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McClinton B, Watson CM, Crinnion LA, McKibbin M, Ali M, Inglehearn CF, Toomes C. Haplotyping Using Long-Range PCR and Nanopore Sequencing to Phase Variants: Lessons Learned From the ABCA4 Locus. J Transl Med 2023; 103:100160. [PMID: 37088464 DOI: 10.1016/j.labinv.2023.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/11/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023] Open
Abstract
Short-read next-generation sequencing has revolutionized our ability to identify variants underlying inherited diseases; however, it does not allow the phasing of variants to clarify their diagnostic interpretation. The advent of widespread, increasingly accurate long-read sequencing has opened up new applications not currently available through short-read next-generation sequencing. One such use is the ability to phase variants to clarify their diagnostic interpretation and to investigate the increasingly prevalent role of cis-acting variants in the pathogenesis of the inherited disease, so-called complex alleles. Complex alleles are becoming an increasingly prevalent part of the study of genes associated with inherited diseases, for example, in ABCA4-related diseases. We sought to establish a cost-effective method to phase contiguous segments of the 130-kb ABCA4 locus by long-read sequencing of overlapping amplification products. Using the comprehensively characterized CEPH sample, NA12878, we verified the accuracy and robustness of our assay. However, in-field assessment of its utility using clinical test cases was hampered by the paucity and distribution of identified variants and by PCR chimerism, particularly where the number of PCR cycles was high. Despite this, we were able to construct robust phase blocks of up to 94.9 kb, representing 73% of the ABCA4 locus. We conclude that, although haplotype analysis of variants located within discrete amplification products was robust and informative, the stitching together of larger phase blocks using overlapping single-molecule reads remained practically challenging.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; Department of Ophthalmology, St. James's University Hospital, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK.
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2
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Yahya S, Watson CM, Carr I, McKibbin M, Crinnion LA, Taylor M, Bonin H, Fletcher T, El-Asrag ME, Ali M, Toomes C, Inglehearn CF. Long-Read Nanopore Sequencing of RPGR ORF15 is Enhanced Following DNase I Treatment of MinION Flow Cells. Mol Diagn Ther 2023; 27:525-535. [PMID: 37284979 PMCID: PMC10299921 DOI: 10.1007/s40291-023-00656-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
INTRODUCTION RPGR ORF15 is an exon present almost exclusively in the retinal transcript of RPGR. It is purine-rich, repetitive and notoriously hard to sequence, but is a hotspot for mutations causing X-linked retinitis pigmentosa. METHODS Long-read nanopore sequencing on MinION and Flongle flow cells was used to sequence RPGR ORF15 in genomic DNA from patients with inherited retinal dystrophy. A flow cell wash kit was used on a MinION flow cell to increase yield. Findings were confirmed by PacBio SMRT long-read sequencing. RESULTS We showed that long-read nanopore sequencing successfully reads through a 2 kb PCR-amplified fragment containing ORF15. We generated reads of sufficient quality and cumulative read-depth to detect pathogenic RP-causing variants. However, we observed that this G-rich, repetitive DNA segment rapidly blocks the available pores, resulting in sequence yields less than 5% of the expected output. This limited the extent to which samples could be pooled, increasing cost. We tested the utility of a MinION wash kit containing DNase I to digest DNA fragments remaining on the flow cell, regenerating the pores. Use of the DNase I treatment allowed repeated re-loading, increasing the sequence reads obtained. Our customised workflow was used to screen pooled amplification products from previously unsolved inherited retinal disease (IRD) in patients, identifying two new cases with pathogenic ORF15 variants. DISCUSSION We report the novel finding that long-read nanopore sequencing can read through RPGR-ORF15, a DNA sequence not captured by short-read next-generation sequencing (NGS), but with a more reduced yield. Use of a flow cell wash kit containing DNase I unblocks the pores, allowing reloading of further library aliquots over a 72-h period, increasing yield. The workflow we describe provides a novel solution to the need for a rapid, robust, scalable, cost-effective ORF15 screening protocol.
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Affiliation(s)
- Samar Yahya
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Medical Genetics, School of Medicine, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Ian Carr
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Martin McKibbin
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Ophthalmology, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Morag Taylor
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Hope Bonin
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Tracy Fletcher
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Mohammed E El-Asrag
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Zoology, Faculty of Science, Benha University, Banha, Egypt
- Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK.
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3
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McClinton B, Crinnion LA, McKibbin M, Mukherjee R, Poulter JA, Smith CEL, Ali M, Watson CM, Inglehearn CF, Toomes C. Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies. Mol Genet Genomic Med 2023:e2164. [PMID: 36934458 DOI: 10.1002/mgg3.2164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/23/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND The widespread adoption of exome sequencing has greatly increased the rate of genetic diagnosis for inherited conditions. However, the detection and validation of large deletions remains challenging. While numerous bioinformatics approaches have been developed to detect deletions from whole - exome sequencing and targeted panels, further work is typically required to define the physical breakpoints or integration sites. Accurate characterisation requires either expensive follow - up whole - genome sequencing or the time - consuming, laborious process of PCR walking, both of which are challenging when dealing with the repeat sequences which frequently intersect deletion breakpoints. The aim of this study was to develop a cost-effective, long-range sequencing method to characterise deletions. METHODS Genomic DNA was amplified with primers spanning the deletion using long-range PCR and the products purified. Sequencing was performed on MinION flongle flowcells. The resulting fast5 files were basecalled using Guppy, trimmed using Porechop and aligned using Minimap2. Filtering was performed using NanoFilt. Nanopore sequencing results were verified by Sanger sequencing. RESULTS Four cases with deletions detected following comparative read-depth analysis of targeted short-read sequencing were analysed. Nanopore sequencing defined breakpoints at the molecular level in all cases including homozygous breakpoints in EYS, CNGA1 and CNGB1 and a heterozygous deletion in PRPF31. All breakpoints were verified by Sanger sequencing. CONCLUSIONS In this study, a quick, accurate and cost - effective method is described to characterise deletions identified from exome, and similar data, using nanopore sequencing.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Department of Ophthalmology, St James's University Hospital, Leeds, UK
| | | | - James A Poulter
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Claire E L Smith
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
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Inglehearn CF, Yahya S, Smith CEL, Poulter JA, Ali M, Toomes C, Ellingford J, Black GC, Arno G, Webster AR. Reply. Ophthalmology 2023; 130:e9-e10. [PMID: 36400608 DOI: 10.1016/j.ophtha.2022.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK.
| | - Samar Yahya
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Claire E L Smith
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - James A Poulter
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Jamie Ellingford
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gavin Arno
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, UK
| | - Andrew R Webster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, UK
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5
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Panneman DM, Hitti-Malin RJ, Holtes LK, de Bruijn SE, Reurink J, Boonen EGM, Khan MI, Ali M, Andréasson S, De Baere E, Banfi S, Bauwens M, Ben-Yosef T, Bocquet B, De Bruyne M, de la Cerda B, Coppieters F, Farinelli P, Guignard T, Inglehearn CF, Karali M, Kjellström U, Koenekoop R, de Koning B, Leroy BP, McKibbin M, Meunier I, Nikopoulos K, Nishiguchi KM, Poulter JA, Rivolta C, Rodríguez de la Rúa E, Saunders P, Simonelli F, Tatour Y, Testa F, Thiadens AAHJ, Toomes C, Tracewska AM, Tran HV, Ushida H, Vaclavik V, Verhoeven VJM, van de Vorst M, Gilissen C, Hoischen A, Cremers FPM, Roosing S. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis. Front Cell Dev Biol 2023; 11:1112270. [PMID: 36819107 PMCID: PMC9936074 DOI: 10.3389/fcell.2023.1112270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are two groups of inherited retinal diseases (IRDs) where the rod photoreceptors degenerate followed by the cone photoreceptors of the retina. A genetic diagnosis for IRDs is challenging since >280 genes are associated with these conditions. While whole exome sequencing (WES) is commonly used by diagnostic facilities, the costs and required infrastructure prevent its global applicability. Previous studies have shown the cost-effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Methods: Here, we introduce a smMIPs panel that targets the exons and splice sites of all currently known genes associated with RP and LCA, the entire RPE65 gene, known causative deep-intronic variants leading to pseudo-exons, and part of the RP17 region associated with autosomal dominant RP, by using a total of 16,812 smMIPs. The RP-LCA smMIPs panel was used to screen 1,192 probands from an international cohort of predominantly RP and LCA cases. Results and discussion: After genetic analysis, a diagnostic yield of 56% was obtained which is on par with results from WES analysis. The effectiveness and the reduced costs compared to WES renders the RP-LCA smMIPs panel a competitive approach to provide IRD patients with a genetic diagnosis, especially in countries with restricted access to genetic testing.
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Affiliation(s)
- Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Daan M. Panneman,
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lara K. Holtes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Sten Andréasson
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Berta de la Cerda
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium,Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Guignard
- Chromosomal Genetics Unit, University Hospital of Montpellier, Montpellier, France
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Marianthi Karali
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy,Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ulrika Kjellström
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Robert Koenekoop
- McGill University Health Center (MUHC) Research Institute, Montreal, QC, Canada,Departments of Paediatric Surgery, Human Genetics, and Adult Ophthalmology, McGill University Health Center, Montreal, QC, Canada
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, Netherlands
| | - Bart P. Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium,Department of Head & Skin, Ghent University, Ghent, Belgium,Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom,Department of Ophthalmology, St. James’s University Hospital, Leeds, United Kingdom
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | | | - Koji M. Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland,Department of Ophthalmology, University of Basel, Basel, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Enrique Rodríguez de la Rúa
- Department of Ophthalmology, Retics Patologia Ocular, OFTARED, Instituto de Salud Carlos III, University Hospital Virgen Macarena, Madrid, Spain
| | | | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Yasmin Tatour
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Anna M. Tracewska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hoai Viet Tran
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Veronika Vaclavik
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus, Rotterdam, Netherlands,Department of Clinical Genetics, Erasmus, Rotterdam, Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
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Mc Clinton B, Corradi Z, McKibbin M, Panneman DM, Roosing S, Boonen EGM, Ali M, Watson CM, Steel DH, Cremers FPM, Inglehearn CF, Hitti-Malin RJ, Toomes C. Effective smMIPs-Based Sequencing of Maculopathy-Associated Genes in Stargardt Disease Cases and Allied Maculopathies from the UK. Genes (Basel) 2023; 14:191. [PMID: 36672932 PMCID: PMC9859292 DOI: 10.3390/genes14010191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Macular dystrophies are a group of individually rare but collectively common inherited retinal dystrophies characterised by central vision loss and loss of visual acuity. Single molecule Molecular Inversion Probes (smMIPs) have proved effective in identifying genetic variants causing macular dystrophy. Here, a previously established smMIPs panel tailored for genes associated with macular diseases has been used to examine 57 UK macular dystrophy cases, achieving a high solve rate of 63.2% (36/57). Among 27 bi-allelic STGD1 cases, only three novel ABCA4 variants were identified, illustrating that the majority of ABCA4 variants in Caucasian STGD1 cases are currently known. We examined cases with ABCA4-associated disease in detail, comparing our results with a previously reported variant grading system, and found this model to be accurate and clinically useful. In this study, we showed that ABCA4-associated disease could be distinguished from other forms of macular dystrophy based on clinical evaluation in the majority of cases (34/36).
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Affiliation(s)
- Benjamin Mc Clinton
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- Department of Ophthalmology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Christopher M. Watson
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - David H. Steel
- Sunderland Eye Infirmary, Sunderland SR2 9HP, UK
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chris F. Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
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7
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Yahya S, Smith CEL, Poulter JA, McKibbin M, Arno G, Ellingford J, Kämpjärvi K, Khan MI, Cremers FPM, Hardcastle AJ, Castle B, Steel DHW, Webster AR, Black GC, El-Asrag ME, Ali M, Toomes C, Inglehearn CF. Late-Onset Autosomal Dominant Macular Degeneration Caused by Deletion of the CRX Gene. Ophthalmology 2023; 130:68-76. [PMID: 35934205 DOI: 10.1016/j.ophtha.2022.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/06/2023] Open
Abstract
PURPOSE To characterize the phenotype observed in a case series with macular disease and determine the cause. DESIGN Multicenter case series. PARTICIPANTS Six families (7 patients) with sporadic or multiplex macular disease with onset at 20 to 78 years, and 1 patient with age-related macular degeneration. METHODS Patients underwent ophthalmic examination; exome, genome, or targeted sequencing; and/or polymerase chain reaction (PCR) amplification of the breakpoint, followed by cloning and Sanger sequencing or direct Sanger sequencing. MAIN OUTCOME MEASURES Clinical phenotypes, genomic findings, and a hypothesis explaining the mechanism underlying disease in these patients. RESULTS All 8 cases carried the same deletion encompassing the genes TPRX1, CRX, and SULT2A1, which was absent from 382 control individuals screened by breakpoint PCR and 13 096 Clinical Genetics patients with a range of other inherited conditions screened by array comparative genomic hybridization. Microsatellite genotypes showed that these 7 families are not closely related, but genotypes immediately adjacent to the deletion breakpoints suggest they may share a distant common ancestor. CONCLUSIONS Previous studies had found that carriers for a single defective CRX allele that was predicted to produce no functional CRX protein had a normal ocular phenotype. Here, we show that CRX whole-gene deletion in fact does cause a dominant late-onset macular disease.
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Affiliation(s)
- Samar Yahya
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom; Department of Medical Genetics, School of Medicine, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Claire E L Smith
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - James A Poulter
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom; Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Gavin Arno
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Jamie Ellingford
- Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | | | - Muhammad I Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alison J Hardcastle
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Bruce Castle
- Peninsula Genetics Service, Royal Devon and Exeter Hospitals NHS Trust, Exeter, United Kingdom
| | - David H W Steel
- Sunderland Eye Infirmary, Sunderland, United Kingdom; The Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew R Webster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Graeme C Black
- Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Mohammed E El-Asrag
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom; Department of Zoology, Faculty of Science, Benha University, Benha, Egypt; Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, United Kingdom
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom.
