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Ahsanuddin S, Wu AY. Single-cell transcriptomics of the ocular anterior segment: a comprehensive review. Eye (Lond) 2023; 37:3334-3350. [PMID: 37138096 PMCID: PMC10156079 DOI: 10.1038/s41433-023-02539-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Elucidating the cellular and genetic composition of ocular tissues is essential for uncovering the pathophysiology of ocular diseases. Since the introduction of single-cell RNA sequencing (scRNA-seq) in 2009, vision researchers have performed extensive single-cell analyses to better understand transcriptome complexity and heterogeneity of ocular structures. This technology has revolutionized our ability to identify rare cell populations and to make cross-species comparisons of gene expression in both steady state and disease conditions. Importantly, single-cell transcriptomic analyses have enabled the identification of cell-type specific gene markers and signalling pathways between ocular cell populations. While most scRNA-seq studies have been conducted on retinal tissues, large-scale transcriptomic atlases pertaining to the ocular anterior segment have also been constructed in the past three years. This timely review provides vision researchers with an overview of scRNA-seq experimental design, technical limitations, and clinical applications in a variety of anterior segment-related ocular pathologies. We review open-access anterior segment-related scRNA-seq datasets and illustrate how scRNA-seq can be an indispensable tool for the development of targeted therapeutics.
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Affiliation(s)
- Sofia Ahsanuddin
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, New York City, NY, USA
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Albert Y Wu
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA.
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Daich Varela M, Georgiou M, Alswaiti Y, Kabbani J, Fujinami K, Fujinami-Yokokawa Y, Khoda S, Mahroo OA, Robson AG, Webster AR, AlTalbishi A, Michaelides M. CRB1-Associated Retinal Dystrophies: Genetics, Clinical Characteristics, and Natural History. Am J Ophthalmol 2023; 246:107-121. [PMID: 36099972 PMCID: PMC10555856 DOI: 10.1016/j.ajo.2022.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE To analyze the clinical characteristics, natural history, and genetics of CRB1-associated retinal dystrophies. DESIGN Multicenter international retrospective cohort study. METHODS Review of clinical notes, ophthalmic images, and genetic testing results of 104 patients (91 probands) with disease-causing CRB1 variants. Macular optical coherence tomography (OCT) parameters, visual function, fundus characteristics, and associations between variables were the main outcome measures. RESULTS The mean age of the cohort at the first visit was 19.8 ± 16.1 (median 15) years, with a mean follow-up of 9.6 ± 10 years. Based on history, imaging, and clinical examination, 26 individuals were diagnosed with retinitis pigmentosa (RP; 25%), 54 with early-onset severe retinal dystrophy / Leber congenital amaurosis (EOSRD/LCA; 52%), and 24 with macular dystrophy (MD; 23%). Severe visual impairment was most frequent after 40 years of age for patients with RP and after 20 years of age for EOSRD/LCA. Longitudinal analysis revealed a significant difference between baseline and follow-up best-corrected visual acuity in the 3 subcohorts. Macular thickness decreased in most patients with EOSRD/LCA and MD, whereas the majority of patients with RP had increased perifoveal thickness. CONCLUSIONS A subset of individuals with CRB1 variants present with mild, adult-onset RP. EOSRD/LCA phenotype was significantly associated with null variants, and 167_169 deletion was exclusively present in the MD cohort. The poor OCT lamination may have a degenerative component, as well as being congenital. Disease symmetry and reasonable window for intervention highlight CRB1 retinal dystrophies as a promising target for trials of novel therapeutics.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom
| | - Michalis Georgiou
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; Jones Eye Institute (M.G.), University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Yahya Alswaiti
- St John of Jerusalem Eye Hospital group, Jerusalem, Palestine (Y.A., A.A.)
| | - Jamil Kabbani
- Imperial College London (J.K.), London, United Kingdom
| | - Kaoru Fujinami
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center (Y.F.-Y.), Tokyo, Japan
| | - Yu Fujinami-Yokokawa
- UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center (Y.F.-Y.), Tokyo, Japan; Department of Health Policy and Management, School of Medicine, Keio University(Y.F.-Y.), Tokyo, Japan
| | - Shaheeni Khoda
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom
| | - Omar A Mahroo
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom
| | - Anthony G Robson
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom
| | - Andrew R Webster
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom
| | - Alaa AlTalbishi
- St John of Jerusalem Eye Hospital group, Jerusalem, Palestine (Y.A., A.A.)
| | - Michel Michaelides
- Moorfields Eye Hospital (M.D.V., M.G., K.F., S.K., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., M.G., K.F., Y.F.-Y., O.A.M., A.G.R., A.R.W., M.M.), London, United Kingdom.
