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Abdi S, Bahloul A, Behlouli A, Hardelin JP, Makrelouf M, Boudjelida K, Louha M, Cheknene A, Belouni R, Rous Y, Merad Z, Selmane D, Hasbelaoui M, Bonnet C, Zenati A, Petit C. Diversity of the Genes Implicated in Algerian Patients Affected by Usher Syndrome. PLoS One 2016; 11:e0161893. [PMID: 27583663 PMCID: PMC5008642 DOI: 10.1371/journal.pone.0161893] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Usher syndrome (USH) is an autosomal recessive disorder characterized by a dual sensory impairment affecting hearing and vision. USH is clinically and genetically heterogeneous. Ten different causal genes have been reported. We studied the molecular bases of the disease in 18 unrelated Algerian patients by targeted-exome sequencing, and identified the causal biallelic mutations in all of them: 16 patients carried the mutations at the homozygous state and 2 at the compound heterozygous state. Nine of the 17 different mutations detected in MYO7A (1 of 5 mutations), CDH23 (4 of 7 mutations), PCDH15 (1 mutation), USH1C (1 mutation), USH1G (1 mutation), and USH2A (1 of 2 mutations), had not been previously reported. The deleterious consequences of a missense mutation of CDH23 (p.Asp1501Asn) and the in-frame single codon deletion in USH1G (p.Ala397del) on the corresponding proteins were predicted from the solved 3D-structures of extracellular cadherin (EC) domains of cadherin-23 and the sterile alpha motif (SAM) domain of USH1G/sans, respectively. In addition, we were able to show that the USH1G mutation is likely to affect the binding interface between the SAM domain and USH1C/harmonin. This should spur the use of 3D-structures, not only of isolated protein domains, but also of protein-protein interaction interfaces, to predict the functional impact of mutations detected in the USH genes.
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Affiliation(s)
- Samia Abdi
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
- Laboratoire central de biologie, CHU Frantz Fanon, 09 Blida, Algérie
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
| | - Amel Bahloul
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
| | - Asma Behlouli
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
- Faculté des sciences biologiques, Université des sciences et de la technologie Houari Boumédiène, 16 Alger, Algérie
| | - Jean-Pierre Hardelin
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
| | - Mohamed Makrelouf
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
| | - Kamel Boudjelida
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ophtalmologie, CHU Frantz Fanon, 09 Blida, Algérie
| | - Malek Louha
- Service de biochimie et de biologie moléculaire, Hôpital Armand Trousseau, APHP, 75012, Paris, France
| | - Ahmed Cheknene
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ORL, CHU Frantz Fanon, 09 Blida, Algérie
| | - Rachid Belouni
- Laboratoire central de biologie, CHU Frantz Fanon, 09 Blida, Algérie
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
| | - Yahia Rous
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ORL, CHU Frantz Fanon, 09 Blida, Algérie
| | - Zahida Merad
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ophtalmologie, CHU Frantz Fanon, 09 Blida, Algérie
| | | | | | - Crystel Bonnet
- INSERM UMRS 1120, Institut de la vision, Université Pierre et Marie Curie, 75005, Paris, France
| | - Akila Zenati
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
| | - Christine Petit
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
- INSERM UMRS 1120, Institut de la vision, Université Pierre et Marie Curie, 75005, Paris, France
- Collège de France, 75005, Paris, France
- * E-mail:
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102
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Nishi E, Masuda K, Arakawa M, Kawame H, Kosho T, Kitahara M, Kubota N, Hidaka E, Katoh Y, Shirahige K, Izumi K. Exome sequencing-based identification of mutations in non-syndromic genes among individuals with apparently syndromic features. Am J Med Genet A 2016; 170:2889-2894. [PMID: 27566442 DOI: 10.1002/ajmg.a.37826] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/19/2016] [Indexed: 12/20/2022]
Abstract
In a clinical setting, the number of organ systems involved is crucial for the differential diagnosis of congenital genetic disorders. When more than one organ system is involved, a syndromic diagnosis is suspected. In this report, we describe three patients with apparently syndromic features. Exome sequencing identified non-syndromic gene mutations as a potential cause of part of their phenotype. The first patient (Patient 1) is a girl with cleft lip/palate, meningoencephalocele, tetralogy of Fallot, and developmental delay. The second and third patients (Patients 2 and 3) are brothers with developmental delay, deafness, and low bone mineral density. Exome sequencing revealed the presence of a CDH1 mutation in Patient 1 and a PLS3 mutation in Patients 2 and 3. CDH1 mutations are known to be associated with non-syndromic cleft lip/palate, while PLS3 mutations are associated with osteoporosis. Thus, these variants may explain a part of the complex phenotype of the patients, although the effects of these missense variants need to be evaluated by functional assays in order to prove pathogenicity. On the basis of these findings, we emphasize the importance of scrutinizing non-syndromic gene mutations even in individuals with apparently syndromic features. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Eriko Nishi
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan.,Life Science Research Center, Nagano Children's Hospital, Azumino, Japan.,Department of Medical Genetics, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Koji Masuda
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Michiko Arakawa
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan
| | - Hiroshi Kawame
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan
| | - Tomoki Kosho
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan.,Department of Medical Genetics, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Masashi Kitahara
- Department of Pediatrics, Matsumoto Medical Center of Chu-shin-Matsumoto Hospital, Matsumoto, Japan
| | - Noriko Kubota
- Life Science Research Center, Nagano Children's Hospital, Azumino, Japan.,Department of Laboratory Medicine, Nagano Children's Hospital, Azumino, Japan
| | - Eiko Hidaka
- Life Science Research Center, Nagano Children's Hospital, Azumino, Japan.,Department of Laboratory Medicine, Nagano Children's Hospital, Azumino, Japan
| | - Yuki Katoh
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Kosuke Izumi
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan. .,Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
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103
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Yan D, Tekin D, Bademci G, Foster J, Cengiz FB, Kannan-Sundhari A, Guo S, Mittal R, Zou B, Grati M, Kabahuma RI, Kameswaran M, Lasisi TJ, Adedeji WA, Lasisi AO, Menendez I, Herrera M, Carranza C, Maroofian R, Crosby AH, Bensaid M, Masmoudi S, Behnam M, Mojarrad M, Feng Y, Duman D, Mawla AM, Nord AS, Blanton SH, Liu XZ, Tekin M. Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents. Hum Genet 2016; 135:953-61. [PMID: 27344577 PMCID: PMC5497215 DOI: 10.1007/s00439-016-1697-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/11/2016] [Indexed: 12/21/2022]
Abstract
Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.
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Affiliation(s)
- Denise Yan
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Demet Tekin
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Guney Bademci
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Joseph Foster
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - F Basak Cengiz
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Abhiraami Kannan-Sundhari
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Shengru Guo
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Rahul Mittal
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Bing Zou
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Mhamed Grati
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Rosemary I Kabahuma
- Department of Otorhinolaryngology, Steve Biko Academic Hospital, University of Pretoria, Cnr Malan and Steve Biko Road, Gezina, Pretoria, South Africa
| | - Mohan Kameswaran
- Madras ENT Research Foundation (MERF), No-1, 1st Cross Street, Off. II Main Road, Raja Annamalai Puram, Chennai, 600028, Tamil Nadu, India
| | - Taye J Lasisi
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Waheed A Adedeji
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Akeem O Lasisi
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ibis Menendez
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Marianna Herrera
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Claudia Carranza
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Reza Maroofian
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Exeter, UK
| | - Andrew H Crosby
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Exeter, UK
| | - Mariem Bensaid
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisia
| | | | - Majid Mojarrad
- Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - Alex M Mawla
- Department of Neurobiology, Physiology, and Behavior, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
- Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
- Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
| | - Susan H Blanton
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
- Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Xue Z Liu
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Mustafa Tekin
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.
- Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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104
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Hartel BP, Löfgren M, Huygen PLM, Guchelaar I, Lo-A-Njoe Kort N, Sadeghi AM, van Wijk E, Tranebjærg L, Kremer H, Kimberling WJ, Cremers CWRJ, Möller C, Pennings RJE. A combination of two truncating mutations in USH2A causes more severe and progressive hearing impairment in Usher syndrome type IIa. Hear Res 2016; 339:60-8. [PMID: 27318125 DOI: 10.1016/j.heares.2016.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Usher syndrome is an inherited disorder that is characterized by hearing impairment (HI), retinitis pigmentosa, and in some cases vestibular dysfunction. Usher syndrome type IIa is caused by mutations in USH2A. HI in these patients is highly heterogeneous and the present study evaluates the effects of different types of USH2A mutations on the audiometric phenotype. Data from two large centres of expertise on Usher Syndrome in the Netherlands and Sweden were combined in order to create a large combined sample of patients to identify possible genotype-phenotype correlations. DESIGN A retrospective study on HI in 110 patients (65 Dutch and 45 Swedish) genetically diagnosed with Usher syndrome type IIa. We used methods especially designed for characterizing and testing differences in audiological phenotype between patient subgroups. These methods included Age Related Typical Audiograms (ARTA) and a method to evaluate the difference in the degree of HI developed throughout life between subgroups. RESULTS Cross-sectional linear regression analysis of last-visit audiograms for the best hearing ear demonstrated a gradual decline of hearing over decades. The congenital level of HI was in the range of 16-33 dB at 0.25-0.5 kHz, and in the range of 51-60 dB at 1-8 kHz. The annual threshold deterioration was in the range of 0.4-0.5 dB/year at 0.25-2 kHz and in the range of 0.7-0.8 dB/year at 4-8 kHz. Patients with two truncating mutations, including homozygotes for the common c.2299delG mutation, developed significantly more severe HI throughout life than patients with one truncating mutation combined with one nontruncating mutation, and patients with two nontruncating mutations. CONCLUSIONS The results have direct implications for patient counselling in terms of prognosis of hearing and may serve as baseline measures for future (genetic) therapeutic interventions.