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8
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Best S, Yu J, Lord J, Roche M, Watson CM, Bevers RPJ, Stuckey A, Madhusudhan S, Jewell R, Sisodiya SM, Lin S, Turner S, Robinson H, Leslie JS, Baple E, Toomes C, Inglehearn C, Wheway G, Johnson CA. Uncovering the burden of hidden ciliopathies in the 100 000 Genomes Project: a reverse phenotyping approach. J Med Genet 2022; 59:1151-1164. [PMID: 35764379 PMCID: PMC9691823 DOI: 10.1136/jmedgenet-2022-108476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND The 100 000 Genomes Project (100K) recruited National Health Service patients with eligible rare diseases and cancer between 2016 and 2018. PanelApp virtual gene panels were applied to whole genome sequencing data according to Human Phenotyping Ontology (HPO) terms entered by recruiting clinicians to guide focused analysis. METHODS We developed a reverse phenotyping strategy to identify 100K participants with pathogenic variants in nine prioritised disease genes (BBS1, BBS10, ALMS1, OFD1, DYNC2H1, WDR34, NPHP1, TMEM67, CEP290), representative of the full phenotypic spectrum of multisystemic primary ciliopathies. We mapped genotype data 'backwards' onto available clinical data to assess potential matches against phenotypes. Participants with novel molecular diagnoses and key clinical features compatible with the identified disease gene were reported to recruiting clinicians. RESULTS We identified 62 reportable molecular diagnoses with variants in these nine ciliopathy genes. Forty-four have been reported by 100K, 5 were previously unreported and 13 are new diagnoses. We identified 11 participants with unreportable, novel molecular diagnoses, who lacked key clinical features to justify reporting to recruiting clinicians. Two participants had likely pathogenic structural variants and one a deep intronic predicted splice variant. These variants would not be prioritised for review by standard 100K diagnostic pipelines. CONCLUSION Reverse phenotyping improves the rate of successful molecular diagnosis for unsolved 100K participants with primary ciliopathies. Previous analyses likely missed these diagnoses because incomplete HPO term entry led to incorrect gene panel choice, meaning that pathogenic variants were not prioritised. Better phenotyping data are therefore essential for accurate variant interpretation and improved patient benefit.
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Affiliation(s)
- Sunayna Best
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jenny Lord
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
| | - Matthew Roche
- Windsor House Group Practice, Mid Yorkshire Hospitals NHS Trust, Leeds, UK
| | - Christopher Mark Watson
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Roel P J Bevers
- Genomics England, Queen Mary University of London, London, UK
| | - Alex Stuckey
- Genomics England, Queen Mary University of London, London, UK
| | | | - Rosalyn Jewell
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sanjay M Sisodiya
- University College London (UCL) Queen Square Institute of Neurology, London, UK
- Chalfont Centre for Epilepsy, Chalfont, UK
| | - Siying Lin
- Department of Ophthalmology, Torbay and South Devon NHS Foundation Trust, Torquay, UK
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Stephen Turner
- Department of Ophthalmology, Torbay and South Devon NHS Foundation Trust, Torquay, UK
| | - Hannah Robinson
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | - Emma Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Chris Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Gabrielle Wheway
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
| | - Colin A Johnson
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
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9
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Best S, Lord J, Roche M, Watson CM, Poulter JA, Bevers RPJ, Stuckey A, Szymanska K, Ellingford JM, Carmichael J, Brittain H, Toomes C, Inglehearn C, Johnson CA, Wheway G. Molecular diagnoses in the congenital malformations caused by ciliopathies cohort of the 100,000 Genomes Project. J Med Genet 2022; 59:737-747. [PMID: 34716235 PMCID: PMC9340050 DOI: 10.1136/jmedgenet-2021-108065] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/27/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Primary ciliopathies represent a group of inherited disorders due to defects in the primary cilium, the 'cell's antenna'. The 100,000 Genomes Project was launched in 2012 by Genomics England (GEL), recruiting National Health Service (NHS) patients with eligible rare diseases and cancer. Sequence data were linked to Human Phenotype Ontology (HPO) terms entered by recruiting clinicians. METHODS Eighty-three prescreened probands were recruited to the 100,000 Genomes Project suspected to have congenital malformations caused by ciliopathies in the following disease categories: Bardet-Biedl syndrome (n=45), Joubert syndrome (n=14) and 'Rare Multisystem Ciliopathy Disorders' (n=24). We implemented a bespoke variant filtering and analysis strategy to improve molecular diagnostic rates for these participants. RESULTS We determined a research molecular diagnosis for n=43/83 (51.8%) probands. This is 19.3% higher than previously reported by GEL (n=27/83 (32.5%)). A high proportion of diagnoses are due to variants in non-ciliopathy disease genes (n=19/43, 44.2%) which may reflect difficulties in clinical recognition of ciliopathies. n=11/83 probands (13.3%) had at least one causative variant outside the tiers 1 and 2 variant prioritisation categories (GEL's automated triaging procedure), which would not be reviewed in standard 100,000 Genomes Project diagnostic strategies. These include four structural variants and three predicted to cause non-canonical splicing defects. Two unrelated participants have biallelic likely pathogenic variants in LRRC45, a putative novel ciliopathy disease gene. CONCLUSION These data illustrate the power of linking large-scale genome sequence to phenotype information. They demonstrate the value of research collaborations in order to maximise interpretation of genomic data.
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Affiliation(s)
- Sunayna Best
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
- Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Jenny Lord
- Department of Human Development and Health, University of Southampton Faculty of Medicine, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Christopher M Watson
- Department of Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, West Yorkshire, UK
- School of Medicine, University of Leeds, Leeds, UK
| | - James A Poulter
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Roel P J Bevers
- Genomics England, Queen Mary University of London, London, UK
| | - Alex Stuckey
- Genomics England, Queen Mary University of London, London, UK
| | - Katarzyna Szymanska
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester, UK
| | - Jenny Carmichael
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Helen Brittain
- Genomics England, Queen Mary University of London, London, UK
| | - Carmel Toomes
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Chris Inglehearn
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Colin A Johnson
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Gabrielle Wheway
- Department of Human Development and Health, University of Southampton Faculty of Medicine, Southampton, UK
- Southampton University Hospitals NHS Trust, Southampton, UK
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10
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El-Asrag ME, Corton M, McKibbin M, Avila-Fernandez A, Mohamed MD, Blanco-Kelly F, Toomes C, Inglehearn CF, Ayuso C, Ali M. Novel homozygous mutations in the transcription factor NRL cause non-syndromic retinitis pigmentosa. Mol Vis 2022; 28:48-56. [PMID: 35693422 PMCID: PMC9122474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/15/2022] [Indexed: 11/02/2022] Open
Abstract
Purpose To describe the clinical phenotype and genetic basis of non-syndromic retinitis pigmentosa (RP) in one family and two sporadic cases with biallelic mutations in the transcription factor neural retina leucine zipper (NRL). Methods Exome sequencing was performed in one affected family member. Microsatellite genotyping was used for haplotype analysis. PCR and Sanger sequencing were used to confirm mutations in and screen other family members where they were available. The SMART tool for domain prediction helped us build the protein schematic diagram. Results For family MM1 of Pakistani origin, whole-exome sequencing and microsatellite genotyping revealed homozygosity on chromosome 14 and identified a homozygous stop-loss mutation in NRL, NM_006177.5: c.713G>T, p.*238Lext57, which is predicted to add an extra 57 amino acids to the normal protein chain. The variant segregated with disease symptoms in the family. For case RP-3051 of Spanish ancestry, clinical exome sequencing focusing on the morbid genome highlighted a homozygous nonsense mutation in NRL, c.238C>T, p.Gln80*, as the most likely disease candidate. For case RP-1553 of Romanian ethnicity, targeted-exome sequencing of 73 RP/LCA genes identified a homozygous nonsense mutation in NRL, c.544C>T, p.Gln182*. The variants were either rare or absent in the gnomAD database. Conclusions NRL mutations predominantly cause dominant retinal disease, but there have been five published reports of mutations causing recessive disease. Here, we present three further examples of recessive RP due to NRL mutations. The phenotypes observed are consistent with those in the previous reports, and the observed mutation types and distribution further confirm distinct patterns for variants in NRL causing recessive and dominant diseases.
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Affiliation(s)
- Mohammed E. El-Asrag
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, UK,Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, UK,The Eye Department, St. James’s University Hospital, Leeds, UK
| | - Almudena Avila-Fernandez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | | | - Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, UK
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, UK
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, UK
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11
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Panagiotou ES, Fernandez-Fuentes N, Farraj LA, McKibbin M, Elçioglu NH, Jafri H, Cerman E, Parry DA, Logan CV, Johnson CA, Inglehearn CF, Toomes C, Ali M. Novel SIX6 mutations cause recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia. Mol Vis 2022; 28:57-69. [PMID: 35693420 PMCID: PMC9122475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/15/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose To investigate the molecular basis of recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia in two consanguineous families. Methods Conventional autozygosity mapping was performed using single nucleotide polymorphism (SNP) microarrays. Whole-exome sequencing was completed on genomic DNA from one affected member of each family. Exome sequence data were also used for homozygosity mapping and copy number variation analysis. PCR and Sanger sequencing were used to confirm the identification of mutations and to screen further patients. Evolutionary conservation of protein sequences was assessed using CLUSTALW, and protein structures were modeled using PyMol. Results In family MEP68, a novel homozygous nucleotide substitution in SIX6 was found, c.547G>C, that converts the evolutionarily conserved aspartic acid residue at the 183rd amino acid in the protein to a histidine, p.(Asp183His). This residue mapped to the third helix of the DNA-binding homeobox domain in SIX6, which interacts with the major groove of double-stranded DNA. This interaction is likely to be disrupted by the mutation. In family F1332, a novel homozygous 1034 bp deletion that encompasses the first exon of SIX6 was identified, chr14:g.60975890_60976923del. Both mutations segregated with the disease phenotype as expected for a recessive condition and were absent from publicly available variant databases. Conclusions Our findings expand the mutation spectrum in this form of inherited eye disease and confirm that homozygous human SIX6 mutations cause a developmental spectrum of ocular phenotypes that includes not only the previously described features of microphthalmia, coloboma, and congenital cataract but also corneal abnormalities.
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Affiliation(s)
- Evangelia S. Panagiotou
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
| | | | - Layal Abi Farraj
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom,Eye Clinic, St. James's University Hospital, Leeds, United Kingdom
| | - Nursel H. Elçioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul, Turkey,Eastern Mediterrean University of Medical School, Cyprus, Turkey
| | | | - Eren Cerman
- Department of Ophthalmology, Marmara University Medical School, Istanbul, Turkey
| | - David A. Parry
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
| | - Clare V. Logan
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
| | - Colin A. Johnson
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, United Kingdom
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12
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Taylor RL, Soriano CS, Williams S, Dzulova D, Ashworth J, Hall G, Gale T, Lloyd IC, Inglehearn CF, Toomes C, Douzgou S, Black GC. Bi-allelic mutation of CTNNB1 causes a severe form of syndromic microphthalmia, persistent foetal vasculature and vitreoretinal dysplasia. Orphanet J Rare Dis 2022; 17:110. [PMID: 35246174 PMCID: PMC8896279 DOI: 10.1186/s13023-022-02239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 02/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Inherited vitreoretinopathies arise as a consequence of congenital retinal vascularisation abnormalities. They represent a phenotypically and genetically heterogeneous group of disorders that can have a major impact on vision. Several genes encoding proteins and effectors of the canonical Wnt/β-catenin pathway have been associated and precise diagnosis, although difficult, is essential for proper clinical management including syndrome specific management where appropriate. This work aimed to investigate the molecular basis of disease in a single proband born to consanguineous parents, who presented with microphthalmia, persistent foetal vasculature, posterior lens vacuoles, vitreoretinal dysplasia, microcephaly, hypotelorism and global developmental delay, and was registered severely visually impaired by 5 months of age. Methods Extensive genomic pre-screening, including microarray comparative genomic hybridisation and sequencing of a 114 gene panel associated with cataract and congenital ophthalmic disorders was conducted by an accredited clinical laboratory. Whole exome sequencing (WES) was undertaken on a research basis and in vitro TOPflash transcriptional reporter assay was utilised to assess the impact of the putative causal variant.
Results In the proband, WES revealed a novel, likely pathogenic homozygous mutation in the cadherin-associated protein beta-1 gene (CTNNB1), c.884C>G; p.(Ala295Gly), which encodes a co-effector molecule of the Wnt/β-catenin pathway. The proband’s parents were shown to be heterozygous carriers but ophthalmic examination did not detect any abnormalities. Functional assessment of the missense variant demonstrated significant reduction of β-catenin activity. Conclusions This is the first report of a biallelic disease-causing variation in CTNNB1. We conclude that this biallelic, transcriptional inactivating mutation of CTNNB1 causes a severe, syndromic form of microphthalmia, persistent foetal vasculature and vitreoretinal dysplasia that results in serious visual loss in infancy. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02239-3.
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Affiliation(s)
- Rachel L Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), 6Th Floor St Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - Carla Sanjuro Soriano
- Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, UK.,Inserm, Institute for Neurosciences of Montpellier, University of Montpellier, Montpellier, France
| | - Simon Williams
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Denisa Dzulova
- Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, UK
| | - Jane Ashworth
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Georgina Hall
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), 6Th Floor St Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), 6Th Floor St Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - I Christopher Lloyd
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK.,Paediatric Ophthalmology, Great Ormond Street Hospital for Children, London, UK
| | - Chris F Inglehearn
- Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), 6Th Floor St Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK.,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Graeme C Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), 6Th Floor St Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK.
