biology. Many tissues are well suited for cell-fate studies, but perhaps none more so than the developing retina. Traditionally, experiments using the retina have been designed to elucidate the influence that individual environmental signals or transcription factors can have on cell-fate decisions. Despite a substantial amount of information gained through these studies, there is still much that we do not yet understand about how cell fate is controlled on a systems level. In addition, new factors such as noncoding RNAs and regulators of chromatin have been shown to play roles in cell-fate determination and with the advent of "omics" technology more factors will most likely be identified. In this chapter we summarize both the traditional view of retinal cell-fate determination and introduce some new ideas that are providing a challenge to the older way of thinking about the acquisition of cell fates.
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Affiliation(s)
- Jillian J Goetz
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Caitlin Farris
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Rebecca Chowdhury
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Jeffrey M Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA.
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Farkas MH, Grant GR, White JA, Sousa ME, Consugar MB, Pierce EA. Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. BMC Genomics 2013; 14:486. [PMID: 23865674 PMCID: PMC3924432 DOI: 10.1186/1471-2164-14-486] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 07/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease. RESULTS We sequenced RNA prepared from three normal human retinas and characterized the retinal transcriptome at an unprecedented level due to the increased depth of sampling provided by the RNA-seq approach. We used a non-redundant reference transcriptome from all of the empirically-determined human reference tracks to identify annotated and novel sequences expressed in the retina. We detected 79,915 novel alternative splicing events, including 29,887 novel exons, 21,757 3' and 5' alternate splice sites, and 28,271 exon skipping events. We also identified 116 potential novel genes. These data represent a significant addition to the annotated human transcriptome. For example, the novel exons detected increase the number of identified exons by 3%. Using a high-throughput RNA capture approach to validate 14,696 of these novel transcriptome features we found that 99% of the putative novel events can be reproducibly detected. Further, 15-36% of the novel splicing events maintain an open reading frame, suggesting they produce novel protein products. CONCLUSIONS To our knowledge, this is the first application of RNA capture to perform large-scale validation of novel transcriptome features. In total, these analyses provide extensive detail about a previously uncharacterized level of transcript diversity in the human retina.
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Affiliation(s)
- Michael H Farkas
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Gregory R Grant
- Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A White
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Maria E Sousa
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Mark B Consugar
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
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9
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Kandpal RP, Rajasimha HK, Brooks MJ, Nellissery J, Wan J, Qian J, Kern TS, Swaroop A. Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs. Mol Vis 2012; 18:1123-46. [PMID: 22605924 PMCID: PMC3351417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 04/28/2012] [Indexed: 11/15/2022] Open
Abstract
PURPOSE To define gene expression changes associated with diabetic retinopathy in a mouse model using next generation sequencing, and to utilize transcriptome signatures to assess molecular pathways by which pharmacological agents inhibit diabetic retinopathy. METHODS We applied a high throughput RNA sequencing (RNA-seq) strategy using Illumina GAIIx to characterize the entire retinal transcriptome from nondiabetic and from streptozotocin-treated mice 32 weeks after induction of diabetes. Some of the diabetic mice were treated with inhibitors of receptor for advanced glycation endproducts (RAGE) and p38 mitogen activated protein (MAP) kinase, which have previously been shown to inhibit diabetic retinopathy in rodent models. The transcripts and alternatively spliced variants were determined in all experimental groups. RESULTS Next generation sequencing-based RNA-seq profiles provided comprehensive signatures of transcripts that are altered in early stages of diabetic retinopathy. These transcripts encoded proteins involved in distinct yet physiologically relevant disease-associated pathways such as inflammation, microvasculature formation, apoptosis, glucose metabolism, Wnt signaling, xenobiotic metabolism, and photoreceptor biology. Significant upregulation of crystallin transcripts was observed in diabetic animals, and the diabetes-induced upregulation of these transcripts was inhibited in diabetic animals treated with inhibitors of either RAGE or p38 MAP kinase. These two therapies also showed dissimilar regulation of some subsets of transcripts that included alternatively spliced versions of arrestin, neutral sphingomyelinase activation associated factor (Nsmaf), SH3-domain GRB2-like interacting protein 1 (Sgip1), and axin. CONCLUSIONS Diabetes alters many transcripts in the retina, and two therapies that inhibit the vascular pathology similarly inhibit a portion of these changes, pointing to possible molecular mechanisms for their beneficial effects. These therapies also changed the abundance of various alternatively spliced versions of signaling transcripts, suggesting a possible role of alternative splicing in disease etiology. Our studies clearly demonstrate RNA-seq as a comprehensive strategy for identifying disease-specific transcripts, and for determining comparative profiles of molecular changes mediated by candidate drugs.