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Affiliation(s)
- Bas P Hartel
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Maria Löfgren
- Swedish Institute for Disability Research (SIDR) Linköping, Sweden; Audiological Research Centre, Örebro University Hospital, Örebro, Sweden; School of Medicine and Health, Örebro University, Örebro, Sweden
| | - Patrick L M Huygen
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris Guchelaar
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicole Lo-A-Njoe Kort
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andre M Sadeghi
- The Sahlgrenska Academy, Institute of Neuroscience and Physiology, Department of Audiology, Göteborg, Sweden; Hearing and Deafness Activities Organization, Habilitation & Health, Göteborg, Sweden
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisbeth Tranebjærg
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark; Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Bispebjerg Hospital/Rigshospitalet, Copenhagen, Denmark
| | - Hannie Kremer
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - William J Kimberling
- Department of Otolaryngology, Molecular Otolaryngology, and Renal Research Laboratories, University of Iowa, Iowa City, IA, USA
| | - Cor W R J Cremers
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claes Möller
- Swedish Institute for Disability Research (SIDR) Linköping, Sweden; Audiological Research Centre, Örebro University Hospital, Örebro, Sweden; School of Medicine and Health, Örebro University, Örebro, Sweden
| | - Ronald J E Pennings
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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105
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Huang L, Xiao X, Li S, Jia X, Wang P, Sun W, Xu Y, Xin W, Guo X, Zhang Q. Molecular genetics of cone-rod dystrophy in Chinese patients: New data from 61 probands and mutation overview of 163 probands. Exp Eye Res 2016; 146:252-258. [DOI: 10.1016/j.exer.2016.03.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 12/27/2015] [Accepted: 03/14/2016] [Indexed: 01/17/2023]
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106
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Lingao MD, Ganesh A, Karthikeyan AS, Al Zuhaibi S, Al-Hosni A, Al Khayat A, Capasso J, Trumler AA, Stroh E, Al Shekaili H, Cater JR, Levin AV. Macular cystoid spaces in patients with retinal dystrophy. Ophthalmic Genet 2016; 37:377-383. [DOI: 10.3109/13816810.2015.1101775] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Michelle D. Lingao
- Wills Eye Hospital, Philadelphia, Pennsylvania, USA
- Asian Eye Institute, Makati, Philippines
| | | | | | | | | | | | | | | | - Eliza Stroh
- Cord Blood Registry, San Bruno, California, USA
| | | | | | - Alex V. Levin
- Wills Eye Hospital, Philadelphia, Pennsylvania, USA
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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107
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NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa. Sci Rep 2015; 5:18287. [PMID: 26667666 PMCID: PMC4678898 DOI: 10.1038/srep18287] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/10/2015] [Indexed: 11/28/2022] Open
Abstract
The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE®) was established in an effort to facilitate basic and clinical research of human inherited eye disease. In order to provide high quality genetic testing to eyeGENE®’s enrolled patients which potentially aids clinical diagnosis and disease treatment, we carried out a pilot study and performed Next-generation sequencing (NGS) based molecular diagnosis for 105 Retinitis Pigmentosa (RP) patients randomly selected from the network. A custom capture panel was designed, which incorporated 195 known retinal disease genes, including 61 known RP genes. As a result, disease-causing mutations were identified in 52 out of 105 probands (solving rate of 49.5%). A total of 82 mutations were identified, and 48 of them were novel. Interestingly, for three probands the molecular diagnosis was inconsistent with the initial clinical diagnosis, while for five probands the molecular information suggested a different inheritance model other than that assigned by the physician. In conclusion, our study demonstrated that NGS target sequencing is efficient and sufficiently precise for molecular diagnosis of a highly heterogeneous patient cohort from eyeGENE®.
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108
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Liquori A, Vaché C, Baux D, Blanchet C, Hamel C, Malcolm S, Koenig M, Claustres M, Roux AF. Whole USH2A Gene Sequencing Identifies Several New Deep Intronic Mutations. Hum Mutat 2015; 37:184-93. [PMID: 26629787 DOI: 10.1002/humu.22926] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/19/2015] [Indexed: 01/01/2023]
Abstract
Deep intronic mutations leading to pseudoexon (PE) insertions are underestimated and most of these splicing alterations have been identified by transcript analysis, for instance, the first deep intronic mutation in USH2A, the gene most frequently involved in Usher syndrome type II (USH2). Unfortunately, analyzing USH2A transcripts is challenging and for 1.8%-19% of USH2 individuals carrying a single USH2A recessive mutation, a second mutation is yet to be identified. We have developed and validated a DNA next-generation sequencing approach to identify deep intronic variants in USH2A and evaluated their consequences on splicing. Three distinct novel deep intronic mutations have been identified. All were predicted to affect splicing and resulted in the insertion of PEs, as shown by minigene assays. We present a new and attractive strategy to identify deep intronic mutations, when RNA analyses are not possible. Moreover, the bioinformatics pipeline developed is independent of the gene size, implying the possible application of this approach to any disease-linked gene. Finally, an antisense morpholino oligonucleotide tested in vitro for its ability to restore splicing caused by the c.9959-4159A>G mutation provided high inhibition rates, which are indicative of its potential for molecular therapy.
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Affiliation(s)
- Alessandro Liquori
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France
| | - Christel Vaché
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Catherine Blanchet
- Service ORL, CHRU Montpellier, Montpellier, France.,CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Christian Hamel
- CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Sue Malcolm
- Genetics and Genomic Medicine Programme, Institute of Child Health, UCL, London, UK
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Mireille Claustres
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
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109
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Abstract
Hearing loss (HL) is one of the most common birth defects in developed countries and is a diverse pathologic condition with different classifications. One of these is based on the association with other clinical features, defined as syndromic hearing loss (SHL). Determining the cause of the HL in these patients is extremely beneficial as it enables a personalized approach to caring for the individual. Early screening can further aid in optimal rehabilitation for a child's development and growth. The advancement of high-throughput sequencing technology is facilitating rapid and low-cost diagnostics for patients with SHL.
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Affiliation(s)
- Tal Koffler
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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110
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Veleri S, Lazar CH, Chang B, Sieving PA, Banin E, Swaroop A. Biology and therapy of inherited retinal degenerative disease: insights from mouse models. Dis Model Mech 2015; 8:109-29. [PMID: 25650393 PMCID: PMC4314777 DOI: 10.1242/dmm.017913] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retinal neurodegeneration associated with the dysfunction or death of photoreceptors is a major cause of incurable vision loss. Tremendous progress has been made over the last two decades in discovering genes and genetic defects that lead to retinal diseases. The primary focus has now shifted to uncovering disease mechanisms and designing treatment strategies, especially inspired by the successful application of gene therapy in some forms of congenital blindness in humans. Both spontaneous and laboratory-generated mouse mutants have been valuable for providing fundamental insights into normal retinal development and for deciphering disease pathology. Here, we provide a review of mouse models of human retinal degeneration, with a primary focus on diseases affecting photoreceptor function. We also describe models associated with retinal pigment epithelium dysfunction or synaptic abnormalities. Furthermore, we highlight the crucial role of mouse models in elucidating retinal and photoreceptor biology in health and disease, and in the assessment of novel therapeutic modalities, including gene- and stem-cell-based therapies, for retinal degenerative diseases.
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Affiliation(s)
- Shobi Veleri
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Csilla H Lazar
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA. Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano Sciences, Babes-Bolyai-University, Cluj-Napoca, 400271, Romania
| | - Bo Chang
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Paul A Sieving
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eyal Banin
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA. Center for Retinal and Macular Degenerations, Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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111
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Zou J, Mathur PD, Zheng T, Wang Y, Almishaal A, Park AH, Yang J. Individual USH2 proteins make distinct contributions to the ankle link complex during development of the mouse cochlear stereociliary bundle. Hum Mol Genet 2015; 24:6944-57. [PMID: 26401052 DOI: 10.1093/hmg/ddv398] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/21/2015] [Indexed: 11/14/2022] Open
Abstract
Usher syndrome (USH) is the leading cause of inherited deaf-blindness, with type 2 (USH2) being the most common clinical form. Studies suggest that proteins encoded by USH2 causative genes assemble into the ankle link complex (ALC) at the hair cell stereociliary bundle; however, little is known about the in vivo assembly and function of this complex. Using various USH2 mutant mice, we showed by immunofluorescence that USH2 proteins play different roles in cochlear ALC assembly, with G protein-coupled receptor 98 being the most important protein. Complex assembly likely occurs at the stereociliary bundle but not along the protein transport route in the cell body. Stereociliary morphological defects in USH2 mutant mice suggest roles for the ALC in regulating inner hair cell stereociliary growth and differentiation as well as outer hair cell stereociliary rigidity and organization during development. These roles are unique from the bundle cohesion role of Usher syndrome type 1 protein complexes. Loss of individual USH2 gene expressions leads to variable morphological and functional consequences, correlating with the severity of ALC disruption. This finding suggests a potential genotype-phenotype correlation in USH2 patients. In summary, this study provides novel insights into the molecular mechanism underlying cochlear stereociliary bundle development and hearing loss pathogenesis of various USH2 subtypes. Our thorough phenotypical characterization of USH2 mouse models is essential for future use of these animal models in therapeutic development.
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Affiliation(s)
- Junhuang Zou
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Pranav D Mathur
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA, Department of Neurobiology and Anatomy, University of Utah, 20 North 1900 East, Salt Lake City, UT 84132, USA
| | - Tihua Zheng
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Yong Wang
- Division of Otolaryngology, Department of Surgery, University of Utah, 30 North 1900 East, Salt Lake City, UT 84132, USA and
| | - Ali Almishaal
- Department of Communication Sciences and Disorders, University of Utah, 390 South 1530 East, Salt Lake City, UT 84112, USA
| | - Albert H Park
- Division of Otolaryngology, Department of Surgery, University of Utah, 30 North 1900 East, Salt Lake City, UT 84132, USA and
| | - Jun Yang
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA, Department of Neurobiology and Anatomy, University of Utah, 20 North 1900 East, Salt Lake City, UT 84132, USA, Division of Otolaryngology, Department of Surgery, University of Utah, 30 North 1900 East, Salt Lake City, UT 84132, USA and
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112
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Novel and recurrent CIB2 variants, associated with nonsyndromic deafness, do not affect calcium buffering and localization in hair cells. Eur J Hum Genet 2015; 24:542-9. [PMID: 26173970 DOI: 10.1038/ejhg.2015.157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/20/2015] [Accepted: 06/07/2015] [Indexed: 12/18/2022] Open
Abstract
Variants in CIB2 can underlie either Usher syndrome type I (USH1J) or nonsyndromic hearing impairment (NSHI) (DFNB48). Here, a novel homozygous missense variant c.196C>T and compound heterozygous variants, c.[97C>T];[196C>T], were found, respectively, in two unrelated families of Dutch origin. Besides, the previously reported c.272 T>C functional missense variant in CIB2 was identified in two families of Pakistani origin. The missense variants are demonstrated not to affect subcellular localization of CIB2 in vestibular hair cells in ex vivo expression experiments. Furthermore, these variants do not affect the ATP-induced calcium responses in COS-7 cells. However, based on the residues affected, the variants are suggested to alter αIIβ integrin binding. HI was nonsyndromic in all four families. However, deafness segregating with the c.272T>C variant in one Pakistani family is remarkably less severe than that in all other families with this mutation. Our results contribute to the insight in genotype-phenotype correlations of CIB2 mutations.