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13
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Best S, Inglehearn CF, Watson CM, Toomes C, Wheway G, Johnson CA. Unlocking the potential of the UK 100,000 Genomes Project-lessons learned from analysis of the "Congenital Malformations caused by Ciliopathies" cohort. Am J Med Genet C Semin Med Genet 2022; 190:5-8. [PMID: 35289502 PMCID: PMC9315030 DOI: 10.1002/ajmg.c.31965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/02/2022] [Accepted: 03/09/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Sunayna Best
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK,Yorkshire Regional Genetics ServiceLeedsUK
| | - Chris F. Inglehearn
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK
| | - Christopher M. Watson
- North East and Yorkshire Genomic Laboratory Hub, Central LabSt. James's University HospitalLeedsUK
| | - Carmel Toomes
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK
| | - Gabrielle Wheway
- University Hospital Southampton NHS Foundation TrustSouthamptonUK,Faculty of Medicine, Human Development and HealthUniversity of SouthamptonSouthamptonUK
| | - Colin A. Johnson
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK
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14
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Best S, Lord J, Roche M, Watson C, Poulter J, Szymanska K, Ellingford J, Carmichael J, Brittain H, Toomes C, Inglehearn C, Johnson C, Wheway G. Molecular diagnoses in the congenital malformations caused by ciliopathies cohort of the 100 000 genomes project. Acta Ophthalmol 2022. [DOI: 10.1111/j.1755-3768.2022.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sunayna Best
- Division of Molecular Medicine Leeds Institute of Medical Research at St. James University of Leeds
- Yorkshire Regional Genetics Service Leeds Teaching Hospitals NHS Trust Leeds
| | - Jenny Lord
- University Hospital Southampton NHS Foundation Trust
- Faculty of Medicine Human Development and Health University of Southampton Southampton
| | | | - Christopher Watson
- Division of Molecular Medicine Leeds Institute of Medical Research at St. James University of Leeds
- Yorkshire Regional Genetics Service Leeds Teaching Hospitals NHS Trust Leeds
| | - James Poulter
- Division of Molecular Medicine Leeds Institute of Medical Research at St. James University of Leeds
| | - Katarzyna Szymanska
- Division of Molecular Medicine Leeds Institute of Medical Research at St. James University of Leeds
| | - Jamie Ellingford
- Division of Evolution and Genomic Sciences Faculty of Biology, Medicine and Health University of Manchester
| | | | | | - Carmel Toomes
- Division of Molecular Medicine Leeds Institute of Medical Research at St. James University of Leeds
| | - Chris Inglehearn
- Division of Molecular Medicine Leeds Institute of Medical Research at St. James University of Leeds
| | - Colin Johnson
- Division of Molecular Medicine Leeds Institute of Medical Research at St. James University of Leeds
| | - Gabrielle Wheway
- University Hospital Southampton NHS Foundation Trust
- Faculty of Medicine Human Development and Health University of Southampton Southampton
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15
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Derar M, Lord EC, Poulter JA, Webster AR, Bell SM, Inglehearn CF, Toomes C. SLC38A8 mutation spectrum in foveal hypoplasia. Acta Ophthalmol 2022. [DOI: 10.1111/j.1755-3768.2022.208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Mohammed Derar
- Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Emma C. Lord
- Leeds Institute of Medical Research University of Leeds Leeds UK
| | - James A. Poulter
- Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Sandra M. Bell
- Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Carmel Toomes
- Leeds Institute of Medical Research University of Leeds Leeds UK
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16
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Hardcastle AJ, Liskova P, Bykhovskaya Y, McComish BJ, Davidson AE, Inglehearn CF, Li X, Choquet H, Habeeb M, Lucas SEM, Sahebjada S, Pontikos N, Lopez KER, Khawaja AP, Ali M, Dudakova L, Skalicka P, Van Dooren BTH, Geerards AJM, Haudum CW, Faro VL, Tenen A, Simcoe MJ, Patasova K, Yarrand D, Yin J, Siddiqui S, Rice A, Farraj LA, Chen YDI, Rahi JS, Krauss RM, Theusch E, Charlesworth JC, Szczotka-Flynn L, Toomes C, Meester-Smoor MA, Richardson AJ, Mitchell PA, Taylor KD, Melles RB, Aldave AJ, Mills RA, Cao K, Chan E, Daniell MD, Wang JJ, Rotter JI, Hewitt AW, MacGregor S, Klaver CCW, Ramdas WD, Craig JE, Iyengar SK, O'Brart D, Jorgenson E, Baird PN, Rabinowitz YS, Burdon KP, Hammond CJ, Tuft SJ, Hysi PG. A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus. Commun Biol 2021; 4:266. [PMID: 33649486 PMCID: PMC7921564 DOI: 10.1038/s42003-021-01784-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.
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Affiliation(s)
- Alison J Hardcastle
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK.
| | - Petra Liskova
- UCL Institute of Ophthalmology, London, UK
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Yelena Bykhovskaya
- The Cornea Eye Institute, Beverly Hills, CA, USA
- Department of Surgery and Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bennet J McComish
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Chris F Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Mahmoud Habeeb
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Sionne E M Lucas
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Srujana Sahebjada
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | | | | | - Anthony P Khawaja
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital, London, UK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Bart T H Van Dooren
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Amphia Hospital, Breda, The Netherlands
| | | | - Christoph W Haudum
- Division of Endocrinology and Diabetology, Endocrinology Lab Platform, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Valeria Lo Faro
- Department of Ophthalmology, University Medical Center Groningen (UMCG), Groningen, the Netherlands
- Department of Ophthalmology, Academic Medical Center, Amsterdam, The Netherlands
| | - Abi Tenen
- Vision Eye Institute, Melbourne, VIC, Australia
- School of Primary and Allied Health Care, Monash University, Melbourne, VIC, Australia
- Melbourne Stem Cell Centre, Melbourne, VIC, 3800, Australia
| | - Mark J Simcoe
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karina Patasova
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Darioush Yarrand
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Salina Siddiqui
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Ophthalmology, St James's University Hospital, Leeds, UK
| | - Aine Rice
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Layal Abi Farraj
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jugnoo S Rahi
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | | | | | - Jac C Charlesworth
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Andrea J Richardson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Paul A Mitchell
- Centre for Vision Research, Department of Ophthalmology, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ronald B Melles
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Anthony J Aldave
- The Jules Stein Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Richard A Mills
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Ke Cao
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Elsie Chan
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Mark D Daniell
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Jie Jin Wang
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Vision Eye Institute, Melbourne, VIC, Australia
- School of Primary and Allied Health Care, Monash University, Melbourne, VIC, Australia
- Melbourne Stem Cell Centre, Melbourne, VIC, 3800, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Wishal D Ramdas
- Department of Ophthalmology, Erasmus Medical Center GD, Rotterdam, The Netherlands
| | - Jamie E Craig
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Sudha K Iyengar
- Department of Ophthalmology, Case Western Reserve University, Cleveland, OH, USA
| | - David O'Brart
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- St Thomas Hospital, Guy's and St. Thomas NHS Trust, London, London, UK
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Paul N Baird
- Department of Surgery, Ophthalmology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Yaron S Rabinowitz
- The Cornea Eye Institute, Beverly Hills, CA, USA
- Department of Surgery and Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Chris J Hammond
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- St Thomas Hospital, Guy's and St. Thomas NHS Trust, London, London, UK
| | - Stephen J Tuft
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital, NHS Foundation Trust, London, UK.
| | - Pirro G Hysi
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK.
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK.
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17
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Poulter JA, Gravett MSC, Taylor RL, Fujinami K, De Zaeytijd J, Bellingham J, Rehman AU, Hayashi T, Kondo M, Rehman A, Ansar M, Donnelly D, Toomes C, Ali M, De Baere E, Leroy BP, Davies NP, Henderson RH, Webster AR, Rivolta C, Zeitz C, Mahroo OA, Arno G, Black GCM, McKibbin M, Harris SA, Khan KN, Inglehearn CF. New variants and in silico analyses in GRK1 associated Oguchi disease. Hum Mutat 2021; 42:164-176. [PMID: 33252155 PMCID: PMC7898643 DOI: 10.1002/humu.24140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/15/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022]
Abstract
Biallelic mutations in G-Protein coupled receptor kinase 1 (GRK1) cause Oguchi disease, a rare subtype of congenital stationary night blindness (CSNB). The purpose of this study was to identify disease causing GRK1 variants and use in-depth bioinformatic analyses to evaluate how their impact on protein structure could lead to pathogenicity. Patients' genomic DNA was sequenced by whole genome, whole exome or focused exome sequencing. Disease associated variants, published and novel, were compared to nondisease associated missense variants. The impact of GRK1 missense variants at the protein level were then predicted using a series of computational tools. We identified twelve previously unpublished cases with biallelic disease associated GRK1 variants, including eight novel variants, and reviewed all GRK1 disease associated variants. Further structure-based scoring revealed a hotspot for missense variants in the kinase domain. In addition, to aid future clinical interpretation, we identified the bioinformatics tools best able to differentiate disease associated from nondisease associated variants. We identified GRK1 variants in Oguchi disease patients and investigated how disease-causing variants may impede protein function in-silico.
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Affiliation(s)
- James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | | | - Rachel L. Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and HealthUniversity of ManchesterManchesterUK
| | - Kaoru Fujinami
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical CentreTokyoJapan
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
- Keio University School of MedicineTokyoJapan
| | | | | | - Atta Ur Rehman
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV)University of LausanneLausanneSwitzerland
| | | | - Mineo Kondo
- Mie University Graduate School of MedicineMieJapan
| | - Abdur Rehman
- Department of Genetics, Faculty of ScienceHazara University MansehraDhodialPakistan
| | - Muhammad Ansar
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB)BaselSwitzerland
| | - Dan Donnelly
- School of Biomedical Sciences, University of LeedsLeedsUK
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | | | | | - Bart P. Leroy
- Ghent UniversityGhentBelgium
- Children's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | | | | | - Andrew R. Webster
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Carlo Rivolta
- Department of Genetics and Genome BiologyUniversity of LeicesterLeicesterUK
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB)BaselSwitzerland
- Department of OphthalmologyUniversity Hospital BaselBaselSwitzerland
| | - Christina Zeitz
- Sorbonne UniversitéINSERM, CNRS, Institut de la VisionParisFrance
| | - Omar A. Mahroo
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Gavin Arno
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical CentreTokyoJapan
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Graeme C. M. Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation TrustManchesterUK
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
- Leeds Teaching Hospitals NHS Trust, St James’ University HospitalLeedsUK
| | | | - Kamron N. Khan
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation TrustManchesterUK
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
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18
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Poulter JA, Gravett MSC, Taylor RL, Fujinami K, De Zaeytijd J, Bellingham J, Rehman AU, Hayashi T, Kondo M, Rehman A, Ansar M, Donnelly D, Toomes C, Ali M, De Baere E, Leroy BP, Davies NP, Henderson RH, Webster AR, Rivolta C, Zeitz C, Mahroo OA, Arno G, Black GCM, McKibbin M, Harris SA, Khan KN, Inglehearn CF. Cover, Volume 42, Issue 2. Hum Mutat 2021. [DOI: 10.1002/humu.24169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Rachel L. Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Kaoru Fujinami
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Centre Tokyo Japan
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
- Keio University School of Medicine Tokyo Japan
| | | | | | - Atta Ur Rehman
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) University of Lausanne Lausanne Switzerland
| | | | - Mineo Kondo
- Mie University Graduate School of Medicine Mie Japan
| | - Abdur Rehman
- Department of Genetics, Faculty of Science Hazara University Mansehra Dhodial Pakistan
| | - Muhammad Ansar
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Dan Donnelly
- School of Biomedical Sciences, University of Leeds Leeds UK
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Bart P. Leroy
- Ghent University Ghent Belgium
- Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | | | | | - Andrew R. Webster
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Carlo Rivolta
- Department of Genetics and Genome Biology University of Leicester Leicester UK
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
- Department of Ophthalmology University Hospital Basel Basel Switzerland
| | - Christina Zeitz
- Sorbonne Université INSERM, CNRS, Institut de la Vision Paris France
| | - Omar A. Mahroo
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Gavin Arno
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Centre Tokyo Japan
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Graeme C. M. Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust Manchester UK
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
- Leeds Teaching Hospitals NHS Trust, St James’ University Hospital Leeds UK
| | - Sarah A. Harris
- School of Physics and Astronomy, University of Leeds Leeds UK
| | - Kamron N. Khan
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust Manchester UK
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
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19
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Vig A, Poulter JA, Ottaviani D, Tavares E, Toropova K, Tracewska AM, Mollica A, Kang J, Kehelwathugoda O, Paton T, Maynes JT, Wheway G, Arno G, Khan KN, McKibbin M, Toomes C, Ali M, Di Scipio M, Li S, Ellingford J, Black G, Webster A, Rydzanicz M, Stawiński P, Płoski R, Vincent A, Cheetham ME, Inglehearn CF, Roberts A, Heon E. DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration. Genet Med 2020; 22:2041-2051. [PMID: 32753734 PMCID: PMC7708302 DOI: 10.1038/s41436-020-0915-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Determining the role of DYNC2H1 variants in nonsyndromic inherited retinal disease (IRD). METHODS Genome and exome sequencing were performed for five unrelated cases of IRD with no identified variant. In vitro assays were developed to validate the variants identified (fibroblast assay, induced pluripotent stem cell [iPSC] derived retinal organoids, and a dynein motility assay). RESULTS Four novel DYNC2H1 variants (V1, g.103327020_103327021dup; V2, g.103055779A>T; V3, g.103112272C>G; V4, g.103070104A>C) and one previously reported variant (V5, g.103339363T>G) were identified. In proband 1 (V1/V2), V1 was predicted to introduce a premature termination codon (PTC), whereas V2 disrupted the exon 41 splice donor site causing incomplete skipping of exon 41. V1 and V2 impaired dynein-2 motility in vitro and perturbed IFT88 distribution within cilia. V3, homozygous in probands 2-4, is predicted to cause a PTC in a retina-predominant transcript. Analysis of retinal organoids showed that this new transcript expression increased with organoid differentiation. V4, a novel missense variant, was in trans with V5, previously associated with Jeune asphyxiating thoracic dystrophy (JATD). CONCLUSION The DYNC2H1 variants discussed herein were either hypomorphic or affecting a retina-predominant transcript and caused nonsyndromic IRD. Dynein variants, specifically DYNC2H1 variants are reported as a cause of non syndromic IRD.
