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      TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum

      research-article
      1 , 2 , 3 , 3 , 1 , 1 , 4 , 5 , 6 , 7 , 6 , 8 , 9 , 8 , 9 , 8 , 8 , 9 , 9 , 9 , 9 , 9 , 9 , NISC Comparative Sequencing Program 9 , 10 , 11 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 7 , 25 , 26 , 26 , 27 , 4 , 28 , 5 , 6 , 9 , 8 , 7 , 29 , 3 , 1 , 2 , 30
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          Abstract

          Ciliary dysfunction leads to a broad range of overlapping phenotypes, termed collectively as ciliopathies. This grouping is underscored by genetic overlap, where causal genes can also contribute modifying alleles to clinically distinct disorders. Here we show that mutations in TTC21B/IFT139, encoding a retrograde intraflagellar transport (IFT) protein, cause both isolated nephronophthisis (NPHP) and syndromic Jeune Asphyxiating Thoracic Dystrophy (JATD). Moreover, although systematic medical resequencing of a large, clinically diverse ciliopathy cohort and matched controls showed a similar frequency of rare changes, in vivo and in vitro evaluations unmasked a significant enrichment of pathogenic alleles in cases, suggesting that TTC21B contributes pathogenic alleles to ∼5% of ciliopathy patients. Our data illustrate how genetic lesions can be both causally associated with diverse ciliopathies, as well as interact in trans with other disease-causing genes, and highlight how saturated resequencing followed by functional analysis of all variants informs the genetic architecture of disorders.

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          Most cited references31

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          Electroporation and RNA interference in the rodent retina in vivo and in vitro.

          The large number of candidate genes made available by comprehensive genome analysis requires that relatively rapid techniques for the study of function be developed. Here, we report a rapid and convenient electroporation method for both gain- and loss-of-function studies in vivo and in vitro in the rodent retina. Plasmid DNA directly injected into the subretinal space of neonatal rodent pups was taken up by a significant fraction of exposed cells after several pulses of high voltage. With this technique, GFP expression vectors were efficiently transfected into retinal cells with little damage to the operated pups. Transfected GFP allowed clear visualization of cell morphologies, and the expression persisted for at least 50 days. DNA-based RNA interference vectors directed against two transcription factors important in photoreceptor development led to photoreceptor phenotypes similar to those of the corresponding knockout mice. Reporter constructs carrying retinal cell type-specific promoters were readily introduced into the retina in vivo, where they exhibited the appropriate expression patterns. Plasmid DNA was also efficiently transfected into retinal explants in vitro by high-voltage pulses.
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            The ciliopathies: an emerging class of human genetic disorders.

            Cilia and flagella are ancient, evolutionarily conserved organelles that project from cell surfaces to perform diverse biological roles, including whole-cell locomotion; movement of fluid; chemo-, mechano-, and photosensation; and sexual reproduction. Consistent with their stringent evolutionary conservation, defects in cilia are associated with a range of human diseases, such as primary ciliary dyskinesia, hydrocephalus, polycystic liver and kidney disease, and some forms of retinal degeneration. Recent evidence indicates that ciliary defects can lead to a broader set of developmental and adult phenotypes, with mutations in ciliary proteins now associated with nephronophthisis, Bardet-Biedl syndrome, Alstrom syndrome, and Meckel-Gruber syndrome. The molecular data linking seemingly unrelated clinical entities are beginning to highlight a common theme, where defects in ciliary structure and function can lead to a predictable phenotypic pattern that has potentially predictive and therapeutic value.
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              • Abstract: found
              • Article: not found

              Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene.

              Cilia and flagella are microtubule-based structures nucleated by modified centrioles termed basal bodies. These biochemically complex organelles have more than 250 and 150 polypeptides, respectively. To identify the proteins involved in ciliary and basal body biogenesis and function, we undertook a comparative genomics approach that subtracted the nonflagellated proteome of Arabidopsis from the shared proteome of the ciliated/flagellated organisms Chlamydomonas and human. We identified 688 genes that are present exclusively in organisms with flagella and basal bodies and validated these data through a series of in silico, in vitro, and in vivo studies. We then applied this resource to the study of human ciliation disorders and have identified BBS5, a novel gene for Bardet-Biedl syndrome. We show that this novel protein localizes to basal bodies in mouse and C. elegans, is under the regulatory control of daf-19, and is necessary for the generation of both cilia and flagella.
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                Author and article information

                Journal
                9216904
                2419
                Nat Genet
                Nature genetics
                1061-4036
                1546-1718
                19 January 2011
                23 January 2011
                March 2011
                1 September 2011
                : 43
                : 3
                : 189-196
                Affiliations
                [1 ]Center for Human Disease Modeling, Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
                [2 ]Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27710, USA
                [3 ]F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, 19104, USA
                [4 ]Department of Medical and Molecular Genetics, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
                [5 ]Laboratoire de Génétique Médicale EA 3949, Faculté de Médecine de Strasbourg, Université Louis Pasteur, 67085 Strasbourg, France
                [6 ]Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, United Kingdom
                [7 ]Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48105, USA
                [8 ]Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
                [9 ]NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
                [10 ]Genoscope Centre National de Séquençage, Crémieux 91057 Evry, France
                [11 ]University Children's Hospital, 69120 Heidelberg, Germany
                [12 ]Hôpital Cantonal, CH-1211 Geneve 14, Switzerland
                [13 ]Department of Pediatrics, Kasralainy School of Medicine, Cairo University, Cairo 11451, Egypt
                [14 ]Division of Nephrology, University Children's Hospital Zurich, 8032 Zurich, Switzerland
                [15 ]Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
                [16 ]Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
                [17 ]Istanbul University, Istanbul Medical Faculty, Medical Genetics, Millet Caddesi, Capa, Fatih, 034104 Istanbul, Turkey
                [18 ]Developmental Pediatrics, University of Hawaii at Manoa, Honolulu, HI 96826, USA
                [19 ]Department of Ophthalmology, Baylor College of Medicine, Houston, Texas 77030, USA
                [20 ]Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
                [21 ]Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
                [22 ]Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
                [23 ]Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany
                [24 ]Department of Human Genetics, RWTH University of Aachen, 52074 Aachen, Germany
                [25 ]Inserm, U574, Université Paris Descartes, Hôpital Necker, Paris, France
                [26 ]Molecular Medicine Unit, Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
                [27 ]Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
                [28 ]Département de Génétique et INSERM U-781, Hôpital Necker-Enfants Malades, Université Paris Descartes, Paris Cedex 15, France
                [29 ]Howard Hughes Medical Institute and Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48105, USA
                [30 ]Wilmer Eye Institute and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore Maryland 21205, USA
                Author notes
                Article
                nihpa260639
                10.1038/ng.756
                3071301
                21258341
                c7ed6cae-9ca4-4f53-ac1b-377db3a5eb33

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                History
                Funding
                Funded by: National Institute of Diabetes and Digestive and Kidney Diseases : NIDDK
                Award ID: F32 DK079541-04 ||DK
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                Genetics
                Genetics

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