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113
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Whole-exome sequencing revealed two novel mutations in Usher syndrome. Gene 2015; 563:215-8. [DOI: 10.1016/j.gene.2015.03.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 11/24/2022]
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114
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Kunstman JW, Juhlin CC, Goh G, Brown TC, Stenman A, Healy JM, Rubinstein JC, Choi M, Kiss N, Nelson-Williams C, Mane S, Rimm DL, Prasad ML, Höög A, Zedenius J, Larsson C, Korah R, Lifton RP, Carling T. Characterization of the mutational landscape of anaplastic thyroid cancer via whole-exome sequencing. Hum Mol Genet 2015; 24:2318-29. [PMID: 25576899 PMCID: PMC4380073 DOI: 10.1093/hmg/ddu749] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 11/26/2014] [Accepted: 12/29/2014] [Indexed: 01/25/2023] Open
Abstract
Anaplastic thyroid carcinoma (ATC) is a frequently lethal malignancy that is often unresponsive to available therapeutic strategies. The tumorigenesis of ATC and its relationship to the widely prevalent well-differentiated thyroid carcinomas are unclear. We have analyzed 22 cases of ATC as well as 4 established ATC cell lines using whole-exome sequencing. A total of 2674 somatic mutations (121/sample) were detected. Ontology analysis revealed that the majority of variants aggregated in the MAPK, ErbB and RAS signaling pathways. Mutations in genes related to malignancy not previously associated with thyroid tumorigenesis were observed, including mTOR, NF1, NF2, MLH1, MLH3, MSH5, MSH6, ERBB2, EIF1AX and USH2A; some of which were recurrent and were investigated in 24 additional ATC cases and 8 ATC cell lines. Somatic mutations in established thyroid cancer genes were detected in 14 of 22 (64%) tumors and included recurrent mutations in BRAF, TP53 and RAS-family genes (6 cases each), as well as PIK3CA (2 cases) and single cases of CDKN1B, CDKN2C, CTNNB1 and RET mutations. BRAF V600E and RAS mutations were mutually exclusive; all ATC cell lines exhibited a combination of mutations in either BRAF and TP53 or NRAS and TP53. A hypermutator phenotype in two cases with >8 times higher mutational burden than the remaining mean was identified; both cases harbored unique somatic mutations in MLH mismatch-repair genes. This first comprehensive exome-wide analysis of the mutational landscape of ATC identifies novel genes potentially associated with ATC tumorigenesis, some of which may be targets for future therapeutic intervention.
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Affiliation(s)
| | | | - Gerald Goh
- Department of Genetics, Howard Hughes Medical Institute and
| | - Taylor C Brown
- Yale Endocrine Neoplasia Laboratory, Department of Surgery
| | | | - James M Healy
- Yale Endocrine Neoplasia Laboratory, Department of Surgery
| | | | - Murim Choi
- Department of Genetics, Howard Hughes Medical Institute and
| | | | | | | | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Manju L Prasad
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - Jan Zedenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital CCK, SE-171 76 Stockholm, Sweden
| | | | - Reju Korah
- Yale Endocrine Neoplasia Laboratory, Department of Surgery
| | | | - Tobias Carling
- Yale Endocrine Neoplasia Laboratory, Department of Surgery,
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115
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Toms M, Bitner-Glindzicz M, Webster A, Moosajee M. Usher syndrome: a review of the clinical phenotype, genes and therapeutic strategies. EXPERT REVIEW OF OPHTHALMOLOGY 2015. [DOI: 10.1586/17469899.2015.1033403] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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116
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Thompson DA, Ali RR, Banin E, Branham KE, Flannery JG, Gamm DM, Hauswirth WW, Heckenlively JR, Iannaccone A, Jayasundera KT, Khan NW, Molday RS, Pennesi ME, Reh TA, Weleber RG, Zacks DN. Advancing therapeutic strategies for inherited retinal degeneration: recommendations from the Monaciano Symposium. Invest Ophthalmol Vis Sci 2015; 56:918-31. [PMID: 25667399 DOI: 10.1167/iovs.14-16049] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although rare in the general population, retinal dystrophies occupy a central position in current efforts to develop innovative therapies for blinding diseases. This status derives, in part, from the unique biology, accessibility, and function of the retina, as well as from the synergy between molecular discoveries and transformative advances in functional assessment and retinal imaging. The combination of these factors has fueled remarkable progress in the field, while at the same time creating complex challenges for organizing collective efforts aimed at advancing translational research. The present position paper outlines recent progress in gene therapy and cell therapy for this group of disorders, and presents a set of recommendations for addressing the challenges remaining for the coming decade. It is hoped that the formulation of these recommendations will stimulate discussions among researchers, funding agencies, industry, and policy makers that will accelerate the development of safe and effective treatments for retinal dystrophies and related diseases.
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Affiliation(s)
- Debra A Thompson
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Robin R Ali
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States Division of Molecular Therapy, University College London Institute of Ophthalmology, London, England, United Kingdom
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California-Berkeley, Berkeley, California, United States
| | - David M Gamm
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - William W Hauswirth
- Department of Ophthalmology, University of Florida College of Medicine, Gainesville, Florida, United States
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Alessandro Iannaccone
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Naheed W Khan
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark E Pennesi
- Casey Eye Institute and the Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, United States
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington, United States
| | - Richard G Weleber
- Casey Eye Institute and the Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, United States Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States
| | - David N Zacks
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
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117
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Lenassi E, Vincent A, Li Z, Saihan Z, Coffey AJ, Steele-Stallard HB, Moore AT, Steel KP, Luxon LM, Héon E, Bitner-Glindzicz M, Webster AR. A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants. Eur J Hum Genet 2015; 23:1318-27. [PMID: 25649381 PMCID: PMC4592079 DOI: 10.1038/ejhg.2014.283] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/20/2014] [Accepted: 12/02/2014] [Indexed: 12/19/2022] Open
Abstract
Defects in USH2A cause both isolated retinal disease and Usher syndrome (ie, retinal disease and deafness). To gain insights into isolated/nonsyndromic USH2A retinopathy, we screened USH2A in 186 probands with recessive retinal disease and no hearing complaint in childhood (discovery cohort) and in 84 probands with recessive retinal disease (replication cohort). Detailed phenotyping, including retinal imaging and audiological assessment, was performed in individuals with two likely disease-causing USH2A variants. Further genetic testing, including screening for a deep-intronic disease-causing variant and large deletions/duplications, was performed in those with one likely disease-causing change. Overall, 23 of 186 probands (discovery cohort) were found to harbour two likely disease-causing variants in USH2A. Some of these variants were predominantly associated with nonsyndromic retinal degeneration (‘retinal disease-specific'); these included the common c.2276 G>T, p.(Cys759Phe) mutation and five additional variants: c.2802 T>G, p.(Cys934Trp); c.10073 G>A, p.(Cys3358Tyr); c.11156 G>A, p.(Arg3719His); c.12295-3 T>A; and c.12575 G>A, p.(Arg4192His). An allelic hierarchy was observed in the discovery cohort and confirmed in the replication cohort. In nonsyndromic USH2A disease, retinopathy was consistent with retinitis pigmentosa and the audiological phenotype was variable. USH2A retinopathy is a common cause of nonsyndromic recessive retinal degeneration and has a different mutational spectrum to that observed in Usher syndrome. The following model is proposed: the presence of at least one ‘retinal disease-specific' USH2A allele in a patient with USH2A-related disease results in the preservation of normal hearing. Careful genotype–phenotype studies such as this will become increasingly important, especially now that high-throughput sequencing is widely used in the clinical setting.
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Affiliation(s)
- Eva Lenassi
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK.,Eye Hospital, University Medical Centre, Ljubljana, Slovenia
| | - Ajoy Vincent
- The Hospital for Sick Children, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Zheng Li
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK.,Ocular Genetics, Singapore Eye Research Institute, Singapore, Singapore
| | - Zubin Saihan
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK
| | | | | | - Anthony T Moore
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK
| | | | - Linda M Luxon
- UCL Ear Institute, London, UK.,National Hospital for Neurology and Neurosurgery, London, UK
| | - Elise Héon
- The Hospital for Sick Children, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | | | - Andrew R Webster
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK
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118
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van Huet RAC, Siemiatkowska AM, Özgül RK, Yücel D, Hoyng CB, Banin E, Blumenfeld A, Rotenstreich Y, Riemslag FCC, den Hollander AI, Theelen T, Collin RWJ, van den Born LI, Klevering BJ. Retinitis pigmentosa caused by mutations in the ciliary MAK gene is relatively mild and is not associated with apparent extra-ocular features. Acta Ophthalmol 2015; 93:83-94. [PMID: 25385675 DOI: 10.1111/aos.12500] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/17/2014] [Indexed: 12/13/2022]
Abstract
PURPOSE Defects in MAK, encoding a protein localized to the photoreceptor connecting cilium, have recently been associated with autosomal recessive retinitis pigmentosa (RP). The aim of this study is to describe our detailed clinical observations in patients with MAK-associated RP, including an assessment of syndromic symptoms frequently observed in ciliopathies. METHODS In this international collaborative study, 11 patients carrying nonsense or missense mutations in MAK were clinically evaluated, including extensive assessment of the medical history, slit-lamp biomicroscopy, ophthalmoscopy, kinetic perimetry, electroretinography (ERG), spectral-domain optical coherence tomography (SD-OCT), autofluorescence imaging and fundus photography. Additionally, we used a questionnaire to evaluate the presence of syndromic features and tested the olfactory function. RESULTS MAK-associated RP is not associated with syndromic features, not even with subclinical dysfunction of the olfactory apparatus. All patients experienced typical RP symptoms of night blindness followed by visual field constriction. Symptoms initiated between childhood and the age of 43 (mean: 23 years). Although some patients experienced vision loss, the visual acuity remained normal in most patients. ERG and ophthalmoscopy revealed classic RP characteristics, and SD-OCT demonstrated thinning of the overall retina, outer nuclear layer and photoreceptor-pigment epithelium complex. CONCLUSION Nonsense and missense mutations in MAK give rise to a non-syndromic recessive RP phenotype without apparent extra-ocular features. When compared to other retinal ciliopathies, MAK-associated RP appears to be relatively mild and shows remarkable resemblance to RP1-associated RP, which could be explained by the close functional relation of these proteins.