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Affiliation(s)
- Anjali Vig
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, The University of Toronto, Toronto, Canada
| | - James A Poulter
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | | | - Erika Tavares
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Katerina Toropova
- Department of Biological Sciences, Birbeck, University of London, London, UK
| | - Anna Maria Tracewska
- DNA Analysis Unit, ŁUKASIEWICZ Research Network-PORT Polish Center for Technology Development, Wrocław, Poland
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Antonio Mollica
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jasmine Kang
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | | | - Tara Paton
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Jason T Maynes
- Department of Anesthesia and Pain Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | - Kamron N Khan
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Martin McKibbin
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Carmel Toomes
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Manir Ali
- Department of Ophthalmology, St James' University Hospital, Leeds, UK
| | - Matteo Di Scipio
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Shuning Li
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jamie Ellingford
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicines and health, The University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
| | - Graeme Black
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicines and health, The University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew Webster
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | | | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Ajoy Vincent
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, The University of Toronto, Toronto, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Anthony Roberts
- Department of Biological Sciences, Birbeck, University of London, London, UK.
| | - Elise Heon
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.
- Institute of Medical Science, The University of Toronto, Toronto, Canada.
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.
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20
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Abdelhamed ZA, Abdelmottaleb DI, El-Asrag ME, Natarajan S, Wheway G, Inglehearn CF, Toomes C, Johnson CA. The ciliary Frizzled-like receptor Tmem67 regulates canonical Wnt/β-catenin signalling in the developing cerebellum via Hoxb5. Sci Rep 2019; 9:5446. [PMID: 30931988 PMCID: PMC6445493 DOI: 10.1038/s41598-019-41940-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
Primary cilia defects result in a group of related pleiotropic malformation syndromes known as ciliopathies, often characterised by cerebellar developmental and foliation defects. Here, we describe the cerebellar anatomical and signalling defects in the Tmem67tm1(Dgen)/H knockout mouse. At mid-gestation, Tmem67 mutant cerebella were hypoplastic and had aberrantly high canonical Wnt/β-catenin signalling, proliferation and apoptosis. Later in development, mutant cerebellar hemispheres had severe foliation defects and inferior lobe malformation, characterized by immature Purkinje cells (PCs). Early postnatal Tmem67 mutant cerebellum had disrupted ciliogenesis and reduced responsiveness to Shh signalling. Transcriptome profiling of Tmem67 mutant cerebella identified ectopic increased expression of homeobox-type transcription factors (Hoxa5, Hoxa4, Hoxb5 and Hoxd3), normally required for early rostral hindbrain patterning. HOXB5 protein levels were increased in the inferior lobe, and increased canonical Wnt signalling, following loss of TMEM67, was dependent on HOXB5. HOXB5 occupancy at the β-catenin promoter was significantly increased by activation of canonical Wnt signalling in Tmem67-/- mutant cerebellar neurones, suggesting that increased canonical Wnt signalling following mutation or loss of TMEM67 was directly dependent on HOXB5. Our results link dysregulated expression of Hox group genes with ciliary Wnt signalling defects in the developing cerebellum, providing new mechanistic insights into ciliopathy cerebellar hypoplasia phenotypes.
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Affiliation(s)
- Zakia A Abdelhamed
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
- Division of Human Genetics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH, 45229-3039, USA
| | - Dina I Abdelmottaleb
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
- Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Mohammed E El-Asrag
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
- Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Subaashini Natarajan
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
| | - Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Chris F Inglehearn
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
| | - Carmel Toomes
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
| | - Colin A Johnson
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK.
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21
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Bedoni N, Haer-Wigman L, Vaclavik V, Tran VH, Farinelli P, Balzano S, Royer-Bertrand B, El-Asrag ME, Bonny O, Ikonomidis C, Litzistorf Y, Nikopoulos K, Yioti GG, Stefaniotou MI, McKibbin M, Booth AP, Ellingford JM, Black GC, Toomes C, Inglehearn CF, Hoyng CB, Bax N, Klaver CCW, Thiadens AA, Murisier F, Schorderet DF, Ali M, Cremers FPM, Andréasson S, Munier FL, Rivolta C. Mutations in the polyglutamylase gene TTLL5, expressed in photoreceptor cells and spermatozoa, are associated with cone-rod degeneration and reduced male fertility. Hum Mol Genet 2018; 25:4546-4555. [PMID: 28173158 DOI: 10.1093/hmg/ddw282] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/19/2016] [Accepted: 08/20/2016] [Indexed: 12/30/2022] Open
Abstract
Hereditary retinal degenerations encompass a group of genetic diseases characterized by extreme clinical variability. Following next-generation sequencing and autozygome-based screening of patients presenting with a peculiar, recessive form of cone-dominated retinopathy, we identified five homozygous variants [p.(Asp594fs), p.(Gln117*), p.(Met712fs), p.(Ile756Phe), and p.(Glu543Lys)] in the polyglutamylase-encoding gene TTLL5, in eight patients from six families. The two male patients carrying truncating TTLL5 variants also displayed a substantial reduction in sperm motility and infertility, whereas those carrying missense changes were fertile. Defects in this polyglutamylase in humans have recently been associated with cone photoreceptor dystrophy, while mouse models carrying truncating mutations in the same gene also display reduced fertility in male animals. We examined the expression levels of TTLL5 in various human tissues and determined that this gene has multiple viable isoforms, being highly expressed in testis and retina. In addition, antibodies against TTLL5 stained the basal body of photoreceptor cells in rat and the centrosome of the spermatozoon flagellum in humans, suggesting a common mechanism of action in these two cell types. Taken together, our data indicate that mutations in TTLL5 delineate a novel, allele-specific syndrome causing defects in two as yet pathogenically unrelated functions, reproduction and vision.
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Affiliation(s)
- Nicola Bedoni
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Lonneke Haer-Wigman
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Veronika Vaclavik
- Jules Gonin Eye Hospital, Lausanne, Switzerland.,Fertas Andrology Laboratory, Lausanne, Switzerland
| | - Viet H Tran
- Jules Gonin Eye Hospital, Lausanne, Switzerland
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Sara Balzano
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Beryl Royer-Bertrand
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Institute for Research in Ophtalmology, University of Lausanne and Ecole Polytechnique Federale de Lausanne, Switzerland
| | - Mohammed E El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Olivier Bonny
- Service of Nephrology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Christos Ikonomidis
- Department of Otorhinolaryngology, Head and Neck Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Yan Litzistorf
- Department of Otorhinolaryngology, Head and Neck Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Konstantinos Nikopoulos
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Georgia G Yioti
- Department of Ophthalmology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Maria I Stefaniotou
- Department of Ophthalmology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Martin McKibbin
- The Eye Department, St. James's University Hospital, Leeds, UK
| | - Adam P Booth
- Royal Eye Infirmary, Derriford Hospital, Plymouth, UK
| | - Jamie M Ellingford
- Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Graeme C Black
- Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Carmel Toomes
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Chris F Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nathalie Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Alberta A Thiadens
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Daniel F Schorderet
- Institute for Research in Ophtalmology, University of Lausanne and Ecole Polytechnique Federale de Lausanne, Switzerland
| | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Frans P M Cremers
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | | | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
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22
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Astuti GDN, van den Born LI, Khan MI, Hamel CP, Bocquet B, Manes G, Quinodoz M, Ali M, Toomes C, McKibbin M, El-Asrag ME, Haer-Wigman L, Inglehearn CF, Black GCM, Hoyng CB, Cremers FPM, Roosing S. Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes. Genes (Basel) 2018; 9:genes9010021. [PMID: 29320387 PMCID: PMC5793174 DOI: 10.3390/genes9010021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/31/2017] [Accepted: 01/03/2018] [Indexed: 01/09/2023] Open
Abstract
Inherited retinal diseases (IRDs) display an enormous genetic heterogeneity. Whole exome sequencing (WES) recently identified genes that were mutated in a small proportion of IRD cases. Consequently, finding a second case or family carrying pathogenic variants in the same candidate gene often is challenging. In this study, we searched for novel candidate IRD gene-associated variants in isolated IRD families, assessed their causality, and searched for novel genotype-phenotype correlations. Whole exome sequencing was performed in 11 probands affected with IRDs. Homozygosity mapping data was available for five cases. Variants with minor allele frequencies ≤ 0.5% in public databases were selected as candidate disease-causing variants. These variants were ranked based on their: (a) presence in a gene that was previously implicated in IRD; (b) minor allele frequency in the Exome Aggregation Consortium database (ExAC); (c) in silico pathogenicity assessment using the combined annotation dependent depletion (CADD) score; and (d) interaction of the corresponding protein with known IRD-associated proteins. Twelve unique variants were found in 11 different genes in 11 IRD probands. Novel autosomal recessive and dominant inheritance patterns were found for variants in Small Nuclear Ribonucleoprotein U5 Subunit 200 (SNRNP200) and Zinc Finger Protein 513 (ZNF513), respectively. Using our pathogenicity assessment, a variant in DEAH-Box Helicase 32 (DHX32) was the top ranked novel candidate gene to be associated with IRDs, followed by eight medium and lower ranked candidate genes. The identification of candidate disease-associated sequence variants in 11 single families underscores the notion that the previously identified IRD-associated genes collectively carry > 90% of the defects implicated in IRDs. To identify multiple patients or families with variants in the same gene and thereby provide extra proof for pathogenicity, worldwide data sharing is needed.
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Affiliation(s)
- Galuh D. N. Astuti
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
| | | | - M. Imran Khan
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
| | - Christian P. Hamel
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
- CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France
| | - Béatrice Bocquet
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
- CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France
| | - Gaël Manes
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1015 Lausanne, Switzerland;
| | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Carmel Toomes
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Martin McKibbin
- Department of Ophthalmology, St. James’s University Hospital, LS9 7TF Leeds, UK;
| | - Mohammed E. El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
- Department of Zoology, Faculty of Science, Benha University, 13511 Benha, Egypt
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
| | - Chris F. Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Graeme C. M. Black
- Centre for Genomic Medicine, St. Mary’s Hospital, Manchester Academic Health Science Centre, University of Manchester, M13 9PL Manchester, UK;
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Center, 6525 EX Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
- Correspondence: ; Tel.: +31-(0)24-365-5266
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23
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Khan KN, El-Asrag ME, Ku CA, Holder GE, McKibbin M, Arno G, Poulter JA, Carss K, Bommireddy T, Bagheri S, Bakall B, Scholl HP, Raymond FL, Toomes C, Inglehearn CF, Pennesi ME, Moore AT, Michaelides M, Webster AR, Ali M. Specific Alleles of CLN7/MFSD8, a Protein That Localizes to Photoreceptor Synaptic Terminals, Cause a Spectrum of Nonsyndromic Retinal Dystrophy. Invest Ophthalmol Vis Sci 2017; 58:2906-2914. [PMID: 28586915 DOI: 10.1167/iovs.16-20608] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Recessive mutations in CLN7/MFSD8 usually cause variant late-infantile onset neuronal ceroid lipofuscinosis (vLINCL), a poorly understood neurodegenerative condition, though mutations may also cause nonsyndromic maculopathy. A series of 12 patients with nonsyndromic retinopathy due to novel CLN7/MFSD8 mutation combinations were investigated in this study. Methods Affected patients and their family members were recruited in ophthalmic clinics at each center where they were examined by retinal imaging and detailed electrophysiology. Whole exome or genome next generation sequencing was performed on genomic DNA from at least one affected family member. Immunofluorescence confocal microscopy of murine retina cross-sections were used to localize the protein. Results Compound heterozygous alleles were identified in six cases, one of which was always p.Glu336Gln. Such combinations resulted in isolated macular disease. Six further cases were homozygous for the variant p.Met454Thr, identified as a founder mutation of South Asian origin. Those patients had widespread generalized retinal disease, characterized by electroretinography as a rod-cone dystrophy with severe macular involvement. In addition, the photopic single flash electroretinograms demonstrated a reduced b- to a-wave amplitude ratio, suggesting dysfunction occurring after phototransduction. Immunohistology identified MFSD8 in the outer plexiform layer of the retina, a site rich in photoreceptor synapses. Conclusions This study highlights a hierarchy of MFSD8 variant severity, predicting three consequences of mutation: (1) nonsyndromic localized maculopathy, (2) nonsyndromic widespread retinopathy, or (3) syndromic neurological disease. The data also shed light on the underlying pathogenesis by implicating the photoreceptor synaptic terminals as the major site of retinal disease.