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3
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Voigt AP, Mullin NK, Stone EM, Tucker BA, Scheetz TE, Mullins RF. Single-cell RNA sequencing in vision research: Insights into human retinal health and disease. Prog Retin Eye Res 2021; 83:100934. [PMID: 33383180 DOI: 10.1016/j.preteyeres.2020.100934] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/03/2023]
Abstract
Gene expression provides valuable insight into cell function. As such, vision researchers have frequently employed gene expression studies to better understand retinal physiology and disease. With the advent of single-cell RNA sequencing, expression experiments provide an unparalleled resolution of information. Instead of studying aggregated gene expression across all cells in a heterogenous tissue, single-cell technology maps RNA to an individual cell, which facilitates grouping of retinal and choroidal cell types for further study. Single-cell RNA sequencing has been quickly adopted by both basic and translational vision researchers, and single-cell level gene expression has been studied in the visual systems of animal models, retinal organoids, and primary human retina, RPE, and choroid. These experiments have generated detailed atlases of gene expression and identified new retinal cell types. Likewise, single-cell RNA sequencing investigations have characterized how gene expression changes in the setting of many retinal diseases, including how choroidal endothelial cells are altered in age-related macular degeneration. In addition, this technology has allowed vision researchers to discover drivers of retinal development and model rare retinal diseases with induced pluripotent stem cells. In this review, we will overview the growing number of single-cell RNA sequencing studies in the field of vision research. We will summarize experimental considerations for designing single-cell RNA sequencing experiments and highlight important advancements in retinal, RPE, choroidal, and retinal organoid biology driven by this technology. Finally, we generalize these findings to genes involved in retinal degeneration and outline the future of single-cell expression experiments in studying retinal disease.
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Fu Y, Xie TH, Zhang YL, Yang N, Shi XN, Gu ZH. Dominant cystoid macular dystrophy associated with mutations in the RP1L1 gene. Int J Ophthalmol 2019; 12:1982-1986. [PMID: 31850186 DOI: 10.18240/ijo.2019.12.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 08/12/2019] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yan Fu
- Department of Ophthalmology, Baoding First Central Hospital, Baoding 071000, Hebei Province, China
| | - Tian-Hao Xie
- Affiliated Hospital of Hebei University, Baoding 071002, Hebei Province, China
| | - Yue-Ling Zhang
- Department of Ophthalmology, Baoding First Central Hospital, Baoding 071000, Hebei Province, China
| | - Na Yang
- Department of Ophthalmology, Baoding First Central Hospital, Baoding 071000, Hebei Province, China
| | - Xiao-Nan Shi
- Department of Ophthalmology, Baoding First Central Hospital, Baoding 071000, Hebei Province, China
| | - Zhao-Hui Gu
- Department of Ophthalmology, Baoding First Central Hospital, Baoding 071000, Hebei Province, China
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May-Simera H, Nagel-Wolfrum K, Wolfrum U. Cilia - The sensory antennae in the eye. Prog Retin Eye Res 2017; 60:144-180. [PMID: 28504201 DOI: 10.1016/j.preteyeres.2017.05.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Abstract
Cilia are hair-like projections found on almost all cells in the human body. Originally believed to function merely in motility, the function of solitary non-motile (primary) cilia was long overlooked. Recent research has demonstrated that primary cilia function as signalling hubs that sense environmental cues and are pivotal for organ development and function, tissue hoemoestasis, and maintenance of human health. Cilia share a common anatomy and their diverse functional features are achieved by evolutionarily conserved functional modules, organized into sub-compartments. Defects in these functional modules are responsible for a rapidly growing list of human diseases collectively termed ciliopathies. Ocular pathogenesis is common in virtually all classes of syndromic ciliopathies, and disruptions in cilia genes have been found to be causative in a growing number of non-syndromic retinal dystrophies. This review will address what is currently known about cilia contribution to visual function. We will focus on the molecular and cellular functions of ciliary proteins and their role in the photoreceptor sensory cilia and their visual phenotypes. We also highlight other ciliated cell types in tissues of the eye (e.g. lens, RPE and Müller glia cells) discussing their possible contribution to disease progression. Progress in basic research on the cilia function in the eye is paving the way for therapeutic options for retinal ciliopathies. In the final section we describe the latest advancements in gene therapy, read-through of non-sense mutations and stem cell therapy, all being adopted to treat cilia dysfunction in the retina.
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Affiliation(s)
- Helen May-Simera
- Institute of Molecular Physiology, Cilia Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany.
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Abstract
The conserved Ski2-family helicase Obelus regulates alternative splicing of the Crumbs polarity protein to control epithelial polarity and junctional organization in Drosophila. Alternative splicing can have profound consequences for protein activity, but the functions of most alternative splicing regulators are not known. We show that Obelus, a conserved Ski2-family helicase, is required for cell polarity and adherens junction organization in the Drosophila melanogaster embryo. In obelus mutants, epithelial cells display an expanded apical domain, aggregation of adherens junctions at the cell membrane, and microtubule-dependent defects in centrosome positioning. Through whole-genome transcriptome analysis, we found that Obelus is required for the alternative splicing of a small number of transcripts in the early embryo, including the pre-mRNA that encodes the apical polarity protein Crumbs. In obelus mutants, inclusion of an alternative exon results in increased expression of a Crumbs isoform that contains an additional epidermal growth factor–like repeat in the extracellular domain. Overexpression of this alternative Crumbs isoform recapitulates the junctional aggregation and centrosome positioning defects of obelus mutants. These results indicate that regulation of Crumbs alternative splicing by the Obelus helicase modulates epithelial polarity during development.