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Affiliation(s)
- Ramon A. C. van Huet
- Department of Ophthalmology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Anna M. Siemiatkowska
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Riza K. Özgül
- Institute of Child Health and Metabolism Unit; Department of Pediatrics; Hacettepe University; Ankara Turkey
| | - Didem Yücel
- Institute of Child Health and Metabolism Unit; Department of Pediatrics; Hacettepe University; Ankara Turkey
| | - Carel B. Hoyng
- Department of Ophthalmology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Eyal Banin
- Department of Ophthalmology; Hadassah-Hebrew University Medical Center; Jerusalem Israel
| | - Anat Blumenfeld
- Department of Ophthalmology; Hadassah-Hebrew University Medical Center; Jerusalem Israel
| | - Ygal Rotenstreich
- Electrophysiology Clinic; Goldschleger Eye Research Institute; Tel Aviv University; Sheba Medical Centre; Ramat Gan Israel
| | - Frans C. C. Riemslag
- The Rotterdam Eye Hospital; Rotterdam The Netherlands
- Bartiméus, Institute for the Visually Handicapped; Zeist The Netherlands
| | - Anneke I. den Hollander
- Department of Ophthalmology; Radboud University Medical Center; Nijmegen The Netherlands
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
- Nijmegen Center for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
| | - Thomas Theelen
- Department of Ophthalmology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
- Nijmegen Center for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - B. Jeroen Klevering
- Department of Ophthalmology; Radboud University Medical Center; Nijmegen The Netherlands
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119
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Mathur P, Yang J. Usher syndrome: Hearing loss, retinal degeneration and associated abnormalities. Biochim Biophys Acta Mol Basis Dis 2014; 1852:406-20. [PMID: 25481835 DOI: 10.1016/j.bbadis.2014.11.020] [Citation(s) in RCA: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 02/06/2023]
Abstract
Usher syndrome (USH), clinically and genetically heterogeneous, is the leading genetic cause of combined hearing and vision loss. USH is classified into three types, based on the hearing and vestibular symptoms observed in patients. Sixteen loci have been reported to be involved in the occurrence of USH and atypical USH. Among them, twelve have been identified as causative genes and one as a modifier gene. Studies on the proteins encoded by these USH genes suggest that USH proteins interact among one another and function in multiprotein complexes in vivo. Although their exact functions remain enigmatic in the retina, USH proteins are required for the development, maintenance and function of hair bundles, which are the primary mechanosensitive structure of inner ear hair cells. Despite the unavailability of a cure, progress has been made to develop effective treatments for this disease. In this review, we focus on the most recent discoveries in the field with an emphasis on USH genes, protein complexes and functions in various tissues as well as progress toward therapeutic development for USH.
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Affiliation(s)
- Pranav Mathur
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA; Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA
| | - Jun Yang
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA; Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA; Department of Otolaryngology Head and Neck Surgery, University of Utah, Salt Lake City, UT 84132, USA.
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120
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Zhao L, Wang F, Wang H, Li Y, Alexander S, Wang K, Willoughby CE, Zaneveld JE, Jiang L, Soens ZT, Earle P, Simpson D, Silvestri G, Chen R. Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland. Hum Genet 2014; 134:217-30. [PMID: 25472526 DOI: 10.1007/s00439-014-1512-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/20/2014] [Indexed: 11/24/2022]
Abstract
Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by progressive photoreceptor degeneration. An accurate molecular diagnosis is essential for disease characterization and clinical prognoses. A retinal capture panel that enriches 186 known retinal disease genes, including 55 known RP genes, was developed. Targeted next-generation sequencing was performed for a cohort of 82 unrelated RP cases from Northern Ireland, including 46 simplex cases and 36 familial cases. Disease-causing mutations were identified in 49 probands, including 28 simplex cases and 21 familial cases, achieving a solving rate of 60 %. In total, 65 pathogenic mutations were found, and 29 of these were novel. Interestingly, the molecular information of 12 probands was neither consistent with their initial inheritance pattern nor clinical diagnosis. Further clinical reassessment resulted in a refinement of the clinical diagnosis in 11 patients. This is the first study to apply next-generation sequencing-based, comprehensive molecular diagnoses to a large number of RP probands from Northern Ireland. Our study shows that molecular information can aid clinical diagnosis, potentially changing treatment options, current family counseling and management.
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Affiliation(s)
- Li Zhao
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
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121
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Chen Q, Zou J, Shen Z, Zhang W, Yang J. Whirlin and PDZ domain-containing 7 (PDZD7) proteins are both required to form the quaternary protein complex associated with Usher syndrome type 2. J Biol Chem 2014; 289:36070-88. [PMID: 25406310 DOI: 10.1074/jbc.m114.610535] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Usher syndrome (USH) is the leading genetic cause of combined hearing and vision loss. Among the three USH clinical types, type 2 (USH2) occurs most commonly. USH2A, GPR98, and WHRN are three known causative genes of USH2, whereas PDZD7 is a modifier gene found in USH2 patients. The proteins encoded by these four USH genes have been proposed to form a multiprotein complex, the USH2 complex, due to interactions found among some of these proteins in vitro, their colocalization in vivo, and mutual dependence of some of these proteins for their normal in vivo localizations. However, evidence showing the formation of the USH2 complex is missing, and details on how this complex is formed remain elusive. Here, we systematically investigated interactions among the intracellular regions of the four USH proteins using colocalization, yeast two-hybrid, and pull-down assays. We show that multiple domains of the four USH proteins interact among one another. Importantly, both WHRN and PDZD7 are required for the complex formation with USH2A and GPR98. In this USH2 quaternary complex, WHRN prefers to bind to USH2A, whereas PDZD7 prefers to bind to GPR98. Interaction between WHRN and PDZD7 is the bridge between USH2A and GPR98. Additionally, the USH2 quaternary complex has a variable stoichiometry. These findings suggest that a non-obligate, short term, and dynamic USH2 quaternary protein complex may exist in vivo. Our work provides valuable insight into the physiological role of the USH2 complex in vivo and informs possible reconstruction of the USH2 complex for future therapy.
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Affiliation(s)
- Qian Chen
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center
| | - Junhuang Zou
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center
| | - Zuolian Shen
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center
| | - Weiping Zhang
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center
| | - Jun Yang
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, the Department of Neurobiology and Anatomy, and the Department of Otolaryngology Head and Neck Surgery, University of Utah, Salt Lake City, Utah 84132
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Reddy R, Fahiminiya S, El Zir E, Mansour A, Megarbane A, Majewski J, Slim R. Molecular genetics of the Usher syndrome in Lebanon: identification of 11 novel protein truncating mutations by whole exome sequencing. PLoS One 2014; 9:e107326. [PMID: 25211151 PMCID: PMC4161397 DOI: 10.1371/journal.pone.0107326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/09/2014] [Indexed: 12/02/2022] Open
Abstract
Background Usher syndrome (USH) is a genetically heterogeneous condition with ten disease-causing genes. The spectrum of genes and mutations causing USH in the Lebanese and Middle Eastern populations has not been described. Consequently, diagnostic approaches designed to screen for previously reported mutations were unlikely to identify the mutations in 11 unrelated families, eight of Lebanese and three of Middle Eastern origins. In addition, six of the ten USH genes consist of more than 20 exons, each, which made mutational analysis by Sanger sequencing of PCR-amplified exons from genomic DNA tedious and costly. The study was aimed at the identification of USH causing genes and mutations in 11 unrelated families with USH type I or II. Methods Whole exome sequencing followed by expanded familial validation by Sanger sequencing. Results We identified disease-causing mutations in all the analyzed patients in four USH genes, MYO7A, USH2A, GPR98 and CDH23. Eleven of the mutations were novel and protein truncating, including a complex rearrangement in GPR98. Conclusion Our data highlight the genetic diversity of Usher syndrome in the Lebanese population and the time and cost-effectiveness of whole exome sequencing approach for mutation analysis of genetically heterogeneous conditions caused by large genes.
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Affiliation(s)
- Ramesh Reddy
- Departments of Human Genetics and Obstetrics-Gynecology, McGill University Health Centre, Montreal, Canada
| | - Somayyeh Fahiminiya
- McGill University and Genome Quebec Innovation Centre and Department of Human Genetics, Montreal, Canada
| | - Elie El Zir
- Department of Otorhinolaryngology, Hôpital Sacré-Coeur, Baabda, Lebanon
| | - Ahmad Mansour
- Department of Ophthalmology, American University of Beirut, Beirut, Lebanon
| | - Andre Megarbane
- Unité de génétique médicale, Faculté de médecine, Université Saint Joseph, Beirut, Lebanon
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre and Department of Human Genetics, Montreal, Canada
| | - Rima Slim
- Departments of Human Genetics and Obstetrics-Gynecology, McGill University Health Centre, Montreal, Canada
- * E-mail:
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Jang HM, Erf GF, Rowland KC, Kong BW. Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model. BMC Genomics 2014; 15:707. [PMID: 25151476 PMCID: PMC4152579 DOI: 10.1186/1471-2164-15-707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 08/18/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Smyth line (SL) chicken is the only animal model for autoimmune vitiligo that spontaneously displays all clinical and biological manifestations of the human disorder. To understand the genetic components underlying the susceptibility to develop SL vitiligo (SLV), whole genome resequencing analysis was performed in SLV chickens compared with non-vitiliginous parental Brown line (BL) chickens, which maintain a very low incidence rate of vitiligo. RESULTS Illumina sequencing technology and reference based assembly on Red Jungle Fowl genome sequences were used. Results of genome resequencing of pooled DNA of each 10 BL and SL chickens reached 5.1x and 7.0x coverage, respectively. The total number of SNPs was 4.8 and 5.5 million in BL and SL genome, respectively. Through a series of filtering processes, a total of ~1 million unique SNPs were found in the SL alone. Eventually of the 156 reliable marker SNPs, which can induce non-synonymous-, frameshift-, nonsense-, and no-start mutations in amino acid sequences in proteins, 139 genes were chosen for further analysis. Of these, 14 randomly chosen SNPs were examined for SNP verification by PCR and Sanger sequencing to detect SNP positions in 20 BL and 70 SL chickens. The results of the analysis of the 14 SNPs clearly showed differential frequencies of nucleotide bases in the SNP positions between BL and SL chickens. Bioinformatic analysis showed that the 156 most reliable marker SNPs included genes involved in dermatological diseases/conditions such as ADAMTS13, ASPM, ATP6V0A2, BRCA2, COL12A1, GRM5, LRP2, OBSCN, PLAU, RNF168, STAB2, and XIRP1. Intermolecular gene network analysis revealed that candidate genes identified in SLV play a role in networks centered on protein kinases (MAPK, ERK1/2, PKC, PRKDC), phosphatase (PPP1CA), ubiquitinylation (UBC) and amyloid production (APP). CONCLUSIONS Various potential genetic markers showing amino acid changes and potential roles in vitiligo development were identified in the SLV chicken through genome resequencing. The genetic markers and bioinformatic interpretations of amino acid mutations found in SLV chickens may provide insight into the genetic component responsible for the onset and the progression of autoimmune vitiligo and serve as valuable markers to develop diagnostic tools to detect vitiligo susceptibility.