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Affiliation(s)
- Kamron N Khan
- University College London Institute of Ophthalmology, London, United Kingdom 2Inherited Eye Disease Service, Moorfields Eye Hospital, London, United Kingdom 3Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St. James's University Hospital, Leeds, United Kingdom 4Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Mohammed E El-Asrag
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St. James's University Hospital, Leeds, United Kingdom 5Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Cristy A Ku
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Graham E Holder
- University College London Institute of Ophthalmology, London, United Kingdom 2Inherited Eye Disease Service, Moorfields Eye Hospital, London, United Kingdom 7Department of Electrophysiology, Moorfields Eye Hospital, London, United Kingdom
| | - Martin McKibbin
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St. James's University Hospital, Leeds, United Kingdom 4Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Gavin Arno
- University College London Institute of Ophthalmology, London, United Kingdom
| | - James A Poulter
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
| | - Keren Carss
- National Institute for Health Research BioResource-Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom 9Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Tejaswi Bommireddy
- Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Saghar Bagheri
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States
| | - Benjamin Bakall
- Associated Retina Consultants, Phoenix, Arizona, United States 12University of Arizona, College of Medicine, Phoenix, Arizona, United States
| | - Hendrik P Scholl
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States
| | - F Lucy Raymond
- National Institute for Health Research BioResource-Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom 13Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Carmel Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
| | - Chris F Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Anthony T Moore
- University College London Institute of Ophthalmology, London, United Kingdom 2Inherited Eye Disease Service, Moorfields Eye Hospital, London, United Kingdom 14Department of Ophthalmology, University of California-San Francisco School of Medicine, San Francisco, California, United States
| | - Michel Michaelides
- University College London Institute of Ophthalmology, London, United Kingdom 2Inherited Eye Disease Service, Moorfields Eye Hospital, London, United Kingdom
| | - Andrew R Webster
- University College London Institute of Ophthalmology, London, United Kingdom 2Inherited Eye Disease Service, Moorfields Eye Hospital, London, United Kingdom
| | - Manir Ali
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
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Mughal S, Moghul I, Yu J, Black G, Hall G, Ingram S, Gillespie R, Manson F, Sergouniotis P, Inglehearn C, Toomes C, Ali M, McKibbin M, Poulter J, Khan K, Lord E, Nemeth A, Downes S, Halford S, Yu J, Lise S, Arno G, Fiorentino A, Pontikos N, Plagnol V, Michaelides M, Hardcastle AJ, Cheetham ME, Webster AR, van Heyningen V, Clark T, Gregory DS, Pontikos N. Pheno4J: a gene to phenotype graph database. Bioinformatics 2017. [DOI: 10.1093/bioinformatics/btx397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Ismail Moghul
- UCL Cancer Institute, University College London, London, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tristan Clark
- Computer Science Department, University College London, London, UK
| | - David S Gregory
- Computer Science Department, University College London, London, UK
| | - Nikolas Pontikos
- UCL Genetics Institute, University College London, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
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25
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Panagiotou ES, Sanjurjo Soriano C, Poulter JA, Lord EC, Dzulova D, Kondo H, Hiyoshi A, Chung BHY, Chu YWY, Lai CH, Tafoya ME, Karjosukarso D, Collin RW, Topping J, Downey LM, Ali M, Inglehearn CF, Toomes C. Defects in the Cell Signaling Mediator β-Catenin Cause the Retinal Vascular Condition FEVR. Am J Hum Genet 2017; 100:960-968. [PMID: 28575650 DOI: 10.1016/j.ajhg.2017.05.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/03/2017] [Indexed: 12/30/2022] Open
Abstract
Familial exudative vitreoretinopathy (FEVR) is an inherited blinding disorder characterized by the abnormal development of the retinal vasculature. The majority of mutations identified in FEVR are found within four genes that encode the receptor complex (FZD4, LRP5, and TSPAN12) and ligand (NDP) of a molecular pathway that controls angiogenesis, the Norrin-β-catenin signaling pathway. However, half of all FEVR-affected case subjects do not harbor mutations in these genes, indicating that further mutated genes remain to be identified. Here we report the identification of mutations in CTNNB1, the gene encoding β-catenin, as a cause of FEVR. We describe heterozygous mutations (c.2142_2157dup [p.His720∗] and c.2128C>T [p.Arg710Cys]) in two dominant FEVR-affected families and a de novo mutation (c.1434_1435insC [p.Glu479Argfs∗18]) in a simplex case subject. Previous studies have reported heterozygous de novo CTNNB1 mutations as a cause of syndromic intellectual disability (ID) and autism spectrum disorder, and somatic mutations are linked to many cancers. However, in this study we show that Mendelian inherited CTNNB1 mutations can cause non-syndromic FEVR and that FEVR can be a part of the syndromic ID phenotype, further establishing the role that β-catenin signaling plays in the development of the retinal vasculature.
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26
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Kamal M, Holliday DL, Morrison EE, Speirs V, Toomes C, Bell SM. Loss of CSMD1 expression disrupts mammary duct formation while enhancing proliferation, migration and invasion. Oncol Rep 2017; 38:283-292. [PMID: 28534981 DOI: 10.3892/or.2017.5656] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 05/11/2017] [Indexed: 11/06/2022] Open
Abstract
The CUB and sushi multiple domains 1 (CSMD1) gene maps to chromosome 8p23, a region deleted in many cancers. Loss of CSMD1 expression is associated with poor prognosis in breast cancer suggesting that it acts as a tumour suppressor in this cancer. However, the function of CSMD1 is largely unknown. Herein, we investigated CSMD1 functions in cell line models. CSMD1 expression was suppressed in MCF10A and LNCaP cells using short hairpin RNA. Functional assays were performed focusing on the 'normal' MCF10A cell line. Suppression of CSMD1 significantly increased the proliferation, cell migration and invasiveness of MCF10A cells compared to shcontrols. shCSMD1 cells also showed significantly reduced adhesion to Matrigel and fibronectin. In a three-dimensional Matrigel model of MCF10A cells, reduced CSMD1 expression resulted in the development of larger and more poorly differentiated breast acini-like structures that displayed impaired lumen formation. Loss of CSMD1 expression disrupts a model of mammary duct formation while enhancing proliferation, migration and invasion. Our data suggest that CSMD1 is involved in the suppression of a transformed phenotype.
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Affiliation(s)
- Mohamed Kamal
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Deborah L Holliday
- Leeds Institute of Cancer and Pathology, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Ewan E Morrison
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Valerie Speirs
- Leeds Institute of Cancer and Pathology, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Carmel Toomes
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Sandra M Bell
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
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Taylor RL, Arno G, Poulter JA, Khan KN, Morarji J, Hull S, Pontikos N, Rueda Martin A, Smith KR, Ali M, Toomes C, McKibbin M, Clayton-Smith J, Grunewald S, Michaelides M, Moore AT, Hardcastle AJ, Inglehearn CF, Webster AR, Black GC. Association of Steroid 5α-Reductase Type 3 Congenital Disorder of Glycosylation With Early-Onset Retinal Dystrophy. JAMA Ophthalmol 2017; 135:339-347. [PMID: 28253385 DOI: 10.1001/jamaophthalmol.2017.0046] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Steroid 5α-reductase type 3 congenital disorder of glycosylation (SRD5A3-CDG) is a rare disorder of N-linked glycosylation. Its retinal phenotype is not well described but could be important for disease recognition because it appears to be a consistent primary presenting feature. Objective To investigate a series of patients with the same mutation in the SRD5A3 gene and thereby characterize its retinal manifestations and other associated features. Design, Setting and Participants Seven affected individuals from 4 unrelated families with early-onset retinal dystrophy as a primary manifestation underwent comprehensive ophthalmic assessment, including retinal imaging and electrodiagnostic testing. Developmental and systemic findings were also recorded. Molecular genetic approaches, including targeted next-generation sequencing, autozygosity mapping, and apex microarray, were tried to reach a diagnosis; all participants were mutation negative. Whole-exome sequencing or whole-genome sequencing was used to identify the causative variant. Biochemical profiling was conducted to confirm a CDG type I defect. Patient phenotype data were collected over the course of ophthalmic follow-up, spanning a period of 20 years, beginning March 20, 1997, through September 15, 2016. Main Outcomes and Measures Detailed clinical phenotypes as well as genetic and biochemical results. Results The cohort consisted of 7 participants (5 females and 2 males) whose mean (SD) age at the most recent examination was 17.1 (3.9) years and who were all of South Asian ethnicity. Whole-exome sequencing and whole-genome sequencing identified the same homozygous SRD5A3 c.57G>A, p.(Trp19Ter) variant as the underlying cause of early-onset retinal dystrophy in each family. Detailed ocular phenotyping identified early-onset (aged ≤3 years) visual loss (mean [SD] best-corrected visual acuity, +0.95 [0.34] logMAR [20/180 Snellen]), childhood-onset nyctalopia, myopia (mean [SD] refractive error, -6.71 [-4.22]), and nystagmus. Six of the 7 patients had learning difficulties and psychomotor delay. Fundus autofluorescence imaging and optical coherence tomographic scans were abnormal in all patients, and electrodiagnostic testing revealed rod and cone dysfunction in the 5 patients tested. Conclusions and Relevance Mutations in the SRD5A3 gene may cause early-onset retinal dystrophy, a previously underdescribed feature of the SRD5A3-CDG disorder that is progressive and may lead to serious visual impairment. SRD5A3 and other glycosylation disorder genes should be considered as a cause of retinal dystrophy even when systemic features are mild. Further delineation of SRD5A3-associated eye phenotypes can help inform genetic counseling for prognostic estimation of visual loss and disease progression.
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Affiliation(s)
- Rachel L Taylor
- Genomic Medicine, Division of Evolution and Genomic Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, England2Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary's Hospital, Manchester, England
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, England
| | - James A Poulter
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, England
| | - Kamron N Khan
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, England 5Department of Ophthalmology, St. James's University Hospital, Leeds, England
| | - Jiten Morarji
- Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, Manchester, England
| | - Sarah Hull
- UCL Institute of Ophthalmology, University College London, London, England 7Moorfields Eye Hospital, London, England
| | - Nikolas Pontikos
- UCL Genetics Institute, University College London, London, England
| | | | | | - Manir Ali
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, England
| | - Carmel Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, England
| | - Martin McKibbin
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, England 5Department of Ophthalmology, St. James's University Hospital, Leeds, England
| | - Jill Clayton-Smith
- Genomic Medicine, Division of Evolution and Genomic Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, England2Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary's Hospital, Manchester, England
| | - Stephanie Grunewald
- Metabolic Unit, Great Ormond Street Hospital, London, England11Institute for Child Health, University College London, London, England
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, England 7Moorfields Eye Hospital, London, England
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, England 12Department of Ophthalmology, University of California, San Francisco, Medical School, San Francisco
| | - Alison J Hardcastle
- UCL Institute of Ophthalmology, University College London, London, England 7Moorfields Eye Hospital, London, England
| | - Chris F Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, England
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, England 7Moorfields Eye Hospital, London, England
| | - Graeme C Black
- Genomic Medicine, Division of Evolution and Genomic Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, England2Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary's Hospital, Manchester, England
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Xu M, Xie Y(A, Abouzeid H, Gordon CT, Fiorentino A, Sun Z, Lehman A, Osman IS, Dharmat R, Riveiro-Alvarez R, Bapst-Wicht L, Babino D, Arno G, Busetto V, Zhao L, Li H, Lopez-Martinez MA, Azevedo LF, Hubert L, Pontikos N, Eblimit A, Lorda-Sanchez I, Kheir V, Plagnol V, Oufadem M, Soens ZT, Yang L, Bole-Feysot C, Pfundt R, Allaman-Pillet N, Nitschké P, Cheetham ME, Lyonnet S, Agrawal SA, Li H, Pinton G, Michaelides M, Besmond C, Li Y, Yuan Z, von Lintig J, Webster AR, Le Hir H, Stoilov P, Amiel J, Hardcastle AJ, Ayuso C, Sui R, Chen R, Allikmets R, Schorderet DF, Black G, Hall G, Gillespie R, Ramsden S, Manson F, Sergouniotis P, Inglehearn C, Toomes C, Ali M, McKibbin M, Poulter J, Lord E, Nemeth A, Halford S, Downes S, Yu J. Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies. Am J Hum Genet 2017; 100:592-604. [PMID: 28285769 DOI: 10.1016/j.ajhg.2017.02.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 02/15/2017] [Indexed: 10/20/2022] Open
Abstract
Pre-mRNA splicing factors play a fundamental role in regulating transcript diversity both temporally and spatially. Genetic defects in several spliceosome components have been linked to a set of non-overlapping spliceosomopathy phenotypes in humans, among which skeletal developmental defects and non-syndromic retinitis pigmentosa (RP) are frequent findings. Here we report that defects in spliceosome-associated protein CWC27 are associated with a spectrum of disease phenotypes ranging from isolated RP to severe syndromic forms. By whole-exome sequencing, recessive protein-truncating mutations in CWC27 were found in seven unrelated families that show a range of clinical phenotypes, including retinal degeneration, brachydactyly, craniofacial abnormalities, short stature, and neurological defects. Remarkably, variable expressivity of the human phenotype can be recapitulated in Cwc27 mutant mouse models, with significant embryonic lethality and severe phenotypes in the complete knockout mice while mice with a partial loss-of-function allele mimic the isolated retinal degeneration phenotype. Our study describes a retinal dystrophy-related phenotype spectrum as well as its genetic etiology and highlights the complexity of the spliceosomal gene network.