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Affiliation(s)
- Athea Vichas
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Matthew T Laurie
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jennifer A Zallen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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7
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Abstract
Myopia, or nearsightedness, is the most common human eye disorder in the world, and is a significant global public health concern. Along with cataract, macular degeneration, infectious disease, and vitamin A deficiency, myopia is one of the most important causes of visual impairment worldwide. Severe or high-grade myopia is a leading cause of blindness because of its associated ocular morbidities of retinal detachment, macular choroidal degeneration, premature cataract, and glaucoma. Ample evidence documents the heritability of the non-syndromic forms of this condition, especially for high-grade myopia, commonly referred to as myopic spherical refractive power of 5 to 6 diopters or higher. Multiple high-grade myopia genetic loci have been identified, and confirmatory studies identifying high-grade and moderate myopia loci have also occurred. In general, myopia susceptibility genes are unknown with few association studies performed, and without confirmation in other research laboratories or testing of separate patient cohorts.
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Affiliation(s)
- Terri L Young
- Department of Ophthalmology and Pediatrics, The Duke Eye Center and the Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Costa V, Conte I, Ziviello C, Casamassimi A, Alfano G, Banfi S, Ciccodicola A. Identification and expression analysis of novel Jakmip1 transcripts. Gene 2007; 402:1-8. [PMID: 17761393 DOI: 10.1016/j.gene.2007.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 05/31/2007] [Accepted: 07/02/2007] [Indexed: 11/20/2022]
Abstract
Janus kinase and microtubule interacting protein 1, (Jakmip1) conserved in vertebrates and predominantly expressed in neural tissues, was identified for its ability to bind Tyk2, a member of the Janus kinase (Jak) family of non-receptor tyrosine kinases. Recently Jakmip1 was also identified as an interacting partner of GABA(B)R1 and as a regulatory protein of GABA(B)R2 mRNA. We have confirmed that this gene is highly expressed in brain and retina tissues and it is also present at lower levels in other tissues. We have identified four new transcripts of 2975 bp, 1743 bp, 2189 bp and 2420 bp respectively, named Jakmip1B, Jakmip1C, Jakmip1D and Jakmip1E. The involvement of the Janus kinase pathway in the development of mouse retina and in the control of survival and proliferation of human retinal ganglion cells, together with the restricted Jakmip1 gene expression pattern, may suggest this gene is a putative candidate for neuro-degenerative and retinal diseases. For this reason, a mutation analysis of the Jakmip1 gene in a panel of 50 unrelated patients with retinitis pigmentosa has been performed, revealing no pathogenic mutations.
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Affiliation(s)
- Valerio Costa
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
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van Driel MA, Cuelenaere K, Kemmeren PPCW, Leunissen JAM, Brunner HG, Vriend G. GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. Nucleic Acids Res 2005; 33:W758-61. [PMID: 15980578 PMCID: PMC1160196 DOI: 10.1093/nar/gki435] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The identification of genes underlying human genetic disorders requires the combination of data related to cytogenetic localization, phenotypes and expression patterns, to generate a list of candidate genes. In the field of human genetics, it is normal to perform this combination analysis by hand. We report on GeneSeeker (), a web server that gathers and combines data from a series of databases. All database searches are performed via the web interfaces provided with the original databases, guaranteeing that the most recent data are queried, and obviating data warehousing. GeneSeeker makes the same selection of candidate genes as the human geneticists would have performed, and thus reducing the time-consuming process to a few minutes. GeneSeeker is particularly well suited for syndromes in which the disease gene displays altered expression patterns in the affected tissue(s).
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Affiliation(s)
| | - K. Cuelenaere
- Dalicon BVPO Box 354, 6700AJ Wageningen, The Netherlands
| | - P. P. C. W. Kemmeren
- Genomics Laboratory, University Medical Centre UtrechtPO Box 85060, 3508AB Utrecht, The Netherlands
| | - J. A. M. Leunissen
- Dalicon BVPO Box 354, 6700AJ Wageningen, The Netherlands
- Wageningen University and Research CentreWageningen, The Netherlands
| | - H. G. Brunner
- Department of Human Genetics, University Medical Centre NijmegenPO Box 9101, 6500HB Nijmegen, The Netherlands
| | - Gert Vriend
- To whom correspondence should be addressed. Tel: +31 24 36 53391; Fax: +31 24 36 52977;
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Schulz HL, Goetz T, Kaschkoetoe J, Weber BHF. The Retinome - defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium. BMC Genomics 2004; 5:50. [PMID: 15283859 PMCID: PMC512282 DOI: 10.1186/1471-2164-5-50] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Accepted: 07/29/2004] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The mammalian retina is a valuable model system to study neuronal biology in health and disease. To obtain insight into intrinsic processes of the retina, great efforts are directed towards the identification and characterization of transcripts with functional relevance to this tissue. RESULTS With the goal to assemble a first genome-wide reference transcriptome of the adult mammalian retina, referred to as the retinome, we have extracted 13,037 non-redundant annotated genes from nearly 500,000 published datasets on redundant retina/retinal pigment epithelium (RPE) transcripts. The data were generated from 27 independent studies employing a wide range of molecular and biocomputational approaches. Comparison to known retina-/RPE-specific pathways and established retinal gene networks suggest that the reference retinome may represent up to 90% of the retinal transcripts. We show that the distribution of retinal genes along the chromosomes is not random but exhibits a higher order organization closely following the previously observed clustering of genes with increased expression. CONCLUSION The genome wide retinome map offers a rational basis for selecting suggestive candidate genes for hereditary as well as complex retinal diseases facilitating elaborate studies into normal and pathological pathways. To make this unique resource freely available we have built a database providing a query interface to the reference retinome 1.