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Affiliation(s)
- Hyeon-Min Jang
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
| | - Gisela F Erf
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
| | - Kaylee C Rowland
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
| | - Byung-Whi Kong
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, POSC O-404, 1260 West Maple, Fayetteville, AR 72701 USA
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Chen X, Sheng X, Liu X, Li H, Liu Y, Rong W, Ha S, Liu W, Kang X, Zhao K, Zhao C. Targeted next-generation sequencing reveals novel USH2A mutations associated with diverse disease phenotypes: implications for clinical and molecular diagnosis. PLoS One 2014; 9:e105439. [PMID: 25133613 PMCID: PMC4136877 DOI: 10.1371/journal.pone.0105439] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/20/2014] [Indexed: 12/15/2022] Open
Abstract
USH2A mutations have been implicated in the disease etiology of several inherited diseases, including Usher syndrome type 2 (USH2), nonsyndromic retinitis pigmentosa (RP), and nonsyndromic deafness. The complex genetic and phenotypic spectrums relevant to USH2A defects make it difficult to manage patients with such mutations. In the present study, we aim to determine the genetic etiology and to characterize the correlated clinical phenotypes for three Chinese pedigrees with nonsyndromic RP, one with RP sine pigmento (RPSP), and one with USH2. Family histories and clinical details for all included patients were reviewed. Ophthalmic examinations included best corrected visual acuities, visual field measurements, funduscopy, and electroretinography. Targeted next-generation sequencing (NGS) was applied using two sequence capture arrays to reveal the disease causative mutations for each family. Genotype-phenotype correlations were also annotated. Seven USH2A mutations, including four missense substitutions (p.P2762A, p.G3320C, p.R3719H, and p.G4763R), two splice site variants (c.8223+1G>A and c.8559-2T>C), and a nonsense mutation (p.Y3745*), were identified as disease causative in the five investigated families, of which three reported to have consanguineous marriage. Among all seven mutations, six were novel, and one was recurrent. Two homozygous missense mutations (p.P2762A and p.G3320C) were found in one individual family suggesting a potential double hit effect. Significant phenotypic divergences were revealed among the five families. Three families of the five families were affected with early, moderated, or late onset RP, one with RPSP, and the other one with USH2. Our study expands the genotypic and phenotypic variability relevant to USH2A mutations, which would help with a clear insight into the complex genetic and phenotypic spectrums relevant to USH2A defects, and is complementary for a better management of patients with such mutations. We have also demonstrated that a targeted NGS approach is a valuable tool for the genetic diagnosis of USH2 and RP.
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Affiliation(s)
- Xue Chen
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, State Key Laboratory of Reproductive Medicine, Nanjing, China
| | - Xunlun Sheng
- Ningxia Eye Hospital, Ningxia People’s Hospital, Ningxia, China
| | - Xiaoxing Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, State Key Laboratory of Reproductive Medicine, Nanjing, China
| | - Huiping Li
- Ningxia Eye Hospital, Ningxia People’s Hospital, Ningxia, China
| | - Yani Liu
- Ningxia Eye Hospital, Ningxia People’s Hospital, Ningxia, China
| | - Weining Rong
- Ningxia Eye Hospital, Ningxia People’s Hospital, Ningxia, China
| | - Shaoping Ha
- Ningxia Eye Hospital, Ningxia People’s Hospital, Ningxia, China
| | - Wenzhou Liu
- Ningxia Eye Hospital, Ningxia People’s Hospital, Ningxia, China
| | - Xiaoli Kang
- Department of Ophthalmology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kanxing Zhao
- Tianjin Medical University, Tianjin Eye Hospital, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, China
| | - Chen Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, State Key Laboratory of Reproductive Medicine, Nanjing, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat Sen University, Guangzhou, China
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125
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The first USH2A mutation analysis of Japanese autosomal recessive retinitis pigmentosa patients: a totally different mutation profile with the lack of frequent mutations found in Caucasian patients. J Hum Genet 2014; 59:521-8. [PMID: 25078356 DOI: 10.1038/jhg.2014.65] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/20/2014] [Accepted: 07/03/2014] [Indexed: 11/09/2022]
Abstract
Retinitis pigmentosa (RP) is a highly heterogeneous genetic disease. The USH2A gene, which accounts for approximately 74-90% of Usher syndrome type 2 (USH2) cases, is also one of the major autosomal recessive RP (arRP) causative genes among Caucasian populations. To identify disease-causing USH2A gene mutations in Japanese RP patients, all 73 exons were screened for mutations by direct sequencing. In total, 100 unrelated Japanese RP patients with no systemic manifestations were identified, excluding families with obvious autosomal dominant inheritance. Of these 100 patients, 82 were included in this present study after 18 RP patients with very likely pathogenic EYS (eyes shut homolog) mutations were excluded. The mutation analysis of the USH2A revealed five very likely pathogenic mutations in four patients. A patient had only one very likely pathogenic mutation and the others had two of them. Caucasian frequent mutations p.C759F in arRP and p.E767fs in USH2 were not found. All the four patients exhibited typical clinical features of RP. The observed prevalence of USH2A gene mutations was approximately 4% among Japanese arRP patients, and the profile of the USH2A gene mutations differed largely between Japanese patients and previously reported Caucasian populations.
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126
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Baux D, Blanchet C, Hamel C, Meunier I, Larrieu L, Faugère V, Vaché C, Castorina P, Puech B, Bonneau D, Malcolm S, Claustres M, Roux AF. Enrichment of LOVD-USHbases with 152 USH2A genotypes defines an extensive mutational spectrum and highlights missense hotspots. Hum Mutat 2014; 35:1179-86. [PMID: 24944099 DOI: 10.1002/humu.22608] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/09/2014] [Indexed: 12/19/2022]
Abstract
Alterations of USH2A, encoding usherin, are responsible for more than 70% of cases of Usher syndrome type II (USH2), a recessive disorder that combines moderate to severe hearing loss and retinal degeneration. The longest USH2A transcript encodes usherin isoform b, a 5,202-amino-acid transmembrane protein with an exceptionally large extracellular domain consisting notably of a Laminin N-terminal domain and numerous Laminin EGF-like (LE) and Fibronectin type III (FN3) repeats. Mutations of USH2A are scattered throughout the gene and mostly private. Annotating these variants is therefore of major importance to correctly assign pathogenicity. We have extensively genotyped a novel cohort of 152 Usher patients and identified 158 different mutations, of which 93 are newly described. Pooling this new data with the existing pathogenic variants already incorporated in USHbases reveals several previously unappreciated features of the mutational spectrum. We show that parts of the protein are more likely to tolerate single amino acid variations, whereas others constitute pathogenic missense hotspots. We have found, in repeated LE and FN3 domains, a nonequal distribution of the missense mutations that highlights some crucial positions in usherin with possible consequences for the assessment of the pathogenicity of the numerous missense variants identified in USH2A.
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Affiliation(s)
- David Baux
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
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127
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Genetics of auditory mechano-electrical transduction. Pflugers Arch 2014; 467:49-72. [PMID: 24957570 PMCID: PMC4281357 DOI: 10.1007/s00424-014-1552-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 12/29/2022]
Abstract
The hair bundles of cochlear hair cells play a central role in the auditory mechano-electrical transduction (MET) process. The identification of MET components and of associated molecular complexes by biochemical approaches is impeded by the very small number of hair cells within the cochlea. In contrast, human and mouse genetics have proven to be particularly powerful. The study of inherited forms of deafness led to the discovery of several essential proteins of the MET machinery, which are currently used as entry points to decipher the associated molecular networks. Notably, MET relies not only on the MET machinery but also on several elements ensuring the proper sound-induced oscillation of the hair bundle or the ionic environment necessary to drive the MET current. Here, we review the most significant advances in the molecular bases of the MET process that emerged from the genetics of hearing.
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128
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Siemiatkowska AM, Collin RWJ, den Hollander AI, Cremers FPM. Genomic approaches for the discovery of genes mutated in inherited retinal degeneration. Cold Spring Harb Perspect Med 2014; 4:a017137. [PMID: 24939053 PMCID: PMC4109577 DOI: 10.1101/cshperspect.a017137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In view of their high degree of genetic heterogeneity, inherited retinal diseases (IRDs) pose a significant challenge for identifying novel genetic causes. Thus far, more than 200 genes have been found to be mutated in IRDs, which together contain causal variants in >80% of the cases. Accurate genetic diagnostics is particularly important for isolated cases, in which X-linked and de novo autosomal dominant variants are not uncommon. In addition, new gene- or mutation-specific therapies are emerging, underlining the importance of identifying causative mutations in each individual. Sanger sequencing of selected genes followed by cost-effective targeted next-generation sequencing (NGS) can identify defects in known IRD-associated genes in the majority of the cases. Exome NGS in combination with genetic linkage or homozygosity mapping studies can aid the identification of the remaining causal genes. As these are thought to be mutated in <1% of the cases, validation through functional modeling in, for example, zebrafish and/or replication through the genotyping of large patient cohorts is required. In the near future, whole genome NGS in combination with transcriptome NGS may reveal mutations that are currently hidden in the noncoding regions of the human genome.
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Affiliation(s)
- Anna M Siemiatkowska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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129
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Novel and recurrent MYO7A mutations in Usher syndrome type 1 and type 2. PLoS One 2014; 9:e97808. [PMID: 24831256 PMCID: PMC4022727 DOI: 10.1371/journal.pone.0097808] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/24/2014] [Indexed: 11/19/2022] Open
Abstract
Usher syndrome (USH) is a group of disorders manifested as retinitis pigmentosa and bilateral sensorineural hearing loss, with or without vestibular dysfunction. Here, we recruited three Chinese families affected with autosomal recessive USH for detailed clinical evaluations and for mutation screening in the genes associated with inherited retinal diseases. Using targeted next-generation sequencing (NGS) approach, three new alleles and one known mutation in MYO7A gene were identified in the three families. In two families with USH type 1, novel homozygous frameshift variant p.Pro194Hisfs*13 and recurrent missense variant p.Thr165Met were demonstrated as the causative mutations respectively. Crystal structural analysis denoted that p.Thr165Met would very likely change the tertiary structure of the protein encoded by MYO7A. In another family affected with USH type 2, novel biallelic mutations in MYO7A, c.[1343+1G>A];[2837T>G] or p.[?];[Met946Arg], were identified with clinical significance. Because MYO7A, to our knowledge, has rarely been correlated with USH type 2, our findings therefore reveal distinguished clinical phenotypes associated with MYO7A. We also conclude that targeted NGS is an effective approach for genetic diagnosis for USH, which can further provide better understanding of genotype-phenotype relationship of the disease.