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Sergouniotis PI, McKibbin M, Robson AG, Bolz HJ, De Baere E, Müller PL, Heller R, El-Asrag ME, Van Schil K, Plagnol V, Toomes C, Consortium UKIRD, Ali M, Holder GE, Charbel Issa P, Leroy BP, Inglehearn CF, Webster AR. Disease Expression in Autosomal Recessive Retinal Dystrophy Associated With Mutations in theDRAM2Gene. ACTA ACUST UNITED AC 2015; 56:8083-90. [DOI: 10.1167/iovs.15-17604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Panagiotis I. Sergouniotis
- UCL Institute of Ophthalmology, London, United Kingdom 2Manchester Royal Eye Hospital, Manchester, United Kingdom 3Centre for Ophthalmology & Vision Sciences, Institute of Human Development, University of Manchester, Manchester, United Kingdom
| | - Martin McKibbin
- Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Anthony G. Robson
- UCL Institute of Ophthalmology, London, United Kingdom 5Moorfields Eye Hospital, London, United Kingdom
| | - Hanno J. Bolz
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany 7Bioscientia Center for Human Genetics, Ingelheim, Germany
| | - Elfride De Baere
- Centre for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | - Raoul Heller
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
| | - Mohammed E. El-Asrag
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom 11Department of Zoology, Benha University, Benha, Egypt
| | - Kristof Van Schil
- Centre for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | - Carmel Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Manir Ali
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Graham E. Holder
- UCL Institute of Ophthalmology, London, United Kingdom 5Moorfields Eye Hospital, London, United Kingdom
| | | | - Bart P. Leroy
- Centre for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium 13Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium 14Division of Ophthalmology and Centre for Cellular and Molecular The
| | - Chris F. Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Andrew R. Webster
- UCL Institute of Ophthalmology, London, United Kingdom 5Moorfields Eye Hospital, London, United Kingdom
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Abdelhamed Z, Natarajan S, Inglehearn C, Toomes C, Johnson C, Jagger D. The Meckel-Gruber Syndrome protein TMEM67 (meckelin) regulates basal body planar polarization and non-canonical Wnt signalling via Wnt5a and ROR2. Cilia 2015. [PMCID: PMC4519161 DOI: 10.1186/2046-2530-4-s1-p40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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El-Asrag M, Sergouniotis P, McKibbin M, Plagnol V, Sheridan E, Waseem N, Abdelhamed Z, McKeefry D, Van Schil K, Poulter J, Johnson CA, Carr IM, Leroy BP, De Baere E, Inglehearn CF, Webster AR, Toomes C, Ali M, Black G, Hall G, Ingram S, Gillespie R, Ramsden S, Manson F, Hardcastle A, Michaelides M, Cheetham M, Arno G, Thomas N, Bhattacharya S, Moore T, Nemeth A, Downes S, Lise S, Lord E. Biallelic mutations in the autophagy regulator DRAM2 cause retinal dystrophy with early macular involvement. Am J Hum Genet 2015; 96:948-54. [PMID: 25983245 DOI: 10.1016/j.ajhg.2015.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/13/2015] [Indexed: 01/08/2023] Open
Abstract
Retinal dystrophies are an overlapping group of genetically heterogeneous conditions resulting from mutations in more than 250 genes. Here we describe five families affected by an adult-onset retinal dystrophy with early macular involvement and associated central visual loss in the third or fourth decade of life. Affected individuals were found to harbor disease-causing variants in DRAM2 (DNA-damage regulated autophagy modulator protein 2). Homozygosity mapping and exome sequencing in a large, consanguineous British family of Pakistani origin revealed a homozygous frameshift variant (c.140delG [p.Gly47Valfs(∗)3]) in nine affected family members. Sanger sequencing of DRAM2 in 322 unrelated probands with retinal dystrophy revealed one European subject with compound heterozygous DRAM2 changes (c.494G>A [p.Trp165(∗)] and c.131G>A [p.Ser44Asn]). Inspection of previously generated exome sequencing data in unsolved retinal dystrophy cases identified a homozygous variant in an individual of Indian origin (c.64_66del [p.Ala22del]). Independently, a gene-based case-control association study was conducted via an exome sequencing dataset of 18 phenotypically similar case subjects and 1,917 control subjects. Using a recessive model and a binomial test for rare, presumed biallelic, variants, we found DRAM2 to be the most statistically enriched gene; one subject was a homozygote (c.362A>T [p.His121Leu]) and another a compound heterozygote (c.79T>C [p.Tyr27His] and c.217_225del [p.Val73_Tyr75del]). DRAM2 encodes a transmembrane lysosomal protein thought to play a role in the initiation of autophagy. Immunohistochemical analysis showed DRAM2 localization to photoreceptor inner segments and to the apical surface of retinal pigment epithelial cells where it might be involved in the process of photoreceptor renewal and recycling to preserve visual function.
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Abdelhamed ZA, Natarajan S, Wheway G, Inglehearn CF, Toomes C, Johnson CA, Jagger DJ. The Meckel-Gruber syndrome protein TMEM67 controls basal body positioning and epithelial branching morphogenesis in mice via the non-canonical Wnt pathway. Dis Model Mech 2015; 8:527-41. [PMID: 26035863 PMCID: PMC4457033 DOI: 10.1242/dmm.019083] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/01/2015] [Indexed: 01/16/2023] Open
Abstract
Ciliopathies are a group of developmental disorders that manifest with multi-organ anomalies. Mutations in TMEM67 (MKS3) cause a range of human ciliopathies, including Meckel-Gruber and Joubert syndromes. In this study we describe multi-organ developmental abnormalities in the Tmem67tm1Dgen/H1 knockout mouse that closely resemble those seen in Wnt5a and Ror2 knockout mice. These include pulmonary hypoplasia, ventricular septal defects, shortening of the body longitudinal axis, limb abnormalities, and cochlear hair cell stereociliary bundle orientation and basal body/kinocilium positioning defects. The basal body/kinocilium complex was often uncoupled from the hair bundle, suggesting aberrant basal body migration, although planar cell polarity and apical planar asymmetry in the organ of Corti were normal. TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 (receptor-tyrosine-kinase-like orphan receptor 2) upon stimulation with Wnt5a-conditioned medium. ROR2 also colocalises and interacts with TMEM67 at the ciliary transition zone. Additionally, the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay. Cultured lungs of Tmem67 mutant mice failed to respond to stimulation of epithelial branching morphogenesis by Wnt5a. Wnt5a also inhibited both the Shh and canonical Wnt/β-catenin signalling pathways in wild-type embryonic lung. Pulmonary hypoplasia phenotypes, including loss of correct epithelial branching morphogenesis and cell polarity, were rescued by stimulating the non-canonical Wnt pathway downstream of the Wnt5a-TMEM67-ROR2 axis by activating RhoA. We propose that TMEM67 is a receptor that has a main role in non-canonical Wnt signalling, mediated by Wnt5a and ROR2, and normally represses Shh signalling. Downstream therapeutic targeting of the Wnt5a-TMEM67-ROR2 axis might, therefore, reduce or prevent pulmonary hypoplasia in ciliopathies and other congenital conditions. Highlighted Article: TMEM67 is a receptor of non-canonical Wnt signalling, implicating the Wnt5a-TMEM67-ROR2 axis during developmental signalling and disruption in ciliopathy disease state.
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Affiliation(s)
- Zakia A Abdelhamed
- Ciliopathy Research Group, Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK Department of Anatomy and Embryology, Faculty of Medicine, Al-Azhar University, Cairo 11844, Egypt
| | - Subaashini Natarajan
- Ciliopathy Research Group, Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Gabrielle Wheway
- Ciliopathy Research Group, Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Christopher F Inglehearn
- Ciliopathy Research Group, Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Carmel Toomes
- Ciliopathy Research Group, Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Colin A Johnson
- Ciliopathy Research Group, Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Daniel J Jagger
- UCL Ear Institute, University College London, 332 Gray's Inn Road, London WC1X 8EE, UK
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Abdelhamed Z, Toomes C, Inglehearn C, Johnson C. Cerebellar Malformations in the Tmem67 Ciliopathy Mouse Model are Caused by Combined Wnt and Shh Signalling Systems Dysregulations. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.lb418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zakia Abdelhamed
- Leeds institue of Biomedical and Cinical Sciences University of LeedsLeedsUnited Kingdom
- Anatomy and Embryology department Faculty of MedicineAl‐Azhar UniversityCairoEgypt
| | - Carmel Toomes
- Leeds institue of Biomedical and Cinical Sciences University of LeedsLeedsUnited Kingdom
| | - Chris Inglehearn
- Leeds institue of Biomedical and Cinical Sciences University of LeedsLeedsUnited Kingdom
| | - Colin Johnson
- Leeds institue of Biomedical and Cinical Sciences University of LeedsLeedsUnited Kingdom
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Ravesh Z, El Asrag ME, Weisschuh N, McKibbin M, Reuter P, Watson CM, Baumann B, Poulter JA, Sajid S, Panagiotou ES, O’Sullivan J, Abdelhamed Z, Bonin M, Soltanifar M, Black GC, Din MAU, Toomes C, Ansar M, Inglehearn CF, Wissinger B, Ali M. Novel C8orf37 mutations cause retinitis pigmentosa in consanguineous families of Pakistani origin. Mol Vis 2015; 21:236-43. [PMID: 25802487 PMCID: PMC4357040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/05/2015] [Indexed: 11/28/2022] Open
Abstract
PURPOSE To investigate the molecular basis of retinitis pigmentosa in two consanguineous families of Pakistani origin with multiple affected members. METHODS Homozygosity mapping and Sanger sequencing of candidate genes were performed in one family while the other was analyzed with whole exome next-generation sequencing. A minigene splicing assay was used to confirm the splicing defects. RESULTS In family MA48, a novel homozygous nucleotide substitution in C8orf37, c.244-2A>C, that disrupted the consensus splice acceptor site of exon 3 was found. The minigene splicing assay revealed that this mutation activated a cryptic splice site within exon 3, causing a 22 bp deletion in the transcript that is predicted to lead to a frameshift followed by premature protein truncation. In family MA13, a novel homozygous null mutation in C8orf37, c.555G>A, p.W185*, was identified. Both mutations segregated with the disease phenotype as expected in a recessive manner and were absent in 8,244 unrelated individuals of South Asian origin. CONCLUSIONS In this report, we describe C8orf37 mutations that cause retinal dystrophy in two families of Pakistani origin, contributing further data on the phenotype and the spectrum of mutations in this form of retinitis pigmentosa.
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Affiliation(s)
- Zeinab Ravesh
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan,Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Mohammed E. El Asrag
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK,Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Martin McKibbin
- The Eye Department, St. James’s University Hospital, Leeds, UK
| | - Peggy Reuter
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | | | - Britta Baumann
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - James A. Poulter
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Sundus Sajid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Evangelia S. Panagiotou
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - James O’Sullivan
- Manchester Centre for Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, UK
| | - Zakia Abdelhamed
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Michael Bonin
- Department of Medical Genetics, Angewandte Genomik, University of Tübingen, Tübingen, Germany
| | - Mehdi Soltanifar
- Department of Ophthalmology, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Graeme C.M. Black
- Manchester Centre for Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, UK
| | | | - Carmel Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Chris F. Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Manir Ali
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
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Siddiqui S, Zenteno JC, Rice A, Chacón-Camacho O, Naylor SG, Rivera-de la Parra D, Spokes DM, James N, Toomes C, Inglehearn CF, Ali M. Congenital hereditary endothelial dystrophy caused by SLC4A11 mutations progresses to Harboyan syndrome. Cornea 2014; 33:247-51. [PMID: 24351571 PMCID: PMC4195577 DOI: 10.1097/ico.0000000000000041] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Supplemental Digital Content is Available in the Text. Purpose: Homozygous mutations in SLC4A11 cause 2 rare recessive conditions: congenital hereditary endothelial dystrophy (CHED), affecting the cornea alone, and Harboyan syndrome consisting of corneal dystrophy and sensorineural hearing loss. In addition, adult-onset Fuchs endothelial corneal dystrophy (FECD) is associated with dominant mutations in SLC4A11. In this report, we investigate whether patients with CHED go on to develop hearing loss and whether their parents, who are carriers of an SLC4A11 mutation, show signs of having FECD. Methods: Patients with CHED were screened for mutations in the SLC4A11 gene and underwent audiometric testing. The patients and their parents underwent a clinical examination and specular microscopy. Results: Molecular analyses confirmed SLC4A11 mutations in 4 affected individuals from 3 families. All the patients were found to have varying degrees of sensorineural hearing loss at a higher frequency range. Guttate lesions were seen in 2 of the 4 parents who were available for examination. Conclusions: Our observations suggest that CHED caused by homozygous SLC4A11 mutations progresses to Harboyan syndrome, but the severity of this may vary considerably. Patients with CHED should therefore be monitored for progressive hearing loss. We could not determine conclusively whether the parents of the patients with CHED were at increased risk of developing late-onset FECD.
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Affiliation(s)
- Salina Siddiqui
- *Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom; †Department of Ophthalmology, St James's University Hospital, Leeds, United Kingdom; ‡Department of Biochemistry, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico; §Department of Genetics, Institute of Ophthalmology "Conde de Valenciana," Mexico City, Mexico; and ¶Department of Ophthalmology, Bradford Royal Infirmary, Bradford, United Kingdom
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Watson CM, El-Asrag M, Parry DA, Morgan JE, Logan CV, Carr IM, Sheridan E, Charlton R, Johnson CA, Taylor G, Toomes C, McKibbin M, Inglehearn CF, Ali M. Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing. PLoS One 2014; 9:e104281. [PMID: 25133751 PMCID: PMC4136783 DOI: 10.1371/journal.pone.0104281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/07/2014] [Indexed: 12/30/2022] Open
Abstract
Purpose Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Methods Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Results Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Conclusions Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics.
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Affiliation(s)
- Christopher M. Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Mohammed El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - David A. Parry
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Joanne E. Morgan
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Clare V. Logan
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Ian M. Carr
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Eamonn Sheridan
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Ruth Charlton
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Colin A. Johnson
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Graham Taylor
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Carmel Toomes
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Martin McKibbin
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
- Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Chris F. Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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Poulter J, Al-Araimi M, Conte I, van Genderen M, Sheridan E, Carr I, Parry D, Shires M, Carrella S, Bradbury J, Khan K, Lakeman P, Sergouniotis P, Webster A, Moore A, Pal B, Mohamed M, Venkataramana A, Ramprasad V, Shetty R, Saktivel M, Kumaramanickavel G, Tan A, Mackey D, Hewitt A, Banfi S, Ali M, Inglehearn C, Toomes C. Recessive mutations in SLC38A8 cause foveal hypoplasia and optic nerve misrouting without albinism. Am J Hum Genet 2013; 93:1143-50. [PMID: 24290379 DOI: 10.1016/j.ajhg.2013.11.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/05/2013] [Accepted: 11/01/2013] [Indexed: 10/26/2022] Open
Abstract
Foveal hypoplasia and optic nerve misrouting are developmental defects of the visual pathway and only co-occur in connection with albinism; to date, they have only been associated with defects in the melanin-biosynthesis pathway. Here, we report that these defects can occur independently of albinism in people with recessive mutations in the putative glutamine transporter gene SLC38A8. Nine different mutations were identified in seven Asian and European families. Using morpholino-mediated ablation of Slc38a8 in medaka fish, we confirmed that pigmentation is unaffected by loss of SLC38A8. Furthermore, by undertaking an association study with SNPs at the SLC38A8 locus, we showed that common variants within this gene modestly affect foveal thickness in the general population. This study reveals a melanin-independent component underpinning the development of the visual pathway that requires a functional role for SLC38A8.