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Affiliation(s)
- Raj P. Kandpal
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD,Department of Basic Medical Sciences and Western Diabetes Institute, Western University of Health Sciences, Pomona, CA
| | - Harsha K. Rajasimha
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Matthew J. Brooks
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Jacob Nellissery
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Jun Wan
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Timothy S. Kern
- Department of Medicine, Case Western Reserve University School of Medicine, and Stokes Veterans Administration Hospital, Cleveland, OH,Department of Pharmacology, Case Western Reserve University School of Medicine, and Stokes Veterans Administration Hospital, Cleveland, OH,Department of Ophthalmology, Case Western Reserve University School of Medicine, and Stokes Veterans Administration Hospital, Cleveland, OH
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
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Gamsiz ED, Ouyang Q, Schmidt M, Nagpal S, Morrow EM. Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing. Genomics 2011; 99:44-51. [PMID: 22032952 DOI: 10.1016/j.ygeno.2011.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 09/05/2011] [Accepted: 09/21/2011] [Indexed: 11/16/2022]
Abstract
Genome-wide characterization of the retinal transcriptome is central to understanding development, physiology and disorders of the visual system. Massively parallel, short-read sequencing of mRNA libraries was used to generate an extensive map of the transcriptome of the adult, murine neural retina. RNA-seq data strongly corroborates prior transcriptome studies by microarray and SAGE. However, several novel features of the retinal transcriptome were discovered. For example, retinal disease genes were discovered to be among the most highly expressed in the transcriptome. We also demonstrate other interesting features of the retinal transcriptome, for example, that the retina appears to employ a very specific and restricted set of synaptic vesicle genes, and also that there is persistence of expression of a majority of "neurodevelopmental" genes into adulthood. Retina transcriptome studies utilizing novel sequencing methods have been highly informative and these data may also serve as a resource for the community of researchers.
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Affiliation(s)
- Ece D Gamsiz
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Box G-E4, Providence, RI 02903, USA
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Lachke SA, Maas RL. Building the developmental oculome: systems biology in vertebrate eye development and disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:305-323. [PMID: 20836031 DOI: 10.1002/wsbm.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate eye is a sophisticated multicomponent organ that has been actively studied for over a century, resulting in the identification of the major embryonic and molecular events involved in its complex developmental program. Data gathered so far provides sufficient information to construct a rudimentary network of the various signaling molecules, transcription factors, and their targets for several key stages of this process. With the advent of genomic technologies, there has been a rapid expansion in our ability to collect and process biological information, and the use of systems-level approaches to study specific aspects of vertebrate eye development has already commenced. This is beginning to result in the definition of the dynamic developmental networks that operate in ocular tissues, and the interactions of such networks between coordinately developing ocular tissues. Such an integrative understanding of the eye by a comprehensive systems-level analysis can be termed the 'oculome', and that of serial developmental stages of the eye as it transits from its initiation to a fully formed functional organ represents the 'developmental oculome'. Construction of the developmental oculome will allow novel mechanistic insights that are essential for organ regeneration-based therapeutic applications, and the generation of computational models for eye disease states to predict the effects of drugs. This review discusses our present understanding of two of the individual components of the developing vertebrate eye--the lens and retina--at both the molecular and systems levels, and outlines the directions and tools required for construction of the developmental oculome.