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130
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Zallocchi M, Binley K, Lad Y, Ellis S, Widdowson P, Iqball S, Scripps V, Kelleher M, Loader J, Miskin J, Peng YW, Wang WM, Cheung L, Delimont D, Mitrophanous KA, Cosgrove D. EIAV-based retinal gene therapy in the shaker1 mouse model for usher syndrome type 1B: development of UshStat. PLoS One 2014; 9:e94272. [PMID: 24705452 PMCID: PMC3976400 DOI: 10.1371/journal.pone.0094272] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/14/2014] [Indexed: 01/21/2023] Open
Abstract
Usher syndrome type 1B is a combined deaf-blindness condition caused by mutations in the MYO7A gene. Loss of functional myosin VIIa in the retinal pigment epithelia (RPE) and/or photoreceptors leads to blindness. We evaluated the impact of subretinally delivered UshStat, a recombinant EIAV-based lentiviral vector expressing human MYO7A, on photoreceptor function in the shaker1 mouse model for Usher type 1B that lacks a functional Myo7A gene. Subretinal injections of EIAV-CMV-GFP, EIAV-RK-GFP (photoreceptor specific), EIAV-CMV-MYO7A (UshStat) or EIAV-CMV-Null (control) vectors were performed in shaker1 mice. GFP and myosin VIIa expression was evaluated histologically. Photoreceptor function in EIAV-CMV-MYO7A treated eyes was determined by evaluating α-transducin translocation in photoreceptors in response to low light intensity levels, and protection from light induced photoreceptor degeneration was measured. The safety and tolerability of subretinally delivered UshStat was evaluated in macaques. Expression of GFP and myosin VIIa was confirmed in the RPE and photoreceptors in shaker1 mice following subretinal delivery of the EIAV-CMV-GFP/MYO7A vectors. The EIAV-CMV-MYO7A vector protected the shaker1 mouse photoreceptors from acute and chronic intensity light damage, indicated by a significant reduction in photoreceptor cell loss, and restoration of the α-transducin translocation threshold in the photoreceptors. Safety studies in the macaques demonstrated that subretinal delivery of UshStat is safe and well-tolerated. Subretinal delivery of EIAV-CMV-MYO7A (UshStat) rescues photoreceptor phenotypes in the shaker1 mouse. In addition, subretinally delivered UshStat is safe and well-tolerated in macaque safety studies These data support the clinical development of UshStat to treat Usher type 1B syndrome.
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Affiliation(s)
- Marisa Zallocchi
- Boys Town National Research Hospital, Omaha, Nebraska, United States of America
| | - Katie Binley
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - Yatish Lad
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - Scott Ellis
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - Peter Widdowson
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - Sharifah Iqball
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - Vicky Scripps
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - Michelle Kelleher
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - Julie Loader
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - James Miskin
- Oxford BioMedica (UK) Ltd, Oxford Science Park, Oxford, United Kingdom
| | - You-Wei Peng
- Boys Town National Research Hospital, Omaha, Nebraska, United States of America
| | - Wei-Min Wang
- Boys Town National Research Hospital, Omaha, Nebraska, United States of America
| | - Linda Cheung
- Boys Town National Research Hospital, Omaha, Nebraska, United States of America
| | - Duane Delimont
- Boys Town National Research Hospital, Omaha, Nebraska, United States of America
| | | | - Dominic Cosgrove
- Boys Town National Research Hospital, Omaha, Nebraska, United States of America
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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131
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The retinal phenotype of Usher syndrome: pathophysiological insights from animal models. C R Biol 2014; 337:167-77. [PMID: 24702843 DOI: 10.1016/j.crvi.2013.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 01/26/2023]
Abstract
The Usher syndrome (USH) is the most prevalent cause of inherited deaf-blindness. Three clinical subtypes, USH1-3, have been defined, and ten USH genes identified. The hearing impairment due to USH gene defects has been shown to result from improper organisation of the hair bundle, the sound receptive structure of sensory hair cells. In contrast, the cellular basis of the visual defect is less well understood as this phenotype is absent in almost all the USH mouse models that faithfully mimic the human hearing impairment. Structural and molecular interspecies discrepancies regarding photoreceptor calyceal processes and the association with the distribution of USH1 proteins have recently been unravelled, and have led to the conclusion that a defect in the USH1 protein complex-mediated connection between the photoreceptor outer segment and the surrounding calyceal processes (in both rods and cones), and the inner segment (in rods only), probably causes the USH1 retinal dystrophy in humans.
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de Castro-Miró M, Pomares E, Lorés-Motta L, Tonda R, Dopazo J, Marfany G, Gonzàlez-Duarte R. Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies. PLoS One 2014; 9:e88410. [PMID: 24516651 PMCID: PMC3917917 DOI: 10.1371/journal.pone.0088410] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/06/2014] [Indexed: 12/30/2022] Open
Abstract
Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3–up to now only associated to Leber Congenital Amaurosis– was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs.
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Affiliation(s)
- Marta de Castro-Miró
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Esther Pomares
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Laura Lorés-Motta
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Raul Tonda
- Centre Nacional d’Anàlisi Genòmica, PCB, Barcelona, Spain
| | - Joaquín Dopazo
- Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
- BIER, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Gemma Marfany
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Roser Gonzàlez-Duarte
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
- * E-mail:
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Wheway G, Parry DA, Johnson CA. The role of primary cilia in the development and disease of the retina. Organogenesis 2014; 10:69-85. [PMID: 24162842 PMCID: PMC4049897 DOI: 10.4161/org.26710] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/01/2013] [Accepted: 10/04/2013] [Indexed: 02/07/2023] Open
Abstract
The normal development and function of photoreceptors is essential for eye health and visual acuity in vertebrates. Mutations in genes encoding proteins involved in photoreceptor development and function are associated with a suite of inherited retinal dystrophies, often as part of complex multi-organ syndromic conditions. In this review, we focus on the role of the photoreceptor outer segment, a highly modified and specialized primary cilium, in retinal health and disease. We discuss the many defects in the structure and function of the photoreceptor primary cilium that can cause a class of inherited conditions known as ciliopathies, often characterized by retinal dystrophy and degeneration, and highlight the recent insights into disease mechanisms.
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Affiliation(s)
- Gabrielle Wheway
- Section of Ophthalmology and Neurosciences; Leeds Institute of Molecular Medicine; The University of Leeds; Leeds, United Kingdom
| | - David A Parry
- Section of Genetics; Leeds Institute of Molecular Medicine; The University of Leeds; Leeds, United Kingdom
| | - Colin A Johnson
- Section of Ophthalmology and Neurosciences; Leeds Institute of Molecular Medicine; The University of Leeds; Leeds, United Kingdom
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Zou J, Zheng T, Ren C, Askew C, Liu XP, Pan B, Holt JR, Wang Y, Yang J. Deletion of PDZD7 disrupts the Usher syndrome type 2 protein complex in cochlear hair cells and causes hearing loss in mice. Hum Mol Genet 2013; 23:2374-90. [PMID: 24334608 DOI: 10.1093/hmg/ddt629] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Usher syndrome type 2 (USH2) is the predominant form of USH, a leading genetic cause of combined deafness and blindness. PDZD7, a paralog of two USH causative genes, USH1C and USH2D (WHRN), was recently reported to be implicated in USH2 and non-syndromic deafness. It encodes a protein with multiple PDZ domains. To understand the biological function of PDZD7 and the pathogenic mechanism caused by PDZD7 mutations, we generated and thoroughly characterized a Pdzd7 knockout mouse model. The Pdzd7 knockout mice exhibit congenital profound deafness, as assessed by auditory brainstem response, distortion product otoacoustic emission and cochlear microphonics tests, and normal vestibular function, as assessed by their behaviors. Lack of PDZD7 leads to the disorganization of stereocilia bundles and a reduction in mechanotransduction currents and sensitivity in cochlear outer hair cells. At the molecular level, PDZD7 determines the localization of the USH2 protein complex, composed of USH2A, GPR98 and WHRN, to ankle links in developing cochlear hair cells, likely through its direct interactions with these three proteins. The localization of PDZD7 to the ankle links of cochlear hair bundles also relies on USH2 proteins. In photoreceptors of Pdzd7 knockout mice, the three USH2 proteins largely remain unchanged at the periciliary membrane complex. The electroretinogram responses of both rod and cone photoreceptors are normal in knockout mice at 1 month of age. Therefore, although the organization of the USH2 complex appears different in photoreceptors, it is clear that PDZD7 plays an essential role in organizing the USH2 complex at ankle links in developing cochlear hair cells. GenBank accession numbers: KF041446, KF041447, KF041448, KF041449, KF041450, KF041451.
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Affiliation(s)
- Junhuang Zou
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, 65 Mario Capecchi Drive, Salt Lake City, UT 84132, USA
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135
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Abstract
The 10 different genes associated with the deaf/blind disorder, Usher syndrome, encode a number of structurally and functionally distinct proteins, most expressed as multiple isoforms/protein variants. Functional characterization of these proteins suggests a role in stereocilia development in cochlear hair cells, likely owing to adhesive interactions in hair bundles. In mature hair cells, homodimers of the Usher cadherins, cadherin 23 and protocadherin 15, interact to form a structural fiber, the tip link, and the linkages that anchor the taller stereocilia's actin cytoskeleton core to the shorter adjacent stereocilia and the elusive mechanotransduction channels, explaining the deafness phenotype when these molecular interactions are perturbed. The conundrum is that photoreceptors lack a synonymous mechanotransduction apparatus, and so a common theory for Usher protein function in the two neurosensory cell types affected in Usher syndrome is lacking. Recent evidence linking photoreceptor cell dysfunction in the shaker 1 mouse model for Usher syndrome to light-induced protein translocation defects, combined with localization of an Usher protein interactome at the periciliary region of the photoreceptors suggests Usher proteins might regulate protein trafficking between the inner and outer segments of photoreceptors. A distinct Usher protein complex is trafficked to the ribbon synapses of hair cells, and synaptic defects have been reported in Usher mutants in both hair cells and photoreceptors. This review aims to clarify what is known about Usher protein function at the synaptic and apical poles of hair cells and photoreceptors and the prospects for identifying a unifying pathobiological mechanism to explain deaf/blindness in Usher syndrome.
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136
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Sadeghi AM, Cohn ES, Kimberling WJ, Halvarsson G, Möller C. Expressivity of hearing loss in cases with Usher syndrome type IIA. Int J Audiol 2013; 52:832-7. [PMID: 24160897 DOI: 10.3109/14992027.2013.839885] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE The purpose of this study was to compare the genotype/phenotype relationship between siblings with identical USH2A pathologic mutations and the consequent audiologic phenotypes, in particular degree of hearing loss (HL). Decade audiograms were also compared among two groups of affected subjects with different mutations of USH2A. DESIGN DNA samples from patients with Usher syndrome type II were analysed. The audiological features of patients and affected siblings with USH2A mutations were also examined to identify genotype-phenotype correlations. STUDY SAMPLE Genetic and audiometric examinations were performed in 18 subjects from nine families with Usher syndrome type IIA. RESULTS Three different USH2A mutations were identified in the affected subjects. Both similarities and differences of the auditory phenotype were seen in families with several affected siblings. A variable degree of hearing loss, ranging from mild to profound, was observed among affected subjects. No significant differences in hearing thresholds were found the group of affected subjects with different pathological mutations. CONCLUSIONS Our results indicate that mutations in the USH2A gene and the resulting phenotype are probably modulated by other variables, such as modifying genes, epigenetics or environmental factors which may be of importance for better understanding the etiology of Usher syndrome.