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Affiliation(s)
- Heidi L Schulz
- Institute of Human Genetics, Biocenter, University of Wuerzburg, D-97074 Wuerzburg, Germany
| | - Thomas Goetz
- Institute of Human Genetics, Biocenter, University of Wuerzburg, D-97074 Wuerzburg, Germany
- German Cancer Research Center, Central Spectroscopic Department, D-69120 Heidelberg, Germany
| | - Juergen Kaschkoetoe
- Institute of Human Genetics, Biocenter, University of Wuerzburg, D-97074 Wuerzburg, Germany
| | - Bernhard HF Weber
- Institute of Human Genetics, Biocenter, University of Wuerzburg, D-97074 Wuerzburg, Germany
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Sifringer M, Uhlenberg B, Lammel S, Hanke R, Neumann B, von Moers A, Koch I, Speer A. Identification of transcripts from a subtraction library which might be responsible for the mild phenotype in an intrafamilially variable course of Duchenne muscular dystrophy. Hum Genet 2003; 114:149-56. [PMID: 14600829 DOI: 10.1007/s00439-003-1041-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2003] [Accepted: 09/18/2003] [Indexed: 10/26/2022]
Abstract
While frame-shift mutations are usually found in Duchenne muscular dystrophy (DMD), in-frame mutations are associated with the less severe phenotype of Becker's muscular dystrophy. Exceptions have been reported in both directions suggesting the existence of modifying genes, which might be helpful for innovation of new therapeutic strategies. We report on the very rare case of an intrafamilially different course of DMD, with the younger brother being far less affected than the older one when compared at the same age. In this context, we constructed a subtraction library enriched for transcripts over-expressed in the patient with the milder phenotype. Twelve random clones were sequenced, followed by database analysis. Six of them, casein kinase 1 alpha 1, RAP2B, dynactin 3 light chain, core binding factor beta, myosin light polypeptide 2 and one hypothetical gene, were further analysed by real-time RT-PCR. All these genes were over-expressed 3-20 times in the less affected patient compared with the more severely affected one. Casein kinase 1 and the hypothetical gene showed even a slightly higher expression than the control. Up-regulation of myosin light polypeptide 2, one of the most sensitive markers of muscle fibre regeneration, obviously reflects the milder phenotype. Casein kinase 1, dynactin and core binding factor are supposed to be involved in cell cycle pathways. RAP is a component of the signalling network which controls fundamental cellular processes such as proliferation and differentiation. All four might be interesting candidates for a therapeutic approach to diminish progression of dystrophy in DMD.
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Affiliation(s)
- Marco Sifringer
- Department of Neuropediatrics, Charité, Humboldt-University Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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Luijendijk MWJ, van de Pol TJR, van Duijnhoven G, den Hollander AI, ten Caat J, van Limpt V, Brunner HG, Kremer H, Cremers FPM. Cloning, characterization, and mRNA expression analysis of novel human fetal cochlear cDNAs☆. Genomics 2003; 82:480-90. [PMID: 13679028 DOI: 10.1016/s0888-7543(03)00150-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To identify novel genes that are expressed specifically or preferentially in the cochlea, we constructed a cDNA library enriched for human cochlear cDNAs using a suppression subtractive hybridization technique. We analyzed 2640 clones by sequencing and BLAST similarity searches. One hundred and fifty-five different cDNA fragments mapped in nonsyndromic hearing impairment loci for which the causative gene has not been cloned yet. Approximately 30% of the clones show no similarity to any known human gene or expressed sequence tag (EST). Clones mapping in nonsyndromic deafness loci and a selection of clones that represent novel ESTs were analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) of RNA derived from 12 human fetal tissues. Our data suggest that a quarter of the novel genes in our library are preferentially expressed in fetal cochlea. These may play a physiologically important role in the hearing process and represent candidate genes for hereditary hearing impairment.
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Affiliation(s)
- M W J Luijendijk
- Department of Human Genetics, University Medical Center Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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13
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Conte I, Lestingi M, den Hollander A, Alfano G, Ziviello C, Pugliese M, Circolo D, Caccioppoli C, Ciccodicola A, Banfi S. Identification and characterisation of the retinitis pigmentosa 1-like1 gene (RP1L1): a novel candidate for retinal degenerations. Eur J Hum Genet 2003; 11:155-62. [PMID: 12634863 DOI: 10.1038/sj.ejhg.5200942] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2002] [Revised: 11/19/2002] [Accepted: 11/27/2002] [Indexed: 11/08/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common form of inherited retinopathy, with an approximate incidence of 1 in 3700 individuals worldwide. Mutations in the retinitis pigmentosa 1 (RP1) gene are responsible for about 5-10% cases of autosomal dominant RP. The RP1 gene is specifically expressed in the photoreceptor layers of the postnatal retina and encodes a predicted protein characterised by the presence of two doublecortin (DC) domains, known to be implicated in microtubule binding. We identified and characterised, both in human and in mouse, a novel mammalian gene, termed Retinitis Pigmentosa1-like1 (RP1L1), because of its significant sequence similarity to the RP1 gene product. The sequence homology between RP1 and RP1L1 was found to be mostly restricted to the DC domains and to the N-terminal region, including the first 350 amino acids. The RP1L1 gene was also found to be conserved in distant vertebrates, since we identified a homologue in Fugu rubripes (pufferfish). Similar to RP1, RP1L1 expression is restricted to the postnatal retina, as determined by semiquantitative reverse transcriptase-PCR and Northern analysis. The retina-specific expression and the sequence similarity to RP1 render RP1L1 a potential candidate for inherited retinal disorders.