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Affiliation(s)
- Salil A Lachke
- Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard L Maas
- Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Abstract
Humans possess the remarkable ability to perceive color, shape, and motion, and to differentiate between light intensities varied by over nine orders of magnitude. Phototransduction—the process in which absorbed photons are converted into electrical responses—is the first stage of visual processing, and occurs in the outer segment, the light-sensing organelle of the photoreceptor cell. Studies of genes linked to human inherited blindness have been crucial to understanding the biogenesis of the outer segment and membrane-trafficking of photoreceptors.
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Affiliation(s)
- Ching-Hwa Sung
- Dyson Vision Research Institute, Department of Ophthalmology, Weill Cornell Medical College, New York, NY 10065, USA.
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Oshikawa M, Sugai Y, Usami R, Ohtoko K, Toyama S, Kato S. Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. DNA Res 2008; 15:123-36. [PMID: 18487259 PMCID: PMC2650634 DOI: 10.1093/dnares/dsn010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recently, we have developed a vector-capping method for constructing a full-length cDNA library. In the present study, we performed in-depth analysis of the vector-capped cDNA library prepared from a single type of cell. As a result of single-pass sequencing analysis of 24 000 clones randomly isolated from the unamplified library, we identified 19 951 full-length cDNA clones whose intactness was confirmed by the presence of an additional G at their 5' end. The full-length cDNA content was >95%. Mapping these sequences to the human genome, we identified 4513 transcriptional units that include 36 antisense transcripts against known genes. Comparison of the frequencies of abundant clones showed that the expression profiles of different libraries, including the distribution of transcriptional start sites (TSSs), were reproducible. The analysis of long-sized cDNAs showed that this library contained many cDNAs with a long-sized insert up to 11 199 bp of golgin B, including multiple slicing variants for filamin A and filamin B. These results suggest that the size-unbiased full-length cDNA library constructed using the vector-capping method will be an ideal resource for fine expression profiling of transcriptional variants with alternative TSSs and alternative splicing.
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Affiliation(s)
- Mio Oshikawa
- Department of Rehabilitation Engineering, Research Institute, National Rehabilitation Center for Persons with Disabilities, 4-1 Namiki, Tokorozawa, Saitama 359-8555, Japan
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Ben-Shlomo G, Ofri R, Bandah D, Rosner M, Sharon D. Microarray-based gene expression analysis during retinal maturation of albino rats. Graefes Arch Clin Exp Ophthalmol 2008; 246:693-702. [PMID: 18286297 DOI: 10.1007/s00417-008-0772-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/03/2008] [Accepted: 01/12/2008] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND In recent years, the rat has become a commonly-used animal model for the study of retinal diseases. Similar to other tissues, the retina undergoes significant functional changes during maturation. Aiming to gain knowledge on additional aspects of retinal maturation, we performed gene expression and histological analyses of the rat retina during maturation. METHODS Rat retinas were dissected at three time points. Histological examination of the samples was performed, and the expression levels of retinal genes were evaluated using the rat whole-genome microarray system. Quantitative real-time PCR analysis was used to validate selected expression patterns. Various statistical and bioinformatic tools were used to identify differentially expressed genes. RESULTS The microarray analysis revealed a relatively high number of highly expressed non-annotated genes. We identified 603 differentially expressed genes, which were grouped into six clusters based on changes in expression levels during the first 20 weeks of life. A bioinformatic analysis of these clusters revealed sets of genes encoding proteins with functions that are likely to be relevant to retinal maturation (potassium, sodium, calcium, and chloride channels, synaptic vesicle transport, and axonogenesis). The histological analysis revealed a significant reduction of outer nuclear layer thickness and retinal ganglion cell number during maturation. CONCLUSIONS These data, taken together with our previously reported electrophysiological data, contribute to our understanding of the retinal maturation processes of this widely-used animal model.