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Affiliation(s)
- André M Sadeghi
- * Department of Audiology, The Sahlgrenska Academy, Institute of Neuroscience and Physiology , Göteborg , Sweden
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137
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Mutai H, Suzuki N, Shimizu A, Torii C, Namba K, Morimoto N, Kudoh J, Kaga K, Kosaki K, Matsunaga T. Diverse spectrum of rare deafness genes underlies early-childhood hearing loss in Japanese patients: a cross-sectional, multi-center next-generation sequencing study. Orphanet J Rare Dis 2013; 8:172. [PMID: 24164807 PMCID: PMC4231469 DOI: 10.1186/1750-1172-8-172] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/05/2013] [Indexed: 11/16/2022] Open
Abstract
Background Genetic tests for hereditary hearing loss inform clinical management of patients and can provide the first step in the development of therapeutics. However, comprehensive genetic tests for deafness genes by Sanger sequencing is extremely expensive and time-consuming. Next-generation sequencing (NGS) technology is advantageous for genetic diagnosis of heterogeneous diseases that involve numerous causative genes. Methods Genomic DNA samples from 58 subjects with hearing loss from 15 unrelated Japanese families were subjected to NGS to identify the genetic causes of hearing loss. Subjects did not have pathogenic GJB2 mutations (the gene most often associated with inherited hearing loss), mitochondrial m.1555A>G or 3243A>G mutations, enlarged vestibular aqueduct, or auditory neuropathy. Clinical features of subjects were obtained from medical records. Genomic DNA was subjected to a custom-designed SureSelect Target Enrichment System to capture coding exons and proximal flanking intronic sequences of 84 genes responsible for nonsyndromic or syndromic hearing loss, and DNA was sequenced by Illumina GAIIx (paired-end read). The sequences were mapped and quality-checked using the programs BWA, Novoalign, Picard, and GATK, and analyzed by Avadis NGS. Results Candidate genes were identified in 7 of the 15 families. These genes were ACTG1, DFNA5, POU4F3, SLC26A5, SIX1, MYO7A, CDH23, PCDH15, and USH2A, suggesting that a variety of genes underlie early-childhood hearing loss in Japanese patients. Mutations in Usher syndrome-related genes were detected in three families, including one double heterozygous mutation of CDH23 and PCDH15. Conclusion Targeted NGS analysis revealed a diverse spectrum of rare deafness genes in Japanese subjects and underscores implications for efficient genetic testing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tatsuo Matsunaga
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan.
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138
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Wang F, Wang H, Tuan HF, Nguyen DH, Sun V, Keser V, Bowne SJ, Sullivan LS, Luo H, Zhao L, Wang X, Zaneveld JE, Salvo JS, Siddiqui S, Mao L, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Wen C, Flagg K, Ferreyra H, Pei J, Khan A, Ren H, Wang K, Lopez I, Qamar R, Zenteno JC, Ayala-Ramirez R, Buentello-Volante B, Fu Q, Simpson DA, Li Y, Sui R, Silvestri G, Daiger SP, Koenekoop RK, Zhang K, Chen R. Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet 2013; 133:331-45. [PMID: 24154662 DOI: 10.1007/s00439-013-1381-5] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
Retinitis pigmentosa (RP) is a devastating form of retinal degeneration, with significant social and professional consequences. Molecular genetic information is invaluable for an accurate clinical diagnosis of RP due to its high genetic and clinical heterogeneity. Using a gene capture panel that covers 163 of the currently known retinal disease genes, including 48 RP genes, we performed a comprehensive molecular screening in a collection of 123 RP unsettled probands from a wide variety of ethnic backgrounds, including 113 unrelated simplex and 10 autosomal recessive RP (arRP) cases. As a result, 61 mutations were identified in 45 probands, including 38 novel pathogenic alleles. Interestingly, we observed that phenotype and genotype were not in full agreement in 21 probands. Among them, eight probands were clinically reassessed, resulting in refinement of clinical diagnoses for six of these patients. Finally, recessive mutations in CLN3 were identified in five retinal degeneration patients, including four RP probands and one cone-rod dystrophy patient, suggesting that CLN3 is a novel non-syndromic retinal disease gene. Collectively, our results underscore that, due to the high molecular and clinical heterogeneity of RP, comprehensive screening of all retinal disease genes is effective in identifying novel pathogenic mutations and provides an opportunity to discover new genotype-phenotype correlations. Information gained from this genetic screening will directly aid in patient diagnosis, prognosis, and treatment, as well as allowing appropriate family planning and counseling.
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Affiliation(s)
- Feng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
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139
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Analysis of the Ush2a gene in medaka fish (Oryzias latipes). PLoS One 2013; 8:e74995. [PMID: 24086419 PMCID: PMC3781144 DOI: 10.1371/journal.pone.0074995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
Patients suffering from Usher syndrome (USH) exhibit sensorineural hearing loss, retinitis pigmentosa (RP) and, in some cases, vestibular dysfunction. USH is the most common genetic disorder affecting hearing and vision and is included in a group of hereditary pathologies associated with defects in ciliary function known as ciliopathies. This syndrome is clinically classified into three types: USH1, USH2 and USH3. USH2 accounts for well over one-half of all Usher cases and mutations in the USH2A gene are responsible for the majority of USH2 cases, but also for atypical Usher syndrome and recessive non-syndromic RP. Because medaka fish (Oryzias latypes) is an attractive model organism for genetic-based studies in biomedical research, we investigated the expression and function of the USH2A ortholog in this teleost species. Ol-Ush2a encodes a protein of 5.445 aa codons, containing the same motif arrangement as the human USH2A. Ol-Ush2a is expressed during early stages of medaka fish development and persists into adulthood. Temporal Ol-Ush2a expression analysis using whole mount in situ hybridization (WMISH) on embryos at different embryonic stages showed restricted expression to otoliths and retina, suggesting that Ol-Ush2a might play a conserved role in the development and/or maintenance of retinal photoreceptors and cochlear hair cells. Knockdown of Ol-Ush2a in medaka fish caused embryonic developmental defects (small eyes and heads, otolith malformations and shortened bodies with curved tails) resulting in late embryo lethality. These embryonic defects, observed in our study and in other ciliary disorders, are associated with defective cell movement specifically implicated in left-right (LR) axis determination and planar cell polarity (PCP).
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141
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Abstract
The very large G protein coupled receptor (Vlgr1) is a member of adhesion receptors or large N-terminal family B-7 transmembrane helixes (LNB7TM) receptors within the seven trans-membrane receptor superfamily. Vlgr1 is the largest GPCR identified to date; its mRNA spans 19 kb and encodes 6,300 amino acids. Vlgr1 is a core component of ankle-link complex in inner ear hair cells. Knock-out and mutation mouse models show that loss of Vlgr1 function leads to abnormal stereociliary development and hearing loss, indicating crucial roles of Vlgr1 in hearing transduction or auditory system development. Over the past 10 or so years, human genetics data suggested that Vlgr1 mutations cause Usher syndromes and seizures. Although significant progresses have been made, the details of Vlgr1's function in hair cells, its signaling cascade, and the mechanisms underlying causative effects of Vlgr1 mutations in human diseases remain elusive and ask for further investigation.
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142
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Sahly I, Dufour E, Schietroma C, Michel V, Bahloul A, Perfettini I, Pepermans E, Estivalet A, Carette D, Aghaie A, Ebermann I, Lelli A, Iribarne M, Hardelin JP, Weil D, Sahel JA, El-Amraoui A, Petit C. Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice. ACTA ACUST UNITED AC 2012; 199:381-99. [PMID: 23045546 PMCID: PMC3471240 DOI: 10.1083/jcb.201202012] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mechanisms underlying retinal dystrophy in Usher syndrome type I (USH1) remain unknown because mutant mice lacking any of the USH1 proteins-myosin VIIa, harmonin, cadherin-23, protocadherin-15, sans-do not display retinal degeneration. We found here that, in macaque photoreceptor cells, all USH1 proteins colocalized at membrane interfaces (i) between the inner and outer segments in rods and (ii) between the microvillus-like calyceal processes and the outer segment basolateral region in rods and cones. This pattern, conserved in humans and frogs, was mediated by the formation of an USH1 protein network, which was associated with the calyceal processes from the early embryonic stages of outer segment growth onwards. By contrast, mouse photoreceptors lacked calyceal processes and had no USH1 proteins at the inner-outer segment interface. We suggest that USH1 proteins form an adhesion belt around the basolateral region of the photoreceptor outer segment in humans, and that defects in this structure cause the retinal degeneration in USH1 patients.
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Affiliation(s)
- Iman Sahly
- Institut de la vision, Syndrome de Usher et autres Atteintes Rétino-Cochléaires, 75012 Paris, France
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143
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Zou J, Lee A, Yang J. The expression of whirlin and Cav1.3α₁ is mutually independent in photoreceptors. Vision Res 2012; 75:53-9. [PMID: 22892111 DOI: 10.1016/j.visres.2012.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 12/18/2022]
Abstract
Whirlin is a gene responsible for Usher syndrome type II (USH2) and congenital deafness. In photoreceptors, it organizes a protein complex through binding to proteins encoded by other USH2 genes, usherin (USH2A) and G-protein-coupled receptor 98 (GPR98). Recently, Ca(v)1.3α(1) (α(1D)) has been discovered to interact with whirlin in vitro and these two proteins are localized to the same subcellular compartments in photoreceptors. Accordingly, it is proposed that Ca(v)1.3α(1) is in the USH2 protein complex and that the USH2 protein complex is involved in regulating Ca(2+) in photoreceptors. To test this hypothesis, we investigated the interdependence of Ca(v)1.3α(1) and whirlin expression in photoreceptors. We found that lack of Ca(v)1.3α(1) did not change the whirlin distribution or expression level in photoreceptors. In the retina, several Ca(v)1.3α(1) splice variants were found at the RNA level. Among them, the whirlin-interacting Ca(v)1.3α(1) long variant had no change in its protein expression level in the absence of whirlin. The localization of Ca(v)1.3α(1) in photoreceptors, published previously, cannot be confirmed. Therefore, the mutual independence of whirlin and Ca(v)1.3α(1) expressions in photoreceptors suggests that Ca(v)1.3α(1) may not be a key member of the USH2 protein complex at the periciliary membrane complex.