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Affiliation(s)
- Ivan Conte
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, 80131 Naples, Italy
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14
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van Driel MA, Cuelenaere K, Kemmeren PPCW, Leunissen JAM, Brunner HG. A new web-based data mining tool for the identification of candidate genes for human genetic disorders. Eur J Hum Genet 2003; 11:57-63. [PMID: 12529706 DOI: 10.1038/sj.ejhg.5200918] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2002] [Revised: 10/01/2002] [Accepted: 10/09/2002] [Indexed: 11/09/2022] Open
Abstract
To identify the gene underlying a human genetic disorder can be difficult and time-consuming. Typically, positional data delimit a chromosomal region that contains between 20 and 200 genes. The choice then lies between sequencing large numbers of genes, or setting priorities by combining positional data with available expression and phenotype data, contained in different internet databases. This process of examining positional candidates for possible functional clues may be performed in many different ways, depending on the investigator's knowledge and experience. Here, we report on a new tool called the GeneSeeker, which gathers and combines positional data and expression/phenotypic data in an automated way from nine different web-based databases. This results in a quick overview of interesting candidate genes in the region of interest. The GeneSeeker system is built in a modular fashion allowing for easy addition or removal of databases if required. Databases are searched directly through the web, which obviates the need for data warehousing. In order to evaluate the GeneSeeker tool, we analysed syndromes with known genesis. For each of 10 syndromes the GeneSeeker programme generated a shortlist that contained a significantly reduced number of candidate genes from the critical region, yet still contained the causative gene. On average, a list of 163 genes based on position alone was reduced to a more manageable list of 22 genes based on position and expression or phenotype information. We are currently expanding the tool by adding other databases. The GeneSeeker is available via the web-interface (http://www.cmbi.kun.nl/GeneSeeker/).
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Affiliation(s)
- Marc A van Driel
- Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands.
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15
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Stöhr H, Mohr N, Fröhlich S, Mehdi SQ, Bhattacharya SS, Weber BHF. Cloning and characterization of WDR17, a novel WD repeat-containing gene on chromosome 4q34. Biochim Biophys Acta 2002; 1579:18-25. [PMID: 12401215 DOI: 10.1016/s0167-4781(02)00499-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As part of our project to generate a catalogue of genes with potential relevance to human retinal disease, we have cloned a transcript abundantly expressed in the human retina and testis. Analysis of the deduced 1322 amino acid protein sequence demonstrates that it encodes a novel WD repeat protein, termed WDR17. The N-terminal moiety of the WDR17 protein is predicted to consist of at least 12 conserved WD repeats that likely adopts a beta-propeller-like structure. Homology searches with the C-terminal region revealed no similarity to known or hypothetical proteins. However, putative orthologous ESTs with 82-91% identity to the human cDNA were found in several mammalian species including rodents, pig and cattle, suggesting that WDR17 represents an evolutionarily novel subtype of WD repeat proteins with unique function(s) in higher eukaryotes. Temporal expression analysis in the murine eye showed that transcription of WDR17 begins prenatally, suggesting a functional role of the protein in the early stages of retinal development. Human WDR17 maps to the same chromosomal interval as the locus for autosomal recessive retinitis pigmentosa (RP29) on 4q34, making it a candidate for this disease gene. Sequencing of the entire coding region of WDR17 in an affected patient of the original RP29 pedigree has not revealed any disease-causing sequence variations likely excluding WDR17 as the gene underlying RP29.
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Affiliation(s)
- Heidi Stöhr
- Institut für Humangenetik, Biozentrum, Universität Würzburg, Am-Hubland, D-97074, Würzburg, Germany
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16
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Abstract
To search for genes that could be involved in genetic disorders primarily involving the retina and the cochlea, we tried to identify mRNAs preferentially expressed in retina and cochlea and to establish their chromosomal localization. Two approaches were employed. First, a mouse subtracted library (retina + cochlea against liver + brain) was generated. Randomly selected cDNA clones were sequenced and compared to databases. Tissue expression of some of them was analyzed by RT-PCR. Using radiation hybrid cell lines, the mouse chromosomal localization was determined for those showing the highest level in the retina and the cochlea. Second, human Expressed Sequence Tags (ESTs) with preferential expression in the retina and the cochlea were searched for in databases, and chromosomal localization was also established. From 171 sequenced clones, 73 were classified as known genes (with 17 clones coding for 6 genes), 86 were homologous to ESTs, and 12 were unidentified. Of 108 selected clones, 22 (18.5%) had the highest level of expression in the retina and/or the cochlea, while expression was higher in another tissue or ubiquitous for 60 (55.5%) and 22 (20.4%) of them, respectively. By RT-PCR, one clone similar to the mouse Asic3 cDNA (proton-gated channel) was found mainly in the retina and cochlea, but its human ortholog was widely expressed. We selected 17 ESTs from the UniGene database with restricted expression including in the retina and cochlea. We mapped 10 of these ESTs as well as four mouse clones from the subtracted library. Some of them localized to morbid intervals. The combined information from expression analysis and chromosomal localization allowed for the identification of potential candidate genes for retinal diseases (CORD8, CORD9) and syndromic blindness/deafness/renal defects.