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Affiliation(s)
- Gil Ben-Shlomo
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot, Israel
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15
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Trimarchi JM, Stadler MB, Roska B, Billings N, Sun B, Bartch B, Cepko CL. Molecular heterogeneity of developing retinal ganglion and amacrine cells revealed through single cell gene expression profiling. J Comp Neurol 2007; 502:1047-65. [PMID: 17444492 DOI: 10.1002/cne.21368] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
During development of the central nervous system (CNS), cycling uncommitted progenitor cells give rise to a variety of distinct neuronal and glial cell types. As these different cell types are born they progress from newly specified cells to fully differentiated neurons and glia. In order to define the developmental processes of individual cell types, single cell expression profiling was carried out on developing ganglion and amacrine cells of the murine retina. Individual cells from multiple developmental stages were isolated and profiled on Affymetrix oligonucleotide arrays. Two-color fluorescent in situ hybridization on dissociated retinas was used to verify and extend the microarray results by allowing quantitative measurements of a large number of cells coexpressing two genes. Together, these experiments have yielded an expanded view of the processes underway in developing retinal ganglion and amacrine cells, as well as several hundred new marker genes for these cell types. In addition, this study has allowed for the definition of some of the molecular heterogeneity both between developing ganglion and amacrine cells and among subclasses of each cell type.
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Affiliation(s)
- Jeffrey M Trimarchi
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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16
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Mordes D, Yuan L, Xu L, Kawada M, Molday RS, Wu JY. Identification of photoreceptor genes affected by PRPF31 mutations associated with autosomal dominant retinitis pigmentosa. Neurobiol Dis 2007; 26:291-300. [PMID: 17350276 PMCID: PMC2014719 DOI: 10.1016/j.nbd.2006.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 07/27/2006] [Accepted: 08/14/2006] [Indexed: 10/23/2022] Open
Abstract
Several ubiquitously expressed genes encoding pre-mRNA splicing factors have been associated with autosomal dominant retinitis pigmentosa (adRP), including PRPF31, PRPF3 and PRPF8. Molecular mechanisms by which defects in pre-mRNA splicing factors cause photoreceptor degeneration are not clear. To investigate the role of pre-mRNA splicing in photoreceptor gene expression and function, we have begun to search for photoreceptor genes whose pre-mRNA splicing is affected by mutations in PRPF31. Using an immunoprecipitation-coupled-microarray method, we identified a number of transcripts associated with PRPF31-containing complexes, including peripherin/RDS, FSCN2 and other photoreceptor-expressed genes. We constructed minigenes to study the effects of PRPF31 mutations on the pre-mRNA splicing of these photoreceptor specific genes. Our experiments demonstrated that mutant PRPF31 significantly inhibited pre-mRNA splicing of RDS and FSCN2. These observations suggest a functional link between ubiquitously expressed and retina-specifically expressed adRP genes. Our results indicate that PRPF31 mutations lead to defective pre-mRNA splicing of photoreceptor-specific genes and that the ubiquitously expressed adRP gene, PRPF31, is critical for pre-mRNA splicing of a subset of photoreceptor genes. Our results provide an explanation for the photoreceptor-specific phenotype of PRPF31 mutations.
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Affiliation(s)
- Daniel Mordes
- Department of Pediatrics, John F. Kennedy Center for Research on Human Development, Vanderbilt University Medical Center, USA
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17
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Mordes D, Luo X, Kar A, Kuo D, Xu L, Fushimi K, Yu G, Sternberg P, Wu JY. Pre-mRNA splicing and retinitis pigmentosa. Mol Vis 2006; 12:1259-71. [PMID: 17110909 PMCID: PMC2683577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Retinitis pigmentosa (RP) is a group of genetically and clinically heterogeneous retinal diseases and a common cause of blindness. Among the 12 autosomal dominant RP (adRP) genes identified, four encode ubiquitously expressed proteins involved in pre-mRNA splicing, demonstrating the important role that pre-mRNA splicing plays in the pathogenesis of retinal degeneration. This review focuses on recent progress in identifying adRP mutations in genes encoding pre-mRNA splicing factors and the potential underlying molecular mechanisms.