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Al-Araimi M, Pal B, Poulter JA, van Genderen MM, Carr I, Cudrnak T, Brown L, Sheridan E, Mohamed MD, Bradbury J, Ali M, Inglehearn CF, Toomes C. A new recessively inherited disorder composed of foveal hypoplasia, optic nerve decussation defects and anterior segment dysgenesis maps to chromosome 16q23.3-24.1. Mol Vis 2013; 19:2165-72. [PMID: 24194637 PMCID: PMC3816992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/29/2013] [Indexed: 11/06/2022] Open
Abstract
PURPOSE We have previously described two families with unique phenotypes involving foveal hypoplasia. The first family (F1) presented with foveal hypoplasia and anterior segment dysgenesis, and the second family (F2) presented with foveal hypoplasia and chiasmal misrouting in the absence of albinism. A genome-wide linkage search in family F1 identified a 6.5 Mb locus for this disorder on chromosome 16q23.2-24.1. The aim of this study was to determine if both families have the same disorder and to see if family F2 is also linked to the 16q locus. METHODS Family members underwent routine clinical examination. Linkage was determined by genotyping microsatellite makers and calculating logarithm of the odds (LOD) scores. Locus refinement was undertaken with single nucleotide polymorphism (SNP) microarray analysis. RESULTS The identification of chiasmal misrouting in family F1 and anterior segment abnormalities in family F2 suggested that the families have the same clinical phenotype. This was confirmed when linkage analysis showed that family F2 also mapped to the 16q locus. The single nucleotide polymorphism microarray analysis excluded a shared founder haplotype between the families and refined the locus to 3.1 Mb. CONCLUSIONS We report a new recessively inherited syndrome consisting of foveal hypoplasia, optic nerve decussation defects and anterior segment dysgenesis, which we have abbreviated to FHONDA syndrome. The gene mutated in this disorder lies within a 3.1 Mb interval containing 33 genes on chromosome 16q23.3-24.1 (chr16:83639061 - 86716445, hg19).
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Affiliation(s)
- Musallam Al-Araimi
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | - Bishwanath Pal
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | - James A. Poulter
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | | | - Ian Carr
- Section of Translational Medicine, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | - Tomas Cudrnak
- Department of Ophthalmology, Bradford Royal Infirmary, Bradford, UK
| | - Lawrence Brown
- Department of Ophthalmology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Eamonn Sheridan
- Section of Genetics, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK,Department of Clinical Genetics, St James’s University Hospital, Leeds, UK
| | - Moin D. Mohamed
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | - John Bradbury
- Department of Ophthalmology, Bradford Royal Infirmary, Bradford, UK
| | - Manir Ali
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | - Chris F. Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | - Carmel Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
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Wheway G, Abdelhamed Z, Natarajan S, Toomes C, Inglehearn C, Johnson CA. Aberrant Wnt signalling and cellular over-proliferation in a novel mouse model of Meckel-Gruber syndrome. Dev Biol 2013; 377:55-66. [PMID: 23454480 DOI: 10.1016/j.ydbio.2013.02.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 02/06/2013] [Accepted: 02/13/2013] [Indexed: 11/19/2022]
Abstract
Meckel-Gruber syndrome (MKS) is an embryonic lethal ciliopathy resulting from mutations in genes encoding proteins localising to the primary cilium. Mutations in the basal body protein MKS1 account for 7% of cases of MKS. The condition affects the development of multiple organs, including brain, kidney and skeleton. Here we present a novel Mks1(tm1a(EUCOMM)Wtsi) knockout mouse which accurately recapitulates the human condition, consistently developing pre-axial polydactyly, complex posterior fossa defects (including the Dandy-Walker malformation), and renal cystic dysplasia. TOPFlash Wnt reporter assays in mouse embryonic fibroblasts (MEFs) showed general de-regulated high levels of canonical Wnt/β-catenin signalling in Mks1(-/-) cells. In addition to these signalling defects, we also observed ectopic high proliferation in the brain and kidney of mutant animals at mid- to late-gestation. The specific role of Mks1 in regulating cell proliferation was confirmed in Mks1 siRNA knockdown experiments which showed increased levels of proliferation after knockdown, an effect not seen after knockdown of other ciliopathy genes. We suggest that this is a result of the de-regulation of multiple signalling pathways (Wnt, mTOR and Hh) in the absence of functional Mks1. This novel model system offers insights into the role of MKS1 in Wnt signalling and proliferation, and the impact of deregulation of these processes on brain and kidney development in MKS, as well as expanding our understanding of the role of Mks1 in multiple signalling pathways.
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Affiliation(s)
- Gabrielle Wheway
- Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, Beckett Street, The University of Leeds, Leeds, LS9 7 TF, UK
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Abdelhamed ZA, Wheway G, Szymanska K, Natarajan S, Toomes C, Inglehearn C, Johnson CA. Variable expressivity of ciliopathy neurological phenotypes that encompass Meckel-Gruber syndrome and Joubert syndrome is caused by complex de-regulated ciliogenesis, Shh and Wnt signalling defects. Hum Mol Genet 2013; 22:1358-72. [PMID: 23283079 DOI: 10.1093/hmg/dds546] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The ciliopathies are a group of heterogeneous diseases with considerable variations in phenotype for allelic conditions such as Meckel-Gruber syndrome (MKS) and Joubert syndrome (JBTS) even at the inter-individual level within families. In humans, mutations in TMEM67 (also known as MKS3) cause both MKS and JBTS, with TMEM67 encoding the orphan receptor meckelin (TMEM67) that localizes to the ciliary transition zone. We now describe the Tmem67(tm1(Dgen/H)) knockout mouse model that recapitulates the brain phenotypic variability of these human ciliopathies, with categorization of Tmem67 mutant animals into two phenotypic groups. An MKS-like incipient congenic group (F6 to F10) manifested very variable neurological features (including exencephaly, and frontal/occipital encephalocele) that were associated with the loss of primary cilia, diminished Shh signalling and dorsalization of the caudal neural tube. The 'MKS-like' group also had high de-regulated canonical Wnt/β-catenin signalling associated with hyper-activated Dishevelled-1 (Dvl-1) localized to the basal body. Conversely, a second fully congenic group (F > 10) had less variable features pathognomonic for JBTS (including cerebellar hypoplasia), and retention of abnormal bulbous cilia associated with mild neural tube ventralization. The 'JBTS-like' group had de-regulated low levels of canonical Wnt signalling associated with the loss of Dvl-1 localization to the basal body. Our results suggest that modifier alleles partially determine the variation between MKS and JBTS, implicating the interaction between Dvl-1 and meckelin, or other components of the ciliary transition zone. The Tmem67(tm1(Dgen/H)) line is unique in modelling the variable expressivity of phenotypes in these two ciliopathies.
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Affiliation(s)
- Zakia A Abdelhamed
- Ciliopathy Research Group, Section of Ophthalmology and Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, UK
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Poulter JA, Davidson AE, Ali M, Gilmour DF, Parry DA, Mintz-Hittner HA, Carr IM, Bottomley HM, Long VW, Downey LM, Sergouniotis PI, Wright GA, MacLaren RE, Moore AT, Webster AR, Inglehearn CF, Toomes C. Recessive mutations in TSPAN12 cause retinal dysplasia and severe familial exudative vitreoretinopathy (FEVR). Invest Ophthalmol Vis Sci 2012; 53:2873-9. [PMID: 22427576 DOI: 10.1167/iovs.11-8629] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Familial exudative vitreoretinopathy (FEVR) is an inherited disorder that disrupts the development of the retinal vasculature and can result in blindness. FEVR is genetically heterogeneous and mutations in four genes, NDP, FZD4, LRP5, and TSPAN12, encoding components of a novel ligand-receptor complex that activates the Norrin-β-catenin signaling pathway, account for approximately 50% of cases. We recently identified mutations in TSPAN12 as a cause of dominant FEVR. The purpose of this study was to identify recessive TSPAN12 mutations in FEVR patients. METHODS Mutation screening was performed by directly sequencing PCR products generated from genomic DNA with primers designed to amplify the coding sequence of TSPAN12. Splicing defects were verified by reverse transcriptase PCR of leukocyte cDNA. RESULTS TSPAN12 screening in a large dominant FEVR family unexpectedly led to the identification of homozygous mutations in severely affected family members, whereas mildly affected family members were heterozygous. Further screening in a cohort of 10 retinal dysplasia/severe FEVR patients identified an additional three cases with recessive TSPAN12 mutations. In all examined cases, single mutation carriers were mildly affected compared to patients harboring two TSPAN12 mutations. CONCLUSIONS We report for the first time recessive mutations in TSPAN12 and describe the first genetic cause for the clinical variation seen in FEVR families. Our data raise the possibility that patients with severe FEVR actually may harbor two mutant alleles, derived either from the same gene or potentially from other genes encoding components of the Norrin-β-catenin signaling pathway.
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Affiliation(s)
- James A Poulter
- Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, United Kingdom
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Edwards TL, Burt BO, Black GCM, Perveen R, Kearns LS, Staffieri SE, Toomes C, Buttery RG, Mackey DA. Familial retinal detachment associated with COL2A1 exon 2 and FZD4 mutations. Clin Exp Ophthalmol 2012; 40:476-83. [PMID: 22574936 DOI: 10.1111/j.1442-9071.2012.02804.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND To characterize the clinical and genetic abnormalities within two Australian pedigrees with high incidences of retinal detachment and visual disability. DESIGN Prospective review of two extended Australian pedigrees with high rates of retinal detachment. PARTICIPANTS Twenty-two family members from two extended Australian pedigrees with high rates of retinal detachment were examined. METHODS A full ophthalmic history and examination were performed, and DNA was analysed by linkage analysis and mutation screening. MAIN OUTCOME MEASURES Characterization of a causative hereditary gene mutation in each family. RESULTS All affected family members of one pedigree carried a C192A COL2A1 exon 2 mutation. None of the affected family members had early-onset arthritis, hearing abnormalities, abnormal clefting or facial features characteristic of classical Stickler syndrome. All affected members of the familial exudative vitreoretinopathy pedigree carried a 957delG FZD4 mutation. CONCLUSIONS Patients with retinal detachment and a positive family history should be investigated for heritable conditions associated with retinal detachment such as Stickler syndrome and familial exudative vitreoretinopathy. The absence of non-ocular features of Stickler syndrome should raise the possibility of mutations in exon 2 of COL2A1. Similarly, late-onset familial exudative vitreoretinopathy may appear more like a rhegmatogenous detachment and not be correctly diagnosed. When a causative gene mutation is identified, cascade genetic screening of the family will facilitate genetic counselling and screening of high-risk relatives, allowing targeted management of the pre-detachment changes in affected patients.
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Affiliation(s)
- Thomas L Edwards
- Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology Vitreo-retinal Unit, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria
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Khan K, Logan CV, McKibbin M, Sheridan E, Elçioglu NH, Yenice O, Parry DA, Fernandez-Fuentes N, Abdelhamed ZIA, Al-Maskari A, Poulter JA, Mohamed MD, Carr IM, Morgan JE, Jafri H, Raashid Y, Taylor GR, Johnson CA, Inglehearn CF, Toomes C, Ali M. Next generation sequencing identifies mutations in Atonal homolog 7 (ATOH7) in families with global eye developmental defects. Hum Mol Genet 2011; 21:776-83. [PMID: 22068589 PMCID: PMC3263993 DOI: 10.1093/hmg/ddr509] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The atonal homolog 7 (ATOH7) gene encodes a transcription factor involved in determining the fate of retinal progenitor cells and is particularly required for optic nerve and ganglion cell development. Using a combination of autozygosity mapping and next generation sequencing, we have identified homozygous mutations in this gene, p.E49V and p.P18RfsX69, in two consanguineous families diagnosed with multiple ocular developmental defects, including severe vitreoretinal dysplasia, optic nerve hypoplasia, persistent fetal vasculature, microphthalmia, congenital cataracts, microcornea, corneal opacity and nystagmus. Most of these clinical features overlap with defects in the Norrin/β-catenin signalling pathway that is characterized by dysgenesis of the retinal and hyaloid vasculature. Our findings document Mendelian mutations within ATOH7 and imply a role for this molecule in the development of structures at the front as well as the back of the eye. This work also provides further insights into the function of ATOH7, especially its importance in retinal vascular development and hyaloid regression.
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Affiliation(s)
- Kamron Khan
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
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Ali M, Hocking PM, McKibbin M, Finnegan S, Shires M, Poulter JA, Prescott K, Booth A, Raashid Y, Jafri H, Ruddle JB, Mackey DA, Jacobson SG, Toomes C, Lester DH, Burt DW, Curry WJ, Inglehearn CF. Mpdz null allele in an avian model of retinal degeneration and mutations in human leber congenital amaurosis and retinitis pigmentosa. Invest Ophthalmol Vis Sci 2011; 52:7432-40. [PMID: 21862650 DOI: 10.1167/iovs.11-7872] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To identify the defective gene in the sex-linked, recessively inherited retinal dysplasia and degeneration (rdd) chicken and to search for the human equivalent disease. METHODS Microsatellites from chicken chromosome Z were genotyped in 77 progeny of a carrier male (rdd/+) and an affected female (rdd/W), and candidate genes were sequenced. Retinal cross-sections from rdd and wild-type birds were analyzed by immunohistology. The human orthologous gene was screened in a panel of archival DNAs from 276 patients with retinitis pigmentosa (RP) or Leber congenital amaurosis (LCA) using melting curve analysis and DNA sequencing. RESULTS The rdd locus was refined to an approximately 3-Mb region on chromosome Z. Sequence analysis identified a C→T change in the mpdz gene that created a premature stop codon (c.1372C→T, p.R458X), which segregated with the disease phenotype. As expected, the full-length mpdz protein was absent in rdd retinas, but in wild-type birds, it localized to the retinal outer limiting membrane, where it may have a role in the interactions between photoreceptors and Müller glia cells. The screen to identify the human equivalent disease found 10 heterozygous variants in the orthologous gene in patients with RP (three missense and two null alleles) and LCA (four missense and one null allele). CONCLUSIONS These findings reveal that MPDZ is essential for normal development of the retina and may have a role in maintaining photoreceptor integrity. The identification of human mutations suggests that MPDZ plays a role in human retinal disease, but the precise nature of this role remains to be determined.