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Affiliation(s)
- Cécilia Maubaret
- Laboratoire de Neurobiologie de l'Audition, Plasticité Synaptique 71, rue de Navacelles, 34090 Montpellier, France
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17
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Katsanis N, Worley KC, Gonzalez G, Ansley SJ, Lupski JR. A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. Proc Natl Acad Sci U S A 2002; 99:14326-31. [PMID: 12391299 PMCID: PMC137883 DOI: 10.1073/pnas.222409099] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Grouping genes by virtue of their sequence similarity, functional association, or spatiotemporal distribution is an important first step in investigating function. Given the recent identification of >30,000 human genes either by analyses of genomic sequence or by derivation/assembly of ESTs, automated means of discerning gene function and association with disease are critical for the efficient processing of this large volume of data. We have designed a series of computational tools to manipulate the EST sequence database (dbEST) to predict EST clusters likely representing genes expressed exclusively or preferentially in a specific tissue. We implemented this tool by extracting 40,000 human retinal ESTs and performing in silico subtraction against 1.4 million human ESTs. This process yielded 925 ESTs likely to be specifically or preferentially expressed in the retina. We mapped all retinal-specific/predominant sequences in the human genome and produced a web-based searchable map of the retina transcriptome, onto which we overlaid the positions of all mapped but uncloned retinopathy genes. This resource has provided positional candidates for 42 of 51 uncloned retinopathies and may expedite substantially the identification of disease-associated genes. More importantly, the ability to systematically group ESTs according to their predicted expression profile is likely to be an important resource for studying gene function in a wide range of tissues and physiological systems and to identify positional candidate genes for human disorders whose phenotypic manifestations are restricted to specific tissues/organs/cell types.
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Affiliation(s)
- Nicholas Katsanis
- Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
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18
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Conte I, Lestingi M, den Hollander A, Miano MG, Alfano G, Circolo D, Pugliese M, Testa F, Simonelli F, Rinaldi E, Baiget M, Banfi S, Ciccodicola A. Characterization of MPP4, a gene highly expressed in photoreceptor cells, and mutation analysis in retinitis pigmentosa. Gene 2002; 297:33-8. [PMID: 12384283 DOI: 10.1016/s0378-1119(02)00872-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Membrane-associated guanylate kinase (MAGUK) proteins are cell-cell contact organizing molecules that mediate targeting, clustering and anchoring of proteins at synapses and other cell junctions. MAGUK proteins may contain multiple protein-protein interaction motifs including PDZ, SH3 and guanylate kinase (GuK) domains. In this study, we performed a detailed analysis of the expression pattern of MPP4, a recently described member of the MAGUK protein family. We confirmed that this gene is highly expressed in retina, and demonstrate that it is also present, at lower levels, in brain. We identified a new retina specific isoform encoding a predicted protein lacking 71 amino acids. This protein region contains a newly identified L27 domain, another module playing a role in protein-protein interaction. By RNA in situ hybridization, Mpp4 expression was found to be localized to photoreceptor cells in postnatal retina. The MPP4 gene is localized to chromosome 2, in band 2q31-33, where a locus for autosomal recessive retinitis pigmentosa (RP26) has been mapped. Mutation analysis of the entire open reading frame of the MPP4 gene in a RP26 family revealed no pathologic mutations. In addition, we did not identify mutations in a panel of 300 unrelated patients with retinitis pigmentosa.