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Affiliation(s)
- Daniel Mordes
- Department of Pediatrics, John F. Kennedy Center for Research on Human Development, Nashville, TN, USA
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18
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Bowes Rickman C, Ebright JN, Zavodni ZJ, Yu L, Wang T, Daiger SP, Wistow G, Boon K, Hauser MA. Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE. Invest Ophthalmol Vis Sci 2006; 47:2305-16. [PMID: 16723438 PMCID: PMC2813776 DOI: 10.1167/iovs.05-1437] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To develop large-scale, high-throughput annotation of the human macula transcriptome and to identify and prioritize candidate genes for inherited retinal dystrophies, based on ocular-expression profiles using serial analysis of gene expression (SAGE). METHODS Two human retina and two retinal pigment epithelium (RPE)/choroid SAGE libraries made from matched macula or midperipheral retina and adjacent RPE/choroid of morphologically normal 28- to 66-year-old donors and a human central retina longSAGE library made from 41- to 66-year-old donors were generated. Their transcription profiles were entered into a relational database, EyeSAGE, including microarray expression profiles of retina and publicly available normal human tissue SAGE libraries. EyeSAGE was used to identify retina- and RPE-specific and -associated genes, and candidate genes for retina and RPE disease loci. Differential and/or cell-type specific expression was validated by quantitative and single-cell RT-PCR. RESULTS Cone photoreceptor-associated gene expression was elevated in the macula transcription profiles. Analysis of the longSAGE retina tags enhanced tag-to-gene mapping and revealed alternatively spliced genes. Analysis of candidate gene expression tables for the identified Bardet-Biedl syndrome disease gene (BBS5) in the BBS5 disease region table yielded BBS5 as the top candidate. Compelling candidates for inherited retina diseases were identified. CONCLUSIONS The EyeSAGE database, combining three different gene-profiling platforms including the authors' multidonor-derived retina/RPE SAGE libraries and existing single-donor retina/RPE libraries, is a powerful resource for definition of the retina and RPE transcriptomes. It can be used to identify retina-specific genes, including alternatively spliced transcripts and to prioritize candidate genes within mapped retinal disease regions.
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19
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Akimoto M, Cheng H, Zhu D, Brzezinski JA, Khanna R, Filippova E, Oh ECT, Jing Y, Linares JL, Brooks M, Zareparsi S, Mears AJ, Hero A, Glaser T, Swaroop A. Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors. Proc Natl Acad Sci U S A 2006; 103:3890-5. [PMID: 16505381 PMCID: PMC1383502 DOI: 10.1073/pnas.0508214103] [Citation(s) in RCA: 256] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Indexed: 11/18/2022] Open
Abstract
The Maf-family transcription factor Nrl is a key regulator of photoreceptor differentiation in mammals. Ablation of the Nrl gene in mice leads to functional cones at the expense of rods. We show that a 2.5-kb Nrl promoter segment directs the expression of enhanced GFP specifically to rod photoreceptors and the pineal gland of transgenic mice. GFP is detected shortly after terminal cell division, corresponding to the timing of rod genesis revealed by birthdating studies. In Nrl-/- retinas, the GFP+ photoreceptors express S-opsin, consistent with the transformation of rod precursors into cones. We report the gene profiles of freshly isolated flow-sorted GFP+ photoreceptors from wild-type and Nrl-/- retinas at five distinct developmental stages. Our results provide a framework for establishing gene regulatory networks that lead to mature functional photoreceptors from postmitotic precursors. Differentially expressed rod and cone genes are excellent candidates for retinopathies.