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Affiliation(s)
- Manir Ali
- Sections of Ophthalmology, Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, United Kingdom.
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Carr IM, Johnson CA, Markham AF, Toomes C, Bonthron DT, Sheridan EG. DominantMapper: rule-based analysis of SNP data for rapid mapping of dominant diseases in related nuclear families. Hum Mutat 2011; 32:1359-66. [PMID: 21905167 DOI: 10.1002/humu.21597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 08/11/2011] [Indexed: 11/10/2022]
Abstract
With the advent of cheap rapid methods for whole-genome SNP genotyping and the completion of the Human Genome Project, mapping disease loci has become primarily a bioinformatic rather than a laboratory problem. Here, we describe DominantMapper, a computer program that implements a rule-based analysis algorithm for the detection of dominant disease loci in either a small number of nuclear families or a single large nuclear family. To demonstrate its utility, we present the successful analysis of two pedigrees in which the affected individuals carry either APC or TSPAN12 mutations.
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Affiliation(s)
- Ian M Carr
- Leeds Institute of Molecular Medicine, University of Leeds, UK.
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Khan K, Rudkin A, Parry D, Burdon K, McKibbin M, Logan C, Abdelhamed Z, Muecke J, Fernandez-Fuentes N, Laurie K, Shires M, Fogarty R, Carr I, Poulter J, Morgan J, Mohamed M, Jafri H, Raashid Y, Meng N, Piseth H, Toomes C, Casson R, Taylor G, Hammerton M, Sheridan E, Johnson C, Inglehearn C, Craig J, Ali M. Homozygous mutations in PXDN cause congenital cataract, corneal opacity, and developmental glaucoma. Am J Hum Genet 2011; 89:464-73. [PMID: 21907015 PMCID: PMC3169830 DOI: 10.1016/j.ajhg.2011.08.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/29/2011] [Accepted: 08/09/2011] [Indexed: 11/17/2022] Open
Abstract
Anterior segment dysgenesis describes a group of heterogeneous developmental disorders that affect the anterior chamber of the eye and are associated with an increased risk of glaucoma. Here, we report homozygous mutations in peroxidasin (PXDN) in two consanguineous Pakistani families with congenital cataract-microcornea with mild to moderate corneal opacity and in a consanguineous Cambodian family with developmental glaucoma and severe corneal opacification. These results highlight the diverse ocular phenotypes caused by PXDN mutations, which are likely due to differences in genetic background and environmental factors. Peroxidasin is an extracellular matrix-associated protein with peroxidase catalytic activity, and we confirmed localization of the protein to the cornea and lens epithelial layers. Our findings imply that peroxidasin is essential for normal development of the anterior chamber of the eye, where it may have a structural role in supporting cornea and lens architecture as well as an enzymatic role as an antioxidant enzyme in protecting the lens, trabecular meshwork, and cornea against oxidative damage.
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Affiliation(s)
- Kamron Khan
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
- Eye Department, St James University Hospital, Leeds LS9 7TF, UK
| | - Adam Rudkin
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - David A. Parry
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Kathryn P. Burdon
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Martin McKibbin
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
- Eye Department, St James University Hospital, Leeds LS9 7TF, UK
| | - Clare V. Logan
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Zakia I.A. Abdelhamed
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
- Anatomy and Embryology Department, Al-Azhar University, Nasr City District 7, Cairo, Egypt
| | - James S. Muecke
- South Australian Institute of Ophthalmology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | | | - Kate J. Laurie
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Mike Shires
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Rhys Fogarty
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Ian M. Carr
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | | | | | - Moin D. Mohamed
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
- St Thomas' Hospital, London SE1 7EH, UK
| | - Hussain Jafri
- Gene Technology Laboratories 146/1, Shadman Jail Road, Lahore 54000, Pakistan
| | - Yasmin Raashid
- Department of Obstetrics and Gynaecology, King Edward Medical University, Lahore 54000, Pakistan
| | - Ngy Meng
- Preah Ang Duong Eye Hospital, Phnom Penh 855, Cambodia
| | - Horm Piseth
- Fred Hollows Foundation, Phnom Penh 518, Cambodia
| | - Carmel Toomes
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Robert J. Casson
- South Australian Institute of Ophthalmology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | | | - Michael Hammerton
- South Australian Institute of Ophthalmology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | | | | | | | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Manir Ali
- Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
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Mackey D, Hewitt A, Ruddle J, Vote B, Buttery R, Toomes C, Metlapally R, Li Y, Tran-Viet K, Malecaze F, Calvas P, Rosenberg T, Guggenheim J, Young T. Pediatric cataract, myopic astigmatism, familial exudative vitreoretinopathy and primary open-angle glaucoma co-segregating in a family. Mol Vis 2011; 17:2118-28. [PMID: 21850187 PMCID: PMC3156798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 07/26/2011] [Indexed: 11/21/2022] Open
Abstract
PURPOSE To describe an Australian pedigree of European descent with a variable autosomal dominant phenotype of: pediatric cortical cataract (CC), asymmetric myopia with astigmatism, familial exudative vitreoretinopathy (FEVR), and primary open-angle glaucoma (POAG). METHODS Probands with CC, FEVR, and POAG were enrolled in three independent genetic eye studies in Tasmania. Genealogy confirmed these individuals were closely related and subsequent examination revealed 11 other family members with some or all of the associated disorders. RESULTS Twelve individuals had CC thought to be of childhood onset, with one child demonstrating progressive lenticular opacification. One individual had severe retinal detachment while five others had dragged retinal vessels. Seven individuals had POAG. Seven individuals had myopia in at least one eye ≤-3 Diopters. DNA testing excluded mutations in myocilin, trabecular meshwork inducible glucocorticoid response (MYOC) and tetraspanin 12 (TSPAN12). Haplotype analysis excluded frizzled family receptor 4 (FZD4) and low density lipoprotein receptor-related protein 5 (LRP5), but only partly excluded EVR3. Multipoint linkage analysis revealed multiple chromosomal single-nucleotide polymorphisms (SNPs) of interest, but no statistically significant focal localization. CONCLUSIONS This unusual clustering of ophthalmic diseases suggests a possible single genetic cause for an apparently new cataract syndrome. This family's clinical ocular features may reflect the interplay between retinal disease with lenticular changes and axial length in the development of myopia and glaucoma.
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Affiliation(s)
- D.A. Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia,Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Australia,Eye Department, University of Tasmania, Royal Hobart Hospital, Hobart, Australia
| | - A.W. Hewitt
- Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - J.B. Ruddle
- Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - B. Vote
- The Launceston Eye Institute, Launceston, Australia
| | - R.G. Buttery
- Vitreoretinal Unit, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - C. Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, UK
| | - R. Metlapally
- Department of Ophthalmology, Duke University Eye Center, Durham, NC,School of Optometry, University of California at Berkeley, Berkeley, CA
| | - Y.J. Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC,Center for Human Genetics, Duke University Medical Center, Durham, NC
| | - K.N. Tran-Viet
- Center for Human Genetics, Duke University Medical Center, Durham, NC
| | - F. Malecaze
- Toulouse University Hospital, Université Paul Sabatier, Toulouse, France
| | - P. Calvas
- Toulouse University Hospital, Université Paul Sabatier, Toulouse, France
| | | | - J.A. Guggenheim
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - T.L. Young
- Department of Ophthalmology, Duke University Eye Center, Durham, NC,Center for Human Genetics, Duke University Medical Center, Durham, NC
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Khan KN, Ali M, Toomes C, Inglehearn CF, Bradbury J. Changing the status quo bias. Br J Ophthalmol 2011; 95:1034. [DOI: 10.1136/bjo.2010.200428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Khan K, Al-Maskari A, McKibbin M, Carr IM, Booth A, Mohamed M, Siddiqui S, Poulter JA, Parry DA, Logan CV, Hashmi A, Sahi T, Jafri H, Raashid Y, Johnson CA, Markham AF, Toomes C, Rice A, Sheridan E, Inglehearn CF, Ali M. Genetic heterogeneity for recessively inherited congenital cataract microcornea with corneal opacity. Invest Ophthalmol Vis Sci 2011; 52:4294-9. [PMID: 21474777 DOI: 10.1167/iovs.10-6776] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To investigate whether three consanguineous families from the Punjab province of Pakistan, with affected members with recessively inherited congenital cataract microcornea with corneal opacity, are genetically homogeneous. METHODS An ophthalmic examination was performed on each family member to establish the diagnosis. The two largest families were analyzed by homozygosity mapping using SNP arrays. Linkage was confirmed using polymorphic microsatellite markers, and logarithm of odds (LOD) scores were calculated. Candidate genes were prioritized using the ENDEAVOUR program. RESULTS Autosomal recessive congenital cataract-microcornea with corneal opacity mapped to chromosome 10cen for family MEP57 and to either chromosomes 2ptel or 20p for family MEP60. For MEP57, the refined interval was 36.8 Mb flanked by D10S1208 (35.3 Mb) and D10S676 (72.1 Mb). For MEP60, the interval containing the mutation was either 6.7 Mb from the telomere of chromosome 2 to marker D2S281 or 3.8 Mb flanked by D20S906 (1.5 Mb) and D20S835 (5.3 Mb). Maximum multipoint LOD scores of 3.09, 1.94, and 3.09 were calculated at D10S567, D2S281, and D20S473 for families MEP57 and MEP60. Linkage to these loci was excluded for family MEP68. SLC4A11 was excluded as a candidate gene for the observed phenotype in MEP60. CONCLUSIONS The authors have identified two new loci, one on chromosome 10cen and the other on 2ptel or 20p, that are associated with recessively inherited congenital cataract-microcornea with corneal opacity. This phenotype is genetically heterogeneous in the Pakistani population. Further genetic studies of this kind, combined with a detailed phenotypic description, will contribute to more precise classification criteria for anterior segment disease.
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Affiliation(s)
- Kamron Khan
- Leeds Institute of Molecular Medicine, Leeds, United Kingdom
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Parmalee NL, Schubert C, Merriam JE, Allikmets K, Bird AC, Gillies MC, Peto T, Figueroa M, Friedlander M, Fruttiger M, Greenwood J, Moss SE, Smith LE, Toomes C, Inglehearn CF, Allikmets R. Analysis of candidate genes for macular telangiectasia type 2. Mol Vis 2010; 16:2718-26. [PMID: 21179236 PMCID: PMC3002960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 12/09/2010] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To find the gene(s) responsible for macular telangiectasia type 2 (MacTel) by a candidate-gene screening approach. METHODS Candidate genes were selected based on the following criteria: those known to cause or be associated with diseases with phenotypes similar to MacTel, genes with known function in the retinal vasculature or macular pigment transport, genes that emerged from expression microarray data from mouse models designed to mimic MacTel phenotype characteristics, and genes expressed in the retina that are also related to diabetes or hypertension, which have increased prevalence in MacTel patients. Probands from eight families with at least two affected individuals were screened by direct sequencing of 27 candidate genes. Identified nonsynonymous variants were analyzed to determine whether they co-segregate with the disease in families. Allele frequencies were determined by TaqMan analysis of the large MacTel and control cohorts. RESULTS We identified 23 nonsynonymous variants in 27 candidate genes in at least one proband. Of these, eight were known single nucleotide polymorphisms (SNPs) with allele frequencies of >0.05; these variants were excluded from further analyses. Three previously unidentified missense variants, three missense variants with reported disease association, and five rare variants were analyzed for segregation and/or allele frequencies. No variant fulfilled the criteria of being causal for MacTel. A missense mutation, p.Pro33Ser in frizzled homolog (Drosophila) 4 (FZD4), previously suggested as a disease-causing variant in familial exudative vitreoretinopathy, was determined to be a rare benign polymorphism. CONCLUSIONS We have ruled out the exons and flanking intronic regions in 27 candidate genes as harboring causal mutations for MacTel.
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Affiliation(s)
- Nancy L. Parmalee
- Department of Ophthalmology, Columbia University, New York, NY,Department of Genetics and Development, Columbia University, New York, NY
| | - Carl Schubert
- Department of Ophthalmology, Columbia University, New York, NY
| | | | - Kaija Allikmets
- Department of Ophthalmology, Columbia University, New York, NY
| | | | - Mark C. Gillies
- Save Sight Institute, Department of Clinical Ophthalmology and Eye Health, The University of Sydney, Sydney, Australia
| | | | | | - Martin Friedlander
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA
| | - Marcus Fruttiger
- Department of Cell Biology, University College London Institute of Ophthalmology, London, UK
| | - John Greenwood
- Department of Cell Biology, University College London Institute of Ophthalmology, London, UK
| | - Stephen E. Moss
- Department of Cell Biology, University College London Institute of Ophthalmology, London, UK
| | - Lois E.H. Smith
- Department of Ophthalmology, Harvard Medical School, Children's Hospital Boston, Boston, MA
| | - Carmel Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds, UK
| | - Chris F. Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds, UK
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY,Department of Pathology and Cell Biology, Columbia University, New York, NY
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