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Affiliation(s)
- Junhuang Zou
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84132, United States
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Estrada-Cuzcano A, Roepman R, Cremers FPM, den Hollander AI, Mans DA. Non-syndromic retinal ciliopathies: translating gene discovery into therapy. Hum Mol Genet 2012; 21:R111-24. [PMID: 22843501 DOI: 10.1093/hmg/dds298] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Homozygosity mapping and exome sequencing have accelerated the discovery of gene mutations and modifier alleles implicated in inherited retinal degeneration in humans. To date, 158 genes have been found to be mutated in individuals with retinal dystrophies. Approximately one-third of the gene defects underlying retinal degeneration affect the structure and/or function of the 'connecting cilium' in photoreceptors. This structure corresponds to the transition zone of a prototypic cilium, a region with increasing relevance for ciliary homeostasis. The connecting cilium connects the inner and outer segments of the photoreceptor, mediating bi-directional transport of phototransducing proteins required for vision. In fact, the outer segment, connecting cilium and associated basal body, forms a highly specialized sensory cilium, fully dedicated to photoreception and subsequent signal transduction to the brain. At least 21 genes that encode ciliary proteins are implicated in non-syndromic retinal dystrophies such as cone dystrophy, cone-rod dystrophy, Leber congenital amaurosis (LCA), macular degeneration or retinitis pigmentosa (RP). The generation and characterization of vertebrate retinal ciliopathy animal models have revealed insights into the molecular disease mechanism which are indispensable for the development and evaluation of therapeutic strategies. Gene augmentation therapy has proven to be safe and successful in restoring long-term sight in mice, dogs and humans suffering from LCA or RP. Here, we present a comprehensive overview of the genes, mutations and modifier alleles involved in non-syndromic retinal ciliopathies, review the progress in dissecting the associated retinal disease mechanisms and evaluate gene augmentation approaches to antagonize retinal degeneration in these ciliopathies.
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145
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Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex. Proc Natl Acad Sci U S A 2012; 109:13046-51. [PMID: 22837400 DOI: 10.1073/pnas.1120685109] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolution of cadherins, which are essential for metazoan multicellularity and restricted to metazoans and their closest relatives, has special relevance for understanding metazoan origins. To reconstruct the ancestry and evolution of cadherin gene families, we analyzed the genomes of the choanoflagellate Salpingoeca rosetta, the unicellular outgroup of choanoflagellates and metazoans Capsaspora owczarzaki, and a draft genome assembly from the homoscleromorph sponge Oscarella carmela. Our finding of a cadherin gene in C. owczarzaki reveals that cadherins predate the divergence of the C. owczarzaki, choanoflagellate, and metazoan lineages. Data from these analyses also suggest that the last common ancestor of metazoans and choanoflagellates contained representatives of at least three cadherin families, lefftyrin, coherin, and hedgling. Additionally, we find that an O. carmela classical cadherin has predicted structural features that, in bilaterian classical cadherins, facilitate binding to the cytoplasmic protein β-catenin and, thereby, promote cadherin-mediated cell adhesion. In contrast with premetazoan cadherin families (i.e., those conserved between choanoflagellates and metazoans), the later appearance of classical cadherins coincides with metazoan origins.
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146
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Pan L, Zhang M. Structures of usher syndrome 1 proteins and their complexes. Physiology (Bethesda) 2012; 27:25-42. [PMID: 22311968 DOI: 10.1152/physiol.00037.2011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Usher syndrome 1 (USH1) is the most common and severe form of hereditary loss of hearing and vision. Genetic, physiological, and cell biological studies, together with recent structural investigations, have not only uncovered the physiological functions of the five USH1 proteins but also provided mechanistic explanations for the hearing and visual deficiencies in humans caused by USH1 mutations. This review focuses on the structural basis of the USH1 protein complex organization.
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Affiliation(s)
- Lifeng Pan
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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147
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Yang J, Wang L, Song H, Sokolov M. Current understanding of usher syndrome type II. Front Biosci (Landmark Ed) 2012; 17:1165-83. [PMID: 22201796 DOI: 10.2741/3979] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Usher syndrome is the most common deafness-blindness caused by genetic mutations. To date, three genes have been identified underlying the most prevalent form of Usher syndrome, the type II form (USH2). The proteins encoded by these genes are demonstrated to form a complex in vivo. This complex is localized mainly at the periciliary membrane complex in photoreceptors and the ankle-link of the stereocilia in hair cells. Many proteins have been found to interact with USH2 proteins in vitro, suggesting that they are potential additional components of this USH2 complex and that the genes encoding these proteins may be the candidate USH2 genes. However, further investigations are critical to establish their existence in the USH2 complex in vivo. Based on the predicted functional domains in USH2 proteins, their cellular localizations in photoreceptors and hair cells, the observed phenotypes in USH2 mutant mice, and the known knowledge about diseases similar to USH2, putative biological functions of the USH2 complex have been proposed. Finally, therapeutic approaches for this group of diseases are now being actively explored.
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Affiliation(s)
- Jun Yang
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, Utah 84132
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148
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Le Quesne Stabej P, Saihan Z, Rangesh N, Steele-Stallard HB, Ambrose J, Coffey A, Emmerson J, Haralambous E, Hughes Y, Steel KP, Luxon LM, Webster AR, Bitner-Glindzicz M. Comprehensive sequence analysis of nine Usher syndrome genes in the UK National Collaborative Usher Study. J Med Genet 2011; 49:27-36. [PMID: 22135276 PMCID: PMC3678402 DOI: 10.1136/jmedgenet-2011-100468] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background Usher syndrome (USH) is an autosomal recessive disorder comprising retinitis pigmentosa, hearing loss and, in some cases, vestibular dysfunction. It is clinically and genetically heterogeneous with three distinctive clinical types (I–III) and nine Usher genes identified. This study is a comprehensive clinical and genetic analysis of 172 Usher patients and evaluates the contribution of digenic inheritance. Methods The genes MYO7A, USH1C, CDH23, PCDH15, USH1G, USH2A, GPR98, WHRN, CLRN1 and the candidate gene SLC4A7 were sequenced in 172 UK Usher patients, regardless of clinical type. Results No subject had definite mutations (nonsense, frameshift or consensus splice site mutations) in two different USH genes. Novel missense variants were classified UV1-4 (unclassified variant): UV4 is ‘probably pathogenic’, based on control frequency <0.23%, identification in trans to a pathogenic/probably pathogenic mutation and segregation with USH in only one family; and UV3 (‘likely pathogenic’) as above, but no information on phase. Overall 79% of identified pathogenic/UV4/UV3 variants were truncating and 21% were missense changes. MYO7A accounted for 53.2%, and USH1C for 14.9% of USH1 families (USH1C:c.496+1G>A being the most common USH1 mutation in the cohort). USH2A was responsible for 79.3% of USH2 families and GPR98 for only 6.6%. No mutations were found in USH1G, WHRN or SLC4A7. Conclusions One or two pathogenic/likely pathogenic variants were identified in 86% of cases. No convincing cases of digenic inheritance were found. It is concluded that digenic inheritance does not make a significant contribution to Usher syndrome; the observation of multiple variants in different genes is likely to reflect polymorphic variation, rather than digenic effects.
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Wang L, Zou J, Shen Z, Song E, Yang J. Whirlin interacts with espin and modulates its actin-regulatory function: an insight into the mechanism of Usher syndrome type II. Hum Mol Genet 2011; 21:692-710. [PMID: 22048959 DOI: 10.1093/hmg/ddr503] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Whirlin mutations cause retinal degeneration and hearing loss in Usher syndrome type II (USH2) and non-syndromic deafness, DFNB31. Its protein recruits other USH2 causative proteins to form a complex at the periciliary membrane complex in photoreceptors and the ankle link of the stereocilia in hair cells. However, the biological function of this USH2 protein complex is largely unknown. Using a yeast two-hybrid screen, we identified espin, an actin-binding/bundling protein involved in human deafness when defective, as a whirlin-interacting protein. The interaction between these two proteins was confirmed by their coimmunoprecipitation and colocalization in cultured cells. This interaction involves multiple domains of both proteins and only occurs when espin does not bind to actin. Espin was partially colocalized with whirlin in the retina and the inner ear. In whirlin knockout mice, espin expression changed significantly in these two tissues. Further studies found that whirlin increased the mobility of espin and actin at the actin bundles cross-linked by espin and, eventually, affected the dimension of these actin bundles. In whirlin knockout mice, the stereocilia were thickened in inner hair cells. We conclude that the interaction between whirlin and espin and the balance between their expressions are required to maintain the actin bundle network in photoreceptors and hair cells. Disruption of this actin bundle network contributes to the pathogenic mechanism of hearing loss and retinal degeneration caused by whirlin and espin mutations. Espin is a component of the USH2 protein complex and could be a candidate gene for Usher syndrome.
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Affiliation(s)
- Le Wang
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
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Garcia-Garcia G, Aparisi MJ, Jaijo T, Rodrigo R, Leon AM, Avila-Fernandez A, Blanco-Kelly F, Bernal S, Navarro R, Diaz-Llopis M, Baiget M, Ayuso C, Millan JM, Aller E. Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations. Orphanet J Rare Dis 2011; 6:65. [PMID: 22004887 PMCID: PMC3207874 DOI: 10.1186/1750-1172-6-65] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 10/17/2011] [Indexed: 11/10/2022] Open
Abstract
Background Usher Syndrome type II (USH2) is an autosomal recessive disorder, characterized by moderate to severe hearing impairment and retinitis pigmentosa (RP). Among the three genes implicated, mutations in the USH2A gene account for 74-90% of the USH2 cases. Methods To identify the genetic cause of the disease and determine the frequency of USH2A mutations in a cohort of 88 unrelated USH Spanish patients, we carried out a mutation screening of the 72 coding exons of this gene by direct sequencing. Moreover, we performed functional minigene studies for those changes that were predicted to affect splicing. Results As a result, a total of 144 DNA sequence variants were identified. Based upon previous studies, allele frequencies, segregation analysis, bioinformatics' predictions and in vitro experiments, 37 variants (23 of them novel) were classified as pathogenic mutations. Conclusions This report provide a wide spectrum of USH2A mutations and clinical features, including atypical Usher syndrome phenotypes resembling Usher syndrome type I. Considering only the patients clearly diagnosed with Usher syndrome type II, and results obtained in this and previous studies, we can state that mutations in USH2A are responsible for 76.1% of USH2 disease in patients of Spanish origin.
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Affiliation(s)
- Gema Garcia-Garcia
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe, Valencia, Spain
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