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Affiliation(s)
- Masayuki Akimoto
- Departments of *Ophthalmology and Visual Sciences
- Translational Research Center, Kyoto University Hospital, Kyoto 606-8507, Japan; and
| | | | - Dongxiao Zhu
- Statistics
- Bioinformatics, University of Michigan, Ann Arbor, MI 48105
| | | | - Ritu Khanna
- Departments of *Ophthalmology and Visual Sciences
| | | | | | | | | | | | | | - Alan J. Mears
- Departments of *Ophthalmology and Visual Sciences
- **University of Ottawa Eye Institute and Ottawa Health Research Institute, Ottawa, ON, Canada K1H 8L6
| | - Alfred Hero
- Statistics
- Electrical Engineering and Computer Science
- Biomedical Engineering, and
- Bioinformatics, University of Michigan, Ann Arbor, MI 48105
| | - Tom Glaser
- Human Genetics
- Internal Medicine, Programs in
| | - Anand Swaroop
- Departments of *Ophthalmology and Visual Sciences
- Human Genetics
- Translational Research Center, Kyoto University Hospital, Kyoto 606-8507, Japan; and
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20
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Qian J, Esumi N, Chen Y, Wang Q, Chowers I, Zack DJ. Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. Nucleic Acids Res 2005; 33:3479-91. [PMID: 15967807 PMCID: PMC1153713 DOI: 10.1093/nar/gki658] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 04/28/2005] [Accepted: 05/26/2005] [Indexed: 01/22/2023] Open
Abstract
Identification of tissue-specific gene regulatory networks can yield insights into the molecular basis of a tissue's development, function and pathology. Here, we present a computational approach designed to identify potential regulatory target genes of photoreceptor cell-specific transcription factors (TFs). The approach is based on the hypothesis that genes related to the retina in terms of expression, disease and/or function are more likely to be the targets of retina-specific TFs than other genes. A list of genes that are preferentially expressed in retina was obtained by integrating expressed sequence tag, SAGE and microarray datasets. The regulatory targets of retina-specific TFs are enriched in this set of retina-related genes. A Bayesian approach was employed to integrate information about binding site location relative to a gene's transcription start site. Our method was applied to three retina-specific TFs, CRX, NRL and NR2E3, and a number of potential targets were predicted. To experimentally assess the validity of the bioinformatic predictions, mobility shift, transient transfection and chromatin immunoprecipitation assays were performed with five predicted CRX targets, and the results were suggestive of CRX regulation in 5/5, 3/5 and 4/5 cases, respectively. Together, these experiments strongly suggest that RP1, GUCY2D, ABCA4 are novel targets of CRX.
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Affiliation(s)
- Jiang Qian
- Wilmer Institute, Johns Hopkins University School of Medicine Baltimore, MD 21287, USA.
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21
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Abstract
Regenerative medicine constitutes a potentially promising therapy for blind people suffering from retinal degenerative diseases such as retinitis pigmentosa and age-related macular degeneration. For the realization of retinal regeneration, it is necessary to establish 1) a method to produce functional photoreceptor cells in vitro and 2) successful transplantation of the donor cells to connect their axons to the recipient secondary neurons so that they can function properly. The results of experimental transplantation of human retinal photoreceptor cells from cadaveric eyes or of fetal retinal cells into the retina of RP patients have not been satisfactory, but encouraging enough to indicate that the transplantation of developing retinal cells may have beneficial results. Recently, attempts have been made to generate photoreceptor-like cells from stem cells, but it remains to be seen whether they are in fact photoreceptor cells. It is therefore important to fully understand the mechanisms involved in the development of these cells, and to characterize them not only by transcriptome but also by functional analysis.
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Affiliation(s)
- Masayuki Akimoto
- Translational Research Center, Kyoto University Hospital, Japan.