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Affiliation(s)
- Ivan Conte
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, 80129, Naples, Italy
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19
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Maugeri A, Flothmann K, Hemmrich N, Ingvast S, Jorge P, Paloma E, Patel R, Rozet JM, Tammur J, Testa F, Balcells S, Bird AC, Brunner HG, Hoyng CB, Metspalu A, Simonelli F, Allikmets R, Bhattacharya SS, D'Urso M, Gonzàlez-Duarte R, Kaplan J, te Meerman GJ, Santos R, Schwartz M, Van Camp G, Wadelius C, Weber BHF, Cremers FPM. The ABCA4 2588G>C Stargardt mutation: single origin and increasing frequency from South-West to North-East Europe. Eur J Hum Genet 2002; 10:197-203. [PMID: 11973624 DOI: 10.1038/sj.ejhg.5200784] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2001] [Revised: 12/19/2001] [Accepted: 01/22/2002] [Indexed: 11/10/2022] Open
Abstract
Inherited retinal dystrophies represent the most important cause of vision impairment in adolescence, affecting approximately 1 out of 3000 individuals. Mutations of the photoreceptor-specific gene ABCA4 (ABCR) are a common cause of retinal dystrophy. A number of mutations have been repeatedly reported for this gene, notably the 2588G>C mutation which is frequent in both patients and controls. Here we ascertained the frequency of the 2588G>C mutation in a total of 2343 unrelated random control individuals from 11 European countries and 241 control individuals from the US, as well as in 614 patients with STGD both from Europe and the US. We found an overall carrier frequency of 1 out of 54 in Europe, compared with 1 out of 121 in the US, confirming that the 2588G>C ABCA4 mutation is one of the most frequent autosomal recessive mutations in the European population. Carrier frequencies show an increasing gradient in Europe from South-West to North-East. The lowest carrier frequency, 0 out of 199 (0%), was found in Portugal; the highest, 11 out of 197 (5.5%), was found in Sweden. Haplotype analysis in 16 families segregating the 2588G>C mutation showed four intragenic polymorphisms invariably present in all 16 disease chromosomes and sharing of the same allele for several markers flanking the ABCA4 locus in most of the disease chromosomes. These results indicate a single origin of the 2588G>C mutation which, to our best estimate, occurred between 2400 and 3000 years ago.
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Affiliation(s)
- Alessandra Maugeri
- Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands.
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20
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Sharon D, Blackshaw S, Cepko CL, Dryja TP. Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE). Proc Natl Acad Sci U S A 2002; 99:315-20. [PMID: 11756676 PMCID: PMC117558 DOI: 10.1073/pnas.012582799] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We used the serial analysis of gene expression (SAGE) technique to catalogue and measure the relative levels of expression of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium (RPE) from one or both of two humans, aged 88 and 44 years. The cone photoreceptor contribution to all transcription in the retina was found to be similar in the macula versus the retinal periphery, whereas the rod contribution was greater in the periphery versus the macula. Genes encoding structural proteins for axons were found to be expressed at higher levels in the macula versus the retinal periphery, probably reflecting the large proportion of ganglion cells in the central retina. In comparison with the younger eye, the peripheral retina of the older eye had a substantially higher proportion of mRNAs from genes encoding proteins involved in iron metabolism or protection against oxidative damage and a substantially lower proportion of mRNAs from genes encoding proteins involved in rod phototransduction. These differences may reflect the difference in age between the two donors or merely interindividual variation. The RPE library had numerous previously unencountered tags, suggesting that this cell type has a large, idiosyncratic repertoire of expressed genes. Comparison of these libraries with 100 reported nonocular SAGE libraries revealed 89 retina-specific or enriched genes expressed at substantial levels, of which 14 are known to cause a retinal disease and 53 are RPE-specific genes. We expect that these libraries will serve as a resource for understanding the relative expression levels of genes in the retina and the RPE and for identifying additional disease genes.
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Affiliation(s)
- Dror Sharon
- Ocular Molecular Genetics Institute, Massachusetts Eye and Ear Infirmary, and Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02114, USA
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21
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Abstract
Bardet-Biedl syndrome (BBS) has been shown to be a genetically heterogeneous disorder involving genes mapping to at least six known loci. One BBS gene (MKKS) has been identified and the form of the disorder caused by this gene is allelic to McKusick-Kaufman syndrome. MKKS codes for a putative chaperonin, suggesting that other BBS genes may also code for components of chaperone complexes or be substrates of chaperone function.
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Affiliation(s)
- V C Sheffield
- Departments of Pediatrics and University of Iowa, 440 EMRB, Iowa City, Iowa 52242, USA.
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22
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Hennebold JD, Tanaka M, Saito J, Hanson BR, Adashi EY. Ovary-selective genes I: the generation and characterization of an ovary-selective complementary deoxyribonucleic acid library. Endocrinology 2000; 141:2725-34. [PMID: 10919256 DOI: 10.1210/endo.141.8.7627] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The importance of several ovary-selective/specific genes, i.e. genes preferentially or exclusively expressed in the ovary, has been established. Indeed, null mutant female mice for the c-mos, growth and differentiation factor-9, alpha-inhibin, and zona pellucida-3 genes proved sterile. A loss of function mutation of the human FSH receptor gene established its critical role in ovarian function. These data support the hypothesis that genes expressed selectively or specifically in the ovary are probably essential for the normal functioning of this organ system. We have used the differential screening technique suppression subtractive hybridization to systematically isolate and clone genes that are expressed in an ovary-selective/specific manner. The resultant target complementary DNA (cDNA) library has been exhaustively screened to a point at which additional sequencing was increasingly unlikely (< or = 4%) to yield additional previously unencountered cDNAs. In toto, 844 clones were sequenced and analyzed for homology to known genes using the Basic Local Alignment Tool (BLAST). Of those, 342 were determined to be independent (nonredundant). One hundred and fifty-nine independent clones proved identical to previously characterized genes, whereas an additional 100 independent clones proved significantly homologous (but not identical) to previously characterized genes. Yet 83 other independent clones did not display significant homology to previously characterized genes now listed in the publicly accessible nonredundant databases. As such, these latter genes were deemed novel. Of these 83 novel genes, a total of 36 displayed ovary-specific/selective expression, as determined by probing mouse multitissue Northern blots with 32P-labeled/PCR-amplified cDNA inserts. Under these circumstances, the false positive rate was minimal, as only one novel clone was expressed at a higher level in nonovarian tissues relative to ovary. Of the 36 ovary-specific/ selective novel genes, 22 proved subject to hormonal regulation during a simulated estrous cycle. In this communication we focus on 2 such novel ovary-specific/hormonally-dependent genes, the full-length sequences of which were isolated using rapid amplification of 3'-cDNA ends technology. Taken together, the present study accomplished systematic identification of those genes that are restricted in their expression to the ovary. These ovary-selective genes may have significant implications for the understanding of ovarian function in molecular terms and for the development of innovative strategies for the promotion of fertility or its control.