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22
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Zhang SSM, Xu X, Li J, Liu MG, Zhao H, Soares MB, Barnstable CJ, Fu XY. Comprehensive in silico functional specification of mouse retina transcripts. BMC Genomics 2005; 6:40. [PMID: 15777472 PMCID: PMC1083414 DOI: 10.1186/1471-2164-6-40] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 03/18/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The retina is a well-defined portion of the central nervous system (CNS) that has been used as a model for CNS development and function studies. The full specification of transcripts in an individual tissue or cell type, like retina, can greatly aid the understanding of the control of cell differentiation and cell function. In this study, we have integrated computational bioinformatics and microarray experimental approaches to classify the tissue specificity and developmental distribution of mouse retina transcripts. RESULTS We have classified a set of retina-specific genes using sequence-based screening integrated with computational and retina tissue-specific microarray approaches. 33,737 non-redundant sequences were identified as retina transcript clusters (RTCs) from more than 81,000 mouse retina ESTs. We estimate that about 19,000 to 20,000 genes might express in mouse retina from embryonic to adult stages. 39.1% of the RTCs are not covered by 60,770 RIKEN full-length cDNAs. Through comparison with 2 million mouse ESTs, spectra of neural, retinal, late-generated retinal, and photoreceptor -enriched RTCs have been generated. More than 70% of these RTCs have data from biological experiments confirming their tissue-specific expression pattern. The highest-grade retina-enriched pool covered almost all the known genes encoding proteins involved in photo-transduction. CONCLUSION This study provides a comprehensive mouse retina transcript profile for further gene discovery in retina and suggests that tissue-specific transcripts contribute substantially to the whole transcriptome.
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Affiliation(s)
- Samuel Shao-Min Zhang
- Departments of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520, USA
- Departments of Ophthalmology and Visual Science, Yale University School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA
| | - Xuming Xu
- Departments of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520, USA
- Departments of Ophthalmology and Visual Science, Yale University School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA
| | - Jinming Li
- Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA
| | - Mu-Gen Liu
- Departments of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520, USA
- Departments of Ophthalmology and Visual Science, Yale University School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA
| | - Hongyu Zhao
- Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - M Bento Soares
- Departments of Pediatrics, Biochemistry, Orthopaedics, Physiology and Biophysics, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, 375 Newton Road, Iowa City, IA 52242, USA
| | - Colin J Barnstable
- Departments of Ophthalmology and Visual Science, Yale University School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA
- Department of Neurobiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Xin-Yuan Fu
- Departments of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520, USA
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23
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Li CM, Presley JB, Zhang X, Dashti N, Chung BH, Medeiros NE, Guidry C, Curcio CA. Retina expresses microsomal triglyceride transfer protein: implications for age-related maculopathy. J Lipid Res 2005; 46:628-40. [PMID: 15654125 DOI: 10.1194/jlr.m400428-jlr200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The principal extracellular lesions of age-related maculopathy (ARM), the leading cause of vision loss in the elderly, involve Bruch's membrane (BrM), a thin vascular intima between the retinal pigment epithelium (RPE) and its blood supply. With age, 80-100 nm solid particles containing esterified cholesterol (EC) accumulate in normal BrM, and apolipoprotein B (apoB) immunoreactivity is detectable in BrM- and ARM-associated lesions. Yet little evidence indicates that increased plasma cholesterol is a risk factor for ARM. To determine if RPE is capable of assembling its own apoB-containing lipoprotein, we examined RPE for the expression of microsomal triglyceride transfer protein (MTP), which is required for this process. Consistent with previous evidence for apoB expression, MTP is expressed in RPE, the ARPE-19 cell line, and, unexpectedly, retinal ganglion cells, which are neurons of the central nervous system. De novo synthesis and secretion of neutral lipid by ARPE-19 was supported by high levels of radiolabeled EC and triglyceride in medium after supplementation with oleate. Lipoprotein assembly and secretion is implicated as a constitutive retinal function and a plausible candidate mechanism involved in forming extracellular cholesterol-containing lesions in ARM. The pigmentary retinopathy and neuropathy of abetalipoproteinemia (Mendelian Inheritance of Man 200100; Bassen-Kornzwieg disease), which is caused by mutations in the MTP gene, may involve loss of function at the retina.