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Affiliation(s)
- J D Hennebold
- Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City 84132, USA
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23
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Abstract
Zebrafish cyclops (cyc) encodes a Transforming Growth Factor beta (TGFbeta) signaling factor closely related to mouse Nodal. By comparing amplified fragment length polymorphisms (AFLP) from cyc mutant and wild-type cDNA pools, we devised a differential gene expression screen to isolate genes whose expression is dependent on Cyc signaling. We report two genes not previously described in the zebrafish that were identified using this approach. The first gene, crestin, is expressed predominantly in premigratory and migrating neural crest cells during somitogenesis stages. crestin expression is reduced in cyc mutants initially but recovers by late somitogenesis. The second gene encodes the zebrafish homologue of the calcium-binding protein, calreticulin. Zebrafish calreticulin is highly expressed in the hatching gland and in the floor plate, tissues that are affected in cyc mutants. During gastrulation, calreticulin transcripts are found in the dorsal mesendoderm, in the same cells that express the cyc gene. Expression is reduced in cyc mutants and is abolished by the one-eyed pinhead (oep) mutation that is presumed to prevent Nodal signaling. The identification of calreticulin suggests that a differential screen between wild-type and mutant cDNA is a useful approach to reveal regulation of unexpected gene expression in response to cellular signals. genesis 26:86-97, 2000.
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Affiliation(s)
- A L Rubinstein
- Carnegie Institution of Washington, Department of Embryology, Baltimore, Maryland 21210, USA
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24
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den Hollander AI, ten Brink JB, de Kok YJ, van Soest S, van den Born LI, van Driel MA, van de Pol DJ, Payne AM, Bhattacharya SS, Kellner U, Hoyng CB, Westerveld A, Brunner HG, Bleeker-Wagemakers EM, Deutman AF, Heckenlively JR, Cremers FP, Bergen AA. Mutations in a human homologue of Drosophila crumbs cause retinitis pigmentosa (RP12). Nat Genet 1999; 23:217-21. [PMID: 10508521 DOI: 10.1038/13848] [Citation(s) in RCA: 316] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Retinitis pigmentosa (RP) comprises a clinically and genetically heterogeneous group of diseases that afflicts approximately 1.5 million people worldwide. Affected individuals suffer from a progressive degeneration of the photoreceptors, eventually resulting in severe visual impairment. To isolate candidate genes for chorioretinal diseases, we cloned cDNAs specifically or preferentially expressed in the human retina and the retinal pigment epithelium (RPE) through a novel suppression subtractive hybridization (SSH) method. One of these cDNAs (RET3C11) mapped to chromosome 1q31-q32.1, a region harbouring a gene involved in a severe form of autosomal recessive RP characterized by a typical preservation of the para-arteriolar RPE (RP12; ref. 3). The full-length cDNA encodes an extracellular protein with 19 EGF-like domains, 3 laminin A G-like domains and a C-type lectin domain. This protein is homologous to the Drosophila melanogaster protein crumbs (CRB), and denoted CRB1 (crumbs homologue 1). In ten unrelated RP patients with preserved para-arteriolar RPE, we identified a homozygous AluY insertion disrupting the ORF, five homozygous missense mutations and four compound heterozygous mutations in CRB1. The similarity to CRB suggests a role for CRB1 in cell-cell interaction and possibly in the maintenance of cell polarity in the retina. The distinct RPE abnormalities observed in RP12 patients suggest that CRB1 mutations trigger a novel mechanism of photoreceptor degeneration.
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MESH Headings
- Alu Elements/genetics
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Base Sequence
- Blotting, Northern
- Cell Line
- Chromosome Mapping
- Chromosomes, Human, Pair 1/genetics
- DNA Mutational Analysis
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Drosophila Proteins
- Drosophila melanogaster/genetics
- Eye Proteins/genetics
- Family Health
- Female
- Gene Expression Regulation, Developmental
- Homozygote
- Humans
- Male
- Membrane Proteins/genetics
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutation
- Pedigree
- Point Mutation
- Polymorphism, Single-Stranded Conformational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Retinitis Pigmentosa/genetics
- Retinitis Pigmentosa/pathology
- Sequence Analysis, DNA
- Tissue Distribution
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Affiliation(s)
- A I den Hollander
- Department of Human Genetics, University Hospital Nijmegen, Geert Grooteplein 10, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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