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Affiliation(s)
- Chuan-Ming Li
- Department of Ophthalmology, University of Alabama School of Medicine, Birmingham, AL, USA
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24
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Abstract
Multiple clinical and physiopathological studies as well as genetic analysis, suggest that diabetic retinopathy (DR) is a consequent of interactions between environmental factors, especially hyperglycaemia, and several genetic factors. The genes of aldose reductase (AR), inducible nitric oxide synthase (NOS2A), endothelial nitric oxide synthase (NOS3), vascular endothelial growth factor (VEGF), pigmented epithelium-derived factor (PEDF), protein kinase C-beta (PKC-beta) and receptor for advanced glycation end products (RAGE) implicated in the pathogenesis of DR. The only genetic marker associated with risk of DR in several studies is a microsatellite (A-C)n at 5'end of AR. The synergistic combination of conventional approaches (e.g. candidate gene association studies) with new emerging technologies (e.g. biochips) will be a key factor in the elucidation of the genetic aspects of DR.
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Affiliation(s)
- M J Taverna
- Laboratoire de Diabétologie, INSERM U.341, Hôpital Hôtel-Dieu, 75004 Paris.
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25
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Yu J, Farjo R, MacNee SP, Baehr W, Stambolian DE, Swaroop A. Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina. Genome Biol 2003; 4:R65. [PMID: 14519200 PMCID: PMC328454 DOI: 10.1186/gb-2003-4-10-r65] [Citation(s) in RCA: 30] [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: 05/21/2003] [Revised: 07/01/2003] [Accepted: 08/19/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal day 2 (M2PN) eye and adult retina (MRA). RESULTS Annotation of 8,633 non-mitochondrial and non-ribosomal high-quality ESTs revealed that 57% of the sequences represent known genes and 43% are unknown or novel ESTs, with M15E having the highest percentage of novel ESTs. Of these, 2,361 ESTs correspond to 747 unique genes and the remaining 6,272 are represented only once. Phototransduction genes are preferentially identified in MRA, whereas transcripts for cell structure and regulatory proteins are highly expressed in the developing eye. Map locations of human orthologs of known genes uncovered a high density of ocular genes on chromosome 17, and identified 277 genes in the critical regions of 37 retinal disease loci. In silico expression profiling identified 210 genes and/or ESTs over-expressed in the eye; of these, more than 26 are known to have vital retinal function. Comparisons between libraries provided a list of temporally regulated genes and/or ESTs. A few of these were validated by qRT-PCR analysis. CONCLUSIONS Our studies present a large number of potentially interesting genes for biological investigation, and the annotated EST set provides a useful resource for microarray and functional genomic studies.
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Affiliation(s)
- Jindan Yu
- Ophthalmology and Visual Science, University of Michigan, 1000 Wall Street, Ann Arbor, MI 48105, USA
| | - Rafal Farjo
- Ophthalmology and Visual Science, University of Michigan, 1000 Wall Street, Ann Arbor, MI 48105, USA
| | - Sean P MacNee
- Ophthalmology and Visual Science, University of Michigan, 1000 Wall Street, Ann Arbor, MI 48105, USA
| | - Wolfgang Baehr
- Moran Eye Center, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Dwight E Stambolian
- Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, PA 19014, USA
| | - Anand Swaroop
- Ophthalmology and Visual Science, University of Michigan, 1000 Wall Street, Ann Arbor, MI 48105, USA
- Human Genetics, University of Michigan, 1000 Wall Street, Ann Arbor, MI 48105, USA
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